# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Nate Coraor <nate@bx.psu.edu> # Date 1286483037 14400 # Node ID b9f3c613c0266e9285679b06e39802a452f4b151 # Parent 4ecbb9b5a360c1d1997890917799f31f5896a01e Convert a bunch of binary requirement tags to package requirements, and change the sputnik tool to call 'sputnik' instead of 'bx-sputnik'. --- a/tools/emboss_5/emboss_lindna.xml +++ b/tools/emboss_5/emboss_lindna.xml @@ -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> --- a/tools/emboss_5/emboss_getorf.xml +++ b/tools/emboss_5/emboss_getorf.xml @@ -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> --- a/tools/emboss_5/emboss_dan.xml +++ b/tools/emboss_5/emboss_dan.xml @@ -1,5 +1,6 @@ <tool id="EMBOSS: dan19" name="dan" version="5.0.0"><description>Calculates DNA RNA/DNA melting temperature</description> + <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements><command interpreter="perl">emboss_single_outputfile_wrapper.pl dan -sequence $input1 -windowsize $window -goutfile $out_file1 -graph png -plot $plot1 -shiftincrement $shift -dnaconc $dnaconc -saltconc $saltconc -product $product -formamide $formamide -mismatch $mismatch -prodlen $prodlen -thermo $thermo -temperature $temperature -rna $rna -outfile $out_file1 -auto</command><inputs> --- a/tools/emboss_5/emboss_banana.xml +++ b/tools/emboss_5/emboss_banana.xml @@ -1,5 +1,6 @@ <tool id="EMBOSS: banana3" name="banana" version="5.0.0"><description>Bending and curvature plot in B-DNA</description> + <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements><command>banana -sequence $input1 -outfile $out_file1 -graph none -auto</command><inputs><param format="data" name="input1" type="data"> --- a/tools/emboss_5/emboss_biosed.xml +++ b/tools/emboss_5/emboss_biosed.xml @@ -1,5 +1,6 @@ <tool id="EMBOSS: biosed4" name="biosed" version="5.0.0"><description>Replace or delete sequence sections</description> + <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements><command>biosed -sequence $input1 -outseq $out_file1 -target $target -replace $replace -osformat2 $out_format1 -auto</command><inputs><param format="fasta" name="input1" type="data"> --- a/tools/emboss_5/emboss_isochore.xml +++ b/tools/emboss_5/emboss_isochore.xml @@ -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> --- a/tools/emboss_5/emboss_helixturnhelix.xml +++ b/tools/emboss_5/emboss_helixturnhelix.xml @@ -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"> --- a/tools/emboss_5/emboss_backtranseq.xml +++ b/tools/emboss_5/emboss_backtranseq.xml @@ -1,5 +1,6 @@ <tool id="EMBOSS: backtranseq2" name="backtranseq" version="5.0.0"><description>Back translate a protein sequence</description> + <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements><command>backtranseq -sequence $input1 -outfile $out_file1 -cfile $cfile -osformat2 $out_format1 -auto</command><inputs><param format="fasta" name="input1" type="data"> --- a/tools/emboss_5/emboss_epestfind.xml +++ b/tools/emboss_5/emboss_epestfind.xml @@ -1,5 +1,6 @@ <tool id="EMBOSS: epestfind29" name="epestfind" version="5.0.0"><description>Finds PEST motifs as potential proteolytic cleavage sites</description> + <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements><command interpreter="perl">emboss_single_outputfile_wrapper.pl epestfind -sequence $input1 -goutfile $ofile2 -outfile $ofile1 -window $window -order $order -potential $potential -poor $poor -invalid $invalid -map $map -graph png -auto</command><inputs> --- a/tools/emboss_5/emboss_infoseq.xml +++ b/tools/emboss_5/emboss_infoseq.xml @@ -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> --- a/tools/emboss_5/emboss_dreg.xml +++ b/tools/emboss_5/emboss_dreg.xml @@ -1,5 +1,6 @@ <tool id="EMBOSS: dreg27" name="dreg" version="5.0.0"><description>Regular expression search of a nucleotide sequence</description> + <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements><command>dreg -sequence $input1 -outfile $out_file1 -pattern "$pattern" -raccshow3 "no" -rusashow3 "no" -rdesshow3 "no" -auto</command><inputs><param format="data" name="input1" type="data"> --- a/tools/emboss_5/emboss_fuzznuc.xml +++ b/tools/emboss_5/emboss_fuzznuc.xml @@ -1,5 +1,6 @@ <tool id="EMBOSS: fuzznuc37" name="fuzznuc" version="5.0.1"><description>Nucleic acid pattern search</description> + <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements><command>fuzznuc -sequence $input1 -outfile $out_file1 -pattern '$pattern' -pmismatch $mismatch -complement $complement -rformat2 $out_format1 -auto</command><inputs><param format="fasta" name="input1" type="data"> --- a/tools/emboss_5/emboss_cutseq.xml +++ b/tools/emboss_5/emboss_cutseq.xml @@ -1,5 +1,6 @@ <tool id="EMBOSS: cutseq18" name="cutseq" version="5.0.0"><description>Removes a specified section from a sequence</description> + <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements><command>cutseq -sequence $input1 -outseq $out_file1 -from $from -to $to -osformat2 $out_format1 -auto</command><inputs><param format="fasta" name="input1" type="data"> --- a/tools/emboss_5/emboss_digest.xml +++ b/tools/emboss_5/emboss_digest.xml @@ -1,5 +1,6 @@ <tool id="EMBOSS: digest23" name="digest" version="5.0.0"><description>Protein proteolytic enzyme or reagent cleavage digest</description> + <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements><command>digest -seqall $input1 -outfile $out_file1 -menu $menu -unfavoured $unfavoured -overlap $overlap -allpartials $allpartials -rformat2 $out_format1 -auto</command><inputs><param format="data" name="input1" type="data"> --- a/tools/emboss_5/emboss_fuzztran.xml +++ b/tools/emboss_5/emboss_fuzztran.xml @@ -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"> --- a/tools/emboss_5/emboss_hmoment.xml +++ b/tools/emboss_5/emboss_hmoment.xml @@ -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"> --- a/tools/emboss_5/emboss_antigenic.xml +++ b/tools/emboss_5/emboss_antigenic.xml @@ -1,5 +1,6 @@ <tool id="EMBOSS: antigenic1" name="antigenic" version="5.0.0"><description>Predicts potentially antigenic regions of a protein sequence, using the method of Kolaskar and Tongaonkar.</description> + <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements><command>antigenic -sequence $input1 -outfile $out_file1 -minlen $minlen -rformat2 $out_format1 -auto</command><inputs><param format="data" name="input1" type="data"> --- a/tools/emboss_5/emboss_cpgplot.xml +++ b/tools/emboss_5/emboss_cpgplot.xml @@ -1,5 +1,6 @@ <tool id="EMBOSS: cpgplot15" name="cpgplot" version="5.0.0"><description>Plot CpG rich areas</description> + <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements><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><inputs><param format="data" name="input1" type="data"> --- a/tools/emboss_5/emboss_codcmp.xml +++ b/tools/emboss_5/emboss_codcmp.xml @@ -1,5 +1,6 @@ <tool id="EMBOSS: codcmp12" name="codcmp" version="5.0.0"><description>Codon usage table comparison</description> + <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements><command>codcmp -first $cfile1 -second $cfile2 -outfile $out_file1 -auto</command><inputs><param name="cfile1" type="select"> --- a/tools/emboss_5/emboss_dottup.xml +++ b/tools/emboss_5/emboss_dottup.xml @@ -1,5 +1,6 @@ <tool id="EMBOSS: dottup26" name="dottup" version="5.0.0"><description>Displays a wordmatch dotplot of two sequences</description> + <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements><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><inputs><param format="data" name="input1" type="data"> --- a/tools/emboss_5/emboss_degapseq.xml +++ b/tools/emboss_5/emboss_degapseq.xml @@ -1,5 +1,6 @@ <tool id="EMBOSS: degapseq20" name="degapseq" version="5.0.0"><description>Removes gap characters from sequences</description> + <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements><command>degapseq -sequence $input1 -outseq $out_file1 -osformat2 $out_format1 -auto</command><inputs><param format="data" name="input1" type="data"> --- a/tools/emboss_5/emboss_descseq.xml +++ b/tools/emboss_5/emboss_descseq.xml @@ -1,5 +1,6 @@ <tool id="EMBOSS: descseq21" name="descseq" version="5.0.0"><description>Alter the name or description of a sequence</description> + <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements><command>descseq -sequence $input1 -outseq $out_file1 -name "$seqname" -description "$desc" -append $append -osformat2 $out_format1 -auto</command><inputs><param format="data" name="input1" type="data"> --- a/tools/emboss_5/emboss_extractseq.xml +++ b/tools/emboss_5/emboss_extractseq.xml @@ -1,5 +1,6 @@ <tool id="EMBOSS: extractseq35" name="extractseq" version="5.0.0"><description>Extract regions from a sequence</description> + <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements><command>extractseq -sequence $input1 -outseq $out_file1 -regions $regions -separate $separate -osformat2 $out_format1 -auto</command><inputs><param format="data" name="input1" type="data"> --- a/tools/emboss_5/emboss_chips.xml +++ b/tools/emboss_5/emboss_chips.xml @@ -1,5 +1,6 @@ <tool id="EMBOSS: chips10" name="chips" version="5.0.0"><description>Codon usage statistics</description> + <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements><command>chips -seqall $input1 -outfile $out_file1 -sum $sum -auto</command><inputs><param format="data" name="input1" type="data"> --- a/tools/emboss_5/emboss_einverted.xml +++ b/tools/emboss_5/emboss_einverted.xml @@ -1,5 +1,6 @@ <tool id="EMBOSS: einverted28" name="einverted" version="5.0.0"><description>Finds DNA inverted repeats</description> + <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements><command>einverted -sequence $input1 -outfile $out_file1 -gap $gap -threshold $threshold -match $match -mismatch $mismatch -maxrepeat $maxrepeat -auto</command><inputs><param format="fasta" name="input1" type="data"> --- a/tools/emboss_5/emboss_fuzzpro.xml +++ b/tools/emboss_5/emboss_fuzzpro.xml @@ -1,5 +1,6 @@ <tool id="EMBOSS: fuzzpro38" name="fuzzpro" version="5.0.0"><description>Protein pattern search</description> + <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"> --- a/tools/emboss_5/emboss_checktrans.xml +++ b/tools/emboss_5/emboss_checktrans.xml @@ -1,5 +1,6 @@ <tool id="EMBOSS: checktrans9" name="checktrans" version="5.0.0"><description>Reports STOP codons and ORF statistics of a protein</description> + <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements><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><inputs><param format="fasta" name="input1" type="data"> --- a/tools/emboss_5/emboss_cusp.xml +++ b/tools/emboss_5/emboss_cusp.xml @@ -1,5 +1,6 @@ <tool id="EMBOSS: cusp17" name="cusp" version="5.0.0"><description>Create a codon usage table</description> + <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements><command>cusp -sequence $input1 -outfile $out_file1 -auto</command><inputs><param format="fasta" name="input1" type="data"> --- a/tools/emboss_5/emboss_extractfeat.xml +++ b/tools/emboss_5/emboss_extractfeat.xml @@ -1,6 +1,7 @@ <tool id="EMBOSS: extractfeat34" name="extractfeat" version="5.0.0"><!-- tool tested with documentation, functional test not designed due to empty files resulting from test input sequences --><description>Extract features from a sequence</description> + <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements><command>extractfeat -sequence $input1 -outseq $out_file1 -before $before -after $after -source "$source" -type "$type" -sense $sense -minscore $minscore -maxscore $maxscore -tag "$tag" -value "$value" -join $join -featinname $featinname -describe "$describe" -osformat2 $out_format1 -auto</command><inputs> --- a/tools/emboss_5/emboss_cirdna.xml +++ b/tools/emboss_5/emboss_cirdna.xml @@ -1,5 +1,6 @@ <tool id="EMBOSS: cirdna11" name="cirdna" version="5.0.0"><description>Draws circular maps of DNA constructs</description> + <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements><command interpreter="perl">emboss_single_outputfile_wrapper.pl cirdna -infile $input1 -graphout png -goutfile $out_file1 -auto</command><inputs><param format="data" name="input1" type="data"> --- a/tools/emboss_5/emboss_btwisted.xml +++ b/tools/emboss_5/emboss_btwisted.xml @@ -1,5 +1,6 @@ <tool id="EMBOSS: btwisted5" name="btwisted" version="5.0.0"><description>Calculates the twisting in a B-DNA sequence</description> + <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements><command>btwisted -sequence $input1 -outfile $out_file1 -auto</command><inputs><param format="data" name="input1" type="data"> --- a/tools/emboss_5/emboss_maskfeat.xml +++ b/tools/emboss_5/emboss_maskfeat.xml @@ -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"> --- a/tools/emboss_5/emboss_cpgreport.xml +++ b/tools/emboss_5/emboss_cpgreport.xml @@ -1,5 +1,6 @@ <tool id="EMBOSS: cpgreport16" name="cpgreport" version="5.0.0"><description>Reports all CpG rich regions</description> + <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements><command>cpgreport -sequence $input1 -outfile $out_file1 -outfeat $out_file2 -offormat3 $out_format2 -score $score -auto</command><inputs><param format="fasta" name="input1" type="data"> --- a/tools/emboss_5/emboss_freak.xml +++ b/tools/emboss_5/emboss_freak.xml @@ -1,5 +1,6 @@ <tool id="EMBOSS: freak36" name="freak" version="5.0.0"><description>Residue/base frequency table or plot</description> + <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements><command>freak -seqall $input1 -outfile $out_file1 -window $window -letters $letters -graph png -step $step -auto</command><inputs><param format="data" name="input1" type="data"> --- a/tools/emboss_5/emboss_dotpath.xml +++ b/tools/emboss_5/emboss_dotpath.xml @@ -1,5 +1,6 @@ <tool id="EMBOSS: dotpath25" name="dotpath" version="5.0.0"><description>Non-overlapping wordmatch dotplot of two sequences</description> + <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements><command interpreter="perl">emboss_single_outputfile_wrapper.pl dotpath -asequence $input1 -bsequence $input2 -goutfile $out_file1 -wordsize $wordsize -overlaps $overlaps -boxit $boxit -graph png -auto</command><inputs> --- a/tools/emboss_5/emboss_iep.xml +++ b/tools/emboss_5/emboss_iep.xml @@ -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"> --- a/tools/emboss_5/emboss_coderet.xml +++ b/tools/emboss_5/emboss_coderet.xml @@ -1,5 +1,6 @@ <tool id="EMBOSS: coderet13" name="coderet" version="5.0.0"><description>Extract CDS, mRNA and translations from feature tables</description> + <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements><!-- <command>coderet -seqall $input1 -outfile $out_file1 -osformat2 $out_format1 -cds $cds -mrna $mrna -translation $translation -auto</command>--><command>coderet -seqall $input1 -outfile $out_file1 -auto</command><inputs> --- a/tools/emboss_5/emboss_charge.xml +++ b/tools/emboss_5/emboss_charge.xml @@ -1,5 +1,6 @@ <tool id="EMBOSS: charge8" name="charge" version="5.0.0"><description>Protein charge plot</description> + <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements><command>charge -seqall $input1 -outfile $out_file1 -window $window -auto</command><inputs><param format="fasta" name="input1" type="data"> --- a/tools/emboss_5/emboss_diffseq.xml +++ b/tools/emboss_5/emboss_diffseq.xml @@ -1,5 +1,6 @@ <tool id="EMBOSS: diffseq22" name="diffseq" version="5.0.0"><description>Find differences between nearly identical sequences</description> + <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements><command>diffseq -asequence $input1 -bsequence $input2 -outfile $out_file1 -aoutfeat $out_file2 -boutfeat $out_file3 -wordsize $wordsize -globaldifferences $globaldifferences -rformat3 $out_format1 -offormat4 $out_format2 -offormat5 $out_format3 -auto</command><inputs> --- a/tools/emboss_5/emboss_dotmatcher.xml +++ b/tools/emboss_5/emboss_dotmatcher.xml @@ -1,5 +1,6 @@ <tool id="EMBOSS: dotmatcher24" name="dotmatcher" version="5.0.0"><description>Displays a thresholded dotplot of two sequences</description> + <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements><command interpreter="perl">emboss_single_outputfile_wrapper.pl dotmatcher -asequence $input1 -bsequence $input2 -goutfile $out_file1 -windowsize $windowsize -threshold $threshold -graph png -xygraph png -auto</command><inputs> --- a/tools/emboss_5/emboss_garnier.xml +++ b/tools/emboss_5/emboss_garnier.xml @@ -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"> --- a/tools/emboss_5/emboss_geecee.xml +++ b/tools/emboss_5/emboss_geecee.xml @@ -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"> --- a/tools/emboss_5/emboss_est2genome.xml +++ b/tools/emboss_5/emboss_est2genome.xml @@ -1,5 +1,6 @@ <tool id="EMBOSS: est2genome32" name="est2genome" version="5.0.0"><description>Align EST and genomic DNA sequences</description> + <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements><command>est2genome -estsequence $input1 -genomesequence $input2 -outfile $out_file1 -match $match -mismatch $mismatch -gappenalty $gappenalty -intronpenalty $intronpenalty -splicepenalty $splicepenalty -minscore $minscore -reverse $reverse -splice $splice -mode $mode -best $best -shuffle $shuffle -seed $seed -align $align -width $width -auto</command><inputs> --- a/tools/emboss_5/emboss_compseq.xml +++ b/tools/emboss_5/emboss_compseq.xml @@ -1,5 +1,6 @@ <tool id="EMBOSS: compseq14" name="compseq" version="5.0.0"><description>Count composition of dimer/trimer/etc words in a sequence</description> + <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements><command>compseq -sequence $input1 -outfile $out_file1 -word $word -frame $frame -auto</command><inputs><param format="fasta" name="input1" type="data"> --- a/tools/emboss_5/emboss_etandem.xml +++ b/tools/emboss_5/emboss_etandem.xml @@ -1,5 +1,6 @@ <tool id="EMBOSS: etandem33" name="etandem" version="5.0.0"><description>Looks for tandem repeats in a nucleotide sequence</description> + <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements><command>etandem -sequence $input1 -outfile $out_file1 -origfile $ofile2 -minrepeat $minrepeat -maxrepeat $maxrepeat -threshold $threshold -mismatch $mismatch -uniform $uniform -rformat2 $out_format1 -auto</command><inputs><param format="fasta" name="input1" type="data"> --- a/tools/emboss_5/emboss_marscan.xml +++ b/tools/emboss_5/emboss_marscan.xml @@ -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"> --- a/tools/emboss_5/emboss_cai_custom.xml +++ b/tools/emboss_5/emboss_cai_custom.xml @@ -1,5 +1,6 @@ <tool id="EMBOSS: cai_custom6" name="cai custom" version="5.0.0"><description>CAI codon adaptation index using custom codon usage file</description> + <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements><command>cai -seqall $input1 -outfile $out_file1 -cfile $input2 -auto</command><inputs><param format="fasta" name="input1" type="data"> --- a/tools/emboss_5/emboss_equicktandem.xml +++ b/tools/emboss_5/emboss_equicktandem.xml @@ -1,5 +1,6 @@ <tool id="EMBOSS: equicktandem31" name="equicktandem" version="5.0.0"><description>Finds tandem repeats</description> + <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements><command>equicktandem -sequence $input1 -outfile $out_file1 -origfile $ofile2 -maxrepeat $maxrepeat -threshold $threshold -rformat2 $out_format1 -auto</command><inputs><param format="fasta" name="input1" type="data"> --- a/tools/emboss_5/emboss_cai.xml +++ b/tools/emboss_5/emboss_cai.xml @@ -1,5 +1,6 @@ <tool id="EMBOSS: cai6" name="cai" version="5.0.0"><description>CAI codon adaptation index</description> + <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements><command>cai -seqall $input1 -outfile $out_file1 -cfile $cfile -auto</command><inputs><param format="fasta" name="input1" type="data"> --- a/tools/emboss_5/emboss_chaos.xml +++ b/tools/emboss_5/emboss_chaos.xml @@ -1,5 +1,6 @@ <tool id="EMBOSS: chaos7" name="chaos" version="5.0.0"><description>Create a chaos game representation plot for a sequence</description> + <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements><command interpreter="perl">emboss_single_outputfile_wrapper.pl chaos -sequence $input1 -graph png -goutfile $out_file1 -auto</command><inputs><param format="data" name="input1" type="data">