mirror of
https://github.com/galaxyproject/galaxy.git
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Convert a bunch of binary requirement tags to package requirements, and change the sputnik tool to call 'sputnik' instead of 'bx-sputnik'.
This commit is contained in:
Nate Coraor
@@ -1,5 +1,6 @@
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<tool id="EMBOSS: antigenic1" name="antigenic" version="5.0.0">
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<description>Predicts potentially antigenic regions of a protein sequence, using the method of Kolaskar and Tongaonkar.</description>
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<requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
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<command>antigenic -sequence $input1 -outfile $out_file1 -minlen $minlen -rformat2 $out_format1 -auto</command>
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<inputs>
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<param format="data" name="input1" type="data">
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@@ -1,5 +1,6 @@
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<tool id="EMBOSS: backtranseq2" name="backtranseq" version="5.0.0">
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<description>Back translate a protein sequence</description>
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<requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
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<command>backtranseq -sequence $input1 -outfile $out_file1 -cfile $cfile -osformat2 $out_format1 -auto</command>
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<inputs>
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<param format="fasta" name="input1" type="data">
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@@ -1,5 +1,6 @@
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<tool id="EMBOSS: banana3" name="banana" version="5.0.0">
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<description>Bending and curvature plot in B-DNA</description>
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<requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
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<command>banana -sequence $input1 -outfile $out_file1 -graph none -auto</command>
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<inputs>
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<param format="data" name="input1" type="data">
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@@ -1,5 +1,6 @@
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<tool id="EMBOSS: biosed4" name="biosed" version="5.0.0">
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<description>Replace or delete sequence sections</description>
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<requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
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<command>biosed -sequence $input1 -outseq $out_file1 -target $target -replace $replace -osformat2 $out_format1 -auto</command>
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<inputs>
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<param format="fasta" name="input1" type="data">
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@@ -1,5 +1,6 @@
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<tool id="EMBOSS: btwisted5" name="btwisted" version="5.0.0">
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<description>Calculates the twisting in a B-DNA sequence</description>
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<requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
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<command>btwisted -sequence $input1 -outfile $out_file1 -auto</command>
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<inputs>
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<param format="data" name="input1" type="data">
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@@ -1,5 +1,6 @@
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<tool id="EMBOSS: cai6" name="cai" version="5.0.0">
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<description>CAI codon adaptation index</description>
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<requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
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<command>cai -seqall $input1 -outfile $out_file1 -cfile $cfile -auto</command>
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<inputs>
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<param format="fasta" name="input1" type="data">
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@@ -1,5 +1,6 @@
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<tool id="EMBOSS: cai_custom6" name="cai custom" version="5.0.0">
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<description>CAI codon adaptation index using custom codon usage file</description>
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<requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
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<command>cai -seqall $input1 -outfile $out_file1 -cfile $input2 -auto</command>
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<inputs>
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<param format="fasta" name="input1" type="data">
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@@ -1,5 +1,6 @@
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<tool id="EMBOSS: chaos7" name="chaos" version="5.0.0">
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<description>Create a chaos game representation plot for a sequence</description>
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<requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
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<command interpreter="perl">emboss_single_outputfile_wrapper.pl chaos -sequence $input1 -graph png -goutfile $out_file1 -auto</command>
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<inputs>
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<param format="data" name="input1" type="data">
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@@ -1,5 +1,6 @@
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<tool id="EMBOSS: charge8" name="charge" version="5.0.0">
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<description>Protein charge plot</description>
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<requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
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<command>charge -seqall $input1 -outfile $out_file1 -window $window -auto</command>
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<inputs>
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<param format="fasta" name="input1" type="data">
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@@ -1,5 +1,6 @@
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<tool id="EMBOSS: checktrans9" name="checktrans" version="5.0.0">
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<description>Reports STOP codons and ORF statistics of a protein</description>
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<requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
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<command>checktrans -sequence $input1 -outfile $out_file1 -outseq $out_file2 -osformat3 $out_format2 -outfeat $out_file3 -offormat4 $out_format3 -orfml $orfml -addlast $addlast -auto</command>
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<inputs>
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<param format="fasta" name="input1" type="data">
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@@ -1,5 +1,6 @@
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<tool id="EMBOSS: chips10" name="chips" version="5.0.0">
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<description>Codon usage statistics</description>
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<requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
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<command>chips -seqall $input1 -outfile $out_file1 -sum $sum -auto</command>
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<inputs>
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<param format="data" name="input1" type="data">
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@@ -1,5 +1,6 @@
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<tool id="EMBOSS: cirdna11" name="cirdna" version="5.0.0">
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<description>Draws circular maps of DNA constructs</description>
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<requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
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<command interpreter="perl">emboss_single_outputfile_wrapper.pl cirdna -infile $input1 -graphout png -goutfile $out_file1 -auto</command>
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<inputs>
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<param format="data" name="input1" type="data">
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@@ -1,5 +1,6 @@
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<tool id="EMBOSS: codcmp12" name="codcmp" version="5.0.0">
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<description>Codon usage table comparison</description>
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<requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
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<command>codcmp -first $cfile1 -second $cfile2 -outfile $out_file1 -auto</command>
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<inputs>
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<param name="cfile1" type="select">
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@@ -1,5 +1,6 @@
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<tool id="EMBOSS: coderet13" name="coderet" version="5.0.0">
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<description>Extract CDS, mRNA and translations from feature tables</description>
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<requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
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<!-- <command>coderet -seqall $input1 -outfile $out_file1 -osformat2 $out_format1 -cds $cds -mrna $mrna -translation $translation -auto</command>-->
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<command>coderet -seqall $input1 -outfile $out_file1 -auto</command>
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<inputs>
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@@ -1,5 +1,6 @@
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<tool id="EMBOSS: compseq14" name="compseq" version="5.0.0">
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<description>Count composition of dimer/trimer/etc words in a sequence</description>
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<requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
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<command>compseq -sequence $input1 -outfile $out_file1 -word $word -frame $frame -auto</command>
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<inputs>
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<param format="fasta" name="input1" type="data">
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@@ -1,5 +1,6 @@
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<tool id="EMBOSS: cpgplot15" name="cpgplot" version="5.0.0">
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<description>Plot CpG rich areas</description>
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<requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
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<command interpreter="perl">emboss_cpgplot_wrapper.pl cpgplot -sequence $input1 -window $window -minlen $minlen -minpc $minpc -outfile $outfile -graph png -goutfile $goutfile -outfeat $outfeat -minoe $minoe -auto</command>
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<inputs>
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<param format="data" name="input1" type="data">
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@@ -1,5 +1,6 @@
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<tool id="EMBOSS: cpgreport16" name="cpgreport" version="5.0.0">
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<description>Reports all CpG rich regions</description>
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<requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
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<command>cpgreport -sequence $input1 -outfile $out_file1 -outfeat $out_file2 -offormat3 $out_format2 -score $score -auto</command>
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<inputs>
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<param format="fasta" name="input1" type="data">
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@@ -1,5 +1,6 @@
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<tool id="EMBOSS: cusp17" name="cusp" version="5.0.0">
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<description>Create a codon usage table</description>
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<requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
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<command>cusp -sequence $input1 -outfile $out_file1 -auto</command>
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<inputs>
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<param format="fasta" name="input1" type="data">
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@@ -1,5 +1,6 @@
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<tool id="EMBOSS: cutseq18" name="cutseq" version="5.0.0">
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<description>Removes a specified section from a sequence</description>
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<requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
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<command>cutseq -sequence $input1 -outseq $out_file1 -from $from -to $to -osformat2 $out_format1 -auto</command>
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<inputs>
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<param format="fasta" name="input1" type="data">
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@@ -1,5 +1,6 @@
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<tool id="EMBOSS: dan19" name="dan" version="5.0.0">
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<description>Calculates DNA RNA/DNA melting temperature</description>
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<requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
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<command interpreter="perl">emboss_single_outputfile_wrapper.pl dan -sequence $input1 -windowsize $window -goutfile $out_file1 -graph png -plot $plot1 -shiftincrement $shift -dnaconc $dnaconc
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-saltconc $saltconc -product $product -formamide $formamide -mismatch $mismatch -prodlen $prodlen -thermo $thermo -temperature $temperature -rna $rna -outfile $out_file1 -auto</command>
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<inputs>
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@@ -1,5 +1,6 @@
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<tool id="EMBOSS: degapseq20" name="degapseq" version="5.0.0">
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<description>Removes gap characters from sequences</description>
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<requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
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<command>degapseq -sequence $input1 -outseq $out_file1 -osformat2 $out_format1 -auto</command>
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<inputs>
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<param format="data" name="input1" type="data">
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@@ -1,5 +1,6 @@
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<tool id="EMBOSS: descseq21" name="descseq" version="5.0.0">
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<description>Alter the name or description of a sequence</description>
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<requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
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<command>descseq -sequence $input1 -outseq $out_file1 -name "$seqname" -description "$desc" -append $append -osformat2 $out_format1 -auto</command>
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<inputs>
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<param format="data" name="input1" type="data">
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@@ -1,5 +1,6 @@
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<tool id="EMBOSS: diffseq22" name="diffseq" version="5.0.0">
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<description>Find differences between nearly identical sequences</description>
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<requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
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<command>diffseq -asequence $input1 -bsequence $input2 -outfile $out_file1 -aoutfeat $out_file2 -boutfeat $out_file3 -wordsize $wordsize -globaldifferences $globaldifferences -rformat3
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$out_format1 -offormat4 $out_format2 -offormat5 $out_format3 -auto</command>
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<inputs>
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@@ -1,5 +1,6 @@
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<tool id="EMBOSS: digest23" name="digest" version="5.0.0">
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<description>Protein proteolytic enzyme or reagent cleavage digest</description>
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<requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
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<command>digest -seqall $input1 -outfile $out_file1 -menu $menu -unfavoured $unfavoured -overlap $overlap -allpartials $allpartials -rformat2 $out_format1 -auto</command>
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<inputs>
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<param format="data" name="input1" type="data">
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@@ -1,5 +1,6 @@
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<tool id="EMBOSS: dotmatcher24" name="dotmatcher" version="5.0.0">
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<description>Displays a thresholded dotplot of two sequences</description>
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<requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
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<command interpreter="perl">emboss_single_outputfile_wrapper.pl dotmatcher -asequence $input1 -bsequence $input2 -goutfile $out_file1 -windowsize $windowsize -threshold $threshold -graph png -xygraph png
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-auto</command>
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<inputs>
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@@ -1,5 +1,6 @@
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<tool id="EMBOSS: dotpath25" name="dotpath" version="5.0.0">
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<description>Non-overlapping wordmatch dotplot of two sequences</description>
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<requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
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<command interpreter="perl">emboss_single_outputfile_wrapper.pl dotpath -asequence $input1 -bsequence $input2 -goutfile $out_file1 -wordsize $wordsize -overlaps $overlaps -boxit $boxit -graph png
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-auto</command>
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<inputs>
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@@ -1,5 +1,6 @@
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<tool id="EMBOSS: dottup26" name="dottup" version="5.0.0">
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<description>Displays a wordmatch dotplot of two sequences</description>
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<requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
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<command interpreter="perl">emboss_single_outputfile_wrapper.pl dottup -asequence $input1 -bsequence $input2 -goutfile $out_file1 -wordsize $wordsize -boxit $boxit -graph png -xygraph png -auto</command>
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<inputs>
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<param format="data" name="input1" type="data">
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@@ -1,5 +1,6 @@
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<tool id="EMBOSS: dreg27" name="dreg" version="5.0.0">
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<description>Regular expression search of a nucleotide sequence</description>
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<requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
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<command>dreg -sequence $input1 -outfile $out_file1 -pattern "$pattern" -raccshow3 "no" -rusashow3 "no" -rdesshow3 "no" -auto</command>
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<inputs>
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<param format="data" name="input1" type="data">
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@@ -1,5 +1,6 @@
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<tool id="EMBOSS: einverted28" name="einverted" version="5.0.0">
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<description>Finds DNA inverted repeats</description>
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<requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
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<command>einverted -sequence $input1 -outfile $out_file1 -gap $gap -threshold $threshold -match $match -mismatch $mismatch -maxrepeat $maxrepeat -auto</command>
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<inputs>
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<param format="fasta" name="input1" type="data">
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@@ -1,5 +1,6 @@
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<tool id="EMBOSS: epestfind29" name="epestfind" version="5.0.0">
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<description>Finds PEST motifs as potential proteolytic cleavage sites</description>
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<requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
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<command interpreter="perl">emboss_single_outputfile_wrapper.pl epestfind -sequence $input1 -goutfile $ofile2 -outfile $ofile1 -window $window -order $order -potential $potential -poor $poor
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-invalid $invalid -map $map -graph png -auto</command>
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<inputs>
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@@ -1,5 +1,6 @@
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<tool id="EMBOSS: equicktandem31" name="equicktandem" version="5.0.0">
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<description>Finds tandem repeats</description>
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<requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
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<command>equicktandem -sequence $input1 -outfile $out_file1 -origfile $ofile2 -maxrepeat $maxrepeat -threshold $threshold -rformat2 $out_format1 -auto</command>
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<inputs>
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<param format="fasta" name="input1" type="data">
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@@ -1,5 +1,6 @@
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<tool id="EMBOSS: est2genome32" name="est2genome" version="5.0.0">
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<description>Align EST and genomic DNA sequences</description>
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<requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
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<command>est2genome -estsequence $input1 -genomesequence $input2 -outfile $out_file1 -match $match -mismatch $mismatch -gappenalty $gappenalty -intronpenalty $intronpenalty -splicepenalty
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$splicepenalty -minscore $minscore -reverse $reverse -splice $splice -mode $mode -best $best -shuffle $shuffle -seed $seed -align $align -width $width -auto</command>
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<inputs>
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@@ -1,5 +1,6 @@
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<tool id="EMBOSS: etandem33" name="etandem" version="5.0.0">
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<description>Looks for tandem repeats in a nucleotide sequence</description>
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<requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
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<command>etandem -sequence $input1 -outfile $out_file1 -origfile $ofile2 -minrepeat $minrepeat -maxrepeat $maxrepeat -threshold $threshold -mismatch $mismatch -uniform $uniform -rformat2 $out_format1 -auto</command>
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<inputs>
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<param format="fasta" name="input1" type="data">
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@@ -1,6 +1,7 @@
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<tool id="EMBOSS: extractfeat34" name="extractfeat" version="5.0.0">
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<!-- tool tested with documentation, functional test not designed due to empty files resulting from test input sequences -->
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<description>Extract features from a sequence</description>
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<requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
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<command>extractfeat -sequence $input1 -outseq $out_file1 -before $before -after $after -source "$source" -type "$type" -sense $sense -minscore $minscore -maxscore $maxscore -tag "$tag" -value
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"$value" -join $join -featinname $featinname -describe "$describe" -osformat2 $out_format1 -auto</command>
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<inputs>
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@@ -1,5 +1,6 @@
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<tool id="EMBOSS: extractseq35" name="extractseq" version="5.0.0">
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<description>Extract regions from a sequence</description>
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<requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
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<command>extractseq -sequence $input1 -outseq $out_file1 -regions $regions -separate $separate -osformat2 $out_format1 -auto</command>
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<inputs>
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<param format="data" name="input1" type="data">
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@@ -1,5 +1,6 @@
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<tool id="EMBOSS: freak36" name="freak" version="5.0.0">
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<description>Residue/base frequency table or plot</description>
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<requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
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<command>freak -seqall $input1 -outfile $out_file1 -window $window -letters $letters -graph png -step $step -auto</command>
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<inputs>
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<param format="data" name="input1" type="data">
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@@ -1,5 +1,6 @@
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<tool id="EMBOSS: fuzznuc37" name="fuzznuc" version="5.0.1">
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<description>Nucleic acid pattern search</description>
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<requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
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<command>fuzznuc -sequence $input1 -outfile $out_file1 -pattern '$pattern' -pmismatch $mismatch -complement $complement -rformat2 $out_format1 -auto</command>
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<inputs>
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||||
<param format="fasta" name="input1" type="data">
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||||
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@@ -1,5 +1,6 @@
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<tool id="EMBOSS: fuzzpro38" name="fuzzpro" version="5.0.0">
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<description>Protein pattern search</description>
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||||
<requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
|
||||
<command>fuzzpro -sequence $input1 -outfile $out_file1 -pattern "$pattern" -pmismatch $mismatch -rformat2 $out_format1 -auto</command>
|
||||
<inputs>
|
||||
<param format="data" name="input1" type="data">
|
||||
|
||||
@@ -1,5 +1,6 @@
|
||||
<tool id="EMBOSS: fuzztran39" name="fuzztran" version="5.0.0">
|
||||
<description>Protein pattern search after translation</description>
|
||||
<requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
|
||||
<command>fuzztran -sequence $input1 -outfile $out_file1 -pattern "$pattern" -pmismatch $mismatch -frame $frame -table $table -rformat2 $out_format1 -auto</command>
|
||||
<inputs>
|
||||
<param format="fasta" name="input1" type="data">
|
||||
|
||||
@@ -1,5 +1,6 @@
|
||||
<tool id="EMBOSS: garnier40" name="garnier" version="5.0.0">
|
||||
<description>Predicts protein secondary structure</description>
|
||||
<requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
|
||||
<command>garnier -sequence $input1 -outfile $out_file1 -idc $idc -rformat2 $out_format1 -auto</command>
|
||||
<inputs>
|
||||
<param format="data" name="input1" type="data">
|
||||
|
||||
@@ -1,5 +1,6 @@
|
||||
<tool id="EMBOSS: geecee41" name="geecee" version="5.0.0">
|
||||
<description>Calculates fractional GC content of nucleic acid sequences</description>
|
||||
<requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
|
||||
<command>geecee -sequence $input1 -outfile $out_file1 -auto</command>
|
||||
<inputs>
|
||||
<param format="data" name="input1" type="data">
|
||||
|
||||
@@ -1,5 +1,6 @@
|
||||
<tool id="EMBOSS: getorf42" name="getorf" version="5.0.0">
|
||||
<description>Finds and extracts open reading frames (ORFs)</description>
|
||||
<requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
|
||||
<command>getorf -sequence $input1 -outseq $out_file1 -table $table -minsize $minsize -maxsize $maxsize -find $find -methionine $methionine -circular $circular -reverse $reverse -flanking $flanking
|
||||
-osformat2 $out_format1 -auto</command>
|
||||
<inputs>
|
||||
|
||||
@@ -1,5 +1,6 @@
|
||||
<tool id="EMBOSS: helixturnhelix43" name="helixturnhelix" version="5.0.0">
|
||||
<description>Report nucleic acid binding motifs</description>
|
||||
<requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
|
||||
<command>helixturnhelix -sequence $input1 -outfile $out_file1 -mean $mean -sd $sd -minsd $minsd -eightyseven $eightyseven -rformat2 $out_format1 -auto</command>
|
||||
<inputs>
|
||||
<param format="data" name="input1" type="data">
|
||||
|
||||
@@ -1,5 +1,6 @@
|
||||
<tool id="EMBOSS: hmoment44" name="hmoment" version="5.0.0">
|
||||
<description>Hydrophobic moment calculation</description>
|
||||
<requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
|
||||
<command>hmoment -seqall $input1 -outfile $out_file1 -window $window -aangle $aangle -graph png -auto</command>
|
||||
<inputs>
|
||||
<param format="data" name="input1" type="data">
|
||||
|
||||
@@ -1,5 +1,6 @@
|
||||
<tool id="EMBOSS: iep45" name="iep" version="5.0.0">
|
||||
<description>Calculates the isoelectric point of a protein</description>
|
||||
<requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
|
||||
<command>iep -sequence $input1 -outfile $out_file1 -step $step -amino $amino -graph png -termini $termini -auto</command>
|
||||
<inputs>
|
||||
<param format="data" name="input1" type="data">
|
||||
|
||||
@@ -1,6 +1,7 @@
|
||||
<tool id="EMBOSS: infoseq46" name="infoseq" version="5.0.0">
|
||||
<!-- info contains file information always -->
|
||||
<description>Displays some simple information about sequences</description>
|
||||
<requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
|
||||
<command>infoseq -sequence $input1 -outfile $out_file1 -html $html_out1 -heading $heading -usa $usa -name $disname -accession $accession -gi $gi -version $version -type $type -length $length -pgc
|
||||
$pgc -description $description -auto</command>
|
||||
<inputs>
|
||||
|
||||
@@ -1,5 +1,6 @@
|
||||
<tool id="EMBOSS: isochore47" name="isochore" version="5.0.0">
|
||||
<description>Plots isochores in large DNA sequences</description>
|
||||
<requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
|
||||
<command interpreter="perl">emboss_single_outputfile_wrapper.pl isochore -sequence $input1 -outfile $ofile2 -goutfile $ofile1 -graph png -window $window -shift $shift -auto</command>
|
||||
<!-- <command interpreter="perl">emboss_single_outputfile_wrapper.pl isochore -sequence $input1 -goutfile $ofile1 -graph png -window $window -shift $shift -auto</command>-->
|
||||
<inputs>
|
||||
|
||||
@@ -1,6 +1,7 @@
|
||||
<tool id="EMBOSS: lindna48" name="lindna" version="5.0.0">
|
||||
<!-- tool produces memory error in ajmem.c -->
|
||||
<description>Draws linear maps of DNA constructs</description>
|
||||
<requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
|
||||
<command>lindna -infile $input1 -graphout png -goutfile $out_file1 -ruler $ruler -blocktype $blocktype -maxgroups $maxgroups -maxlabels $maxlabels -intersymbol $intersymbol -intercolour $intercolour
|
||||
-interticks $interticks -gapsize $gapsize -ticklines $ticklines -textheight $textheight -textlength $textlength -margin $margin -tickheight $tickheight -blockheight $blockheight -rangeheight
|
||||
$rangeheight -gapgroup $gapgroup -postext $postext -auto</command>
|
||||
|
||||
@@ -1,5 +1,6 @@
|
||||
<tool id="EMBOSS: marscan49" name="marscan" version="5.0.0">
|
||||
<description>Finds MAR/SAR sites in nucleic sequences</description>
|
||||
<requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
|
||||
<command>marscan -sequence $input1 -outfile $out_file1 -rformat2 $out_format1 -auto</command>
|
||||
<inputs>
|
||||
<param format="data" name="input1" type="data">
|
||||
|
||||
@@ -1,5 +1,6 @@
|
||||
<tool id="EMBOSS: maskfeat50" name="maskfeat" version="5.0.0">
|
||||
<description>Mask off features of a sequence</description>
|
||||
<requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
|
||||
<command>maskfeat -sequence $input1 -outseq $out_file1 -type "$type" -tolower $tolower -maskchar "$maskchar" -osformat2 $out_format1 -auto</command>
|
||||
<inputs>
|
||||
<param format="data" name="input1" type="data">
|
||||
|
||||
@@ -1,5 +1,6 @@
|
||||
<tool id="EMBOSS: maskseq51" name="maskseq" version="5.0.0">
|
||||
<description>Mask off regions of a sequence</description>
|
||||
<requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
|
||||
<command>maskseq -sequence $input1 -outseq $out_file1 -regions "$regions" -tolower $tolower -maskchar "$maskchar" -osformat2 $out_format1 -auto</command>
|
||||
<inputs>
|
||||
<param format="data" name="input1" type="data">
|
||||
|
||||
@@ -1,5 +1,6 @@
|
||||
<tool id="EMBOSS: matcher52" name="matcher" version="5.0.0">
|
||||
<description>Finds the best local alignments between two sequences</description>
|
||||
<requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
|
||||
<command>matcher -asequence $input1 -bsequence $input2 -outfile $out_file1 -alternatives $alternatives -gapopen $gapopen -gapextend $gapextend -aformat3 $out_format1 -auto</command>
|
||||
<inputs>
|
||||
<param format="data" name="input1" type="data">
|
||||
|
||||
@@ -1,5 +1,6 @@
|
||||
<tool id="EMBOSS: megamerger53" name="megamerger" version="5.0.0">
|
||||
<description>Merge two large overlapping nucleic acid sequences</description>
|
||||
<requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
|
||||
<command>megamerger -asequence $input1 -bsequence $input2 -outseq $out_file1 -outfile $out_file2 -wordsize $wordsize -prefer $prefer -osformat3 $out_format1 -auto</command>
|
||||
<inputs>
|
||||
<param format="data" name="input1" type="data">
|
||||
|
||||
@@ -1,5 +1,6 @@
|
||||
<tool id="EMBOSS: merger54" name="merger" version="5.0.0">
|
||||
<description>Merge two overlapping nucleic acid sequences</description>
|
||||
<requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
|
||||
<command>merger -asequence $input1 -bsequence $input2 -outseq $out_file1 -outfile $out_file2 -gapopen $gapopen -gapextend $gapextend -osformat4 $out_format1 -aformat3 $out_format2 -auto</command>
|
||||
<inputs>
|
||||
<param format="data" name="input1" type="data">
|
||||
|
||||
@@ -1,5 +1,6 @@
|
||||
<tool id="EMBOSS: msbar55" name="msbar" version="5.0.0">
|
||||
<description>Mutate sequence beyond all recognition</description>
|
||||
<requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
|
||||
<command>msbar -sequence $input1 -outseq $out_file1 -count $count -point $point -block $block -codon $codon -inframe $inframe -minimum $minimum -maximum $maximum -osformat2 $out_format1
|
||||
-auto</command>
|
||||
<inputs>
|
||||
|
||||
@@ -1,5 +1,6 @@
|
||||
<tool id="EMBOSS: needle56" name="needle" version="5.0.0">
|
||||
<description>Needleman-Wunsch global alignment</description>
|
||||
<requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
|
||||
<command>needle -asequence $input1 -bsequence $input2 -outfile $out_file1 -gapopen $gapopen -gapextend $gapextend -brief $brief -aformat3 $out_format1 -auto</command>
|
||||
<inputs>
|
||||
<param format="fasta" name="input1" type="data">
|
||||
|
||||
@@ -1,5 +1,6 @@
|
||||
<tool id="EMBOSS: newcpgreport57" name="newcpgreport" version="5.0.0">
|
||||
<description>Report CpG rich areas</description>
|
||||
<requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
|
||||
<command>newcpgreport -sequence $input1 -window $window -shift $shift -minlen $minlen -minpc $minpc -outfile $out_file1 -minoe $minoe -auto</command>
|
||||
<inputs>
|
||||
<param format="data" name="input1" type="data">
|
||||
|
||||
@@ -1,5 +1,6 @@
|
||||
<tool id="EMBOSS: newcpgseek58" name="newcpgseek" version="5.0.0">
|
||||
<description>Reports CpG rich region</description>
|
||||
<requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
|
||||
<command>newcpgseek -sequence $input1 -outfile $out_file1 -score $score -auto</command>
|
||||
<inputs>
|
||||
<param format="fasta" name="input1" type="data">
|
||||
|
||||
@@ -1,5 +1,6 @@
|
||||
<tool id="EMBOSS: newseq59" name="newseq" version="5.0.0">
|
||||
<description>Type in a short new sequence</description>
|
||||
<requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
|
||||
<command>newseq -outseq $out_file1 -name "$seqname" -description "$description" -type $type -sequence "$sequence" -osformat5 $out_format1 -auto</command>
|
||||
<inputs>
|
||||
<param name="seqname" size="10" type="text" value="">
|
||||
|
||||
@@ -1,5 +1,6 @@
|
||||
<tool id="EMBOSS: noreturn60" name="noreturn" version="5.0.0">
|
||||
<description>Removes carriage return from ASCII files</description>
|
||||
<requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
|
||||
<command>noreturn -infile $input1 -outfile $out_file1 -system $system -auto</command>
|
||||
<inputs>
|
||||
<param format="data" name="input1" type="data">
|
||||
|
||||
@@ -1,5 +1,6 @@
|
||||
<tool id="EMBOSS: notseq61" name="notseq" version="5.0.0">
|
||||
<description>Exclude a set of sequences and write out the remaining ones</description>
|
||||
<requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
|
||||
<command>notseq -sequence $input1 -outseq $out_file1 -exclude "$exclude" -osformat3 $out_format1 -auto</command>
|
||||
<inputs>
|
||||
<param format="fasta" name="input1" type="data">
|
||||
|
||||
@@ -1,5 +1,6 @@
|
||||
<tool id="EMBOSS: nthseq62" name="nthseq" version="5.0.0">
|
||||
<description>Writes one sequence from a multiple set of sequences</description>
|
||||
<requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
|
||||
<command>nthseq -sequence $input1 -outseq $out_file1 -number $number -osformat2 $out_format1 -auto</command>
|
||||
<inputs>
|
||||
<param format="fasta" name="input1" type="data">
|
||||
|
||||
@@ -1,6 +1,7 @@
|
||||
<tool id="EMBOSS: octanol63" name="octanol" version="5.0.0">
|
||||
<!-- graphics output with filename, no functional tests added -->
|
||||
<description>Displays protein hydropathy</description>
|
||||
<requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
|
||||
<command interpreter="perl">emboss_single_outputfile_wrapper.pl octanol -sequence $input1 -graph png -goutfile $out_file1 -width $width -octanolplot $octanolplot -interfaceplot $interfaceplot
|
||||
-differenceplot $differenceplot -auto</command>
|
||||
<inputs>
|
||||
|
||||
@@ -1,6 +1,7 @@
|
||||
<tool id="EMBOSS: oddcomp64" name="oddcomp" version="5.0.0">
|
||||
<!-- output contains file location info, commented out functional tests -->
|
||||
<description>Find protein sequence regions with a biased composition</description>
|
||||
<requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
|
||||
<command>oddcomp -sequence $input1 -infile $input2 -outfile $out_file1 -window $window -ignorebz $ignorebz -auto</command>
|
||||
<inputs>
|
||||
<param format="data" name="input1" type="data">
|
||||
|
||||
@@ -1,5 +1,6 @@
|
||||
<tool id="EMBOSS: palindrome65" name="palindrome" version="5.0.0">
|
||||
<description>Looks for inverted repeats in a nucleotide sequence</description>
|
||||
<requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
|
||||
<command>palindrome -sequence $input1 -outfile $out_file1 -minpallen $minpallen -maxpallen $maxpallen -gaplimit $gaplimit -nummismatches $nummismatches -overlap $overlap -auto</command>
|
||||
<inputs>
|
||||
<param format="fasta" name="input1" type="data">
|
||||
|
||||
@@ -1,5 +1,6 @@
|
||||
<tool id="EMBOSS: pasteseq66" name="pasteseq" version="5.0.0">
|
||||
<description>Insert one sequence into another</description>
|
||||
<requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
|
||||
<command>pasteseq -asequence $input2 -bsequence $input1 -outseq $out_file1 -pos $pos -osformat3 $out_format1 -auto</command>
|
||||
<inputs>
|
||||
<param format="fasta" name="input1" type="data">
|
||||
|
||||
@@ -1,5 +1,6 @@
|
||||
<tool id="EMBOSS: patmatdb67" name="patmatdb" version="5.0.0">
|
||||
<description>Search a protein sequence with a motif</description>
|
||||
<requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
|
||||
<command>patmatdb -sequence $input1 -outfile $out_file1 -motif "$motif" -rformat3 $out_format1 -auto</command>
|
||||
<inputs>
|
||||
<param format="data" name="input1" type="data">
|
||||
|
||||
@@ -1,5 +1,6 @@
|
||||
<tool id="EMBOSS: pepcoil68" name="pepcoil" version="5.0.0">
|
||||
<description>Predicts coiled coil regions</description>
|
||||
<requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
|
||||
<command>pepcoil -sequence $input1 -outfile $out_file1 -window $window -coil $coil -frame $frame -other $other -auto</command>
|
||||
<inputs>
|
||||
<param format="data" name="input1" type="data">
|
||||
|
||||
@@ -1,6 +1,7 @@
|
||||
<tool id="EMBOSS: pepinfo69" name="pepinfo" version="5.0.0">
|
||||
<!-- puts file info in output files -->
|
||||
<description>Plots simple amino acid properties in parallel</description>
|
||||
<requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
|
||||
<command interpreter="perl">emboss_single_outputfile_wrapper.pl pepinfo -sequence $input1 -outfile $out_file1 -goutfile $out_file2 -graph png -hwindow $hwindow $plot_type -auto</command>
|
||||
<inputs>
|
||||
<param format="data" name="input1" type="data">
|
||||
|
||||
@@ -1,6 +1,7 @@
|
||||
<tool id="EMBOSS: pepnet70" name="pepnet" version="5.0.0">
|
||||
<!-- graphical output file with path information -->
|
||||
<description>Displays proteins as a helical net</description>
|
||||
<requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
|
||||
<command>pepnet -sequence $input1 -graph png -goutfile $out_file1 -squares $squares -diamonds $diamonds -octags $octags -amphipathic $amphipathic -auto</command>
|
||||
<inputs>
|
||||
<param format="data" name="input1" type="data">
|
||||
|
||||
@@ -1,5 +1,6 @@
|
||||
<tool id="EMBOSS: pepstats71" name="pepstats" version="5.0.0">
|
||||
<description>Protein statistics</description>
|
||||
<requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
|
||||
<command>pepstats -sequence $input1 -outfile $out_file1 -termini $termini -auto</command>
|
||||
<inputs>
|
||||
<param format="data" name="input1" type="data">
|
||||
|
||||
@@ -1,6 +1,7 @@
|
||||
<tool id="EMBOSS: pepwheel72" name="pepwheel" version="5.0.0">
|
||||
<!-- produces png file -->
|
||||
<description>Shows protein sequences as helices</description>
|
||||
<requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
|
||||
<command interpreter="perl">emboss_single_outputfile_wrapper.pl pepwheel -sequence $input1 -graph png -goutfile $out_file1 -squares $squares -diamonds $diamonds -octags $octags -amphipathic
|
||||
$amphipathic -steps $steps -turns $turns -wheel $wheel -auto</command>
|
||||
<inputs>
|
||||
|
||||
@@ -1,6 +1,7 @@
|
||||
<tool id="EMBOSS: pepwindow73" name="pepwindow" version="5.0.0">
|
||||
<!-- produces png file -->
|
||||
<description>Displays protein hydropathy</description>
|
||||
<requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
|
||||
<command interpreter="perl">emboss_single_outputfile_wrapper.pl pepwindow -sequence $input1 -graph png -goutfile $out_file1 -length $length -auto</command>
|
||||
<inputs>
|
||||
<param format="data" name="input1" type="data">
|
||||
|
||||
@@ -1,6 +1,7 @@
|
||||
<tool id="EMBOSS: pepwindowall74" name="pepwindowall" version="5.0.0">
|
||||
<!-- produces png file -->
|
||||
<description>Displays protein hydropathy of a set of sequences</description>
|
||||
<requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
|
||||
<command interpreter="perl">emboss_single_outputfile_wrapper.pl pepwindowall -sequence $input1 -graph png -goutfile $out_file1 -length $length -auto</command>
|
||||
<inputs>
|
||||
<param format="data" name="input1" type="data">
|
||||
|
||||
@@ -1,6 +1,7 @@
|
||||
<tool id="EMBOSS: plotcon75" name="plotcon" version="5.0.0">
|
||||
<!-- produces png file -->
|
||||
<description>Plot quality of conservation of a sequence alignment</description>
|
||||
<requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
|
||||
<command interpreter="perl">emboss_single_outputfile_wrapper.pl plotcon -sequences $input1 -graph png -goutfile $out_file1 -winsize $winsize -auto</command>
|
||||
<inputs>
|
||||
<param format="data" name="input1" type="data">
|
||||
|
||||
@@ -1,6 +1,7 @@
|
||||
<tool id="EMBOSS: plotorf76" name="plotorf" version="5.0.0">
|
||||
<!-- produces png file output -->
|
||||
<description>Plot potential open reading frames</description>
|
||||
<requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
|
||||
<command interpreter="perl">emboss_single_outputfile_wrapper.pl plotorf -sequence $input1 -graph png -goutfile $out_file1 -start $start -stop $stop -auto</command>
|
||||
<inputs>
|
||||
<param format="fasta" name="input1" type="data">
|
||||
|
||||
@@ -1,6 +1,7 @@
|
||||
<tool id="EMBOSS: polydot77" name="polydot" version="5.0.0">
|
||||
<!-- produces png file, not added functional tests -->
|
||||
<description>Displays all-against-all dotplots of a set of sequences</description>
|
||||
<requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
|
||||
<command interpreter="perl">emboss_single_outputfile_wrapper.pl polydot -sequence $input1 -graph png -goutfile $output2 -outfeat $output1 -wordsize $wordsize -boxit $boxit -dumpfeat yes -gap
|
||||
$gap -auto</command>
|
||||
<inputs>
|
||||
|
||||
@@ -1,5 +1,6 @@
|
||||
<tool id="EMBOSS: preg78" name="preg" version="5.0.0">
|
||||
<description>Regular expression search of a protein sequence</description>
|
||||
<requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
|
||||
<command>preg -sequence $input1 -outfile $out_file1 -pattern "$pattern" -auto</command>
|
||||
<inputs>
|
||||
<param format="data" name="input1" type="data">
|
||||
|
||||
@@ -1,6 +1,7 @@
|
||||
<tool id="EMBOSS: prettyplot79" name="prettyplot" version="5.0.0">
|
||||
<!-- produces png output with file name -->
|
||||
<description>Displays aligned sequences, with colouring and boxing</description>
|
||||
<requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
|
||||
<command>prettyplot -sequences $input1 -graph png -goutfile $out_file1 -residuesperline $residuesperline -resbreak $resbreak -ccolours $ccolours -cidentity $cidentity -csimilarity $csimilarity
|
||||
-cother $cother -docolour $docolour -gtitle $title -pair $pair -identity $identity -box $box -boxcol $boxcol -boxcolval $boxcolval -name $name -maxnamelen $maxnamelen -number $number -listoptions
|
||||
$listoptions -consensus $consensus -collision $collision -alternative $alternative -showscore $showscore -portrait $portrait -auto</command>
|
||||
|
||||
@@ -1,5 +1,6 @@
|
||||
<tool id="EMBOSS: prettyseq80" name="prettyseq" version="5.0.0">
|
||||
<description>Output sequence with translated ranges</description>
|
||||
<requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
|
||||
<command>prettyseq -sequence $input1 -outfile $out_file1 -ruler $ruler -plabel $plabel -nlabel $nlabel -width $width -auto</command>
|
||||
<inputs>
|
||||
<param format="fasta" name="input1" type="data">
|
||||
|
||||
@@ -1,5 +1,6 @@
|
||||
<tool id="EMBOSS: primersearch81" name="primersearch" version="5.0.0">
|
||||
<description>Searches DNA sequences for matches with primer pairs</description>
|
||||
<requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
|
||||
<command>primersearch -seqall $input1 -infile $input2 -outfile $out_file1 -mismatchpercent $mismatchpercent -auto</command>
|
||||
<inputs>
|
||||
<param format="fasta" name="input1" type="data">
|
||||
|
||||
@@ -1,5 +1,6 @@
|
||||
<tool id="EMBOSS: revseq82" name="revseq" version="5.0.0">
|
||||
<description>Reverse and complement a sequence</description>
|
||||
<requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
|
||||
<command>revseq -sequence $input1 -outseq $out_file1 -reverse $reverse -complement $complement -osformat2 $out_format1 -auto</command>
|
||||
<inputs>
|
||||
<param format="fasta" name="input1" type="data">
|
||||
|
||||
@@ -1,5 +1,6 @@
|
||||
<tool id="EMBOSS: seqmatchall83" name="seqmatchall" version="5.0.0">
|
||||
<description>All-against-all comparison of a set of sequences</description>
|
||||
<requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
|
||||
<command>seqmatchall -sequence $input1 -outfile $out_file1 -wordsize $wordsize -aformat2 $out_format1 -auto</command>
|
||||
<inputs>
|
||||
<param format="fasta" name="input1" type="data">
|
||||
|
||||
@@ -1,5 +1,6 @@
|
||||
<tool id="EMBOSS: seqret84" name="seqret" version="5.0.0">
|
||||
<description>Reads and writes sequences</description>
|
||||
<requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
|
||||
<command>seqret -sequence $input1 -outseq $out_file1 -feature $feature -firstonly $firstonly -osformat2 $out_format1 -auto</command>
|
||||
<inputs>
|
||||
<param format="data" name="input1" type="data">
|
||||
|
||||
@@ -1,6 +1,7 @@
|
||||
<tool id="EMBOSS: showfeat85" name="showfeat" version="5.0.0">
|
||||
<!-- tool gives memory errors -->
|
||||
<description>Show features of a sequence</description>
|
||||
<requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
|
||||
<command>showfeat -sequence $input1 -outfile $out_file1 -matchsource "$matchsource" -matchtype "$matchtype" -matchtag "$matchtag" -matchvalue "$matchvalue" -sort $sort -annotation "$annotation" -id
|
||||
$id -description "$description" -scale "$scale" -width "$width" -collapse $collapse -forward $forward -reverse $reverse -unknown $unknown -strand $strand -source $source -position $position -type
|
||||
$type -tags $tags -values $values -stricttags $stricttags -html $html_out1 -auto</command>
|
||||
|
||||
@@ -1,6 +1,7 @@
|
||||
<tool id="EMBOSS: shuffleseq87" name="shuffleseq" version="5.0.0">
|
||||
<!-- produces random outputs each time -->
|
||||
<description>Shuffles a set of sequences maintaining composition</description>
|
||||
<requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
|
||||
<command>shuffleseq -sequence $input1 -outseq $out_file1 -shuffle "$shuffle" -osformat2 $out_format1 -auto</command>
|
||||
<inputs>
|
||||
<param format="fasta" name="input1" type="data">
|
||||
|
||||
@@ -1,5 +1,6 @@
|
||||
<tool id="EMBOSS: sigcleave88" name="sigcleave" version="5.0.0">
|
||||
<description>Reports protein signal cleavage sites</description>
|
||||
<requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
|
||||
<command>sigcleave -sequence $input1 -outfile $out_file1 -minweight "$minweight" -prokaryote $prokaryote -rformat2 $out_format1 -auto</command>
|
||||
<inputs>
|
||||
<param format="data" name="input1" type="data">
|
||||
|
||||
@@ -1,5 +1,6 @@
|
||||
<tool id="EMBOSS: sirna89" name="sirna" version="5.0.0">
|
||||
<description>Finds siRNA duplexes in mRNA</description>
|
||||
<requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
|
||||
<command>sirna -sequence $input1 -outfile $ofile1 -outseq $ofile2 -poliii $poliii -aa $aa -tt $tt -polybase $polybase -context $context -rformat2 $out_format1 -osformat3 $out_format2
|
||||
-auto</command>
|
||||
<inputs>
|
||||
|
||||
@@ -1,6 +1,7 @@
|
||||
<tool id="EMBOSS: sixpack90" name="sixpack" version="5.0.0">
|
||||
<!-- tool adds file description and timestamp to output data -->
|
||||
<description>Display a DNA sequence with 6-frame translation and ORFs</description>
|
||||
<requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
|
||||
<command>sixpack -sequence $input1 -outfile $ofile1 -outseq $ofile2 -table $table -firstorf $firstorf -lastorf $lastorf -mstart $mstart -reverse $reverse -orfminsize $orfminsize -uppercase
|
||||
"$uppercase" -number $number -width "$width" -length "$length" -margin "$margin" -name $disp_name -description $description -offset "$offset" -html $html_out1 -osformat $out_format2 -auto</command>
|
||||
<inputs>
|
||||
|
||||
@@ -1,5 +1,6 @@
|
||||
<tool id="EMBOSS: skipseq91" name="skipseq" version="5.0.0">
|
||||
<description>Reads and writes sequences, skipping first few</description>
|
||||
<requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
|
||||
<command>skipseq -sequence $input1 -outseq $out_file1 -skip "$skip" -feature $feature -osformat2 $out_format1 -auto</command>
|
||||
<inputs>
|
||||
<param format="data" name="input1" type="data">
|
||||
|
||||
@@ -1,5 +1,6 @@
|
||||
<tool id="EMBOSS: splitter92" name="splitter" version="5.0.0">
|
||||
<description>Split a sequence into (overlapping) smaller sequences</description>
|
||||
<requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
|
||||
<command>splitter -sequence $input1 -outseq $out_file1 -size "$size" -overlap "$overlap" -addoverlap $addoverlap -osformat2 $out_format1 -auto</command>
|
||||
<inputs>
|
||||
<param format="fasta" name="input1" type="data">
|
||||
|
||||
@@ -1,6 +1,7 @@
|
||||
<tool id="EMBOSS: supermatcher95" name="supermatcher" version="5.0.0">
|
||||
<!-- puts file information in output report -->
|
||||
<description>Match large sequences against one or more other sequences</description>
|
||||
<requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
|
||||
<command>supermatcher -asequence $input1 -bsequence $input2 -gapopen "$gapopen" -gapextend "$gapextend" -width "$width" -wordlen "$wordlen" -outfile $ofile1 -errorfile $ofile2 -aformat3
|
||||
$out_format1 -auto</command>
|
||||
<inputs>
|
||||
|
||||
@@ -1,6 +1,7 @@
|
||||
<tool id="EMBOSS: syco96" name="syco" version="5.0.0">
|
||||
<!-- graphics output -->
|
||||
<description>Synonymous codon usage Gribskov statistic plot</description>
|
||||
<requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
|
||||
<command interpreter="perl">emboss_single_outputfile_wrapper.pl syco -sequence $input1 -graph png -goutfile $ofile1 -outfile $ofile2 -cfile $cfile -window "$window" -uncommon $uncommon -minimum "$minimum"
|
||||
-auto</command>
|
||||
<inputs>
|
||||
|
||||
@@ -1,5 +1,6 @@
|
||||
<tool id="EMBOSS: tcode97" name="tcode" version="5.0.0">
|
||||
<description>Fickett TESTCODE statistic to identify protein-coding DNA</description>
|
||||
<requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
|
||||
<command>tcode -sequence $input1 -outfile $out_file1 -window "$window" -step "$step" -rformat $out_format1 -auto</command>
|
||||
<inputs>
|
||||
<param format="data" name="input1" type="data">
|
||||
|
||||
@@ -1,5 +1,6 @@
|
||||
<tool id="EMBOSS: textsearch98" name="textsearch" version="5.0.0">
|
||||
<description>Search sequence documentation. Slow, use SRS and Entrez!</description>
|
||||
<requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
|
||||
<command>textsearch -sequence $input1 -outfile $out_file1 -pattern "$pattern" -casesensitive -heading $heading -usa $usa -accession $accession -name $search_name -description $description -html
|
||||
$html_out1 -auto</command>
|
||||
<inputs>
|
||||
|
||||
@@ -1,5 +1,6 @@
|
||||
<tool id="EMBOSS: tmap99" name="tmap" version="5.0.0">
|
||||
<description>Displays membrane spanning regions</description>
|
||||
<requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
|
||||
<command interpreter="perl">emboss_single_outputfile_wrapper.pl tmap -sequences $input1 -outfile $out_file1 -goutfile $out_file2 -graph png -rformat $out_format1 -auto</command>
|
||||
<inputs>
|
||||
<param format="data" name="input1" type="data">
|
||||
|
||||
@@ -1,5 +1,6 @@
|
||||
<tool id="EMBOSS: tranalign100" name="tranalign" version="5.0.0">
|
||||
<description>Align nucleic coding regions given the aligned proteins</description>
|
||||
<requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
|
||||
<command>tranalign -asequence $input1 -bsequence $input2 -outseq $out_file1 -table $table -osformat3 $out_format1 -auto</command>
|
||||
<inputs>
|
||||
<param format="fasta" name="input1" type="data">
|
||||
|
||||
@@ -1,5 +1,6 @@
|
||||
<tool id="EMBOSS: transeq101" name="transeq" version="5.0.0">
|
||||
<description>Translate nucleic acid sequences</description>
|
||||
<requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
|
||||
<command>transeq -sequence $input1 -outseq $out_file1 -frame $frame -table $table -regions "$regions" -trim $trim -clean $clean -alternative $alternative -osformat2 $out_format1 -auto</command>
|
||||
<inputs>
|
||||
<param format="fasta" name="input1" type="data">
|
||||
|
||||
@@ -1,5 +1,6 @@
|
||||
<tool id="EMBOSS: trimest102" name="trimest" version="5.0.0">
|
||||
<description>Trim poly-A tails off EST sequences</description>
|
||||
<requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
|
||||
<command>trimest -sequence $input1 -outseq $out_file1 -minlength "$minlength" -mismatches "$mismatches" -reverse $reverse -tolower $tolower -fiveprime $fiveprime -osformat2 $out_format1
|
||||
-auto</command>
|
||||
<inputs>
|
||||
|
||||
@@ -1,5 +1,6 @@
|
||||
<tool id="EMBOSS: trimseq103" name="trimseq" version="5.0.0">
|
||||
<description>Trim ambiguous bits off the ends of sequences</description>
|
||||
<requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
|
||||
<command>trimseq -sequence $input1 -outseq $out_file1 -window "$window" -percent "$percent" -strict $strict -star $star -left $left -right $right -osformat2 $out_format1 -auto</command>
|
||||
<inputs>
|
||||
<param format="fasta" name="input1" type="data">
|
||||
|
||||
Some files were not shown because too many files have changed in this diff Show More
Reference in New Issue
Block a user