("", " -sequence=" + str(value))[value is not None]
("", " -targetregion=" + str(value))[value is not None and value!=vdef]
("", " -delete")[ bool(value) ]
not e_delete
("", " -replace=" + str(value))[value is not None and value!=vdef]
("", " -position=" + str(value))[value is not None and value!=vdef]
value >= 0
("" , " -outseq=" + str(value))[value is not None]
("", " -osformat=" + str(value))[value is not None and value!=vdef]
e_outseq
" -auto -stdout"
"drawtree <drawtree.params"
"drawtree <drawtree.params"
"ln -s $treefile intree && "
"ln -s "+str( treefile ) + " intree && "
"0\\n"
"0\n"
(defined $value and $value ne $vdef) ? "P\\n$value\\n" : ""
("" , "P\n" + str(value) + "\n")[ value is not None and value != vdef ]
$plotter =~ /^[XW]$/
plotter in [ "X" , "W" ]
"$value\\n"
str( value ) + "\n"
$value <= 2500
value <= 2500
"$value\\n"
str( value ) + "\n"
$value <= 2500
value <= 2500
$plotter eq "J"
plotter == "J"
"$value\\n"
str(value) + "\n"
$plotter eq "P"
plotter == "P"
"$value\\n"
str(value) + "\n"
$plotter eq "V"
plotter == "V"
"Y\\n"
"Y\n"
$plotter eq "L"
plotter == "L"
(defined $value and $value ne $vdef) ? "F\\n$value\\n" : ""
("", "F\n"+str(value)+"\n")[value is not None and value != vdef]
$plotter eq "Z"
plotter == "Z"
"Y\\n"
"Y\n"
$plotter eq "R"
plotter == "R"
"Y\\n"
"Y\n"
"V\\nN\\n"
"V\nN\n"
($value) ? "" : "B\\n"
("B\n" , "")[ value ]
"L\\nA\\n"
"L\nA\n"
"L\\nR\\n"
"L\nR\n"
""
""
""
""
$angle eq "" or $angle eq "F"
angle == "" or angle == "F"
(defined $value and $value != $vdef) ? "L\\nF\\n$value\\n" : ""
( "" , "L\nF\n"+ str( value ) +"\n")[ value is not None and value != vdef ]
$value >= -90.0 and $value <= 90.0
value >= -90.0 and value <= 90.0
(defined $value and $value != $vdef) ? "R\\n$value\\n" : ""
("" , "R\n" +str( value ) +"\n" )[ value is not None and value != vdef]
(defined $value and $value != $vdef) ? "A\\n$value\\n" : ""
( "" , "A\n" + str( value ) +"\n" )[ value is not None and value != vdef]
""
""
"I\\n"
"I\n"
"I\\nI\\n"
"I\nI\n"
(defined $value) ? "S\\n$value\\n" : ""
( "" , "S\n"+ str( value )+ "\n")[ value is not None ]
$iterate ne "N"
iterate != "N"
($value) ? "D\\n" : ""
( "" , "D\n" )[ value ]
(defined $value and $value != $vdef) ? "M\\n$value\\n$vertical_margins\\n" : ""
("" , "M\n" + str( value ) + "\n" + str(vertical_margins ) + "\n")[ value is not None and value != vdef ]
""
""
(defined $value and $value != $vdef) ? "C\\n$value\\n" : ""
("", "C\n" + str( value ) + "\n" )[ value is not None and value != vdef ]
$plotter !~ /^[LMWX]$/
plotter not in [ "L" , "M" , "W", "X" ]
"plotfile"
"plotfile"
$plotter eq "L"
plotter == "L"
" && ln -s plotfile plotfile.ps"
" && ln -s plotfile plotfile.ps"
"plotfile.ps"
"plotfile.ps"
$plotter eq "M"
plotter == "M"
" && ln -s plotfile plotfile.pict"
" && ln -s plotfile plotfile.pict"
"plotfile.pict"
"plotfile.pict"
$plotter eq "X"
plotter == "X"
" && ln -s plotfile plotfile.xbm"
" && ln -s plotfile plotfile.xbm"
"plotfile.xbm"
"plotfile.xbm"
$plotter eq "W"
plotter == "W"
" && ln -s plotfile plotfile.bmp"
" && ln -s plotfile plotfile.bmp"
"plotfile.bmp"
"plotfile.bmp"
"Y\\n"
"Y\n"
("", " -infile=" + str(value))[value is not None]
(" -noplot", "")[ bool(value) ]
("" , " -outfile=" + str(value))[value is not None]
e_outfile
(" -graphlb=" + str(vdef), " -graphlb=" + str(value))[value is not None and value!=vdef]
("" , " -goutfile=" + str(value))[value is not None]
e_graphlb == "png"
"*.png"
e_graphlb == "gif"
"*.gif"
e_graphlb == "ps" or e_graphlb == "cps"
"*.ps"
e_graphlb == "meta"
"*.meta"
e_graphlb == "data"
"*.dat"
" -auto -stdout"
" < $value"
" < " + str(value)
(defined $value and $value ne $vdef)? " -X$value" : ""
("", " -X" + str(value) )[value is not None and value != vdef]
(defined $value)? " -B $value" : ""
("" , " -B " + str(value))[ value is not None ]
(defined $value and $value != $vdef)? " -T $value" : ""
( "" , " -T " + str(value) )[ value is not None and value != vdef]
($value)? " -4" : ""
( "" , " -4" )[ value ]
(defined $value and $value ne $vdef)? " $value" : ""
( "" , " " + str(value) )[ value is not None and value != vdef]
($value)? " -noGU" : ""
( "" , " -noGU" )[ value ]
($value)? " -noCloseGU" : ""
( "" , " -noCloseGU" )[ value ]
(defined $value)? " -nsp $value" : ""
( "" , " -nsp " + str(value) )[ value is not None ]
(defined $value)? " -P $value" : ""
( "" , " -P " + str(value) )[ value is not None ]
"
"
"*.ps"
"*.ps"
defined $alignment_file
alignment_file is not None
"$alignment_file"
str(alignment_file)
("", " -sequence=" + str(value))[value is not None]
("", " -datafile=" + str(value))[value is not None]
("", " -mfile=" + str(value))[value is not None ]
("", " -seqcomp=" + str(value))[value is not None]
("", " -min=" + str(value))[value is not None and value!=vdef]
value >= 1
value <= 1000
("", " -max=" + str(value))[value is not None and value!=vdef]
("", " -single")[ bool(value) ]
("", " -threeprime")[ bool(value) ]
(" -noblunt", "")[ bool(value) ]
(" -nosticky", "")[ bool(value) ]
(" -noambiguity", "")[ bool(value) ]
("", " -plasmid")[ bool(value) ]
("", " -methylation")[ bool(value) ]
(" -nocommercial", "")[ bool(value) ]
("", " -html")[ bool(value) ]
(" -nolimit", "")[ bool(value) ]
("", " -alphabetic")[ bool(value) ]
("", " -fragments")[ bool(value) ]
("" , " -outfile=" + str(value))[value is not None]
e_outfile
" -auto -stdout"
("", " -sequence=" + str(value))[value is not None]
("", " -regions=" + str(value))[value is not None]
("", " -separate")[ bool(value) ]
("" , " -outseq=" + str(value))[value is not None]
("", " -osformat=" + str(value))[value is not None and value!=vdef]
e_outseq
" -auto -stdout"
("", " -sequence=" + str(value))[value is not None]
("", " -minrepeat=" + str(value))[value is not None and value!=vdef]
value >= 2
e_minrepeat
("", " -maxrepeat=" + str(value))[value is not None]
("", " -threshold=" + str(value))[value is not None and value!=vdef]
("", " -mismatch")[ bool(value) ]
("", " -uniform")[ bool(value) ]
("" , " -outfile=" + str(value))[value is not None]
("", " -rformat=" + str(value))[value is not None and value!=vdef]
e_rformat_outfile in ['DASGFF', 'DBMOTIF', 'DIFFSEQ', 'EMBL', 'EXCEL', 'FEATTABLE', 'GENBANK', 'GFF', 'LISTFILE', 'MOTIF', 'NAMETABLE', 'CODATA', 'REGIONS', 'SEQTABLE', 'SIMPLE', 'SRS', 'SWISS', 'TABLE', 'TAGSEQ']
e_outfile
("" , " -origfile=" + str(value))[value is not None]
e_origfile
" -auto -stdout"
" $value"
" " + str(value)
" $value"
" " + str(value)
defined $sec_struc_seq_filename
sec_struc_seq_filename is not None
(defined $value)? " $value" : ""
("", " "+str(value))[value is not None]
defined $ref_seq_name_
ref_seq_name is not None
(defined $value)? " $value" : ""
( "" , " " + str(value) )[ value is not None ]
(defined $value and $value != $vdef)? " -c $value " : ""
( "" , " -c " + str(value) )[ value is not None and value != vdef]
(defined $value)? " -d $value" : ""
( "" , " -d " + str(value) )[ value is not None ]
(defined $value)? " -i $value" : ""
( "" , " -i " + str(value) )[ value is not None ]
(defined $value)? " -l $value" : ""
( "" , " -l " + str(value) )[ value is not None ]
(defined $value and $value ne $vdef and $value ne "user")? " -m $value" : ""
( "" , " -m " + str(value) )[ value is not None and value !=vdef and value !="user"]
$mat_file eq "user"
mat_file == "user"
(defined $value)? " -m $value" : ""
( "" , " -m " + str(value) )[ value is not None ]
($value)? " -n" : ""
( "" , " -n" )[ value ]
(defined $value)? " -t $value " : ""
( "" , " -t " + str(value) + " " )[ value is not None ]
"*.cluster"
*.pattern"
*.pima"
"*.cluster"
"*.pattern"
"*.pima"
("", " -sequence=" + str(value))[value is not None]
("", " -matrix=" + str(value))[value is not None and value!=vdef]
("", " -refseq=" + str(value))[value is not None and value!=vdef]
("", " -plurality=" + str(value))[value is not None and value!=vdef]
value >= 0.0
value <= 100.0
("", " -identity=" + str(value))[value is not None and value!=vdef]
value >= 0.0
value <= 100.0
("" , " -outfile=" + str(value))[value is not None]
e_outfile
("", " -html")[ bool(value) ]
("", " -only")[ bool(value) ]
not e_only
("", " -heading")[ bool(value) ]
not e_only
("", " -usa")[ bool(value) ]
not e_only
("", " -name")[ bool(value) ]
not e_only
("", " -seqlength")[ bool(value) ]
not e_only
("", " -alignlength")[ bool(value) ]
not e_only
("", " -gaps")[ bool(value) ]
not e_only
("", " -gapcount")[ bool(value) ]
not e_only
("", " -idcount")[ bool(value) ]
not e_only
("", " -simcount")[ bool(value) ]
not e_only
("", " -diffcount")[ bool(value) ]
not e_only
("", " -change")[ bool(value) ]
not e_only
("", " -weight")[ bool(value) ]
not e_only
("", " -description")[ bool(value) ]
" -auto -stdout"
" $value -g"
" "+str(value)+" -g"
(defined $value and $value ne $vdef) ? " -t=$value" : ""
("", " -t="+str(value))[value is not None and value!=vdef]
(defined $value) ? " -b1=$value" : ""
("" , " -b1="+str(value))[value is not None]
(defined $value) ? " -b2=$value" : ""
("" , " -b2="+str(value))[value is not None]
(defined $value and $value != $vdef) ? " -b4=$value" : ""
("" , " -b4="+str(value))[value is not None and value!=vdef]
(defined $value and $value ne $vdef) ? " -b5=$value" : ""
("", " -b5="+str(value))[value is not None and value!=vdef]
(defined $value and $value != $vdef) ? " -b3=$value" : ""
("" , " -b3="+str(value))[value is not None and value!=vdef]
($value) ? "" , " -s=n"
(" -s=n" , "")[value]
(defined $value and $value ne $vdef) ? " -p=$value" : ""
("" , " -p="+str(value))[value is not None and value!=vdef]
(defined $value and $value != $vdef) ? " -v=$value" : ""
("" , " -v="+str(value))[value is not None and value!=vdef]
($value) ? "-n=y" , ""
("" , " -n=y")[value]
($value) ? "-u=y" , ""
("" , " -u=y")[value]
($value) ? "-k=y" , ""
("" , " -k=y")[value]
($value) ? "-d=y" , ""
("" , " -d=y")[value]
$Res_Param ne 't' and $Res_Param ne 's' and $Res_Param ne 'n'
Res_Param != 't' and Res_Param != 's' and Res_Param != 'n'
"*-gb.htm"
"*-gb.htm"
$Res_Param eq 't'
Res_Param == 't'
"*-gb.txt"
$Res_Param eq 's'
Res_Param == 's'
"*-gb.txts"
"*-gb.txts"
$sb
sb
"*-gb"
"*-gb"
$nc
nc
"*-gbComp"
"*-gbComp"
$ua
ua
"*--"
"*--"
$mask
mask
"*-gbMask"
"*-gbMask"
$ps
ps
"*-gbPS"
"*-gbPS"
("", " -asequence=" + str(value))[value is not None]
("", " -bsequence=" + str(value))[value is not None]
("", " -datafile=" + str(value))[value is not None and value!=vdef]
("", " -gapopen=" + str(value))[value is not None]
value >= 0.0
value <= 100.0
("", " -gapextend=" + str(value))[value is not None]
value >= 0.0
value <= 10.0
("", " -endweight")[ bool(value) ]
("", " -endopen=" + str(value))[value is not None]
value >= 0.0
value <= 100.0
("", " -endextend=" + str(value))[value is not None]
value >= 0.0
value <= 10.0
("", " -minscore=" + str(value))[value is not None and value!=vdef]
value >= -10.0
value <= 100.0
(" -nobrief", "")[ bool(value) ]
("" , " -outfile=" + str(value))[value is not None]
("", " -aformat=" + str(value))[value is not None and value!=vdef]
e_aformat_outfile in ['FASTA', 'MSF']
e_outfile
e_aformat_outfile in ['PAIR', 'MARKX0', 'MARKX1', 'MARKX2', 'MARKX3', 'MARKX10', 'SRS', 'SRSPAIR', 'SCORE', 'UNKNOWN', 'MULTIPLE', 'SIMPLE', 'MATCH']
e_outfile
("" , " -errorfile=" + str(value))[value is not None]
e_errorfile
" -auto -stdout"
"toppred"
"toppred"
" $value"
" "+ str( value )
($value) ? "" : " -t none"
(" -t none","")[ value ]
(defined $value and $value ne $vdef) ? "-H $value" : ""
( "" , " -H " + str( value ) )[ value is not None and value != vdef ]
($value) ? " -e" : ""
( "" , " -e" )[ value ]
(defined $value and $value != $vdef) ? " -c $value" : ""
( "" , " -c " + str(value) ) [ value is not None and value!= vdef ]
$certain > $putative
certain > putative
(defined $value and $value != $vdef) ? "-p $value" : ""
( "" , " -p " + str(value) )[ value is not None and value != vdef ]
$certain > $putative
certain > putative
(defined $value and $value != $vdef) ? " -n $value" : ""
( "" , " -n " + str(value) )[ value is not None and value != vdef ]
(defined $value and $value != $vdef) ? " -q $value" : ""
( "" , " -q " + str(value) )[ value is not None and value != vdef ]
(defined $value and $value != $vdef) ? " -s $value" : ""
( "" , " -s " + str(value) )[ value is not None and value != vdef ]
(defined $value and $value != $vdef) ? " -d $value" : ""
( "" , " -d " + str( value ) )[ value is not None and value!= vdef ]
(defined $value and $value ne $vdef) ? " -O $value" : ""
( "" , " -O " + str(value) )[ value is not None and value != vdef ]
$graph_output
graph_output
($graph_output) ? " -g $value" : " -g none"
( " -g none" , " -g " + str(value) )[ graph_output ]
$graph_output
graph_output
*.$profile_format
'*.' + profile_format
*.hydro*
'*.hydro*'
outformat eq 'html'
outformat == 'html'
*.html
'*.html'
("", " -name=" + str(value))[value is not None]
("", " -description=" + str(value))[value is not None]
("", " -type=" + str(value))[value is not None and value!=vdef]
("", " -sequence=" + str(value))[value is not None]
("" , " -outseq=" + str(value))[value is not None]
("", " -osformat=" + str(value))[value is not None and value!=vdef]
e_outseq
" -auto -stdout"
("", " -sequence=" + str(value))[value is not None]
("", " -window=" + str(value))[value is not None and value!=vdef]
value >= 1
("", " -shift=" + str(value))[value is not None and value!=vdef]
value >= 1
("" , " -outfile=" + str(value))[value is not None]
e_outfile
(" -graph=" + str(vdef), " -graph=" + str(value))[value is not None and value!=vdef]
("" , " -goutfile=" + str(value))[value is not None]
e_graph == "png"
"*.png"
e_graph == "gif"
"*.gif"
e_graph == "ps" or e_graph == "cps"
"*.ps"
e_graph == "meta"
"*.meta"
e_graph == "data"
"*.dat"
" -auto -stdout"
("", " -sequence=" + str(value))[value is not None]
("", " -enzymes=" + str(value))[value is not None and value!=vdef]
("", " -sshow")[ bool(value) ]
("", " -tshow")[ bool(value) ]
("", " -allmut")[ bool(value) ]
("" , " -outfile=" + str(value))[value is not None]
("", " -rformat=" + str(value))[value is not None and value!=vdef]
e_rformat_outfile in ['DASGFF', 'DBMOTIF', 'DIFFSEQ', 'EMBL', 'EXCEL', 'FEATTABLE', 'GENBANK', 'GFF', 'LISTFILE', 'MOTIF', 'NAMETABLE', 'CODATA', 'REGIONS', 'SEQTABLE', 'SIMPLE', 'SRS', 'SWISS', 'TABLE', 'TAGSEQ']
e_outfile
" -auto -stdout"
("", " -sequence=" + str(value))[value is not None]
("", " -cfile=" + str(value))[value is not None and value!=vdef]
("" , " -outfile=" + str(value))[value is not None]
("", " -osformat=" + str(value))[value is not None and value!=vdef]
e_outfile
" -auto -stdout"
("", " -sequence=" + str(value))[value is not None]
("", " -mean=" + str(value))[value is not None and value!=vdef]
value >= 1.
value <= 10000.
("", " -sd=" + str(value))[value is not None and value!=vdef]
value >= 1.
value <= 10000.
("", " -minsd=" + str(value))[value is not None and value!=vdef]
value >= 0.
value <= 100.
("", " -eightyseven")[ bool(value) ]
("" , " -outfile=" + str(value))[value is not None]
("", " -rformat=" + str(value))[value is not None and value!=vdef]
e_rformat_outfile in ['DASGFF', 'DBMOTIF', 'DIFFSEQ', 'EMBL', 'EXCEL', 'FEATTABLE', 'GENBANK', 'GFF', 'LISTFILE', 'MOTIF', 'NAMETABLE', 'CODATA', 'REGIONS', 'SEQTABLE', 'SIMPLE', 'SRS', 'SWISS', 'TABLE', 'TAGSEQ']
e_outfile
" -auto -stdout"
("", " -seqall=" + str(value))[value is not None]
("", " -aadata=" + str(value))[value is not None ]
("", " -window=" + str(value))[value is not None and value!=vdef]
value >= 1
("", " -plot")[ bool(value) ]
e_plot
(" -graph=" + str(vdef), " -graph=" + str(value))[value is not None and value!=vdef]
e_plot
("" , " -goutfile=" + str(value))[value is not None]
e_plot and e_graph == "png"
"*.png"
e_plot and e_graph == "gif"
"*.gif"
e_plot and e_graph == "ps" or e_graph == "cps"
"*.ps"
e_plot and e_graph == "meta"
"*.meta"
e_plot and e_graph == "data"
"*.dat"
not e_plot
("" , " -outfile=" + str(value))[value is not None]
e_outfile
" -auto -stdout"
(defined $value) ? " $value " : ""
( "" , " " + str(value) )[ value is not None]
(defined $value) ? "
( "" , "
(defined $value and $value ne $vdef) ? " $value " : ""
( "" , " " + str(value) )[ value is not None and value !=vdef]
$reference eq '--refgene'
reference == '--refgene'
($value) ? "--name2 " : ""
( "" , " --name2 " )[ value]
$reference ne '--knowngene'
reference != '--knowngene'
($value) ? "--reflink
( "" , " --reflink
$reference eq '--knowngene'
reference == '--knowngene'
($value) ? "--kgxref
( "" , " --kgxref
($value) ? "--condense_query " : ""
( "" , " --condense_query " )[ value]
(defined $value) ? " --score_threshold $value " : ""
( "" , " --score_threshold " + str(value) )[ value is not None]
(defined $value) ? " --normscore_threshold $value " : ""
( "" , " --normscore_threshold " + str(value) )[ value is not None]
($reference eq '--knowngene' or $reference eq '--refgene') and (not $expandmax)
(reference == '--knowngene' or reference == '--refgene') and (not expandmax)
(defined $value) ? " --expandleft $value " : ""
( "" , " --expandleft " + str(value) )[ value is not None]
($reference eq '--knowngene' or $reference eq '--refgene') and (not $expandmax)
(reference == '--knowngene' or reference == '--refgene') and (not expandmax)
(defined $value) ? " --expandright $value " : ""
( "" , " --expandright " + str(value) )[ value is not None]
$reference eq '--knowngene' or $reference eq '--refgene'
reference == '--knowngene' or reference == '--refgene'
(defined $value) ? " --expandmax $value " : ""
( "" , " --expandmax " + str(value) )[ value is not None]
(defined $value) ? " --expanddb $value " : ""
( "" , " --expanddb " + str(value) )[ value is not None]
($value) ? "--overlap " : ""
( "" , " --overlap " )[ value]
($value) ? "--dbregion " : ""
( "" , " --dbregion " )[ value]
($value) ? "--append " : ""
( "" , " --append " )[ value]
$dbregion
dbregion
($value) ? "--queryinfo " : ""
( "" , " --queryinfo " )[ value]
"scan_region.out"
"scan_region.out"
" < $value"
" < "+ str(value)
(defined $value and $value!=$vdef)? " -e $value" : ""
( "" , " -e " + str(value))[ value is not None and value != vdef ]
(defined $value and $value != $vdef)? " -T $value" : ""
( "" , " -T " + str(value) )[ value is not None and value != vdef]
($value)? " -4" : ""
( "" , " -4" )[ value ]
($value)? " -noGU" : ""
( "" , " -noGU" )[ value ]
($value)? " -noCloseGU" : ""
( "" , " -noCloseGU" )[ value ]
(defined $value)? " -P $value" : ""
( "" , " -P " + str(value) )[ value is not None ]
"
"
"*.ps"
"*.ps"
" $value"
" "+str(value)
($value)? " -m":""
("" , " -m")[ value ]
(defined $value)? " -f $value" : ""
( "" , " -f " + str(value) )[ value is not None ]
($value)? " -g":""
("" , " -g")[ value ]
($value)? " -b":""
("" , " -b")[ value ]
(defined $value)? " -d$value" : ""
( "" , " -d" + str(value) )[ value is not None ]
(defined $value)? " -e $value" : ""
( "" , " -e " + str(value) )[ value is not None ]
(defined $value)? " -c $value" : ""
( "" , " -c " + str(value) )[ value is not None ]
($value)? " -o":""
("" , " -o")[ value ]
" --infile=$value"
" --infile=" + str( value )
" --profile1=$value"
" --profile1=" + str( value )
(defined $value and $value neq $vdef)? " --seqtype=$value" : ""
("", " --seqtype="+str(value))[value is not None and value != vdef]
$alignment_input
bool( alignment_input )
(defined $value and $value) " --dealign " : ""
( "" , " --dealign ")[ value is not None and value !=vdef ]
(defined $value and $value)? " --distmat-out=$value ":""
( "" , " --distmat-out="+str(value))[ value is not None ]
$full
full
(defined $value )? " --guidetree-in= $value" : ""
( "" , " --guidetree-in="+str(value))[ value is not None ]
(defined $value and $value)? " --guidetree-out=$value ":""
( "" , " --guidetree-out="+str(value))[ value is not None ]
(defined $full and $ full)? " --full ": ""
( "" , " --full ")[ value is not None and value ]
(defined $full and $ full)? " --full-iter ": ""
( "" , " --full-iter ")[ value is not None and value ]
(defined $value and $value ne $vdef)? " --outfmt=$value" : ""
( "" , " --outfmt=" + value )[ value is not None and value != vdef ]
(defined $value)? " --iter=$value ": ""
( "" , " --iter="+str(value) )[ value is not None ]
(defined $value)? " --max-guidetree-iterations=$value ": ""
( "" , " --max-guidetree-iterations="+str(value) )[ value is not None ]
(defined $value)? " --max-hmm-iterations=$value ": ""
( "" , " --max-hmm-iterations="+str(value) )[ value is not None ]
(defined $value and $value)? " --auto ": ""
( "" , " --auto ")[value is not None and value]
" -v --force --log=clustalO_log"
" -v --force --log=clustalO_log"
"clustalO-sequence.out"
"clustalO-sequence.out"
defined $guidetree_out
guidetree_out is not None
$guidetree_out
guidetree_out
defined $distmat_out
distmat_out is not None
$distmat_out
distmat_out
"clustalO_log"
"clustalO_log"
("", " -sequence=" + str(value))[value is not None]
("", " -pattern=@" + str(value))[value is not None]
("", " -pmismatch=" + str(value))[value is not None and value!=vdef]
("" , " -outfile=" + str(value))[value is not None]
("", " -rformat=" + str(value))[value is not None and value!=vdef]
e_rformat_outfile in ['DASGFF', 'DBMOTIF', 'DIFFSEQ', 'EMBL', 'EXCEL', 'FEATTABLE', 'GENBANK', 'GFF', 'LISTFILE', 'MOTIF', 'NAMETABLE', 'CODATA', 'REGIONS', 'SEQTABLE', 'SIMPLE', 'SRS', 'SWISS', 'TABLE', 'TAGSEQ']
e_outfile
" -auto -stdout"
("", " -sequence=" + str(value))[value is not None]
("", " -full")[ bool(value) ]
(" -noprune", "")[ bool(value) ]
("" , " -outfile=" + str(value))[value is not None]
("", " -rformat=" + str(value))[value is not None and value!=vdef]
e_rformat_outfile in ['DASGFF', 'DBMOTIF', 'DIFFSEQ', 'EMBL', 'EXCEL', 'FEATTABLE', 'GENBANK', 'GFF', 'LISTFILE', 'MOTIF', 'NAMETABLE', 'CODATA', 'REGIONS', 'SEQTABLE', 'SIMPLE', 'SRS', 'SWISS', 'TABLE', 'TAGSEQ']
e_outfile
" -auto -stdout"
("", " -sequence=" + str(value))[value is not None]
("", " -mfile=" + str(value))[value is not None ]
("", " -format=" + str(value))[value is not None and value!=vdef]
e_format=="0"
("", " -things=" + str(value))[value is not None and value!=vdef]
("", " -translate=" + str(value))[value is not None]
("", " -revtranslate=" + str(value))[value is not None]
("", " -uppercase=" + str(value))[value is not None]
("", " -highlight=" + str(value))[value is not None]
("", " -annotation=" + str(value))[value is not None]
("", " -enzymes=" + str(value))[value is not None and value!=vdef]
("", " -table=" + str(value))[value is not None and value!=vdef]
("", " -sourcematch=" + str(value))[value is not None]
("", " -typematch=" + str(value))[value is not None]
("", " -sensematch=" + str(value))[value is not None and value!=vdef]
value >= -1
value <= 1
("", " -minscore=" + str(value))[value is not None and value!=vdef]
("", " -maxscore=" + str(value))[value is not None and value!=vdef]
("", " -tagmatch=" + str(value))[value is not None]
("", " -valuematch=" + str(value))[value is not None]
("", " -stricttags")[ bool(value) ]
("", " -flatreformat")[ bool(value) ]
("", " -mincuts=" + str(value))[value is not None and value!=vdef]
value >= 1
value <= 1000
("", " -maxcuts=" + str(value))[value is not None and value!=vdef]
("", " -sitelen=" + str(value))[value is not None and value!=vdef]
value >= 2
value <= 20
("", " -single")[ bool(value) ]
(" -noblunt", "")[ bool(value) ]
(" -nosticky", "")[ bool(value) ]
(" -noambiguity", "")[ bool(value) ]
("", " -plasmid")[ bool(value) ]
("", " -methylation")[ bool(value) ]
(" -nocommercial", "")[ bool(value) ]
(" -nolimit", "")[ bool(value) ]
("", " -orfminsize=" + str(value))[value is not None and value!=vdef]
value >= 0
("", " -threeletter")[ bool(value) ]
("", " -number")[ bool(value) ]
("", " -width=" + str(value))[value is not None and value!=vdef]
value >= 1
("", " -length=" + str(value))[value is not None and value!=vdef]
value >= 0
("", " -margin=" + str(value))[value is not None and value!=vdef]
value >= 0
(" -noname", "")[ bool(value) ]
(" -nodescription", "")[ bool(value) ]
("", " -offset=" + str(value))[value is not None and value!=vdef]
("", " -html")[ bool(value) ]
("" , " -outfile=" + str(value))[value is not None]
e_outfile
" -auto -stdout"
"$value"
str(value)
not $hmmer
hmmer is None
" $value"
" " +str(value)
not ($hmmer)
not (hmmer)
$protein is not defined
protein is None
" $value"
" " + str(value)
not ($protein)
not (protein)
defined $hmmer
hmmer is not None
" -hmmer"
" -hmmer"
" $value"
" " + str(value)
" -silent -quiet"
" -silent -quiet"
(defined $value) ? " -u $value" : ""
( "" , " -u " + str(value) )[ value is not None ]
(defined $value) ? " -v $value" : ""
( "" , " -v " + str(value) )[ value is not None ]
(defined $value and $value ne $vdef) ? " $value" : ""
( "" , " " + str(value) )[ value is not None and value != vdef]
($value) ? " -tabs" : ""
( "" , " -tabs" )[ value ]
not $hmmer
hmmer is None
(defined $value) ? " -s $value" : ""
( "" , " -s " + str(value) )[ value is not None ]
(defined $value) ? " -t $value" : ""
( "" , " -t " + str(value) )[ value is not None ]
(defined $value and $value != $vdef) ? " -g $value" : ""
( "" , " -g " + str(value) )[ value is not None and value != vdef]
(defined $value and $value != $vdef) ? " -e $value" : ""
( "" , " -e " + str(value) )[ value is not None and value != vdef]
(defined $value and $value ne $vdef) ? " -m $value" : ""
( "" , " -m" + str(value) )[ value is not None and value != vdef]
(defined $value and $value ne $vdef) ? " -init $value" : ""
( "" , " -init " + str(value) )[ value is not None and value != vdef]
(defined $value and $value != $vdef) ? " -subs $value" : ""
( "" , " -subs " + str(value) )[ value is not None and value != vdef]
(defined $value and $value != $vdef) ? " -indel $value" : ""
( "" , " -indel " + str(value) )[ value is not None and value != vdef]
(defined $value and $value ne $vdef) ? " -null $value" : ""
( "" , " -null " + str(value) )[ value is not None and value != vdef]
(defined $value and $value != $vdef) ? " -alln $value" : ""
( "" , " -alln " + str(value) )[ value is not None and value != vdef]
$wise2 eq "genewise"
wise2 == "genewise"
(defined $value and $value ne $vdef) ? " -gene $value" : ""
( "" , " -gene " + str(value) )[ value is not None and value != vdef]
(defined $value and $value ne $vdef) ? " -cfreq $value" : ""
( "" , " -cfreq " + str(value) )[ value is not None and value != vdef]
(defined $value and $value ne $vdef) ? " -splice $value" : ""
( "" , " -splice " + str(value) )[ value is not None and value != vdef]
(defined $value and $value ne $vdef) ? " -intron $value" : ""
( "" , " -intron " + str(value) )[ value is not None and value != vdef]
(defined $value and $value ne $vdef) ? " -insert $value" : ""
( "" , " -insert " + str(value) )[ value is not None and value != vdef]
($value) ? " -pretty" : ""
( "" , " -pretty" )[ value ]
($value) ? " -para" : ""
( "" , " -para" )[ value ]
($value) ? " -sum" : ""
( "" , " -sum" )[ value ]
($value) ? " -pep" : ""
( "" , " -pep" )[ value ]
($value) ? " -alb" : ""
( "" , " -alb" )[ value ]
($value) ? " -pal" : ""
( "" , " -pal" )[ value ]
(defined $value and $value != $vdef) ? " -block $value" : ""
( "" , " -block " + str(value) )[ value is not None and value != vdef]
(defined $value) ? " -divide \"$value\"" : ""
( "" , " -divide " + str(value) )[ value is not None ]
$wise2 eq "genewise"
wise2 == "genewise"
($value) ? " -pseudo" : ""
( "" , " -pseudo" )[ value ]
($value) ? " -genes" : ""
( "" , " -genes" )[ value ]
($value) ? " -genesf" : ""
( "" , " -genesf" )[ value ]
($value) ? " -embl" : ""
( "" , " -embl" )[ value ]
($value) ? " -diana" : ""
( "" , " -diana" )[ value ]
($value) ? " -cdna" : ""
( "" , " -cdna" )[ value ]
($value) ? " -trans" : ""
( "" , " -trans" )[ value ]
($value) ? " -ace" : ""
( "" , " -ace" )[ value ]
($value) ? " -gff" : ""
( "" , " -gff" )[ value ]
($value) ? " -gener" : ""
( "" , " -gener" )[ value ]
$wise2 eq "genewise"
wise2 == "genewise"
(defined $value and $value != $vdef) ? " -splice_max_collar $value" : ""
( "" , " -splice_max_collar " + str(value) )[ value is not None and value != vdef]
(defined $value and $value != $vdef) ? " -splice_min_collar $value" : ""
( "" , " -splice_min_collar " + str(value) )[ value is not None and value != vdef]
(defined $value and $value != $vdef) ? " -splice_score_offset $value" : ""
( "" , " -splice_score_offset " + str(value) )[ value is not None and value != vdef]
($value) ? " -erroroffstd" : ""
( "" , " -erroroffstd" )[ value ]
("", " -infile=" + str(value))[value is not None]
("", " -sequence=" + str(value))[value is not None]
("" , " -outfile=" + str(value))[value is not None]
e_outfile
" -auto -stdout"
" -i $value "
( "" , " -i " + str( value ) + " " )[value is not None]
($value) ?"-T $value ": ""
( "" , " -T " + str( value ) )[value != vdef]
($value) ?"-S $value ": ""
( "" , " -S " + str( value ) )[value != vdef]
($value) ?"-D $value ": ""
( "" , " -D " + str( value ) )[value != vdef]
($value) ?"-L $value ": ""
( "" , " -L " + str( value ) )[value is not None and value!=vdef]
($value) ?"-V": ""
( "" , " -V " )[value]
$variant == 1
variant == 1
($value) ?"-X": ""
( "" , " -X " )[value]
($value) ?"-C $value ": ""
( "" , " -C " + str( value ) )[value is not None]
($value) ?"-E $value ": ""
( "" , " -E " + str( value ) )[value is not None]
$enztype == 0 or $enztype eq 'blunt'
enztype == 0 or enztype == 'blunt'
($value) ?"-P": ""
( "" , " -P " )[value]
($value) ?"-N": ""
( "" , " -N " )[value]
$enztype ne 'cohesive'
enztype != 'cohesive'
($value) ?"-A": ""
( "" , " -A " )[value]
($value) ?"-F $value ": ""
( "" , " -F " + str( value ) )[value != vdef]
$outputstyle eq 'image'
outputstyle == 'image'
*.png
"*.png"
("", " -asequence=" + str(value))[value is not None]
("", " -bsequence=" + str(value))[value is not None]
("", " -datafile=" + str(value))[value is not None and value!=vdef]
("", " -gapopen=" + str(value))[value is not None]
value >= 0
("", " -gapextend=" + str(value))[value is not None]
value >= 0
("" , " -outfile=" + str(value))[value is not None]
("", " -aformat=" + str(value))[value is not None and value!=vdef]
e_aformat_outfile in ['FASTA', 'MSF']
e_outfile
e_aformat_outfile in ['PAIR', 'MARKX0', 'MARKX1', 'MARKX2', 'MARKX3', 'MARKX10', 'SRS', 'SRSPAIR', 'SCORE', 'UNKNOWN', 'MULTIPLE', 'SIMPLE', 'MATCH']
e_outfile
" -auto -stdout"
" $value"
" "+str(value)
($value) ? " -w" : ""
("", " -w")[ value ]
" >psort.html"
" >psort.html"
"psort.html"
"psort.html"
' -i ' + str(value)
('', ' -n ' + str(value) )[value is not None]
('', ' -s rankoptimizer' )[value]
splitOut
"*.offset"
splitOut
"*.seq"
"kronaextract.out"
not splitOut
' -o kronaextract.out'
"blastall"
"blastall"
" -p $value"
" -p "+ str(value)
$blast2 =~ /^blast[px]$/
blast2 in [ "blastx" , "blastp" ]
" -d $value"
" -d "+ str(value)
$blast2 =~ /^(blastn|tblast[nx]|psitblastn)$/
blast2 in [ "blastn" , "tblastx", "tblastn" , "psitblastn" ]
" -d $value"
" -d "+ str(value)
" -i $query"
" -i "+ str(query_seq)
defined $start_region
start_region is not None
(defined $value) ? " -L \"$start_region $value\"" : " -L \"$start_region\""
(' -L "%s"' % (str(start_region)), ' -L "%s %s"' % (str(start_region), str(value)))[value is not None]
$blast2 =~ /^t?blastn$/
blast2 in [ "blastn" , "tblastn" ]
(defined $value) ? " -B $value" : ""
("" , " -B "+str(value))[value is not None]
(defined $value) ? " -G $value" : ""
("" , " -G "+str(value))[value is not None]
(defined $value) ? " -E $value" : ""
("" , " -E "+str(value))[value is not None]
$blast2 ne "blastn"
blast2 != "blastn"
(defined $value and $value ne $vdef) ? " -M $value" : ""
("" , " -M "+str(value))[value is not None and value != vdef]
$blast2 eq "blastn"
blast2 == "blastn"
(defined $value and $value != $vdef) ? " -q $value" : ""
("" , " -q "+str(value))[value is not None and value != vdef]
(defined $value and $value != $vdef) ? " -r $value" : ""
("" , " -r "+str(value))[value is not None and value != vdef]
(defined $value) ? " -w $value" : ""
("", " -w "+str(value))[value is not None]
($value) ? "" : " -F F"
(" -F F" , "")[value]
$filter and not $other_masking
filter and not other_masking
""
""
" -F C"
" -F C"
" -F \"C;S\""
" -F \"C;S\""
" -F D"
" -F D"
$filter and not $other_filters
filter and not other_filters
""
""
" -F \"m S\""
" -F \"m S\""
" -F \"m D\""
" -F \"m D\""
" -F \"m C\""
" -F \"m C\""
" -F m"
" -F m"
($value eq 'null' or $value eq 'v1' or $value eq 'v2' or $value eq 'v3']) or ($value eq 'v4' and $lower_case)
value in ['null', 'v1', 'v2', 'v3'] or (value == 'v4' and lower_case)
($value) ? " -U T" : ""
("", " -U T")[value]
(defined $value and $value != $vdef) ? " -e $value" : ""
("" , " -e "+str(value))[value is not None and value != vdef]
(defined $value) ? " -W $value" : ""
("" , " -W "+str(value))[value is not None]
(defined $value) ? " -A $value" : ""
("" , " -A "+str(value))[value is not None]
(defined $value)? " -f $value" : ""
("" , " -f " + str(value))[ value is not None ]
(defined $value) ? " -X $value" : ""
("" , " -X "+str(value))[value is not None]
(defined $value and $value != $vdef ) ? " -y $value" : ""
("" , " -y "+str(value))[value is not None and value != vdef]
(defined $value) ? " -Z $value" : ""
("" , " -Z "+str(value))[value is not None]
(defined $value) ? " -Y $value" : ""
("" , " -Y "+str(value))[value is not None]
(defined $value) ? " -K $value" : ""
("" , " -K "+str(value))[value is not None]
$blast2 ne "tblastx"
blast2 != "tblastx"
($value) ? "" : " -g F "
(" -g F " , "")[value]
$blast2 ne "blastn"
blast2 != "blastn"
($value ne "0") ? " -P $value" : ""
("" , " -P "+str(value))[value != "0"]
$blast2 =~ /^t?blastx$/
blast2 in [ "blastx" , "tblastx" ]
(defined $value and $value ne $vdef) ? " -Q $value" : ""
("" , " -Q "+str(value))[value is not None and value != vdef]
$blast2 =~ /^tblast[nx]$/
blast2 in [ "tblastn", "tblastx" ]
($value ne $vdef) ? " -D $value" : ""
("" , " -D "+str(value))[value != vdef]
$blast2 =~ /^(blastn|t?blastx)$/
blast2 in [ "blastn" ,"blastx" , "tblastx" ]
(defined $value and $value ne $vdef) ? " -S $value" : ""
("" , " -S "+str(value))[value is not None and value != vdef]
(defined $value and $value != $vdef) ? " -v $value" : ""
("" , " -v "+str(value))[value is not None and value != vdef]
(defined $value and $value != $vdef) ? " -b $value" : ""
("" , " -b "+str(value))[value is not None and value != vdef]
(defined $value and $value ne $vdef) ? " -m $value" : ""
("" , " -m "+str(value))[value is not None and value != vdef]
$view_alignments ne "7"
view_alignments != "7"
" -o blast2.txt"
" -o blast2.txt"
$view_alignments eq "7"
view_alignments == "7"
" -o blast2.xml"
" -o blast2.xml"
$view_alignments !~ /^[78]$/
view_alignments not in [ "7" , "8" ]
($value) ? " && html4blast -g -o blast2.html blast2.txt" : ""
("" , " && html4blast -g -o blast2.html blast2.txt")[value]
$view_alignments ne "7"
view_alignments != "7"
"blast2.txt"
"blast2.txt"
$view_alignments eq "7"
view_alignments == "7"
"blast2.xml"
"blast2.xml"
$view_alignments !~ /^[78]$/
view_alignments not in [ "7" , "8" ]
"blast2.html"
"blast2.html"
$view_alignments !~ /^[78]$/
view_alignments not in ["7", "8"]
"*.png"
"*.gif"
"*.png"
"*.gif"
not $oldhmmfile
oldhmmfile is not None
" $oldhmmfile"
" " + str(oldhmmfile)
not defined $oldbinfile
oldbinfile is None
not $oldhmmfile
oldbinfile is not None
" $oldbinfile"
" " + str(oldbinfile)
not defined $oldhmmfile
oldhmmfile is None
($value)? " $value":""
" "+str(value)
$new_format ne '-2'
new_format != '-2'
($value ne $vdef)? " --outfmt $value":""
("", " --outfmt "+str(value))[value !=vdef]
$new_format eq '-a' or $new_format eq '-2'
new_format == '-a' or new_format == '-2'
(defined $oldhmmfile)? "> $oldhmmfile.convert": "> $oldbinfile.convert"
("> " + str(oldbinfile) + ".convert", "> " + str(oldhmmfile) + ".convert")[oldhmmfile is not None]
(defined $oldhmmfile)? "$oldhmmfile.convert": "$oldbinfile.convert"
(str(oldbinfile) + ".convert" , str(oldhmmfile) + ".convert")[oldhmmfile is not None]
$new_format eq '-b'
new_format == '-b'
(defined $oldhmmfile)? "> $oldhmmfile.bin": "> $oldbinfile.bin"
("> " + str(oldbinfile) + ".bin", "> " + str(oldhmmfile) + ".bin")[oldhmmfile is not None]
(defined $oldhmmfile)? "$oldhmmfile.bin":"oldbinfile.bin"
(str(oldbinfile) + ".bin" , str(oldhmmfile) + ".bin")[oldhmmfile is not None]
("", " -sequence=" + str(value))[value is not None]
("", " -table=" + str(value))[value is not None and value!=vdef]
("" , " -outfile=" + str(value))[value is not None]
("", " -osformat=" + str(value))[value is not None and value!=vdef]
e_outfile
" -auto -stdout"
" $value"
" "+str(value)
" $value"
" "+str(value)
not defined $Bit_cutoff and $model_specific ne '--cut_ga' and $model_specific ne '--cut_nc'
Bit_cutoff is None and model_specific != '--cut_ga' and model_specific != '--cut_nc'
(defined $value and $value != $vdef) ? " -E $value" : ""
( "" , " -E " + str(value) )[ value is not None and value != vdef]
$E_value_cutoff == 10.0 and $model_specific ne '--cut_ga' and $model_specific ne '--cut_nc'
E_value_cutoff == 10.0 and model_specific != '--cut_ga' and model_specific != '--cut_nc'
(defined $value)? " -T $value" : ""
( "" , " -T " + str(value) )[ value is not None ]
not defined $domT and $model_specific ne '--cut_ga' and $model_specific ne '--cut_nc'
domT is None and model_specific != '--cut_ga' and model_specific != '--cut_nc'
(defined $value and $value != $vdef) ? " --domE $value" : ""
( "" , " --domE " + str(value) )[ value is not None and value !=vdef ]
$domE == 10.0 and $model_specific ne '--cut_ga' and $model_specific ne '--cut_nc'
domE == 10.0 and model_specific != '--cut_ga' and model_specific != '--cut_nc'
(defined $value) ? " --domT $value" : ""
( "" , " --domT " + str(value) )[ value is not None ]
not defined $incT and $model_specific ne '--cut_ga'
incT is None and model_specific != '--cut_ga'
(defined $value and value != vdef) ? " --incE $value" : ""
( "" , " --incE " + str(value) )[ value is not None and value != vdef]
defined $incdomT and not defined model_specific
incdomT is not None and model_specific is None
(defined $value and value != vdef) ? " --incdomE $value" : ""
( "" , " --incdomE " + str(value) )[ value is not None and value != vdef]
$incE == 0.01 and $model_specific ne '--cut_ga'
incE == 0.01 and model_specific != '--cut_ga'
(defined $value) ? " --incT $value" : ""
( "" , " --incT " + str(value) )[ value is not None ]
$incdomE == 0.01 and not defined $model_specific
incdomE == 0.01 and model_specific is None
(defined $value) ? " --incdomT $value" : ""
( "" , " --incdomT " + str(value) )[ value is not None ]
not defined $Bit_cutoff and not $E_value_cutoff == 10.0 and not defined $incdomT and $incdomE == 0.01
not Bit_cutoff and E_value_cutoff == 10.0 and incdomT is None and incdomE == 0.01
(defined $value and $value ne $vdef) ? " $value" : ""
( "" , " " + str(value) )[ value is not None and value != vdef]
($value) ? " --max" : ""
( "" , " --max " )[ value ]
not max
not max
(defined $value and $value != $vdef ) ? " --F1 $value" : ""
( "" , " --F1 " + str(value) )[ value is not None and value != vdef]
not max
not max
(defined $value and $value != $vdef ) ? " --F2 $value" : ""
( "" , " --F2 " + str(value) )[ value is not None and value != vdef]
not max
not max
(defined $value and $value != $vdef ) ? " --F3 $value" : ""
( "" , " --F3 " + str(value) )[ value is not None and value != vdef]
not max
not max
($value) ? " --nobias" : ""
( "" , " --nobias " )[ value ]
($value) ? " --nonull2" : ""
( "" , " --nonull2 " )[ value ]
(defined $value) ? " -Z $value" : ""
( "" , " -Z " + str(value) )[ value is not None ]
(defined $value) ? " --domZ $value" : ""
( "" , " --domZ " + str(value) )[ value is not None ]
(defined $value and $value != $vdef) ? " --seed $value " : ""
( "" , " --seed " + str(value) )[ value is not None and value !=vdef ]
0 <= $value
0 <= value
(defined $value ) ? " -o $value" : ""
( " " , " -o " + str(value) )[ value is not None ]
defined $outfile_name
outfile_name is not None
$outfile_name
str(outfile_name)
(defined $value) ? " --tblout $value" : ""
( "" , " --tblout " + str(value) )[ value is not None ]
$perseqfile_name
perseqfile_name
$perseqfile_name
str(perseqfile_name)
(defined $value) ? " --domtblout $value" : ""
( "" , " --domtblout " + str(value) )[ value is not None ]
($value) ? " --acc " : ""
( "" , " --acc " )[ value ]
($value) ? " --noali " : ""
( "" , " --noali " )[ value ]
textw == 120
textw == 120
($value) ? " --notextw " : ""
( "" , " --notextw " )[ value ]
(defined $value and $value != $vdef) ? " --textw $value " : ""
( "" , " --textw " + str(value) )[ value is not None and value !=vdef ]
$perdomfile_name
perdomfile_name
$perdomfile_name
str(perdomfile_name)
(defined $value) ? " $value" : " -- "
( " -- " , " " + str(value) )[ value is not None ]
not defined $pdbid and defined $pdbfile
pdbfile is not None and pdbid is None
(defined $value) ? "cat
( "" , "cat
defined $pdbid and not defined $pdbfile
pdbid is not None and pdbfile is None
($value) ? " -na " : ""
( "" , " -na " )[ value ]
($value) ? " -c " : ""
( "" , " -c " )[ value ]
($value) ? " -ssa " : ""
( "" , " -ssa " )[ value ]
($value) ? " -x " : ""
( "" , " -x " )[ value ]
($value) ? " -alt2 " : ""
( "" , " -alt2 " )[ value ]
"dssp.out"
"dssp.out"
"hmmalign"
"hmmalign"
" $seqfile"
" " + str(seqfile)
" $value"
" "+str(value)
(defined $value and $value ne $vdef)? " $value" : ""
("", " " + str(value))[ value is not None and value != vdef]
($value) ? " --allcol : ""
( "" , " --allcol " )[ value ]
(defined $value) ? " --mapali $value" : ""
( "" , " --mapali " + str(value) )[ value is not None ]
($value) ? " --trim" : ""
( "", " --trim" )[ value ]
(defined $value)? " -o $value" : ""
("", " -o " + str(value))[value is not None]
defined($outfile_name)
outfile_name is not None
"$outfile_name"
str(outfile_name)
not defined($outfile_name)
outfile_name is None
"hmmalign.out"
"hmmalign.out"
(defined $value and $value ne $vdef) ? " --outformat $value" : ""
( "" , " --outformat " + str( value) )[ value is not None and value != vdef ]
("", " -sequence=" + str(value))[value is not None]
("", " -amino=" + str(value))[value is not None and value!=vdef]
value >= 0
("", " -carboxyl=" + str(value))[value is not None and value!=vdef]
value >= 0
(" -notermini", "")[ bool(value) ]
("", " -lysinemodified=" + str(value))[value is not None and value!=vdef]
value >= 0
("", " -disulphides=" + str(value))[value is not None and value!=vdef]
value >= 0
("", " -step=" + str(value))[value is not None and value!=vdef]
value >= .01
value <= 1.
("", " -plot")[ bool(value) ]
(" -noreport", "")[ bool(value) ]
e_plot
(" -graph=" + str(vdef), " -graph=" + str(value))[value is not None and value!=vdef]
e_plot
("" , " -goutfile=" + str(value))[value is not None]
e_plot and e_graph == "png"
"*.png"
e_plot and e_graph == "gif"
"*.gif"
e_plot and e_graph == "ps" or e_graph == "cps"
"*.ps"
e_plot and e_graph == "meta"
"*.meta"
e_plot and e_graph == "data"
"*.dat"
e_report
("" , " -outfile=" + str(value))[value is not None]
e_outfile
" -auto -stdout"
("", " -seqall=" + str(value))[value is not None]
("", " -infile=" + str(value))[value is not None]
("", " -mismatchpercent=" + str(value))[value is not None and value!=vdef]
("" , " -outfile=" + str(value))[value is not None]
e_outfile
" -auto -stdout"
"seq-gen"
"seq-gen"
"< $value"
"< " + str(value)
(defined $value and $value != $vdef)? " -l $value":""
("" , " -l " + str(value))[ value is not None and value != vdef]
(defined $value and $value != $vdef)? " -n $value":""
("" , " -n " + str(value))[ value is not None and value != vdef]
(defined $value and $value != $vdef)? " -p $value":""
("" , " -p " + str(value))[ value is not None and value != vdef]
not defined $scale_tree
scale_tree is None
(defined $value and $value != $vdef)? " -s $value":""
("" , " -s " + str(value))[ value is not None and value != vdef]
$value > 0
value > 0
$scale_branch != 1.0
scale_branch != 1.0
(defined $value)? " -d $value":""
("" , " -d " + str(value))[ value is not None ]
$value > 0
value > 0
(defined $value)? " -k $value":""
("" , " -k " + str(value))[ value is not None ]
(defined $value )? " -m $value" : ""
( "" , " -m " + str(value) )[ value is not None ]
(defined $value)? " -a $value":""
("" , " -a " + str(value))[ value is not None ]
(defined $value)? " -g $value":""
("" , " -g " + str(value))[ value is not None ]
$value >= 2 and $value <= 32
value >= 2 and value <= 32
(defined $value and $value != $vdef)? " -i $value":""
("" , " -i " + str(value))[ value is not None and value != vdef]
$value >= 0.0 and $value <= 1.0
value >= 0.0 and value <= 1.0
""
""
""
""
""
""
defined $rate1 and defined $rate2 and defined $rate3
rate1 is not None and rate2 is not None and rate3 is not None
" -c $rate1 $rate2 $rate3"
" -c %f %f %f " %(rate1,rate2,rate3)
$model eq 'HKY' or $model eq 'F84'
model =='HKY' or model == 'F84'
(defined $value)? " -t $value":""
("" , " -t " + str(value))[ value is not None ]
(defined $value and $value ne $vdef)? " -r $value":""
("" , " -r " + str(value))[ value is not None and value != vdef]
""
""
""
""
""
""
""
""
defined $freqA and defined $freqC and defined $freqG and defined $freqT
freqA is not None and freqC is not None and freqG is not None and freqT is not None
" -f $freqA,$freqC,$freqG,$freqT"
" -f " + str(freqA) + "," + str(freqC) + "," + str(freqG) + "," + str(freqT)
(defined $value)? "-z $value":""
("" , "-z " + str(value))[ value is not None ]
(defined $value and $value ne $vdef)? " -o$value":""
("" , " -o" + str(value))[ value is not None and value != vdef]
($value)? " -q":""
("" , " -q")[ value ]
($value)? " -wa":""
("" , " -wa")[ value ]
($value)? " -wr":""
("" , " -wr")[ value ]
"seqgen.out"
"seqgen.out"
(defined $value) ? " -profile1=$value" : ""
( "" , " -profile1=" + str( value ) )[value is not None]
(defined $value) ? " -profile2=$value" : ""
( "" , " -profile2=" + str( value ) )[value is not None]
(defined $value) ? " -type=$value" : ""
("", " -type="+str(value))[value is not None]
($value eq "fast") ? " -quicktree" : ""
( "" , " -quicktree")[ value == "fast"]
$quicktree eq "fast"
quicktree == "fast"
(defined $value and $value != $vdef) ? " -ktuple=$value" : ""
( "" , " -ktuple=" + str( value ) )[value is not None and value != vdef ]
(defined $value and $value != $vdef) ? " -topdiags=$value" : ""
( "" , " -topdiags=" + str( value ))[value is not None and value != vdef ]
(defined $value and $value != $vdef) ? " -window=$value" : ""
( "" , " -window=" + str( value ) )[ value is not None and value != vdef ]
(defined $value and $value != $vdef) ? " -pairgap=$value" : ""
( "" , " -pairgap=" + str( value ))[ value is not None and value != vdef ]
(defined $value and $value ne $vdef) ? " -score=$value" : ""
( "" , " -score=" +str( value ) )[value is not None and value !=vdef]
$quicktree eq "slow"
quicktree == "slow"
(defined $value and $value != $vdef) ? " -pwgapopen=$value" : ""
( "" , " -pwgapopen=" + str( value ) )[ value is not None and value != vdef ]
(defined $value and $value != $vdef) ? " -pwgapext=$value" : ""
( "" , " -pwgapext=" + str( value ) )[ value is not None and value != vdef ]
$typeseq eq "protein"
typeseq == "protein"
(defined $value and $value ne $vdef) ? " -pwmatrix=$value" : ""
( "" , " -pwmatrix=" + str(value) )[value is not None and value != vdef ]
$typeseq eq "dna"
typeseq == "dna"
(defined $value and $value ne $vdef) ? " -pwdnamatrix=$value" : ""
( "" , " -pwdnamatrix=" + str(value) )[ value is not None and value != vdef ]
($value) ? " -nosecstr1" : ""
( "" , " -nosecstr1")[ value ]
($value) ? " -nosecstr2" : ""
( "" , " -nosecstr2")[ value ]
(defined $value and $value != $vdef) ? " -helixgap=$value" : ""
( "" , " -helixgap=" + str( value ) )[ value is not None and value != vdef ]
(defined $value and $value != $vdef) ? " -strandgap=$value" : ""
( "" , " -strandgap=" + str( value ) )[ value is not None and value != vdef ]
(defined $value and $value != $vdef) ? " -loopgap=$value" : ""
( "" , " -loopgap=" + str( value ) )[ value is not None and value != vdef ]
(defined $value and $value != $vdef) ? " -terminalgap=$value" : ""
( "" , " -terminalgap=" + str( value ) )[ value is not None and value != vdef ]
(defined $value and $value != $vdef) ? " -helixendin=$value" : ""
( "" , " -helixendin=" + str( value ) )[ value is not None and value != vdef ]
(defined $value and $value != $vdef) ? " -helixendout=$value" : ""
( "" , " -helixendout=" + str( value ) )[ value is not None and value != vdef ]
(defined $value and $value != $vdef) ? " -strandendin=$value" : ""
( "" , " -strandendin=" + str( value ) )[ value is not None and value != vdef ]
(defined $value and $value != $vdef) ? " -strandendout=$value" : ""
( "" , " -strandendout=" + str( value ) )[ value is not None and value != vdef ]
(defined $value and $value ne $vdef) ? " -secstrout=$value" : ""
( "" , " -secstrout=" + str( value ) )[ value is not None and value != vdef ]
(defined $value and $value ne $vdef) ? " -output=$value" : ""
( "" , " -output=" + str( value) )[ value is not None and value != vdef ]
not defined $outputformat
outputformat is None
(defined $value and $value != $vdef) ? " -seqnos=on" : ""
( "" , " -seqnos=on")[ value is not None and value != vdef]
(defined $value and $value ne $vdef) ? " -outorder=$value" : ""
( "" , " -outorder=" + str(value))[ value is not None and value != vdef ]
(defined $value) ? " -outfile=$value" : ""
( "" , " -outfile=" + str( value))[ value is not None ]
not defined $outputformat
outputformat is None
(defined $outfile)? "$outfile":"*.aln"
("*.aln", str(outfile))[outfile is not None]
$outputformat =~ /^(NEXUS|GCG|PHYLIPI|FASTA)$/
outputformat in [ "NEXUS", "GCG", "PHYLIPI","FASTA"]
(defined $outfile)? "$outfile":"*.fasta *.nxs *.phy *.msf"
{ "OUTFILE":outfile, "FASTA":"*.fasta", "NEXUS": "*.nxs", "PHYLIPI": "*.phy" , 'GCG': '*.msf' }[( "OUTFILE", outputformat)[outfile is None]]
$outputformat =~ /^(GDE|PIR)$/
outputformat in [ 'GDE', 'PIR' ]
(defined $outfile)? "$outfile":"*.gde *.pir"
{ "OUTFILE":outfile, 'GDE':'*.gde', 'PIR':'*.pir}[( "OUTFILE", outputformat)[outfile is None]]
"*.dnd"
"*.dnd"
("", " -sequence=" + str(value))[value is not None]
("", " -angledata=" + str(value))[value is not None ]
("", " -energydata=" + str(value))[value is not None ]
("" , " -outfile=" + str(value))[value is not None]
e_outfile
" -auto -stdout"
" $value"
" "+str(value)
($value) ? " -P":""
("" , " -P")[ value ]
($value) ? " -A" : ""
( "" , " -A" )[ value ]
($value) ? " -O":""
("" , " -O")[ value ]
($value) ? " -G" : ""
( "" , " -G" )[ value ]
($value) ? " -C":""
("" , " -C")[ value ]
($value) ? " -H" : ""
( "" , " -H" )[ value ]
($value) ? " -D":""
("" , " -D")[ value ]
($value) ? " -T":""
("" , " -T")[ value ]
($value) ? " -E":""
("" , " -E")[ value ]
(defined $value and $value ne $vdef) ? " -t $value":""
("" , " -t "+ str(value))[ value is not None and value != vdef]
(defined $value) ? " -e $value":""
("" , " -e "+ str(value))[ value is not None ]
($value) ? " -r\\#":""
("" , " -r#")[ value ]
$matching or $start
matching and start
(defined $value) ? " -u $value":""
("" , " -u "+ str(value))[ value is not None ]
($value) ? " -F\\#":""
("" , " -F#")[ value ]
(defined $value and $value != $vdef) ? " -X $value":""
("" , " -X "+ str(value))[ value is not None and value != vdef]
(defined $value and $value !=$vdef) ? " -L $value":""
("" , " -L "+ str(value))[ value is not None and value !=vdef]
(defined $value and $value != $vdef) ? " -z $value" : ""
( "" , " -z "+ str(value) )[ value is not None and value != vdef]
not $trnascan_only and not $eufindtrna_only
not trnascan_only and not eufindtrna_only
(defined $value and $value ne $vdef) ? " -g $value":""
("" , " -g "+ str(value))[ value is not None and value != vdef]
(defined $value) ? " -c $value":""
("" , " -c " + str(value))[ value is not None]
(defined $value) ? " -n $value":""
("" , " -n "+ str(value))[ value is not None]
(defined $value) ? " -s $value":""
("" , " -s "+ str(value))[ value is not None ]
($value) ? " -f\\#":""
("" , " -f#")[ value ]
($value) ? " -a":""
("" , " -a")[ value ]
($value) ? " -m\\#":""
("" , " -m#")[ value ]
($value) ? " -d":""
("" , " -d")[ value ]
($value) ? " -l\\#":""
("" , " -l#")[ value ]
($value) ? " -q":""
("" , " -q")[ value ]
($value) ? " -b":""
("" , " -b")[ value ]
($value) ? " -N":""
("" , " -N")[ value ]
(defined $value) ? " -p $value":""
("" , " -p "+str(value))[ value is not None ]
($value) ? " -y":""
("" , " -y")[ value ]
"*.stats"
"*.log"
"*.ss"
"*.fpos"
"*.stats"
"*.log"
"*.ss"
"*.fpos"
"*.fpass.out"
"*.fpass.out"
("", " -seqall=" + str(value))[value is not None]
("", " -mwdata=" + str(value))[value is not None ]
("", " -menu=" + str(value))[value is not None and value!=vdef]
("", " -mono")[ bool(value) ]
("", " -unfavoured")[ bool(value) ]
("", " -ragging")[ bool(value) ]
("", " -termini=" + str(value))[value is not None and value!=vdef]
("", " -overlap")[ bool(value) ]
("", " -allpartials")[ bool(value) ]
("" , " -outfile=" + str(value))[value is not None]
("", " -rformat=" + str(value))[value is not None and value!=vdef]
e_rformat_outfile in ['DASGFF', 'DBMOTIF', 'DIFFSEQ', 'EMBL', 'EXCEL', 'FEATTABLE', 'GENBANK', 'GFF', 'LISTFILE', 'MOTIF', 'NAMETABLE', 'CODATA', 'REGIONS', 'SEQTABLE', 'SIMPLE', 'SRS', 'SWISS', 'TABLE', 'TAGSEQ']
e_outfile
" -auto -stdout"
("", " -feature")[ bool(value) ]
("", " -sequence=" + str(value))[value is not None]
("", " -firstonly")[ bool(value) ]
("" , " -outseq=" + str(value))[value is not None]
("", " -osformat=" + str(value))[value is not None and value!=vdef]
e_outseq
" -auto -stdout"
" $value"
" "+str(value)
(defined $value and $value ne $vdef)? " -c $value" : ""
( "" , " -c " + str(value) )[ value is not None and value != vdef]
($value)? " -g ":""
("" , " -g ")[ value ]
($value)? " -a":""
("" , " -a")[ value ]
(defined $value and $value != $vdef)? " -b $value" : ""
( "" , " -b " + str(value) )[ value is not None and value != vdef]
$intensity >= 0.0 and $intensity <= 1.0
intensity >= 0.0 and intensity <= 1.0
(defined $value and $value != $vdef)? " -l $value" : ""
( "" , " -l " + str(value) )[ value is not None and value != vdef]
(defined $value and $value != $vdef)? " -w $value" : ""
( "" , " -w " + str(value) )[ value is not None and value != vdef]
" -q"
" -q"
(defined $value and $value ne $vdef)? " -f $value" : ""
( "" , " -f " + str(value) )[ value is not None and value != vdef]
" -o"
" -o"
$output_format eq "2" or $output_format eq "3"
output_format == "2" or output_format == "3"
"dca.out"
"dca.out"
$output_format eq "1" or $output_format eq "4"
output_format == "1" or output_format == "4"
"dca.out"
"dca.out"
"blastpgp -p $value"
"blastpgp -p " + str(value)
" -i $query"
" -i " + str(value)
(defined $value and $value != $vdef)? " -S $value" : ""
( "" , " -S " + str(value) )[ value is not None and value != vdef]
(defined $value and $value != $vdef)? " -H $value" : ""
( "" , " -H " + str(value) )[ value is not None and value != vdef]
" -k $value"
" -k " + str(value)
" -d $value"
" -d " + str(value)
(defined $value and $value != $vdef) ? " -G $value" : ""
( "" , " -G " + str(value) )[ value is not None and value != vdef]
(defined $value and $value != $vdef) ? " -E $value" : ""
( "" , " -E " + str(value) )[ value is not None and value != vdef]
(defined $value and $value ne $vdef)? " -M $value" : ""
( "" , " -M " + str(value) )[ value is not None and value != vdef]
($value) ? " -F T" : ""
( "" , " -F T" )[ value ]
($value) ? " -U T" : ""
("", " -U T")[value]
(defined $value and $value != $vdef)? " -e $value":""
("" , " -e " + str(value))[ value is not None and value != vdef]
(defined $value) ? " -W $value" : ""
("" , " -W "+str(value))[value is not None]
$value >= 2 and $value <=3
value >= 2 and value <=3
(defined $value and $value != $vdef)? " -A $value" : ""
( "" , " -A " + str(value) )[ value is not None and value != vdef]
(defined $value and $value != $vdef)? " -f $value" : ""
( "" , " -f " + str(value) )[ value is not None and value !=vdef]
(defined $value)? " -X $value":""
("" , " -X " + str(value))[ value is not None ]
(defined $value and $value != $vdef)? " -Z $value" : ""
( "" , " -Z " + str(value) )[ value is not None and value != vdef]
(defined $value and $value != $vdef) ? " -y $value" : ""
( "" , " -y " + str(value) )[ value is not None and value != vdef]
(defined $value and $value != $vdef) ? " -Y $value" : ""
("" , " -Y "+str(value))[value is not None and value !=vdef]
(defined $value) ? " -K $value" : ""
("" , " -K "+str(value))[value is not None]
($value eq "0") ? " -P $value" : ""
("" , " -P "+str(value))[value != "0"]
(defined $value and $value != $vdef) ? " -N $value" : ""
("" , " -N "+str(value))[value is not None and value !=vdef]
(defined $value and $value != $vdef) ? " -j $value" : ""
("" , " -j "+str(value))[value is not None and value !=vdef]
(defined $value and $value != $vdef) ? " -c $value" : ""
("" , " -c "+str(value))[value is not None and value !=vdef]
(defined $value and $value != $vdef) ? " -h $value" : ""
("" , " -h "+str(value))[value is not None and value !=vdef]
(defined $value and $value != $vdef) ? " -v $value" : ""
( "" , " -v " + str(value) )[ value is not None and value != vdef]
(defined $value and $value != $vdef) ? " -b $value" : ""
( "" , " -b " + str(value) )[ value is not None and value != vdef]
(defined $value and $value ne $vdef)? " -m $value" : ""
( "" , " -m " + str(value) )[ value is not None and value != vdef]
$view_alignments ne "7"
view_alignments != "7"
" -o phiblast.txt"
" -o phiblast.txt"
$view_alignments eq "7"
view_alignments == "7"
" -o phiblast.xml"
" -o phiblast.xml"
$view_alignments !~ /^[78]$/
view_alignments not in [ "7" , "8" ]
($value) ? " && html4blast -g -o phiblast.html phiblast.txt" : ""
("" , " && html4blast -g -o phiblast.html phiblast.txt")[value]
($value)? " -J":""
("" , " -J")[ value ]
$believe
believe
(defined $value)? " -O $value" : ""
( "" , " -O " + str(value) )[ value is not None ]
$view_alignments ne "7"
view_alignments != "7"
"phiblast.txt"
"phiblast.txt"
$view_alignments eq "7"
view_alignments == "7"
"phiblast.xml"
"phiblast.xml"
$view_alignments !~ /^[78]$/
view_alignments not in ["7", "8"]
"phiblast.html"
"phiblast.html"
$view_alignments !~ /^[78]$/
view_alignments not in ["7", "8"]
"*.png"
"*.gif"
"*.png"
"*.gif"
("", " -sequence=" + str(value))[value is not None]
("", " -nucmethod=" + str(value))[value is not None and value!=vdef]
("", " -protmethod=" + str(value))[value is not None and value!=vdef]
("", " -ambiguous")[ bool(value) ]
("", " -gapweight=" + str(value))[value is not None and value!=vdef]
("", " -position=" + str(value))[value is not None and value!=vdef]
("", " -calculatea")[ bool(value) ]
("", " -parametera=" + str(value))[value is not None and value!=vdef]
("" , " -outfile=" + str(value))[value is not None]
e_outfile
" -auto -stdout"
("", " -feature")[ bool(value) ]
("", " -sequence=" + str(value))[value is not None]
("" , " -outseq=" + str(value))[value is not None]
("", " -osformat=" + str(value))[value is not None and value!=vdef]
e_outseq
" -auto -stdout"
("", " -sequence=" + str(value))[value is not None]
("", " -idc=" + str(value))[value is not None and value!=vdef]
value >= 0
value <= 6
("" , " -outfile=" + str(value))[value is not None]
("", " -rformat=" + str(value))[value is not None and value!=vdef]
e_rformat_outfile in ['DASGFF', 'DBMOTIF', 'DIFFSEQ', 'EMBL', 'EXCEL', 'FEATTABLE', 'GENBANK', 'GFF', 'LISTFILE', 'MOTIF', 'NAMETABLE', 'CODATA', 'REGIONS', 'SEQTABLE', 'SIMPLE', 'SRS', 'SWISS', 'TABLE', 'TAGSEQ']
e_outfile
" -auto -stdout"
" @" + str(value)
"fetchSequences.out"
" -auto -stdout"
"fitch <fitch.params"
"fitch <fitch.params"
$infile ne "infile"
infile != "infile"
"ln -s $infile infile && "
"ln -s " + str( value ) + " infile && "
""
""
"D\\n"
"D\n"
($value) ? "-\\n" : ""
( "" , "-\n" )[ value ]
(defined $value and $value != $vdef) ? "P\\n$value\\n" : ""
( "" , "P\n" + str(value ) + "\n" )[ value is not None and value != vdef ]
not $user_tree
not user_tree
($value) ? "J\\n$jumble_seed\\n$jumble_number\\n" : ""
( "" , "J\n"+str( jumble_seed ) +"\n" + str( jumble_number ) +"\n" )[ value ]
$jumble
jumble
""
""
$value > 0 and ($value % 2) != 0
value > 0 and (value % 2) != 0
$jumble
jumble
""
""
($value) ? "M\\n$multiple_number\\n$multiple_seed\\n" : ""
( "", "M\n"+str(multiple_number)+"\n"+str(multiple_seed)+"\n")[value]
$multiple
multiple
""
""
$value <= 1000
value <= 1000
$multiple
multiple
""
""
$value > 0 and ($value % 2) != 0
value > 0 and (value % 2) != 0
$multiple and $print_treefile
multiple and print_treefile
($value) ? " && cp infile fitch.infile && cp fitch.outtree intree && consense <consense.params && mv outtree consense.outtree && mv outfile consense.outfile" : ""
( "" , " && cp infile fitch.infile && cp fitch.outtree intree && consense <consense.params && mv outtree consense.outtree && mv outfile consense.outfile" )[ value ]
$consense
consense
"Y\\n"
"Y\n"
$consense
consense
"T\\n"
"T\n"
$consense
consense
"consense.outfile"
"consense.outfile"
$consense
consense
"consense.outtree"
"consense.outtree"
defined $tree_file
tree_file is not None
($value) ? "U\\n" : ""
( "" , "U\n")[ value ]
not ( $user_tree and $jumble )
not ( user_tree and jumble )
$user_tree
user_tree
(defined $value) ? "cat $tree_file >> intree; " : ""
("" , "cat "+str( tree_file ) + " >> intree; " )[ value is not None ]
$user_tree
user_tree
($value) ? "N\\n" : ""
( "" , "N\n" )[ value ]
($value) ? "" : "3\\n"
( "3\n" , "" )[ value ]
($value) ? "" : "4\\n"
( "4\n" , "" )[ value ]
($value) ? "1\\n" : ""
( "" , "1\n" )[ value ]
(defined $value and $value != $vdef) ? "O\\n$value\\n" : ""
( "" , "O\n" +str( value )+ "\n" )[ value is not None and value != vdef]
$value > 0
value > 0
""
""
"L\\n"
"L\n"
"R\\n"
"R\n"
($value) ? "S\\n" : ""
( "" , "S\n" )[ value ]
($value) ? "G\\n" : ""
( "", "G\n")[ value ]
" && mv outfile fitch.outfile"
" && mv outfile fitch.outfile"
"fitch.outfile"
"fitch.outfile"
$print_treefile
print_treefile
" && mv outtree fitch.outtree"
" && mv outtree fitch.outtree"
"fitch.outtree"
"fitch.outtree"
"Y\\n"
"Y\n"
"0\\n"
"0\n"
" $db:"
" " + db + ":"
"$value"
str(value)
($value) ? " -a" : ""
( "" , " -a" )[ value ]
($value) ? " -i" : ""
( "" , " -i" )[ value ]
$db =~ /^(embl|genbank|imgt|rdpii)$/
db in ( 'embl' , 'genbank' , 'imgt' ,'rdpii' )
"golden.out"
"golden.out"
$db =~ /^(genpept|uniprot)$/
db in ( 'genpept' , 'uniprot' )
"golden.out"
"golden.out"
$db eq 'refseq'
db == 'refseq'
"golden.out"
"golden.out"
$db eq 'prosite'
db == 'prosite'
"golden.out"
"golden.out"
$db eq 'enzyme'
db == 'enzyme'
"golden.out"
"golden.out"
("", " -seqall=" + str(value))[value is not None]
("", " -cfile=" + str(value))[value is not None and value!=vdef]
("" , " -outfile=" + str(value))[value is not None]
e_outfile
" -auto -stdout"
"html4blast"
"html4blast"
" $value"
" %s" % str(value)
" -n"
" -n"
""
""
" -s"
" -s"
" -e"
" -e"
($value) ? " -g" : ""
("" , " -g")[ value ]
$graph
graph
($value) ? " -l" : ""
("" , " -l")[ value ]
$graph
graph
($value) ? " -q" : ""
("" , " -q")[ value ]
(defined $value and $value ne $vdef) ? " -o $value" : ""
("", " -o " + str(value))[value is not None and value != vdef]
$outfile
outfile
$graph
graph
"*.png"
"*.gif"
"*.png"
"*.gif"
not $alignment_input or ($sequences_input and $alignment_input)
not alignment_input or (sequences_input and alignment_input)
" -infile=$value"
" -infile=" + str( value )
not $alignment_input
not alignment_input
not $sequences_input or ($sequences_input and $alignment_input)
not sequences_input or (sequences_input and alignment_input)
" -infile=$value"
" -infile=" + str( value )
not $sequences_input
not sequences_input
($value eq "fast") ? " -quicktree" : ""
( "" , " -quicktree")[ value == "fast"]
(defined $value) ? " -type=$value" : ""
("", " -type="+str(value))[value is not None]
(defined $value and $value != $vdef) ? " -gapopen=$value" : ""
( "" , " -gapopen=" + str( value ))[ value is not None and value != vdef ]
(defined $value and $value != $vdef) ? " -gapext=$value" : ""
( "" , " -gapext=" + str( value ))[ value is not None and value != vdef ]
($value) ? " -endgaps" : ""
( "" ," -endgaps" )[ value ]
(defined $value and $value != $vdef) ? " -gapdist=$value" : ""
( "" , " -gapdist=" + str( value ))[ value is not None and value != vdef]
(defined $value and $value != $vdef) ? " -maxdiv=$value" : ""
( "" , " -maxdiv=" + str( value ))[ value is not None and value != vdef ]
(defined $value) ? " -newtree=$value" : ""
( "" , " -newtree=" + str( value ))[value is not None]
defined $newtree
newtree is not None
$newtree
newtree
(defined $value) ? " -usetree=$value" : ""
( "" ," -usetree=" + str( value ))[value is not None]
$typeseq eq "protein"
typeseq == "protein"
(defined $value and $value ne $vdef) ? " -matrix=$value" : ""
("", " -matrix="+str(value))[value is not None and value!=vdef]
($value) ? " -negative" : ""
( "" , " -negative" )[ value ]
($value) ? " -nopgap" : ""
( "" , " -nopgap" )[ value ]
($value) ? " -nohgap" : ""
( "" , " -nohgap" )[ value ]
($value and $value ne $vdef) ? " -hgapresidues=\\"$value\\"" : ""
( '' , ' -hgapresidues="%s"' % str(value) )[ value and value != vdef ]
$typeseq eq "dna"
typeseq == "dna"
(defined $value and $value ne $vdef) ? " -dnamatrix=$value" : ""
("", " -dnamatrix=" + str(value))[value is not None and value!=vdef]
(defined $value and $value != $vdef) ? " -transweight=$value" : ""
( "" , " -transweight=" + str( value ) )[ value is not None and value != vdef ]
$quicktree eq "fast"
quicktree == "fast"
(defined $value and $value != $vdef) ? " -ktuple=$value" : ""
( "" , " -ktuple=" + str( value ) )[value is not None and value != vdef ]
(defined $value and $value != $vdef) ? " -topdiags=$value" : ""
( "" , " -topdiags=" + str( value ))[value is not None and value != vdef ]
(defined $value and $value != $vdef) ? " -window=$value" : ""
( "" , " -window=" + str( value ) )[ value is not None and value != vdef ]
(defined $value and $value != $vdef) ? " -pairgap=$value" : ""
( "" , " -pairgap=" + str( value ))[ value is not None and value != vdef ]
(defined $value and $value ne $vdef) ? " -score=$value" : ""
( "" , " -score=" +str( value ) )[value is not None or value != vdef]
$quicktree eq "slow"
quicktree == "slow"
(defined $value and $value != $vdef) ? " -pwgapopen=$value" : ""
( "" , " -pwgapopen=" + str( value ) )[ value is not None and value != vdef ]
(defined $value and $value != $vdef) ? " -pwgapext=$value" : ""
( "" , " -pwgapext=" + str( value ) )[ value is not None and value != vdef ]
$typeseq eq "protein"
typeseq == "protein"
(defined $value and $value ne $vdef) ? " -pwmatrix=$value" : ""
( "" , " -pwmatrix=" + str(value) )[value is not None and value != vdef ]
$typeseq eq "dna"
typeseq == "dna"
(defined $value and $value ne $vdef) ? " -pwdnamatrix=$value" : ""
( "" , " -pwdnamatrix=" + str(value) )[ value is not None and value != vdef ]
(defined $value ) ? " -output=$value" : ""
( "" , " -output=" + str( value) )[ value is not None ]
not defined $outputformat
outputformat is None
(defined $value and $value != $vdef) ? " -seqnos=on" : ""
( "" , " -seqnos=on")[ value is not None and value != vdef]
(defined $value and $value ne $vdef) ? " -outorder=$value" : ""
( "" , " -outorder=" + str(value))[ value is not None and value != vdef ]
(defined $value) ? " -outfile=$value" : ""
( "" , " -outfile=" + str( value))[ value is not None ]
not defined $outputformat
outputformat is None
(defined $outfile)? "$outfile":"*.aln"
("*.aln", str(outfile))[outfile is not None]
$outputformat =~ /^(NEXUS|GCG|PHYLIPI|FASTA)$/
outputformat in [ "NEXUS", "GCG", "PHYLIPI","FASTA"]
(defined $outfile)? "$outfile":"*.fasta *.nxs *.phy *.msf"
{ "OUTFILE":outfile, "FASTA":"*.fasta", "NEXUS": "*.nxs", "PHYLIPI": "*.phy" , 'GCG': '*.msf' }[( "OUTFILE", outputformat)[outfile is None]]
$outputformat =~ /^(GDE|PIR)$/
outputformat in [ 'GDE', 'PIR' ]
(defined $outfile)? "$outfile":"*.gde *.pir"
{ "OUTFILE":outfile, 'GDE':'*.gde', 'PIR':'*.pir}[( "OUTFILE", outputformat)[outfile is None]]
not defined $newtree
newtree is None
"*.dnd"
"*.dnd"
$outputformat eq "GDE"
outputformat == "GDE"
($value) ? " -case=upper" : ""
( "" , " -case=upper" )[ value ]
("", " -sequence=" + str(value))[value is not None]
("", " -window=" + str(value))[value is not None and value!=vdef]
value >= 7
value <= 28
(" -nocoil", "")[ bool(value) ]
e_coil
("", " -frame")[ bool(value) ]
("", " -other")[ bool(value) ]
("" , " -outfile=" + str(value))[value is not None]
("", " -rformat=" + str(value))[value is not None and value!=vdef]
e_rformat_outfile in ['DASGFF', 'DBMOTIF', 'DIFFSEQ', 'EMBL', 'EXCEL', 'FEATTABLE', 'GENBANK', 'GFF', 'LISTFILE', 'MOTIF', 'NAMETABLE', 'CODATA', 'REGIONS', 'SEQTABLE', 'SIMPLE', 'SRS', 'SWISS', 'TABLE', 'TAGSEQ']
e_outfile
" -auto -stdout"
" $value"
" " + str(value)
($value) ? " -s" : ""
("", " -s")[value]
($value ne $vdef) ? " -m $value" : ""
("", " -m " + str(value))[value != vdef]
($value) ? " -c" : ""
("", " -c")[value]
(defined $value) ? " -l $value" : ""
("", " -l " + str(value))[value is not None]
("", " -sequence=" + str(value))[value is not None]
("" , " -outfile=" + str(value))[value is not None]
e_outfile
" -auto -stdout"
("", " -firstsequences=" + str(value))[value is not None]
("", " -secondsequences=" + str(value))[value is not None]
("", " -operator=" + str(value))[value is not None and value!=vdef]
("" , " -outfile=" + str(value))[value is not None]
e_outfile
" -auto -stdout"
("", " -sequence=" + str(value))[value is not None]
(" -nowheel", "")[ bool(value) ]
("", " -steps=" + str(value))[value is not None and value!=vdef]
value >= 2
value <= 100
("", " -turns=" + str(value))[value is not None and value!=vdef]
value >= 1
value <= 100
(" -graph=" + str(vdef), " -graph=" + str(value))[value is not None and value!=vdef]
("" , " -goutfile=" + str(value))[value is not None]
e_graph == "png"
"*.png"
e_graph == "gif"
"*.gif"
e_graph == "ps" or e_graph == "cps"
"*.ps"
e_graph == "meta"
"*.meta"
e_graph == "data"
"*.dat"
("", " -amphipathic")[ bool(value) ]
not e_amphipathic
("", " -squares=" + str(value))[value is not None and value!=vdef]
not e_amphipathic
("", " -diamonds=" + str(value))[value is not None and value!=vdef]
not e_amphipathic
("", " -octags=" + str(value))[value is not None and value!=vdef]
" -auto -stdout"
("", " -sequence=" + str(value))[value is not None]
("", " -cfile=" + str(value))[value is not None and value!=vdef]
("", " -window=" + str(value))[value is not None and value!=vdef]
("", " -uncommon")[ bool(value) ]
("", " -minimum=" + str(value))[value is not None and value!=vdef]
value >= 0.0
value <= .99
(" -noplot", "")[ bool(value) ]
e_plot
(" -graph=" + str(vdef), " -graph=" + str(value))[value is not None and value!=vdef]
e_plot
("" , " -goutfile=" + str(value))[value is not None]
e_plot and e_graph == "png"
"*.png"
e_plot and e_graph == "gif"
"*.gif"
e_plot and e_graph == "ps" or e_graph == "cps"
"*.ps"
e_plot and e_graph == "meta"
"*.meta"
e_plot and e_graph == "data"
"*.dat"
not e_plot
("" , " -outfile=" + str(value))[value is not None]
e_outfile
" -auto -stdout"
("", " -sequences=" + str(value))[value is not None]
("", " -scorefile=" + str(value))[value is not None and value!=vdef]
("", " -winsize=" + str(value))[value is not None and value!=vdef]
(" -graph=" + str(vdef), " -graph=" + str(value))[value is not None and value!=vdef]
("" , " -goutfile=" + str(value))[value is not None]
e_graph == "png"
"*.png"
e_graph == "gif"
"*.gif"
e_graph == "ps" or e_graph == "cps"
"*.ps"
e_graph == "meta"
"*.meta"
e_graph == "data"
"*.dat"
" -auto -stdout"
("", " -sequence=" + str(value))[value is not None]
("", " -exclude=" + str(value))[value is not None]
("" , " -outseq=" + str(value))[value is not None]
("", " -osformat=" + str(value))[value is not None and value!=vdef]
e_outseq
("" , " -junkoutseq=" + str(value))[value is not None]
("", " -osformat=" + str(value))[value is not None and value!=vdef]
e_junkoutseq
" -auto -stdout"
" -f$value"
" -f" + str(value)
(defined $value and $value != $vdef) ? " -s$value" : ""
( "" , " -s" + str(value) )[ value is not None and value != vdef]
(defined $value and $value != $vdef) ? " -n$value" : ""
( "" , " -n" + str(value) )[ value is not None and value != vdef]
(defined $value and $value != $vdef) ? " -i$value" : ""
( "" , " -i" + str(value) )[ value is not None and value != vdef]
(defined $value) ? " -l$value" : ""
( "" , " -l" + str(value) )[ value is not None]
(defined $value) ? " -t$value" : ""
( "" , " -t" + str(value) )[ value is not None ]
(defined $value and $value != $vdef) ? " -c$value" : ""
( "" , " -c" + str(value) )[ value is not None and value != vdef]
($value) ? " -a" : ""
( "" , " -a" )[ value ]
("", " -seqall=" + str(value))[value is not None]
("" , " -outfile=" + str(value))[value is not None]
e_outfile
("" , " -cdsoutseq=" + str(value))[value is not None]
("", " -osformat=" + str(value))[value is not None and value!=vdef]
e_cdsoutseq
("" , " -mrnaoutseq=" + str(value))[value is not None]
("", " -osformat=" + str(value))[value is not None and value!=vdef]
e_mrnaoutseq
("" , " -translationoutseq=" + str(value))[value is not None]
("", " -osformat=" + str(value))[value is not None and value!=vdef]
e_translationoutseq
("" , " -restoutseq=" + str(value))[value is not None]
("", " -osformat=" + str(value))[value is not None and value!=vdef]
e_restoutseq
" -auto -stdout"
("", " -sequence=" + str(value))[value is not None]
("", " -minpallen=" + str(value))[value is not None and value!=vdef]
value >= 1
("", " -maxpallen=" + str(value))[value is not None and value!=vdef]
("", " -gaplimit=" + str(value))[value is not None and value!=vdef]
value >= 0
("", " -nummismatches=" + str(value))[value is not None and value!=vdef]
value >= 0
("" , " -outfile=" + str(value))[value is not None]
e_outfile
(" -nooverlap", "")[ bool(value) ]
" -auto -stdout"
("", " -asequence=" + str(value))[value is not None]
("", " -bsequence=" + str(value))[value is not None]
("", " -pos=" + str(value))[value is not None]
value >= 0
("" , " -outseq=" + str(value))[value is not None]
("", " -osformat=" + str(value))[value is not None and value!=vdef]
e_outseq
" -auto -stdout"
"$value -v"
str(value) + " -v"
" -f"
" -f"
$pftools eq "pfscan"
pftools == "pfscan"
" $value"
" " + str(value)
($value) ? "
( "" , "
not $prosite
not prosite
" $value"
" " + str(value)
$pftools eq "pfsearch"
pftools == "pfsearch"
" $value"
" " + str(value)
""
""
($aa_or_nuc_db eq "protein" and $aadb ne "null") or ( $aa_or_nuc_db eq "user" and defined $userdb) or ($aa_or_nuc_db eq "dna" and $nucdb ne "null")
(aa_or_nuc_db == "protein" and aadb != "null") or (aa_or_nuc_db == "user" and userdb is not None) or (aa_or_nuc_db == "dna" and nucdb != "null")
$aa_or_nuc_db eq "protein"
aa_or_nuc_db == "protein"
(defined $value and $value ne $vdef) ? "
("", "
$aa_or_nuc_db eq "dna"
aa_or_nuc_db == "dna"
(defined $value and $value ne $vdef) ? "
("", "
$aa_or_nuc_db eq "user"
aa_or_nuc_db == "user"
(defined $value) ? " $value" : ""
("", " "+str(value) )[value is not None]
($value) ? " | psa2msa - " : ""
( "" , " | psa2msa - " )[ value ]
not $optimal
not optimal
(defined $value and $value != $vdef) ? " -C $value" : ""
("" , " -C " + str(value))[ value is not None and value != vdef]
(defined $value) ? " -M $value" : ""
("" , " -M " + str(value))[value is not None]
($value) ? " -b" : ""
("" , " -b")[ value ]
($value) ? " -r" : ""
("" , " -r")[ value ]
($value) ? " -u" : ""
("" , " -u")[ value ]
($value) ? " -a" : ""
("" , " -a")[ value ]
($value) ? " -m" : ""
("" , " -m")[ value ]
($value) ? " -l" : ""
("" , " -l")[ value ]
($value) ? " -L" : ""
("" , " -L")[ value ]
not $xpsa
not xpsa
($value) ? " -d" : ""
("" , " -d")[ value ]
not $Length
not Length
($value) ? " -k" : ""
("" , " -k")[ value ]
($value) ? " -s" : ""
("" , " -s")[ value ]
($value) ? " -x" : ""
("" , " -x")[ value ]
($value) ? " -y" : ""
("" , " -y")[ value ]
($value) ? " -z" : ""
("" , " -z")[ value ]
$listseq or $psa_format or $between
listseq or psa_format or between
(defined $value and $value != $vdef) ? " -W $value" : ""
("" , " -W "+str(value))[value is not None and value != vdef]
" < $value"
" < " + str(value)
($value)? " -a" : ""
( "" , " -a" )[ value ]
($value)? " -c" : ""
( "" , " -c" )[ value ]
($value)? " -p" : ""
( "" , " -p" )[ value ]
($value)? " -p0" : ""
( "" , " -p0" )[ value ]
(defined $value and $value != $vdef)? " -T $value" : ""
( "" , " -T " + str(value) )[ value is not None and value != vdef]
($value)? " -4" : ""
( "" , " -4" )[ value ]
(defined $value and $value ne $vdef)? " $value" : ""
( "" , " " + str(value) )[ value is not None and value != vdef]
(defined $value)? " -S $value" : ""
( "" , " -S " + str(value) )[ value is not None ]
($value)? " -C" : ""
( "" , " -C" )[ value ]
($value)? " -noLP" : ""
( "" , " -noLP" )[ value ]
($value)? " -noGU" : ""
( "" , " -noGU" )[ value ]
($value)? " -noCloseGU" : ""
( "" , " -noCloseGU" )[ value ]
(defined $value)? " -nsp $value" : ""
( "" , " -nsp " + str(value) )[ value is not None ]
(defined $value)? " -P $value" : ""
( "" , " -P " + str(value) )[ value is not None ]
Read energy parameters from paramfile, instead of using the default parameter set. ( documentation for details on the file format.)
($value)? " -noPS ": ""
( "" , " -noPS ")[ value ]
"*.ps"
"*.ps"
"protpars <protpars.params"
"protpars <protpars.params"
$infile ne "infile"
infile != "infile"
"ln -s $infile infile && "
"ln -s " + str(infile) + " infile && "
($value) ? "T\\n$threshold\\n" : ""
( "" , "T\n" + str( threshold ) + "\n" )[ value ]
$use_threshold
use_threshold
$value > 1
value > 1
(defined $value and $value ne $vdef) ? "C\\n$code\\n" : ""
( "" , "C\n"+str( code ) +"\n" )[ value is not None and value != vdef ]
($value) ? "J\\n$jumble_seed\\n$times2jumble\\n" : ""
( "" , "J\n" + str( jumble_seed ) + "\n" + str(times2jumble) + "\n" )[ value ]
not( $jumble and $seqboot)
not (jumble and seqboot)
$jumble
jumble
$value > 0 and ($value % 2) != 0
value > 0 and (value % 2) != 0
$jumble
jumble
($value) ? "seqboot <seqboot.params && mv outfile seqboot.outfile && rm infile && ln -s seqboot.outfile infile && " : ""
( "" , "seqboot < seqboot.params && mv outfile seqboot.outfile && rm infile && ln -s seqboot.outfile infile && " )[ value ]
not( $seqboot and $jumble)
not( seqboot and jumble)
$seqboot
seqboot
""
""
"J\\n"
""
"J\\nJ\\n"
"J\nJ\n"
"J\\nJ\\nJ\\n"
"J\nJ\nJ\n"
"J\\nJ\\nJ\\nJ\\n"
"J\nJ\nJ\nJ\n"
$seqboot
seqboot
(defined $value and $value != $vdef) ? "R\\n$value\\n" : ""
( "" , "R\n" + str( value ) + "\n" )[ value is not None and value != vdef ]
$replicates <= 1000
replicates <= 1000
$value > 1
value > 1
$seqboot
seqboot
"$value\\n"
str(value) + "\n"
$value > 0 and ($value % 2) != 0
value > 0 and (value % 2) != 0
$seqboot
seqboot
($seqboot_times2jumble * (defined $replicates) ? $replicates : 1) <= 100000
seqboot_times2jumble * ( 1 , replicates)[replicates is not None] <= 100000
$seqboot
seqboot
"M\\nD\\n$replicates\\n$seqboot_seed\\n$times2jumble\\n"
"M\nD\n" + str( replicates ) + "\n" + str( seqboot_seed ) + "\n"+ str( seqboot_times2jumble ) + "\n"
$seqboot and $print_treefile
seqboot and print_treefile
($value) ? " && cp infile protpars.infile && cp protpars.outtree intree && consense <consense.params && mv outtree consense.outtree && mv outfile consense.outfile" : ""
("" , " && cp infile protpars.infile && cp protpars.outtree intree && consense < consense.params && mv outtree consense.outtree && mv outfile consense.outfile" )[ value ]
($value) ? "U\\n" : ""
( "" , "U\n" )[ value ]
not ( $user_tree and $seqboot )
not ( user_tree and seqboot )
not ( $user_tree and $jumble )
not ( user_tree and jumble )
$user_tree
user_tree
(defined $value) ? "ln -s $tree_file intree && " : ""
( "" , "ln -s " + str( tree_file ) + " intree && ")[ value is not None ]
($value != $vdef) ? "" : "3\\n"
( "" , "3\n" )[ value != vdef ]
($value) ? "5\\n" : ""
( "" , "5\n" )[ value ]
($value != $vdef) ? "" : "6\\n"
( "" , "6\n" )[ value != vdef ]
($value) ? "1\\n" : ""
( "" , "1\n" )[ value ]
($value) ? "4\\n" : ""
( "" , "4\n" )[ value ]
(defined $value and $value != $vdef) ? "O\\n$value\\n" : ""
( "" , "O\n" + str( value ) +"\n" )[ value is not None and value != vdef ]
$value > 0
value > 0
" && mv outfile protpars.outfile"
" && mv outfile protpars.outfile"
"protpars.outfile"
"protpars.outfile"
$print_treefile
print_treefile
" && mv outtree protpars.outtree"
" && mv outtree protpars.outtree"
"protpars.outtree"
"protpars.outtree"
$seqboot
seqboot
"seqboot.outfile"
"seqboot.outfile"
"y\\n"
"y\n"
"0\\n"
"0\n"
$seqboot
seqboot
"y\\n"
"y\n"
$seqboot
seqboot
"0\\n"
"0\n"
$consense
consense
"Y\\n"
"Y\n"
$consense
consense
"T\\n"
"T\n"
$consense and $outgroup > 1
consense and outgroup > 1
"O\\n$outgroup\\n"
"0\n" + str(outgroup) + "\n"
$consense
consense
"consense.outfile"
"consense.outfile"
$consense
consense
"consense.outtree"
"consense.outtree"
($bootstrap) ? "cat > $infile.tmp;" : "fastDNAml"
("fastDNAml", "cat > %s.tmp;" % infile )[bootstrap]
" && clean_checkpoints"
" && clean_checkpoints"
"cat $value | "
"cat " + str(value) + " | "
(not $value and not ($fA and $fC and $fG and $fT )) ? "": "frequencies $fA $fC $fG $fT | "
( "" ,"frequencies %s %s %s %s | " % (str(fA), str(fC), str(fG), str(fT)) )[ not ( value and fA is None and fC is None and fG is None and fT is None) ]
not $frequencies
not frequencies
(defined $value and $value!=$vdef) ? " transition $value | " : ""
( "" , " transition " + str(value) + " | " )[ value is not None and value != vdef]
not $bootstrap
not bootstrap
($value) ? "jumble | " : ""
( "" , "jumble | " )[ value ]
defined $transition or $bootstrap or $jumble
transition is not None or bootstrap or jumble
($value) ? " global " : ""
( "" , " global ")[ value ]
(defined $transition or $bootstrap or $jumble) and $global_opp
(transition is not None or bootstrap or jumble) and global_opp
(defined $value) ? " $final_arrgt " : ""
( "" , " %s " % str(final_arrgt))[ value is not None]
(defined $transition or $bootstrap or $jumble) and $global_opp
(transition is not None or bootstrap or jumble) and global_opp
(defined $value) ? "$partial_arrgt " : ""
( "" , " %s " % str(partial_arrgt))[ value is not None]
(defined $transition or $bootstrap or $jumble) and $global_opp
(transition is not None or bootstrap or jumble) and global_opp
" | "
" | "
($value)? "quickadd | " : ""
( "" , " quickadd | " )[ value ]
(defined $value) ? "outgroup $value | " : ""
( "" , "outgroup " + str(value) + " | " )[ value is not None ]
not $bootstrap
not bootstrap
(defined $value) ? "usertree $value |" : ""
( "" , " usertree %s |" % str(value) )[ value is not None ]
not $bootstrap
not bootstrap
($value) ? "userlengths |" : ""
( "" , "userlengths |" )[ value ]
($value) ? " fastdnaml " : ""
( "" , " fastdnaml " )[ value ]
$bootstrap
bootstrap
(defined $value and $value != $vdef) ? " -boots $value" : ""
( "" , " -boots " + str(value) )[ value is not None and value != vdef]
$value <= 1000
value <= 1000
(defined $value) ? " -seed $value" : ""
( "" , " -seed " + str(value) )[ value is not None ]
$bootstrap
bootstrap
(defined $value and $value != $vdef) ? " -jumble $value" : ""
( "" , " -jumble " + str(value) )[ value is not None and value != vdef]
" $infile.tmp"
" %s.tmp" % str(infile)
not $bootstrap
not bootstrap
(defined $value and $value ne $vdef) ? " > $outfile" : ""
( "" , " > " + str(outfile) )[ value is not None ]
not $bootstrap and not defined $outfile
not bootstrap and outfile is None
"fastdnaml.out"
"fastdnaml.out"
not $bootstrap and defined $outfile
not bootstrap and outfile is not None
"$outfile"
str(outfile)
not $bootstrap
not bootstrap
($value) ? "" : "treefile | "
( "treefile | ", "" )[ value ]
($value) ? "printdata | " : ""
( "" , "printdata | " )[ value ]
(defined $value) ? "categories $value |" : ""
( "" , "categories "+ str(value) + " |" )[ value is not None ]
(defined $value) ? "weights $value |" : ""
( "" , "weights " + str(value) + " |" )[ value is not None ]
not $bootstrap
not bootstrap
"_treefile.[0-9]*"
"_treefile.[0-9]*"
$bootstrap
bootstrap
"$infile.tmp.out"
"%s.tmp.out" % str(infile)
$bootstrap
bootstrap
"$infile.tmp.tree"
"%s.tmp.tree" % str(infile)
$bootstrap
bootstrap
"$infile.tmp"
"%s.tmp" % str(infile)
" -i $value"
" -i " + str(value)
(defined $value) ? " -L $value" : ""
( "" , " -L " + str(value) )[ value is not None ]
(defined $value and $value != $vdef) ? " -b $value" : ""
( "" , " -b " + str(value) )[ value is not None and value != vdef]
(defined $value and $value ne $vdef) ? " $value" : ""
( "" , " " + str(value) )[ value is not None and value != vdef]
" -o weighbor.treefile"
" -o weighbor.treefile"
"weighbor.treefile"
"weighbor.treefile"
"bambe <bambe.params"
"bambe <bambe.params"
"data-file=$value\\n"
"data-file="+str(value)+"\n"
(defined $value and $value != $vdef) ? "seed=$value\\n" : ""
("", "seed="+str(value)+"\n")[value is not None and value!=vdef]
(defined $value and $value != $vdef) ?"cycles=$value\\n" : ""
("", "cycles="+str(value)+"\n")[value is not None and value!=vdef]
(defined $value and $value != $vdef) ? "window-interval=$value\\n" : ""
("", "window-interval="+str(value)+"\n")[value is not None and value!=vdef]
(defined $value and $value ne $vdef) ? "main-algorithm=$value\\n" : ""
("", "main-algorithm="+str(value)+"\n")[value is not None and value != vdef]
(defined $value and $value != $vdef) ? "burn=$value\\n" : ""
("", "burn="+str(value)+"\n")[value is not None and value!=vdef]
(defined $value and $value ne $vdef) ? "burn-algorithm=$value\\n" : ""
("","burn-algorithm="+str(value)+"\n")[value is not None and value!=vdef]
$main_algorithm eq "local" or $burn_algorithm eq "local"
main_algorithm == "local" or burn_algorithm == "local"
($value) ? "use-beta=true\\n" : ""
("", "use-beta=true\n")[ value ]
($value) ? "" :"molecular-clock=false\\n"
("molecular-clock=false\n", "")[ value ]
(defined $value and $value ne $vdef) ? "likelihood-model=$value\\n" : ""
("", "likelihood-model="+str(value)+"\n")[value is not None and value!=vdef]
(defined $value) ? "category-list=$value\\n" :""
("", "category-list="+str(value)+"\n" )[value is not None]
($value) ? "single-kappa=true\\n" : ""
("", "single-kappa=true\n")[ value ]
$likelihood_model eq "HKY85" or $likelihood_model eq "F84"
likelihood_model=="HKY85" or likelihood_model=="F84"
(defined $value and $value ne $vdef) ? "initial-kappa=$value\\n" : ""
("", "initial-kappa="+str(value)+"\n")[value is not None and value!=vdef]
(defined $value and $value ne $vdef) ? "initial-theta=$value\\n" : ""
("", "initial-theta="+str(value)+"\n")[value is not None and value!=vdef]
($value) ? "" : "estimate-pi=false\\n"
("estimate-pi=false\n","")[ value ]
not $estimate_pi
not estimate_pi
(defined $value and $value ne $vdef) ? "initial-pia=$value\\n" : ""
("", "initial-pia="+str(value)+"\n")[value is not None and value!=vdef]
not $estimate_pi
not estimate_pi
(defined $value and $value ne $vdef) ? "initial-pig=$value\\n" : ""
("", "initial-pig="+str(value)+"\n")[value is not None and value!=vdef]
not $estimate_pi
not estimate_pi
(defined $value and $value ne $vdef) ? "initial-pic=$value\\n" : ""
("", "initial-pic="+str(value)+"\n")[value is not None and value!=vdef]
not $estimate_pi
not estimate_pi
(defined $value and $value ne $vdef) ? "initial-pit=$value\\n" : ""
("","initial-pit="+str(value)+"\n")[value is not None and value!=vdef]
$likelihood_model eq "TN93"
likelihood_model == "TN93"
(defined $value and $value ne $vdef) ? "initial-ttp=$value\\n" : ""
("", "initial-ttp="+str(value)+"\n")[value is not None and value!=vdef]
$likelihood_model eq "TN93"
likelihood_model == "TN93"
(defined $value and $value ne $vdef) ? "initial-gamma=$value\\n" : ""
("", "initial-gamma="+str(value)+"\n")[value is not None and value!=vdef]
$likelihood_model eq "GREV"
likelihood_model == "GREV"
(defined $value and $value ne $vdef) ? "initial-rac=$value\\n" : ""
("", "initial-rac="+str(value)+"\n")[value is not None and value!=vdef]
$likelihood_model eq "GREV"
likelihood_model == "GREV"
(defined $value and $value ne $vdef) ? "initial-rag=$value\\n" : ""
("", "initial-rag="+str(value)+"\n")[value is not None and value!=vdef]
$likelihood_model eq "GREV"
likelihood_model == "GREV"
(defined $value and $value ne $vdef) ? "initial-rat=$value\\n" : ""
("", "initial-rat="+str(value)+"\n")[value is not None and value!=vdef]
$likelihood_model eq "GREV"
likelihood_model == "GREV"
(defined $value and $value ne $vdef) ? "initial-rcg=$value\\n" : ""
("", "initial-rcg="+str(value)+"\n")[value is not None and value!=vdef]
$likelihood_model eq "GREV"
likelihood_model == "GREV"
(defined $value and $value ne $vdef) ? "initial-rct=$value\\n" : ""
("", "initial-rct="+str(value)+"\n")[value is not None and value!=vdef]
$likelihood_model eq "GREV"
likelihood_model == "GREV"
(defined $value and $value ne $vdef) ? "initial-rgt=$value\\n" : ""
("", "initial-rgt="+str(value)+"\n")[value is not None and value!=vdef]
(defined $value and $value != $vdef) ? "parameter-update-interval=$value\\n" : ""
("", "parameter-update-interval="+str(value)+"\n")[value is not None and value!=vdef]
$likelihood_model eq "HKY85" or $likelihood_model eq "F84"
likelihood_model=="HKY85" or likelihood_model=="F84"
($value) ? "" : "update-kappa=false\\n"
("update-kappa=false\n", "")[ value ]
($value) ? "" : "update-theta=false\\n"
("update-theta=false\n", "")[ value ]
($value) ? "" : "update-pi=false\\n"
("update-pi=false\n", "")[ value ]
$likelihood_model eq "TN93"
likelihood_model == "TN93"
($value) ? "" : "update-ttp=false\\n"
("update-ttp=false\n", "")[ value ]
$likelihood_model eq "TN93"
likelihood_model == "TN93"
($value) ? "" : "update-gamma=false\\n"
("update-gamma=false\n", "")[ value ]
$likelihood_model eq "GREV"
likelihood_model == "GREV"
($value) ? "" : "update-grev=false\\n"
("update-grev=false\n", "")[ value ]
($value) ? "update-invariant-prob=true\\n" : ""
("", "update-invariant-prob=true\n")[ value ]
$burn_algorithm eq "local" or $main_algorithm eq "local"
burn_algorithm == "local" or main_algorithm == "local"
(defined $value and $value != $vdef) ? "local-tune=$value\\n" : ""
("", "local-tune="+str(value)+"\n")[value is not None and value!=vdef]
$parameter_update_interval != 0 and $update_theta
parameter_update_interval != 0 and update_theta
(defined $value and $value != $vdef) ? "theta-tune=$value\\n" : ""
("","theta-tune="+str(value)+"\n")[value is not None and value!=vdef]
$parameter_update_interval != 0 and $update_pi
parameter_update_interval != 0 and update_pi
(defined $value and $value != $vdef) ? "pi-tune=$value\\n" : ""
("", "pi-tune="+str(value)+"\n")[value is not None and value!=vdef]
$parameter_update_interval != 0 and $update_kappa and ($likelihood_model eq "HKY85" or $likelihood_model eq "F84")
parameter_update_interval != 0 and update_kappa and (likelihood_model == "HKY85" or likelihood_model == "F84")
(defined $value and $value != $vdef) ? "kappa-tune=$value\\n" : ""
("","kappa-tune="+str(value)+"\n")[value is not None and value!=vdef]
$parameter_update_interval != 0 and $update_ttp and $likelihood_model eq "TN93"
parameter_update_interval != 0 and update_ttp and likelihood_model == "TN93"
(defined $value and $value != $vdef) ? "ttp-tune=$value\\n" : ""
("","ttp-tune="+str(value)+"\n")[value is not None and value!=vdef]
$parameter_update_interval != 0 and $update_gamma and $likelihood_model eq "TN93"
parameter_update_interval != 0 and update_gamma and likelihood_model == "TN93"
(defined $value and $value != $vdef) ? "gamma-tune=$value\\n" : ""
("","gamma-tune="+str(value)+"\n")[value is not None and value!=vdef]
$parameter_update_interval != 0 and $update_grev and $likelihood_model eq "GREV"
parameter_update_interval != 0 and update_grev and likelihood_model=="GREV"
(defined $value and $value != $vdef) ? "grev-tune=$value\\n" : ""
("","grev-tune="+str(value)+"\n")[value is not None and value!=vdef]
$use_beta
use_beta
(defined $value and $value != $vdef) ? "beta-tune=$value\\n" : ""
("","beta-tune="+str(value)+"\n")[value is not None and value!=vdef]
$parameter_update_interval != 0 and $update_invariant_prob
parameter_update_interval != 0 and update_invariant_prob
(defined $value and $value != $vdef) ? "invariant-prob-tune=$value\\n" : ""
("","invariant-prob-tune="+str(value)+"\n")[value is not None and value!=vdef]
(defined $value and $value != $vdef) ? "sample-interval=$value\\n" : ""
("","sample-interval="+str(value)+"\n")[value is not None and value!=vdef]
($value) ? "newick-format=false\\n" : ""
("newick-format=false\n", "")[ value ]
"bambe_results.lpd" and "bambe_results.par" and "bambe_results.out"
"bambe_results.lpd"
"bambe_results.par"
"bambe_results.out"
"bambe_results.tre"
"bambe_results.tre"
"bambe_results.top"
"bambe_results.top"
"file-root=bambe_results\\n"
"file-root=bambe_results\n"
$molecular_clock
molecular_clock
(defined $value and $value != $vdef) ? "outgroup=$value\\n" : ""
("", "outgroup="+str(value)+"\n")[value is not None and value!=vdef]
$initial_tree_type eq "bambe" or $initial_tree_type eq "newick"
initial_tree_type=="bambe" or initial_tree_type=="newick"
(defined $value) ? "tree-file=$value\\n" : ""
("", "tree-file="+str(value)+"\n")[value is not None]
(defined $value and $value ne $vdef) ? "initial-tree-type=$value\\n" : ""
("", "initial-tree-type="+str(value)+"\n")[value is not None and value != vdef]
($value) ? "" : "print-all-trees=false\\n"
("print-all-trees=false\n", "")[value ]
(defined $value and $value != $vdef) ? "max-initial-tree-height=$value\\n" : ""
("", "max-initial-tree-height="+str(value)+"\n")[value is not None and value!=vdef]
("", " -sequence=" + str(value))[value is not None]
("", " -mwdata=" + str(value))[value is not None ]
("", " -window=" + str(value))[value is not None and value!=vdef]
value >= 2
("", " -order=" + str(value))[value is not None and value!=vdef]
("", " -threshold=" + str(value))[value is not None and value!=vdef]
value >= -55.0
value <= +55.0
("", " -mono")[ bool(value) ]
(" -nopotential", "")[ bool(value) ]
(" -nopoor", "")[ bool(value) ]
("", " -invalid")[ bool(value) ]
(" -nomap", "")[ bool(value) ]
("" , " -outfile=" + str(value))[value is not None]
e_outfile
(" -graph=" + str(vdef), " -graph=" + str(value))[value is not None and value!=vdef]
("" , " -goutfile=" + str(value))[value is not None]
e_graph == "png"
"*.png"
e_graph == "gif"
"*.gif"
e_graph == "ps" or e_graph == "cps"
"*.ps"
e_graph == "meta"
"*.meta"
e_graph == "data"
"*.dat"
" -auto -stdout"
("", " -sequence=" + str(value))[value is not None]
("", " -regions=" + str(value))[value is not None]
("", " -tolower")[ bool(value) ]
not e_tolower
("", " -maskchar=" + str(value))[value is not None]
("" , " -outseq=" + str(value))[value is not None]
("", " -osformat=" + str(value))[value is not None and value!=vdef]
e_outseq
" -auto -stdout"
" <$value"
" <"+str(value)
not $pf
not pf
($value)? " -p" : ""
( "" , " -p" )[ value ]
not $partition
not partition
(defined $value)? " -p0" : ""
( "" , " -p0" )[ value ]
(defined $value)? " -p2" : ""
( "" , " -p2 " )[ value ]
defined $partition
partition
(defined $value and $value != $vdef)? " -MEA $value" : ""
( "" , " -MEA " + str(value) )[ value is not None and value != vdef]
(defined $value and $value != $vdef)? " -T $value" : ""
( "" , " -T " + str(value) )[ value is not None and value != vdef]
($value)? " -4" : ""
( "" , " -4" )[ value ]
(defined $value and $value ne $vdef)? " $value" : ""
( "" , " " + str(value) )[ value is not None and value != vdef]
(defined $value)? " -S $value" : ""
( "" , " -S " + str(value) )[ value is not None ]
($value)? " -C" : ""
( "" , " -C" )[ value ]
($value)? " -noLP" : ""
( "" , " -noLP" )[ value ]
($value)? " -noGU" : ""
( "" , " -noGU" )[ value ]
($value)? " -noCloseGU" : ""
( "" , " -noCloseGU" )[ value ]
(defined $value)? " -nsp $value" : ""
( "" , " -nsp " + str(value) )[ value is not None ]
(defined $value)? " -P $value" : ""
( "" , " -P " + str(value) )[ value is not None ]
"$seqin.tmp"
str(seqin)+'.tmp'
"rnafold.out"
"rnafold.out"
not $constraints/
not constraints
"mv $seqin $seqin.ori &&
"mv %s %s.ori &&
"*.ps"
"*.ps"
("", " -sequence=" + str(value))[value is not None]
("", " -motif=" + str(value))[value is not None]
("" , " -outfile=" + str(value))[value is not None]
("", " -rformat=" + str(value))[value is not None and value!=vdef]
e_rformat_outfile in ['DASGFF', 'DBMOTIF', 'DIFFSEQ', 'EMBL', 'EXCEL', 'FEATTABLE', 'GENBANK', 'GFF', 'LISTFILE', 'MOTIF', 'NAMETABLE', 'CODATA', 'REGIONS', 'SEQTABLE', 'SIMPLE', 'SRS', 'SWISS', 'TABLE', 'TAGSEQ']
e_outfile
" -auto -stdout"
"mfold"
"mfold"
" SEQ=$value"
" SEQ=" + str(value)
(defined $value and $value ne $vdef) ? " NA=$value" : ""
("" , " NA=" + str(value))[ value is not None and value != vdef]
(defined $value and $value ne $vdef) ? " LC=$value" : ""
("" , " LC=" + str(value))[ value is not None and value != vdef]
(defined $value and $value != $vdef) ? " T=$value" : ""
("" , " T=" + str(value))[ value is not None and value != vdef]
$value <= 100 and $value >= 0
value <= 100 and value >= 0
(defined $value and $value != $vdef) ? " P=$value" : ""
("", " P="+str(value))[value is not None and value != vdef]
(defined $value and $value != $vdef) ? " NA_CONC=$value" : ""
("" , " NA_CONC=" + str(value))[ value is not None and value != vdef]
(defined $value and $value != $vdef) ? " MG_CONC=$value" : ""
("" , " MG_CONC=" + str(value))[ value is not None and value != vdef]
(defined $value) ? " W=$value" : ""
("" , " W=" + str(value))[ value is not None ]
(defined $value) ? " MAXBP=$value" : ""
("" , " MAXBP=" + str(value))[ value is not None ]
(defined $value and $value != $vdef) ? " MAX_LP=$value" : ""
("" , " MAX_LP=" + str(value))[ value is not None and value != vdef]
(defined $value and $value != $vdef) ? " MAX_AS=$value" : ""
("" , " MAX_AS=" + str(value))[ value is not None and value != vdef]
(defined $value and $value != $vdef) ? " MAX=$value" : ""
("" , " MAX=" + str(value))[ value is not None and value != vdef]
(defined $value and $value ne $vdef) ? " ANN=$value" : ""
("" , " ANN=" + str(value))[ value is not None and value != vdef]
(defined $value and $value ne $vdef) ? " MODE=$value" : ""
("" , " MODE=" + str(value))[ value is not None and value != vdef]
(defined $value and $value != $vdef) ? " ROT_ANG=$value" : ""
("" , " ROT_ANG=" + str(value))[ value is not None and value != vdef]
(defined $value and $value != $vdef) ? " START=$value" : ""
("" , " START=" + str(value))[ value is not None and value != vdef]
(defined $value) ? " STOP=$value" : ""
("" , " STOP=" + str(value))[ value is not None ]
(defined $value) ? " AUX=$value" : ""
( "" , " AUX=" + str(value) )[ value is not None]
""
""
$txt_format
txt_format
"*.out"
"*.out"
""
""
$det_format and $html_format
det_format and html_format
"*.det.html"
"*.det.html"
$det_format and not $html_format
det_format and not html_format
"*.det"
"*.det"
($value) ? " RUN_TYPE=html" : ""
("" , " RUN_TYPE=html")[ value ]
$html_format
html_format
"*.html"
"*.html"
$rnaml_format
rnaml_format
"*.rnaml"
"*.rnaml"
$plot_format
plot_format
"*.plot"
"*.plot"
$ann_format
ann_format
"*.ann"
"*.ann"
$hnum_format
hnum_format
"*.h-num"
"*.h-num"
$gif_format
gif_format
*.gif
"*.gif"
$pdf_format
pdf_format
"*.pdf"
"*.pdf"
$ps_format
ps_format
"*.ps"
"*.ps"
$ct_format
ct_format
"*.ct"
"*.ct"
$ss_format
ss_format
"*.ss"
"*.ss-count"
"*.ss"
"*.ss-count"
("", " -asequence=" + str(value))[value is not None]
("", " -bsequence=" + str(value))[value is not None]
("", " -datafile=" + str(value))[value is not None and value!=vdef]
("", " -minscore=" + str(value))[value is not None and value!=vdef]
value >= 0
("", " -gapopen=" + str(value))[value is not None]
value >= 0.0
value <= 100.0
("", " -gapextend=" + str(value))[value is not None]
value >= 0.0
value <= 10.0
("", " -width=" + str(value))[value is not None and value!=vdef]
value >= 1
("", " -wordlen=" + str(value))[value is not None and value!=vdef]
value >= 3
("" , " -outfile=" + str(value))[value is not None]
("", " -aformat=" + str(value))[value is not None and value!=vdef]
e_aformat_outfile in ['FASTA', 'MSF']
e_outfile
e_aformat_outfile in ['PAIR', 'MARKX0', 'MARKX1', 'MARKX2', 'MARKX3', 'MARKX10', 'SRS', 'SRSPAIR', 'SCORE', 'UNKNOWN', 'MULTIPLE', 'SIMPLE', 'MATCH']
e_outfile
("" , " -errorfile=" + str(value))[value is not None]
e_errorfile
" -auto -stdout"
("", " -sequence=" + str(value))[value is not None]
("", " -aaproperties=" + str(value))[value is not None ]
("", " -aahydropathy=" + str(value))[value is not None ]
("", " -hwindow=" + str(value))[value is not None and value!=vdef]
value >= 1
(" -graph=" + str(vdef), " -graph=" + str(value))[value is not None and value!=vdef]
("" , " -goutfile=" + str(value))[value is not None]
e_graph == "png"
"*.png"
e_graph == "gif"
"*.gif"
e_graph == "ps" or e_graph == "cps"
"*.ps"
e_graph == "meta"
"*.meta"
e_graph == "data"
"*.dat"
("" , " -outfile=" + str(value))[value is not None]
e_outfile
(" -nogeneralplot", "")[ bool(value) ]
(" -nohydropathyplot", "")[ bool(value) ]
" -auto -stdout"
not defined $distfile or (defined $aligfile and defined $distfile)
distfile is None or (distfile and aligfile)
(defined $value) ? " -in a $value" : ""
( "" , " -in a " + str(value) )[ value is not None ]
not $distfile
distfile is None
not defined $aligfile
aligfile is None
(defined $value) ? " -in m $value" : ""
( "" , " -in m " + str(value) )[ value is not None ]
not defined $aligfile
aligfile is None
(defined $value and $value ne $vdef) ? " -out $value" : ""
( "" , " -out " + str(value) )[ value is not None and value != vdef]
$out ne "m"
out != "m"
($value) ? " -upgma" : ""
( "" , " -upgma" )[ value ]
not defined $distfile and $out ne "m"
distfile is None and out != "m"
(defined $value) ? " -boot $value" : ""
( "" , " -boot " + str(value))[ value is not None ]
defined $aligfile
aligfile is not None
($value) ? " -kimura" : ""
( "" , " -kimura" )[ value ]
$out ne "m"
out != "m"
"quicktree.out"
"quicktree.out"
$out eq "m"
out == "m"
"quicktree.out"
"quicktree.out"
"retree < retree.params"
"retree < retree.params"
"ln -s $treefile intree && "
"ln -s "+str( treefile ) +" intree && "
" && mv outtree unroot.outtree"
" && mv outtree unroot.outtree"
"unroot.outtree"
"unroot.outtree"
"0\\nY\\nW\\nU\\nQ\\n"
"0\nY\nW\nU\nQ\n"
("", " -pepstatsfile=" + str(value))[value is not None]
("", " -amount=" + str(value))[value is not None and value!=vdef]
value >= 1
("", " -length=" + str(value))[value is not None and value!=vdef]
value >= 1
("", " -useinsert")[ bool(value) ]
e_useinsert
("", " -insert=" + str(value))[value is not None]
e_useinsert
("", " -start=" + str(value))[value is not None and value!=vdef]
value >= 1
("" , " -outseq=" + str(value))[value is not None]
("", " -osformat=" + str(value))[value is not None and value!=vdef]
e_outseq
" -auto -stdout"
("", " -sequence=" + str(value))[value is not None]
("", " -sourcematch=" + str(value))[value is not None]
("", " -typematch=" + str(value))[value is not None]
("", " -tagmatch=" + str(value))[value is not None]
("", " -valuematch=" + str(value))[value is not None]
("", " -sort=" + str(value))[value is not None and value!=vdef]
("", " -joinfeatures")[ bool(value) ]
("", " -annotation=" + str(value))[value is not None]
("", " -html")[ bool(value) ]
(" -noid", "")[ bool(value) ]
(" -nodescription", "")[ bool(value) ]
(" -noscale", "")[ bool(value) ]
("", " -width=" + str(value))[value is not None and value!=vdef]
value >= 0
("", " -collapse")[ bool(value) ]
(" -noforward", "")[ bool(value) ]
(" -noreverse", "")[ bool(value) ]
(" -nounknown", "")[ bool(value) ]
("", " -strand")[ bool(value) ]
("", " -origin")[ bool(value) ]
("", " -position")[ bool(value) ]
(" -notype", "")[ bool(value) ]
("", " -tags")[ bool(value) ]
(" -novalues", "")[ bool(value) ]
("", " -stricttags")[ bool(value) ]
("" , " -outfile=" + str(value))[value is not None]
e_outfile
" -auto -stdout"
" --sequence=$value"
" --sequence=" + str(value)
(defined $value and $value != $vdef) ? " --z=$value" : ""
( "" , " --z=" + str(value))[ value is not None and value != vdef ]
(defined $value) ? " --onlydirect=1" : ""
( "" , " --onlydirect=1")[ value ]
(defined $value and $value != $vdef) ? "" : " --extend=0"
( " --extend=0" , "" )[ value ]
(defined $value) ? "" : " --large-repeats=0"
( " --large-repeats=0" , "" )[ value ]
(defined $value and $value != $vdef) ? " --minreplen=$value" : ""
( "" , " --minreplen=" + str(value))[ value is not None and value != vdef ]
(defined $value and $value != $vdef) ? " --maxmulti=$value" : ""
( "" , " --maxmulti=" + str(value))[ value is not None and value != vdef ]
(defined $value and $value != $vdef) ? " --minmulti=$value" : ""
( "" , " --minmulti=" + str(value))[ value is not None and value != vdef ]
(defined $value) ? " --solid=1" : ""
( "" , " --solid=1")[ value ]
(defined $value) ? " --allow-redundant=1" : ""
( "" , " --allow-redundant=1" )[ value ]
(defined $value) ? " --two-hits=1" : ""
( "" , " --two-hits=1" )[ value ]
(defined $value) ? "" : " --chain=0"
( " --chain=0" , "" )[ value ]
(defined $value) ? " --xml=repeatoire.xml" : ""
( "" , " --xml=repeatoire.xml" )[ value ]
"reps.out"
"reps.out"
"stats.highest"
"stats.highest"
$xml
xml
"repeatoire.xml"
"repeatoire.xml"
" $value"
" " + str(value)
(defined $value) ? " $value" : ""
("" , " " + str(value))[value is not None]
"nw_cat.out"
"nw_cat.out"
' -i ' + str(value)
' -c ' + str(value)
('',' -d '+ str(value))[value is not None]
('',' -e ')[value]
('',' -x ')[value]
('',' -f ')[value]
NoTaxonomyInfo is not None
' -f noTaxo' + OutputFileName
"noTaxo"+ OutputFileName
OutputFileName
' -o ' + OutputFileName
"-rt $value"
" -rt "+str(value)
"-ct $value "
" -ct "+str(value)+" "
($value) ? " -t"
("", " -t")[ value ]
($value) ? " -p"
("", " -p")[ value ]
($value) ? " -s"
("", " -s")[ value ]
($value) ? " -r"
("", " -r")[ value ]
($value) ? " -n"
("", " -n")[ value ]
($value) ? " -a"
("", " -a")[ value ]
$output_res or $output_all
output_res or output_all
"*.tab"
"*.tab"
$output_part or $output_all
output_part or output_all
"*.part"
"*.part"
$output_comp or $output_all
output_comp or output_all
"*.scaled"
"*.scaled"
("", " -sequence=" + str(value))[value is not None]
("", " -maxrepeat=" + str(value))[value is not None and value!=vdef]
("", " -threshold=" + str(value))[value is not None and value!=vdef]
("" , " -outfile=" + str(value))[value is not None]
("", " -rformat=" + str(value))[value is not None and value!=vdef]
e_rformat_outfile in ['DASGFF', 'DBMOTIF', 'DIFFSEQ', 'EMBL', 'EXCEL', 'FEATTABLE', 'GENBANK', 'GFF', 'LISTFILE', 'MOTIF', 'NAMETABLE', 'CODATA', 'REGIONS', 'SEQTABLE', 'SIMPLE', 'SRS', 'SWISS', 'TABLE', 'TAGSEQ']
e_outfile
("" , " -origfile=" + str(value))[value is not None]
e_origfile
" -auto -stdout"
("", " -sequence=" + str(value))[value is not None]
("", " -from=" + str(value))[value is not None]
("", " -to=" + str(value))[value is not None]
("" , " -outseq=" + str(value))[value is not None]
("", " -osformat=" + str(value))[value is not None and value!=vdef]
e_outseq
" -auto -stdout"
("", " -feature")[ bool(value) ]
("", " -sequence=" + str(value))[value is not None]
("", " -skip=" + str(value))[value is not None and value!=vdef]
("" , " -outseq=" + str(value))[value is not None]
("", " -osformat=" + str(value))[value is not None and value!=vdef]
e_outseq
" -auto -stdout"
" netOglyc "
" netOglyc "
" " + str( value )
( $value ) ? "-sp ": ""
( "","-sp ")[ bool( value ) ]
( $value )? "-g " : ""
( "" , "-g " )[ bool( value ) ]
"netOglyc.out"
"netOglyc.out"
Each input sequence is displayed with the predicted sites indicated, labelled with ``S'' and ``T'' for serine and threonine, respectively. The signal peptide (if predicted) is labelled with ``_''. The details of the prediction for each serine and threonine residue are then shown in a table. The columns are:
The final answer is calculated as follows. If the G-score is >0.5 the residue is predicted as glycosy†lated; the higher the score the more confident the prediction. If the G-score is < 0.5 but the I-score >0.5 and there are no predicted neighbouring sites (distance <10 residues) the residue is also predicted as gly†cosylated.
If a residue in a predicted signal peptide is predicted as glycosylated there is a warning in the comment field.
graphics
graphics
"*.ps"
"*.ps"
graphics
graphics
"*.gif"
"*.gif"
("", " -sequence=" + str(value))[value is not None]
("", " -format=" + str(value))[value is not None and value!=vdef]
e_format=="0"
("", " -things=" + str(value))[value is not None and value!=vdef]
("", " -uppercase=" + str(value))[value is not None]
("", " -highlight=" + str(value))[value is not None]
("", " -annotation=" + str(value))[value is not None]
("", " -sourcematch=" + str(value))[value is not None]
("", " -typematch=" + str(value))[value is not None]
("", " -minscore=" + str(value))[value is not None and value!=vdef]
("", " -maxscore=" + str(value))[value is not None and value!=vdef]
("", " -tagmatch=" + str(value))[value is not None]
("", " -valuematch=" + str(value))[value is not None]
("", " -stricttags")[ bool(value) ]
("", " -threeletter")[ bool(value) ]
("", " -number")[ bool(value) ]
("", " -width=" + str(value))[value is not None and value!=vdef]
value >= 1
("", " -length=" + str(value))[value is not None and value!=vdef]
value >= 0
("", " -margin=" + str(value))[value is not None and value!=vdef]
value >= 0
(" -noname", "")[ bool(value) ]
(" -nodescription", "")[ bool(value) ]
("", " -offset=" + str(value))[value is not None and value!=vdef]
("", " -html")[ bool(value) ]
("" , " -outfile=" + str(value))[value is not None]
e_outfile
" -auto -stdout"
("", " -sequences=" + str(value))[value is not None]
("", " -nucmode=" + str(value))[value is not None and value!=vdef]
("", " -revcomp")[ bool(value) ]
("", " -overlapw=" + str(value))[value is not None and value!=vdef]
("", " -linkage=" + str(value))[value is not None and value!=vdef]
("", " -maxfragl=" + str(value))[value is not None and value!=vdef]
value >= 0
("", " -fragmat")[ bool(value) ]
("", " -fragsim=" + str(value))[value is not None and value!=vdef]
value >= 0
("", " -itscore")[ bool(value) ]
("", " -threshold=" + str(value))[value is not None and value!=vdef]
value >= 0.0
("", " -mask")[ bool(value) ]
("", " -dostars")[ bool(value) ]
("", " -starnum=" + str(value))[value is not None and value!=vdef]
value >= 0
("" , " -outfile=" + str(value))[value is not None]
e_outfile
("" , " -outseq=" + str(value))[value is not None]
e_outseq
" -auto -stdout"
"hmmemit"
"hmmemit"
" $hmmfile"
" " + str(hmmfile)
(defined $value) ? " -o $value" : ""
( "" , " -o " + str(value) )[ value is not None ]
defined $outfile_name
outfile_name is not None
$outfile_name
str(outfile_name)
not defined $outfile_name
outfile_name is None
"hmmemit.out"
"hmmemit.out"
$number == 1 and not sample
number == 1 and not sample
($value) ? " -c" : ""
( "" , " -c" )[ value ]
(defined $value and $value != $vdef) ? " -N $value " : ""
( "" , " -N " + str(value) )[ value is not None and value != vdef]
0 < $value
0 < value
( $value ) ? " -p " : ""
( "" , " -p " )[ value ]
define $sample
sample
(defined $value and $value != $vdef) ? " -L $value " : ""
( "" , " -L " + str(value) )[ value is not None and value != vdef]
(defined $value) ? " --$value " : ""
( "" , " --" + str(value) )[ value is not None ]
(defined $value and $value != $vdef) ? " --seed $value " : ""
( "" , " --seed " + str(value) )[ value is not None and value !=vdef ]
0 <= $value
0 <= value
("", " -enzyme=" + str(value))[value is not None and value!=vdef]
(" -noisoschizomers", "")[ bool(value) ]
(" -noreferences", "")[ bool(value) ]
(" -nosuppliers", "")[ bool(value) ]
("" , " -outfile=" + str(value))[value is not None]
e_outfile
" -auto -stdout"
("", " -sequence=" + str(value))[value is not None]
("", " -score=" + str(value))[value is not None and value!=vdef]
value >= 1
value <= 200
("" , " -outfile=" + str(value))[value is not None]
e_outfile
" -auto -stdout"
("", " -sequence=" + str(value))[value is not None]
("", " -menu=" + str(value))[value is not None and value!=vdef]
("", " -matrices=" + str(value))[value is not None and value!=vdef]
("", " -threshold=" + str(value))[value is not None and value!=vdef]
("", " -exclude=" + str(value))[value is not None]
("", " -both")[ bool(value) ]
("" , " -outfile=" + str(value))[value is not None]
("", " -rformat=" + str(value))[value is not None and value!=vdef]
e_rformat_outfile in ['DASGFF', 'DBMOTIF', 'DIFFSEQ', 'EMBL', 'EXCEL', 'FEATTABLE', 'GENBANK', 'GFF', 'LISTFILE', 'MOTIF', 'NAMETABLE', 'CODATA', 'REGIONS', 'SEQTABLE', 'SIMPLE', 'SRS', 'SWISS', 'TABLE', 'TAGSEQ']
e_outfile
" -auto -stdout"
" $value"
" " + str( value )
(defined $value?)"ln -sf $value $seq.qual" : ""
("" , "ln -sf %s %s.qual && " %( value , seq ) )[value is not None and value != seq + ".qual" ]
(defined $value?)"ln -sf $value $seq.con" : ""
( "" , "ln -sf %s %s.con && " %( value , seq ) )[value is not None ]
CAP3 computes clipping positions of each read using both base quality values and similarity information. Clipping of a poor end region of a read f is controlled by three parameters: quality value cutoff qualcut, clipping range crange, and depth of good coverage gdepth. The value for qualcut can specified with the "-c" option, the value for crange with the "-y" option, and the value for gdepth with the "-z" option.
If there are quality values, CAP3 computes two positions qualpos5 and qualpos3 of read f such that the region of read f from position qualpos5 to position qualpos3 consists mostly of quality values greater than qualcut. If there are no quality values, then qualpos5 is set to 1 and qualpos3 is set the length of read f. The range for the left clipping position of read f is from 1 to qualpos5 + crange. The range for the right clipping position of read f is from qualpos3 - crange to the end of read f. The minimum depth of good coverage at the left and right clipping positions of read f is expected to be gdepth.
Let realdepth5 be the maximum real depth of coverage for the initial region of read f ending at position qualpos5 + crange. Let depth5 be the smaller of realdepth5 and gdepth. If depth5 is 0, then left clipping position of read f is set to qualpos5 by CAP3. The given value for the parameter crange may be too small for read f. CAP3 reports at the start of a .info file that "No overlap is found in the given 5' clipping range for read f." If there are overlaps beyond the given 5' clipping range for read f, CAP3 reports a new clipping range for each overlap. One of the reported range values can be used as a new value for the parameter crange for read f.
If depth5 is greater than 0, the left clipping position of read f is the smallest position x such that x is less than qualpos5 + crange and the region of read f beginning at position x is similar to depth5 other reads. The right clipping position of read f is computed similarly by CAP3. Larger values for the parameters crange and gdepth result in more aggressive clipping of poor end regions. A larger value for crange allows CAP3 to search for the left clipping position in a larger area. A larger value for gdepth may cause CAP3 to clip more bases so that the resulting good portion of read f is similar to more reads.
The user may provide specific values for the parameters crange and gdepth for individual reads in a file. Each line in the file has the following format: file has the following format:
ReadName crange5 gdepth5 crange3 gdepth3
where ReadName is the name of a read, crange5 & gdepth5 are values for the 5' end, and crange3 & gdepth3 are for the 3' end.
(defined $value and $value != $vdef) ? " -c $value" : ""
( "" , " -c "+ str( value ) )[ value is not None and value != vdef ]
$value > 5
value > 5
(defined $value and $value != $vdef) ? " -y $value" : ""
( "" , " -y "+ str( value ) )[ value is not None and value != vdef ]
$value > 5
value > 5
(defined $value and $value != $vdef)? " -z $value" : ""
( "" , " -z "+ str( value ) )[ value is not None and value != vdef ]
$value > 0
value > 0
(defined $value)? " -w $value" : ""
( "" , " -w "+ str( value ) )[ value is not None ]
(defined $value and $value != $vdef) ? " -a $value" : ""
( "" , " -a "+ str( value ) )[ value is not None and value != vdef ]
$value > 10
value > 10
(defined $value and $value != $vdef) ? "-b $value" : ""
( "" , " -b "+ str( value ) )[ value is not None and value != vdef ]
$value > 15
value > 15
(defined $value and $value != $vdef) ? " -d $value" : ""
( "" , " -d "+ str( value ) )[ value is not None and value != vdef ]
$value > 20
value > 20
(defined $value and $value != $vdef)? " -e $value" : ""
( "" , " -e "+ str( value ) )[ value is not None and value != vdef ]
$value > 10
value > 10
(defined $value and $value != $vdef)? " -m $value" : ""
( "" , " -m "+ str( value ) )[ value is not None and value != vdef ]
$value > 0
value > 0
(defined $value and $value != $vdef)? " -n $value" : ""
( "" , " -n "+ str( value ) )[ value is not None and value != vdef ]
$value < 0
value < 0
(defined $value and $value != $vdef)? " -g $value" : ""
( "" , " -g "+ str( value ) )[ value is not None and value != vdef ]
$value > 0
value > 0
(defined $value and $value != $vdef) ? " -o $value" : ""
( "" , " -o "+ str( value ) )[ value is not None and value != vdef ]
$value > 20
value > 20
(defined $value and $value != $vdef) ? " -p $value" : ""
( "" , " -p "+ str( value ) )[ value is not None and value != vdef ]
$value > 65
value > 65
(defined $value and $value != $vdef) ? " -f $value" : ""
( "" , " -f "+ str( value ) )[ value is not None and value != vdef ]
$value > 1
value > 1
(defined $value and $value != $vdef)? " -h $value" : ""
( "" , " -h "+ str( value ) )[ value is not None and value != vdef ]
$value > 2
value > 2
(defined $value and $value != $vdef) ? " -s $value" : ""
( "" , " -s "+ str( value ) )[ value is not None and value != vdef ]
$value > 400
value > 400
(defined $value and $value != $vdef) ? " -r $value" : ""
( "" , " -r "+ str( value ) )[ value is not None and value != vdef ]
$value >= 0
value >= 0
(defined $value and $value != $vdef) ? " -t $value" : ""
( "" , " -t "+ str( value ) )[ value is not None and value != vdef ]
$value > 30
value > 30
(defined $value and $value != $vdef) ? " -u $value" : ""
( "" , " -u "+ str( value ) )[ value is not None and value != vdef ]
$value > 0
value > 0
(defined $value and $value != $vdef) ? " -v $value" : ""
( "" , " -v "+ str( value ) )[ value is not None and value != vdef ]
$value > 0
value > 0
"*.cap.ace"
"*.cap.ace"
"*.cap.contigs"
"*.cap.contigs"
"*.cap.contigs.links"
"*.cap.contigs.links"
"*.cap.contigs.qual"
"*.cap.contigs.qual"
"*.cap.info"
"*.cap.info"
"*.cap.singlets"
"*.cap.singlets"
not $infile_aln or ($infile_seq and $infile_aln)
not infile_aln or (infile_seq and infile_aln)
" ($value)"
" "+str(value)
not $infile_aln
not infile_aln
(defined $value) ? " -S -c $value" : ""
("", " -S -c "+str(value))[value is not None]
defined $infile_seq
infile_seq is not None
"squizz_convert.out"
"squizz_convert.out"
not $infile_seq or ($infile_seq and $infile_aln)
not infile_seq or (infile_seq and infile_aln)
" $value"
" "+str(value)
not $infile_seq
not infile_seq
not defined $convert_seq2 or (defined $convert_aln and defined $convert_seq2)
convert_seq2 is None or (convert_aln is not None and convert_seq2 is not None)
(defined $value) ? "-A -c $value" : ""
("", " -A -c "+str(value))[value is not None]
defined $convert_aln and not defined $convert_seq2
convert_aln is not None and convert_seq2 is None
not defined $convert_aln or (defined $convert_aln and defined $convert_seq2)
convert_aln is None or (convert_aln is not None and convert_seq2 is not None)
(defined $value) ? " -c $value" : ""
("", " -c "+str(value))[value is not None]
not defined $convert_aln and defined $convert_seq2
convert_aln is None and convert_seq2 is not None
defined $infile_aln and defined $convert_aln
infile_aln is not None and convert_aln is not None
"squizz_convert.out"
"squizz_convert.out"
defined $infile_aln and defined $convert_seq2
infile_aln is not None and convert_seq2 is not None
"squizz_convert.out"
"squizz_convert.out"
("", " -asequence=" + str(value))[value is not None]
("", " -bsequence=" + str(value))[value is not None]
("", " -wordsize=" + str(value))[value is not None and value!=vdef]
value >= 2
(" -nodumpalign", "")[ bool(value) ]
("" , " -outfile=" + str(value))[value is not None]
("", " -aformat=" + str(value))[value is not None and value!=vdef]
e_aformat_outfile in ['FASTA', 'MSF']
e_outfile
e_aformat_outfile in ['PAIR', 'MARKX0', 'MARKX1', 'MARKX2', 'MARKX3', 'MARKX10', 'SRS', 'SRSPAIR', 'SCORE', 'UNKNOWN', 'MULTIPLE', 'SIMPLE', 'MATCH']
e_outfile
("" , " -logfile=" + str(value))[value is not None]
e_logfile
(" -nodumpfeat", "")[ bool(value) ]
("" , " -aoutfeat=" + str(value))[value is not None]
("", " -offormat=" + str(value))[value is not None and value!=vdef]
e_aoutfeat
("" , " -boutfeat=" + str(value))[value is not None]
("", " -offormat=" + str(value))[value is not None and value!=vdef]
e_boutfeat
" -auto -stdout"
" $value"
" " + str(value)
" split $value -heading 3 --name_by_header -tab -out $filename"
" split " + str(value) + " -heading 3 --name_by_header -tab --out "+ str(infile)
defined $infile
infile is not None
"$infile.*"
infile + ".*"
(defined $value and $value ne $vdef) ? " && detect_cnv.pl $value " : ""
( "" , " && detect_cnv.pl " + str(value) )[ value is not None and value !=vdef]
(defined $value and not defined $rawcnv) or (not defined $value and defined $rawcnv)
(value is not None and rawcnv is None) or (value is None and rawcnv is not None)
(defined $value and $value ne $vdef) ? " && detect_cnv.pl $value " : ""
( "" , " && detect_cnv.pl " + str(value) )[ value is not None and value !=vdef]
(defined $value and defined $cnvfile and not defined $type) or (not defined $value and defined $type)
(value is not None and cnvfile is not None and type is None) or (value is None and type is not None)
$type eq '--test' or $type eq '--joint' or $type eq '--validate' or $type eq '--summary' or $rawcnv eq '--trio' or $rawcnv eq '--quartet' or $rawcnv eq '--cctest' or $rawcnv eq '--exclude_heterosomic'
type =='--test' or type =='--joint' or type =='--validate' or type =='--summary' or rawcnv =='--trio' or rawcnv =='--quartet' or rawcnv =='--cctest' or rawcnv =='--exclude_heterosomic'
" $infile.*"
" " + infile + ".*"
defined $rawcnv
rawcnv is not None
(defined $value) ? "--cnv $value " : ""
( "" , " --cnv " + str(value) )[ value is not None]
$type eq '--test' and $infile
type == '--test' and infile
" --out $infile_rawcnv"
" --out " + infile + "_rawcnv "
$type eq '--test' and $infile
type == '--test' and infile
"$infile_rawcnv"
infile + "_rawcnv"
($type is not None or $rawcnv is not None) and ($type and $rawcnv and $rawcnv ne '--cctest' and $rawcnv ne '--exclude_heterosomic'
(type is not None or rawcnv is not None) and (type != '--summary' and (rawcnv !='--cctest' and rawcnv !='--exclude_heterosomic'))
(defined $value) ? "--hmm
( "" , " --hmm
($type is not None or $rawcnv is not None) and ($rawcnv ne '--exclude_heterosomic')
(type is not None or rawcnv is not None) and (rawcnv !='--exclude_heterosomic')
(defined $value) ? "--pfb
( "" , " --pfb
$type eq '--test' or $rawcnv eq '--trio' or $rawcnv eq '--quartet' or $type eq '--joint' or $type eq '--validate'
(type == '--test' or type =='--joint' or type =='--validate') or (rawcnv =='--trio' or rawcnv =='--quartet')
(defined $value) ? "--gcmodel
( "" , " --gcmodel
($type is not None or $rawcnv is not None)
(type is not None or rawcnv is not None)
(defined $value and $value ne $vdef) ? " && visualize_cnv.pl --format $value " : ""
( "" , " && visualize_cnv.pl --format %s " % str(value) )[ value is not None and value !=vdef]
$type eq '--test' and $infile and $outputformat ne 'output'
type == '--test' and infile and outputformat != 'output'
"$infile.$outputformatcnv"
infile + "_" + outputformat + "cnv"
($type is not None or $rawcnv is not None) and $type ne '--test' and $outputformat ne 'output'
(type is not None or rawcnv is not None) and type != '--test' and outputformat != 'output'
"$infile.$outputformat"
infile + "_" + outputformat
$type eq '--test' and $infile and $outputformat ne 'output'
type == '--test' and infile and outputformat != 'output'
" --out $infile.$outputformatcnv $infile.rawcnv "
" --out " + infile + "_" + outputformat + "cnv " + infile + "_rawcnv "
($type is not None or $rawcnv is not None) and $type eq '--test' and $outputformat ne 'output'
(type is not None or rawcnv is not None) and type != '--test' and outputformat != 'output'
" --out $infile.$outputformat detect_cnv.out "
" --out " + infile + "_" + outputformat + " detect_cnv.out "
$type eq '--test' or $rawcnv eq '--trio' or $rawcnv eq '--quartet' or $type eq '--joint' or $type eq '--validate'
type =='--test' or rawcnv =='--trio' or rawcnv =='--quartet' or type =='--joint' or type =='--validate'
(defined $value and $value != $vdef) ? "--minsnp $value " : ""
( "" , " --minsnp " + str(value) )[ value is not None and value != vdef]
$type eq '--test' or $rawcnv eq '--trio' or $rawcnv eq '--quartet' or $type eq '--joint' or $type eq '--validate'
type =='--test' or rawcnv =='--trio' or rawcnv =='--quartet' or type =='--joint' or type =='--validate'
(defined $value) ? "--minlength $value " : ""
( "" , " --minlength " + str(value) )[ value is not None ]
$minlength =~ m/^\d+(k|m)?$/i
minlength > 0
$type eq '--test' or $type eq '--validate'
type =='--test' or type =='--validate'
(defined $value) ? "--minconf $value " : ""
( "" , " --minconf " + str(value) )[ value is not None ]
$type eq '--test' or $type eq '--validate'
type =='--test' or type =='--validate'
($value) ? "--confidence" : ""
( "" , " --confidence " )[ value ]
$type eq '--test' or $rawcnv eq '--trio' or $rawcnv eq '--quartet' or $type eq '--joint' or $type eq '--validate'
type =='--test' or rawcnv =='--trio' or rawcnv =='--quartet' or type =='--joint' or type =='--validate'
($value) ? "--chrx" : ""
( "" , " --chrx " )[ value ]
$chrx and not $bafxhet
chrx and not bafxhet
(defined $value) ? "--sex $value " : ""
( "" , " --sex " + str(value) )[ value is not None]
$chrx and not $sexfile
chrx and not sexfile
(defined $value and $value != $vdef) ? "--bafxhet $value" : ""
( "" , " --bafxhet " + str(value) )[ value is not None and value != vdef]
$bafxhet_threshold > 0 and $bafxhet_threshold < 1
bafxhet > 0 and bafxhet_threshold < 1
$type eq '--validate'
type == '--validate'
not candlist
not candlist
(defined $value) ? "--startsnp $value" : ""
( "" , " --startsnp " + str(value) )[ value is not None ]
not candlist
not candlist
(defined $value) ? "--endsnp $value" : ""
( "" , " --endsnp " + str(value) )[ value is not None ]
not candlist
not candlist
(defined $value) ? "--delfreq $value" : ""
( "" , " --delfreq " + str(value) )[ value is not None ]
$delfreq < 1 and $delfreq >=0 and (delfrep+dupfreq) <1
delfreq < 1 and delfreq >=0
not candlist
not candlist
(defined $value) ? "--dupfreq $value" : ""
( "" , " --dupfreq " + str(value) )[ value is not None ]
$dupfreq < 1 and $dupfreq >=0
dupfreq < 1 and dupfreq >=0
not $delfreq and not $dupfreq
not delfreq and not dupfreq
(defined $value) ? "--backfreq $value" : ""
( "" , " --backfreq " + str(value) )[ value is not None ]
$backfreq > 0 and $backfreq < 0.5
backfreq > 0 and backfreq < 0.5
not $startsnp and not $endsnp and not $delfreq and not $dupfreq
not startsnp and not endsnp and not delfreq and not dupfreq
(defined $value) ? "--candlist $value " : ""
( "" , " --candlist " + str(value) )[ value is not None]
$rawcnv eq '--cctest'
rawcnv == '--cctest'
$rawcnv eq '--cctest'
rawcnv == '--cctest'
(defined $value) ? "--phenofile $value " : ""
( "" , " --phenofile " + str(value) )[ value is not None]
(defined $value) ? "--control_label $value " : ""
( "" , " --control_label " + str(value) )[ value is not None ]
($value) ? "--onesided" : ""
( "" , " --onesided " )[ value ]
(defined $value and $value ne $vdef) ? "--type_filter $value " : ""
( "" , " --type_filter " + str(value) )[ value is not None and value !=vdef ]
$rawcnv eq '--trio' or $rawcnv eq '--quartet'
rawcnv =='--trio' or rawcnv =='--quartet'
(defined $value) ? "--fmprior $value " : ""
( "" , " --fmprior " + str(value) )[ value is not None ]
$value ~= /\d+(,\d+){5}/
len(value.split(',')) == 6
$rawcnv eq '--trio' or $rawcnv eq '--quartet'
rawcnv =='--trio' or rawcnv =='--quartet'
(defined $value and $value != $vdef) ? "--denovo_rate $value" : ""
( "" , " --denovo_rate " + str(value) )[ value is not None and value != vdef]
$type eq '--test' or $rawcnv eq '--trio' or $rawcnv eq '--quartet' or $type eq '--joint' or $type eq '--validate'
type =='--test' or rawcnv =='--trio' or rawcnv =='--quartet' or type =='--joint' or type =='--validate'
(not $value) ? "--nomedianadjust" : ""
( "" , " --nomedianadjust " )[ not value ]
$type eq '--test' or $rawcnv eq '--trio' or $rawcnv eq '--quartet' or $type eq '--joint' or $type eq '--validate'
type =='--test' or rawcnv =='--trio' or rawcnv =='--quartet' or type =='--joint' or type =='--validate'
(not $value) ? "--nobafadjust" : ""
( "" , " --nobafadjust " )[ not value ]
$type eq '--test' or $rawcnv eq '--trio' or $rawcnv eq '--quartet' or $type eq '--joint' or $type eq '--validate'
type =='--test' or rawcnv =='--trio' or rawcnv =='--quartet' or type =='--joint' or type =='--validate'
(not $value) ? "--nosdadjust" : ""
( "" , " --nosdadjust " )[ not value ]
(not $value) ? "--noflush" : ""
( "" , " --noflush " )[ not value ]
($type is not None or $rawcnv is not None) and $type ne '--test'
(type is not None or rawcnv is not None) and type != '--test'
" --out detect_cnv.out "
" --out detect_cnv.out "
$type ne '--test'
type != '--test'
"detect_cnv.out"
"detect_cnv.out"
("", " -sequence=" + str(value))[value is not None]
("", " -wordsize=" + str(value))[value is not None and value!=vdef]
value >= 2
("" , " -outfile=" + str(value))[value is not None]
("", " -aformat=" + str(value))[value is not None and value!=vdef]
e_aformat_outfile in ['FASTA', 'MSF']
e_outfile
e_aformat_outfile in ['PAIR', 'MARKX0', 'MARKX1', 'MARKX2', 'MARKX3', 'MARKX10', 'SRS', 'SRSPAIR', 'SCORE', 'UNKNOWN', 'MULTIPLE', 'SIMPLE', 'MATCH']
e_outfile
" -auto -stdout"
("", " -sequence=" + str(value))[value is not None]
("", " -pattern=@" + str(value))[value is not None]
("" , " -outfile=" + str(value))[value is not None]
("", " -rformat=" + str(value))[value is not None and value!=vdef]
e_rformat_outfile in ['DASGFF', 'DBMOTIF', 'DIFFSEQ', 'EMBL', 'EXCEL', 'FEATTABLE', 'GENBANK', 'GFF', 'LISTFILE', 'MOTIF', 'NAMETABLE', 'CODATA', 'REGIONS', 'SEQTABLE', 'SIMPLE', 'SRS', 'SWISS', 'TABLE', 'TAGSEQ']
e_outfile
" -auto -stdout"
("", " -sequence=" + str(value))[value is not None]
("", " -pattern=@" + str(value))[value is not None]
("", " -pmismatch=" + str(value))[value is not None and value!=vdef]
("", " -complement")[ bool(value) ]
("" , " -outfile=" + str(value))[value is not None]
("", " -rformat=" + str(value))[value is not None and value!=vdef]
e_rformat_outfile in ['DASGFF', 'DBMOTIF', 'DIFFSEQ', 'EMBL', 'EXCEL', 'FEATTABLE', 'GENBANK', 'GFF', 'LISTFILE', 'MOTIF', 'NAMETABLE', 'CODATA', 'REGIONS', 'SEQTABLE', 'SIMPLE', 'SRS', 'SWISS', 'TABLE', 'TAGSEQ']
e_outfile
" -auto -stdout"
("", " -features=" + str(value))[value is not None]
("" , " -outfeat=" + str(value))[value is not None]
("", " -offormat=" + str(value))[value is not None and value!=vdef]
e_outfeat
" -auto -stdout"
("", " -sequence=" + str(value))[value is not None]
("", " -gap=" + str(value))[value is not None and value!=vdef]
("", " -threshold=" + str(value))[value is not None and value!=vdef]
("", " -match=" + str(value))[value is not None and value!=vdef]
("", " -mismatch=" + str(value))[value is not None and value!=vdef]
("", " -maxrepeat=" + str(value))[value is not None and value!=vdef]
("" , " -outfile=" + str(value))[value is not None]
e_outfile
("" , " -outseq=" + str(value))[value is not None]
("", " -osformat=" + str(value))[value is not None and value!=vdef]
e_outseq
" -auto -stdout"
"netChop "
"netChop "
" $value"
" " + str( value )
(defined $value and $value ne $vdef)? " -v $value": ""
( "" , " -v "+ value )[ value is not None and value != vdef ]
(defined $value and $value ne $vdef)? " -t $value": ""
( "" , " -t "+str(value) )[value is not None and value != vdef]
($value)? " -s": ""
( ""," -s ")[ bool( value ) ]
"netchop.out"
"netchop.out"
"smile smile.params"
"smile smile.params"
"FASTA file\t\t\t$value\\n"
"FASTA file\t\t\t" + str(value) + "\n"
"Alphabet file\t\t\t
"Alphabet file\t\t\t
$alphabet ne "dna.alphabet"
alphabet != "dna.alphabet"
"Composition in *\t\t$value\\n"
"Composition in *\t\t" + str(value)+"\n"
$alphabet eq "dnadeg.alphabet"
alphabet == "dnadeg.alphabet"
"Composition in AG\t\t$value\\n"
"Composition in AG\t\t" + str(value)+"\n"
$alphabet eq "dnadeg.alphabet"
alphabet == "dnadeg.alphabet"
"Composition in CT\t\t$value\\n"
"Composition in CT\t\t" + str(value)+"\n"
"Quorum\t\t\t\t$value\\n"
"Quorum\t\t\t\t" + str(value)+"\n"
"Total min length\t\t$value\\n"
"Total min length\t\t" + str(value)+"\n"
(defined $value)? "Total max length\t\t$value\\n" : ""
( "" , "Total max length\t\t" + str(value)+"\n" )[ value is not None ]
"Total substitutions\t\t$value\\n"
"Total substitutions\t\t" + str(value)+"\n"
defined $subst and $subst <= $minlen
subst is not None and subst <= minlen
"Boxes\t\t\t\t\1\\n"
"Boxes\t\t\t\t1\n"
(defined $value)? "Shufflings\t\t\t$value\\n":""
( "" , "Shufflings\t\t\t"+ str(value)+"\n")[value is not None]
(defined $value)? "Size k-mer\t\t\t$value\\n":""
("" , "Size k-mer\t\t\t"+ str(value)+"\n")[value is not None]
"Output file\t\t\tsmile.result\\n"
"Output file\t\t\tsmile.result\n"
"smile.result"
"smile.result"
"smile.result.shuffle"
"smile.result.shuffle"
("", " -sequence=" + str(value))[value is not None]
("" , " -outfile=" + str(value))[value is not None]
e_outfile
" -auto -stdout"
" -quiet"
" -quiet"
not defined($profile1) and not defined($profile2)
profile1 is None and profile2 is None
"-in $value"
" -in " + str(value)
(defined $value and $value ne $vdef) ? " -seqtype $value " : ""
( "" , " -seqtype " + str(value) )[ value is not None and value != vdef ]
(defined $value and $value != $vdef) ? " -maxiters $value" : ""
( "" , " -maxiters " + str( value ) )[ value is not None and value != vdef]
(defined $value and $value != $vdef) ? "-maxtrees $value" : ""
( "" , " -maxtrees " + str( value ) )[ value is not None and value != vdef]
(defined $maxhours) ? "-maxhours $value" : ""
( "" , " -maxhours " + str( value ) )[ maxhours is not None ]
(defined $value and $value != $vdef) ? " -diags " : ""
( "" , " -diags " )[ value is not None and value != vdef]
$seqtype ne "nucleo"
seqtype != "nucleo"
""
""
" -sp "
" -sp "
" -sv "
" -sv "
not defined($sequence)
sequence is None
"-in1 $value"
" -in1 " + str(value)
not defined($sequence)
sequence is None
"-in2 $value"
" -in2 " + str(value)
not defined($sequence) and defined($profile1) and defined($profile2)
sequence is None and profile1 is not None and profile2 is not None
""
" -profile "
""
""
" -html "
" -html "
" -msf "
" -msf "
" -phyi "
" -phyi "
" -clw "
" -clw "
" -clwstrict "
" -clwstrict "
" -out $value"
("", " -out " + str(value))[value is not None]
$outformat =~ /^(fasta|msf|phyi|clwstrict|clw)$/
outformat in [ 'fasta' , 'msf' , 'phyi' , 'clwstrict' , 'clw']
(defined $outfile) ? "$outfile" : "muscle.out"
( outfile , "muscle.out")[outfile is None]
$outformat == 'html'
outformat == 'html'
(defined $outfile) ? "$outfile" : "muscle.out"
( outfile , "muscle.out")[outfile is None]
("", " -asequence=" + str(value))[value is not None]
("", " -bsequence=" + str(value))[value is not None]
("", " -wordsize=" + str(value))[value is not None and value!=vdef]
value >= 2
("", " -stretch")[ bool(value) ]
not e_stretch
(" -graph=" + str(vdef), " -graph=" + str(value))[value is not None and value!=vdef]
not e_stretch
("" , " -goutfile=" + str(value))[value is not None]
not e_stretch and e_graph == "png"
"*.png"
not e_stretch and e_graph == "gif"
"*.gif"
not e_stretch and e_graph == "ps" or e_graph == "cps"
"*.ps"
not e_stretch and e_graph == "meta"
"*.meta"
not e_stretch and e_graph == "data"
"*.dat"
e_stretch
(" -xygraph=" + str(vdef), " -xygraph=" + str(value))[value is not None and value!=vdef]
e_stretch
("" , " -goutfile=" + str(value))[value is not None]
e_stretch and e_xygraph == "png"
"*.png"
e_stretch and e_xygraph == "gif"
"*.gif"
e_stretch and e_xygraph == "ps" or e_xygraph == "cps"
"*.ps"
e_stretch and e_xygraph == "meta"
"*.meta"
e_stretch and e_xygraph == "data"
"*.dat"
not e_stretch
(" -noboxit", "")[ bool(value) ]
" -auto -stdout"
("", " -asequence=" + str(value))[value is not None]
("", " -bsequence=" + str(value))[value is not None]
("", " -datafile=" + str(value))[value is not None and value!=vdef]
("", " -gapopen=" + str(value))[value is not None]
value >= 0.0
value <= 100.0
("", " -gapextend=" + str(value))[value is not None]
value >= 0.0
value <= 10.0
(" -nobrief", "")[ bool(value) ]
("" , " -outfile=" + str(value))[value is not None]
("", " -aformat=" + str(value))[value is not None and value!=vdef]
e_aformat_outfile in ['FASTA', 'MSF']
e_outfile
e_aformat_outfile in ['PAIR', 'MARKX0', 'MARKX1', 'MARKX2', 'MARKX3', 'MARKX10', 'SRS', 'SRSPAIR', 'SCORE', 'UNKNOWN', 'MULTIPLE', 'SIMPLE', 'MATCH']
e_outfile
" -auto -stdout"
" $value"
" "+str(value)
" $value"
" "+str(value)
($value != $vdef) ? " -o phmmer.output" : ""
("", " -o phmmer.output") [ value != vdef]
($value != $vdef) ? " -A phmmer.alig" : ""
("", " -A phmmer.alig") [ value != vdef]
$value != $vdef) ? " --tblout phmmer.tblout" : ""
("", " --tblout phmmer.tblout") [ value != vdef]
($value != $vdef) ? " --domtblout phmmer.domtblout" : ""
("", " --domtblout phmmer.domtblout") [ value != vdef]
($value != $vdef) ? " --acc" : ""
("", " --acc") [ value != vdef]
($value != $vdef) ? " --noali" : ""
("", " --noali") [ value != vdef]
($value != $vdef) ? " --notextw" : ""
("", " --notextw" ) [ value != vdef]
$notextw == 0
notextw == 0
($value != $vdef) ? " --textw $value" : ""
("", " --textw " + str(value) ) [ value != vdef]
120 <=$value
120 <=value
($value != $vdef) ? " --popen $value" : ""
("", " --popen " + str(value)) [ value != vdef]
0 <= $value <0.5
0 <= value <0.5
($value != $vdef) ? " --pextend $value" : ""
("", " --pextend " + str(value)) [ value != vdef]
0 <= $value <1
0 <= value <1
($value != $vdef) ? " --mxfile $value" : ""
("", " --mxfile " + str(value)) [ value != vdef]
$s_threshold is None
s_threshold is None
($value != $vdef) ? " -E $value" : ""
("", " -E " + str(value)) [ value != vdef]
0 <$value
0 < value
($value) ? " -T $value" : ""
("", " -T " + str(value)) [ value is not None]
0 <$value
0 < value
$d_s_threshold is None
d_s_threshold is None
($value != $vdef) ? " --domE $value" : ""
("", " --domE " + str(value)) [ value is not None and value != vdef]
0 <$value
0 < value
($value) ? " --domT $value" : ""
("", " --domT " + str(value)) [ value is not None]
0 <$value
0 < value
$aligfile==1
aligfile==1
$a_s_threshold is None
a_s_threshold is None
($value != $vdef) ? " --incE $value" : ""
("", " --incE " + str(value)) [ value is not None and value != vdef]
($value) ? " --incT $value" : ""
("", " --incT " + str(value)) [ value is not None]
$a_d_s_threshold is None
a_d_s_threshold is None
($value != $vdef) ? " --incdomE $value" : ""
("", " --incdomE " + str(value)) [ value is not None and value != vdef ]
($value) ? " --incdomT $value" : ""
("", " --incdomT " + str(value)) [ value is not None]
($value != $vdef) ? " --max" : ""
("", " --max") [ value != vdef ]
$max==0
max==0
($value != $vdef) ? " --F1 $value" : ""
("", " --F1 " + str(value) ) [ value != vdef ]
$max==0
max==0
($value != $vdef) ? " --F2 $value" : ""
("", " --F2 " + str(value) ) [ value != vdef ]
$max==0
max==0
($value != $vdef) ? " --F3 $value" : ""
("", " --F3 " + str(value) ) [ value != vdef ]
$max==0
max==0
($value != $vdef) ? " --nobias" : ""
("", " --nobias" ) [ value != vdef ]
($value != $vdef) ? " --EmL $value" : ""
("", " --EmL " + str(value) ) [ value != vdef ]
0 <$value
0 < value
($value != $vdef) ? " --EmN $value" : ""
("", " --EmN " + str(value) ) [ value != vdef ]
0 <$value
0 < value
($value != $vdef) ? " --EvL $value" : ""
("", " --EvL " + str(value) ) [ value != vdef ]
0 <$value
0 < value
($value != $vdef) ? " --EvN $value" : ""
("", " --EvN " + str(value) ) [ value != vdef ]
0 <$value
0 < value
($value != $vdef) ? " --EfL $value" : ""
("", " --EfL " + str(value) ) [ value != vdef ]
0 <$value
0 < value
($value != $vdef) ? " --EfN $value" : ""
("", " --EfN " + str(value) ) [ value != vdef ]
0 <$value
0 < value
($value != $vdef) ? " --Eft $value" : ""
("", " --Eft " + str(value) ) [ value != vdef ]
0 <$value
0 < value
$max==0
max==0
($value != $vdef) ? " --nonull2" : ""
("", " --nonull2" ) [ value != vdef]
($value) ? " -Z $value" : ""
("", " -Z " + str(value)) [ value is not None]
0 <$value
0 < value
($value) ? " --domZ $value" : ""
("", " --domZ " + str(value)) [ value is not None]
0 <$value
0 < value
($value != $vdef) ? " --seed $value" : ""
("", " --seed " + str(value) ) [ value != vdef]
$outfile==1
outfile==1
*.output
"*.output"
$aligfile==1
aligfile==1
*.alig
"*.alig"
$seqtab==1
seqtab==1
*.tblout
"*.tblout"
$domaintab==1
domaintab==1
*.domtblout
"*.domtblout"
("", " -sequence=" + str(value))[value is not None]
("", " -range=" + str(value))[value is not None]
("", " -table=" + str(value))[value is not None and value!=vdef]
(" -noruler", "")[ bool(value) ]
(" -noplabel", "")[ bool(value) ]
(" -nonlabel", "")[ bool(value) ]
("", " -width=" + str(value))[value is not None and value!=vdef]
value >= 10
("" , " -outfile=" + str(value))[value is not None]
e_outfile
" -auto -stdout"
"RNAinverse"
"RNAinverse"
" < $value"
" < " + str(value)
(defined $value and $value ne $vdef)? " -F$value" : ""
("", " -F" + str(value))[ value is not None]
$folding eq 'mp' or $folding eq 'p'
folding == 'mp' or folding == 'p'
(defined $value)? " -f $value" : ""
("", " -f " + str(value))[ value is not None]
(defined $value)? " -R $value" : ""
("", " -R " + str(value))[ value is not None]
(defined $value)? " -a $value" : ""
("", " -a " + str(value))[ value is not None]
(defined $value and $value != $vdef)? " -T $value" : ""
( "" , " -T " + str(value) )[ value is not None and value != vdef]
($value)? " -4" : ""
( "" , " -4" )[ value ]
(defined $value and $value ne $vdef)? " $value" : ""
( "" , " " + str(value) )[ value is not None and value != vdef]
($value)? " -noGU" : ""
( "" , " -noGU" )[ value ]
($value)? " -noCloseGU" : ""
( "" , " -noCloseGU" )[ value ]
(defined $value)? " -nsp $value" : ""
( "" , " -nsp " + str(value) )[ value is not None ]
(defined $value)? " -P $value" : ""
( "" , " -P " + str(value) )[ value is not None ]
"boxshade <boxshade.params"
"boxshade <boxshade.params"
"$value\\n"
str(value) + "\n"
"2\\n"
"2\n"
"$value\\n"
str(value) + "\n"
($value) ? "y\\n" : "n\\n"
( "n\n" , "y\n" )[ value ]
($value) ? "y\\n" : "n\\n"
( "n\n" , "y\n" )[ value ]
not $ruler
not ruler
($value) ? "y\\n" : "n\\n"
( "n\n" , "y\n" )[ value ]
"$value\\n"
str( value ) + "\n"
$value <= 254
value <= 254
"$value\\n"
str(value) + "\n"
$value > 0
value > 0
$output_format !~ /^[89be]$/
output_format not in ["8","9","b","e"]
"$value\\n"
str(value) + "\n"
$output_format eq "d"
output_format == "d"
"$value\\n"
str(value) + "\n"
$output_format eq "1" or $output_format eq "3" or $output_format eq "d"
output_format == "1" or output_format == "3" or output_format == "d"
($value) ? "y\\n" : "n\\n"
( "n\n" , "y\n" )[ value ]
($value) ? "y\\n" : "n\\n"
( "n\n" , "y\n" )[ value ]
($value) ? "y\\n" : "n\\n"
( "n\n" , "y\n" )[ value ]
($value) ? "y\\n .*\\n" : "n\\n"
( "n\n" , "y\n .*\n" )[ value ]
$output_format ne "b"
output_format != "b"
"$value\\n"
str(value) + "\n"
0 <= $value <= 1
0 <= value <= 1
$output_format ne "b"
output_format != "b"
"$value\\n"
str(value) + "\n"
"$value\\n"
str(value) + "\n"
$output_format ne "b"
output_format != "b"
"$value\\n"
str(value) + "\n"
"$value\\n"
str(value) + "\n"
$label_similar and $output_format ne "b"
label_similar and output_format != "b"
"$value\\n"
str(value) + "\n"
$label_similar
label_similar
"$value\\n"
str(value) + "\n"
label_identical and output_format ne "b"
label_identical and output_format != "b"
"$value\\n"
str(value) + "\n"
$label_identical
label_identical
"$value\\n"
str(value) + "\n"
$output_format ne "b"
output_format != "b"
($value) ? "y\\n" : "n\\n"
( "n\n" , "y\n" )[ value ]
$single
single
"$value\\n"
str(value) + "\n"
$seq_no >= 0
seq_no >= 0
$single
single
($value) ? "y\\n" : "n\\n"
( "n\n" , "y\n" )[ value ]
$single
single
($value) ? "y\\n" : "n\\n"
( "n\n" , "y\n" )[ value ]
($value) ? "y\\n" : "n\\n"
( "n\n" , "y\n" )[ value ]
$output_format ne "1" and $output_format ne "e" and $output_format ne "2" and $output_format ne "d" and $output_format ne "c" and $output_format ne "4"
output_format != "1" and output_format != "e" and output_format != "2" and output_format != "d" and output_format != "c" and output_format != "4"
"boxshade.result\\n"
"boxshade.result\n"
$output_format ne "1" and $output_format ne "e" and $output_format ne "2" and $output_format ne "d" and $output_format ne "c" and $output_format ne "4"
output_format != "1" and output_format != "e" and output_format != "2" and output_format != "d" and output_format != "c" and output_format != "4"
"boxshade.result"
"boxshade.result"
$output_format eq "1" or $output_format eq "2"
output_format == "1" or output_format == "2"
"boxshade.ps\\n"
"boxshade.ps\n"
$output_format eq "1" or $output_format eq "2"
output_format == "1" or output_format == "2"
"boxshade.ps"
"boxshade.ps"
$output_format eq "e"
output_format == "e"
"boxshade.html\\n"
"boxshade.html\n"
$output_format eq "e"
output_format == "e"
"boxshade.html"
"boxshade.html"
$output_format eq "4"
output_format == "4"
"boxshade.rtf\\n"
"boxshade.rtf\n"
$output_format eq "4"
output_format == "4"
"boxshade.rtf"
"boxshade.rtf"
$output_format eq "c"
output_format == "c"
"boxshade.fig\\n"
"boxshade.fig\n"
$output_format eq "c"
output_format == "c"
"boxshade.fig"
"boxshade.fig"
$output_format eq "d"
output_format == "d"
"boxshade.pict\\n"
"boxshade.pict\n"
$output_format eq "d"
output_format == "d"
"boxshade.pict"
"boxshade.pict"
$matrix
matrix
"boxshade.matrix\\n"
"boxshade.matrix\n"
$matrix
matrix
"boxshade.matrix"
"boxshade.matrix"
("", " -sequence=" + str(value))[value is not None]
("", " -matrix=" + str(value))[value is not None and value!=vdef]
("", " -refseq=" + str(value))[value is not None and value!=vdef]
(" -nobottom", "")[ bool(value) ]
("", " -show=" + str(value))[value is not None and value!=vdef]
("", " -order=" + str(value))[value is not None and value!=vdef]
(" -nosimilarcase", "")[ bool(value) ]
(" -noconsensus", "")[ bool(value) ]
("", " -uppercase=" + str(value))[value is not None]
(" -nonumber", "")[ bool(value) ]
(" -noruler", "")[ bool(value) ]
("", " -width=" + str(value))[value is not None and value!=vdef]
value >= 1
("", " -margin=" + str(value))[value is not None and value!=vdef]
value >= -1
("", " -html")[ bool(value) ]
("", " -highlight=" + str(value))[value is not None]
("", " -plurality=" + str(value))[value is not None and value!=vdef]
value >= 0.0
value <= 100.0
("", " -setcase=" + str(value))[value is not None]
("", " -identity=" + str(value))[value is not None and value!=vdef]
value >= 0.0
value <= 100.0
(" -nogaps", "")[ bool(value) ]
("" , " -outfile=" + str(value))[value is not None]
e_outfile
" -auto -stdout"
("", " -infile=" + str(value))[value is not None]
("", " -datafile=" + str(value))[value is not None ]
("", " -tolerance=" + str(value))[value is not None and value!=vdef]
("", " -showdel")[ bool(value) ]
("" , " -outfile=" + str(value))[value is not None]
e_outfile
" -auto -stdout"
("", " -sequence=" + str(value))[value is not None]
("", " -emin=" + str(value))[value is not None and value!=vdef]
value >= 1
value <= 20
("", " -emax=" + str(value))[value is not None and value!=vdef]
value <= 20
("" , " -outfile=" + str(value))[value is not None]
e_outfile
" -auto -stdout"
("", " -sequence=" + str(value))[value is not None]
("", " -type=" + str(value))[value is not None and value!=vdef]
e_type !="F"
("", " -datafile=" + str(value))[value is not None and value!=vdef]
("", " -name=" + str(value))[value is not None and value!=vdef]
e_type =="F"
("", " -threshold=" + str(value))[value is not None and value!=vdef]
value >= 1
value <= 100
e_type !="F"
("", " -open=" + str(value))[value is not None and value!=vdef]
e_type !="F"
("", " -extension=" + str(value))[value is not None and value!=vdef]
("" , " -outfile=" + str(value))[value is not None]
e_outfile
" -auto -stdout"
("", " -sequences=" + str(value))[value is not None]
("", " -wordsize=" + str(value))[value is not None and value!=vdef]
value >= 2
("", " -gap=" + str(value))[value is not None and value!=vdef]
value >= 0
(" -noboxit", "")[ bool(value) ]
("", " -dumpfeat")[ bool(value) ]
e_dumpfeat
("" , " -outfeat=" + str(value))[value is not None]
e_dumpfeat
("", " -offormat=" + str(value))[value is not None and value!=vdef]
e_outfeat
(" -graph=" + str(vdef), " -graph=" + str(value))[value is not None and value!=vdef]
("" , " -goutfile=" + str(value))[value is not None]
e_graph == "png"
"*.png"
e_graph == "gif"
"*.gif"
e_graph == "ps" or e_graph == "cps"
"*.ps"
e_graph == "meta"
"*.meta"
e_graph == "data"
"*.dat"
" -auto -stdout"