Mercurial > repos > iuc > transdecoder
diff transdecoder.xml @ 4:0db979fead3a draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit f0e5f4748034bc0f1faafcec65bffa34b64a4781
| author | iuc |
|---|---|
| date | Thu, 01 Jun 2017 06:04:12 -0400 |
| parents | b408e5a8b137 |
| children | c6334cb383ff |
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--- a/transdecoder.xml Wed Jul 06 11:30:14 2016 -0400 +++ b/transdecoder.xml Thu Jun 01 06:04:12 2017 -0400 @@ -1,63 +1,38 @@ -<tool id="transdecoder" name="TransDecoder" version="1.1"> +<tool id="transdecoder" name="TransDecoder" version="3.0.1"> <description>Find coding regions within transcripts</description> <requirements> - <requirement type="package" version="2.1.0">transdecoder</requirement> + <requirement type="package" version="3.0.1">transdecoder</requirement> </requirements> - <stdio> - <exit_code range="1:" level="fatal" description="Error occurred" /> - </stdio> - - <command><![CDATA[ - TransDecoder.LongOrfs -t "${input}" - - #if ($min_len): - -m ${min_len} - #end if - + <command detect_errors="exit_code"><![CDATA[ + TransDecoder.LongOrfs -t '${input}' + -m ${min_len} ${adv.stranded} - - #if ($adv.gen_code): - -G ${adv.gen_code} + -G ${adv.gen_code} + #if str($adv.partials) + -p ${adv.partials} #end if - && - - TransDecoder.Predict --cpu \${GALAXY_SLOTS:-1} -t "${input}" - - #if ($adv.retain_long_orfs): - --retain_long_orfs ${adv.retain_long_orfs} - #end if - + TransDecoder.Predict --cpu \${GALAXY_SLOTS:-1} -t '${input}' + --retain_long_orfs ${adv.retain_long_orfs} + ${adv.single_best_orf} #if str( $training_sect.training.training_selector ) == "training_top": - #if ($training_sect.training.top_longest): - -T ${training_sect.training.top_longest} - #end if + -T ${training_sect.training.top_longest} #else - #if ($training_sect.training.train): - --train ${training_sect.training.train} - #end if + --train '${training_sect.training.train}' #end if - && - - out_prefix=`basename "${input}"` - - mv `basename "${input}"`.transdecoder.pep transcript.transdecoder.pep && - mv `basename "${input}"`.transdecoder.cds transcript.transdecoder.cds && - mv `basename "${input}"`.transdecoder.bed transcript.transdecoder.bed && - mv `basename "${input}"`.transdecoder.gff3 transcript.transdecoder.gff3 && - mv `basename "${input}"`.transdecoder.mRNA transcript.transdecoder.mRNA + mv `basename '${input}'`.transdecoder.pep '$transdecoder_pep' && + mv `basename '${input}'`.transdecoder.cds '$transdecoder_cds' && + mv `basename '${input}'`.transdecoder.bed '$transdecoder_bed' && + mv `basename '${input}'`.transdecoder.gff3 '$transdecoder_gff3' ]]></command> - <inputs> - <param format="fasta" name="input" type="data" label="Transcripts"/> - - <param name="min_len" size="5" type="integer" optional='true' value="100" label="Minimum protein length (default: 100aa)"/> - + <param name="input" argument="-t" type="data" format="fasta" label="Transcripts" /> + <param name="min_len" argument="-m" type="integer" value="100" label="Minimum protein length" /> <section name="adv" title="Advanced Options" expanded="False"> - <param name="stranded" type="boolean" checked="false" truevalue="-S" falsevalue="" label="Strand-specific" help="Only analyzes top strand"/> - <param name="gen_code" type="select" label="Genetic code"> + <param name="stranded" argument="-S" type="boolean" truevalue="-S" falsevalue="" label="Strand-specific" help="Only analyzes top strand" /> + <param name="gen_code" argument="-G" type="select" label="Genetic code"> <option value="universal" selected="True">universal</option> <option value="Euplotes">Euplotes</option> <option value="Tetrahymena">Tetrahymena</option> @@ -75,10 +50,10 @@ <option value="Mitochondrial-Euascomycetes">Mitochondrial-Euascomycetes</option> <option value="Mitochondrial-Protozoans">Mitochondrial-Protozoans</option> </param> - - <param name="retain_long_orfs" type="integer" optional="true" label="Retain long orfs" help="Retain all ORFs found that are equal or longer than these many nucleotides even if no other evidence marks it as coding (default: 900 bp => 300aa)" /> + <param name="partials" argument="-p" type="integer" value="" optional="true" label="Shorten potential 5' partials if they are this percentage of the original protein or longer" /> + <param name="retain_long_orfs" argument="--retain_long_orfs" type="integer" value="900" label="Retain long ORFs" help="Retain all ORFs found that are equal or longer than these many nucleotides even if no other evidence marks it as coding (default: 900 bp => 300aa)" /> + <param argument="--single_best_orf" type="boolean" truevalue="--single_best_orf" falsevalue="" label="Retain only the single best ORF per transcript" help="Best is defined as having (optionally Pfam and/or BLAST support) and longest ORF" /> </section> - <section name="training_sect" title="Training Options" expanded="False"> <conditional name="training"> <param name="training_selector" type="select" label="Select the training method"> @@ -86,33 +61,26 @@ <option value="training_set">Train with a set of known ORFs</option> </param> <when value="training_top"> - <param name="top_longest" type="integer" optional="true" label="Number of top longest ORFs" help="Number of top longest ORFs to train Markov Model (hexamer stats) (default: 500 sequences)" /> + <param name="top_longest" argument="-T" type="integer" value="500" label="Number of top longest ORFs" help="Number of top longest ORFs to train Markov Model (hexamer stats). Note, 10x this value are first selected for use with cd-hit to remove redundancies, and then this value of longest ORFs are selected from the non-redundant set" /> </when> <when value="training_set"> - <param format="fasta" name="train" type="data" label="Training set of transcripts" optional="true" help="FASTA file with ORFs to train Markov Mod for protein identification" /> + <param name="train" argument="--train" type="data" format="fasta" label="Training set of transcripts" help="FASTA file with ORFs to train Markov Mod for protein identification" /> </when> </conditional> </section> - </inputs> - - <outputs> - <data name='transdecoder_pep' format='fasta' label="${tool.name} on ${on_string}: pep" from_work_dir="transcript.transdecoder.pep"/> - <data name='transdecoder_cds' format='fasta' label="${tool.name} on ${on_string}: cds" from_work_dir="transcript.transdecoder.cds"/> - <data name='transdecoder_bed' format='bed' label="${tool.name} on ${on_string}: bed" from_work_dir="transcript.transdecoder.bed"/> - <data name='transdecoder_gff3' format='gff3' label="${tool.name} on ${on_string}: gff3" from_work_dir="transcript.transdecoder.gff3"/> - <data name='transdecoder_mRNA' format='fasta' label="${tool.name} on ${on_string}: mRNA" from_work_dir="transcript.transdecoder.mRNA"/> + <data name="transdecoder_pep" format="fasta" label="${tool.name} on ${on_string}: pep" /> + <data name="transdecoder_cds" format="fasta" label="${tool.name} on ${on_string}: cds" /> + <data name="transdecoder_bed" format="bed" label="${tool.name} on ${on_string}: bed" /> + <data name="transdecoder_gff3" format="gff3" label="${tool.name} on ${on_string}: gff3" /> </outputs> - - <tests> <test> <param name="input" value="test.fa"/> <output name="transdecoder_gff3" file="raw/test.fa.transdecoder.gff3" compare="sim_size" /> <output name="transdecoder_bed" file="raw/test.fa.transdecoder.bed" compare="sim_size" /> <output name="transdecoder_cds" file="raw/test.fa.transdecoder.cds" compare="sim_size" /> - <output name="transdecoder_mRNA" file="raw/test.fa.transdecoder.mRNA" compare="sim_size" /> <output name="transdecoder_pep" file="raw/test.fa.transdecoder.pep" compare="sim_size" /> </test> <test> @@ -122,7 +90,6 @@ <output name="transdecoder_gff3" file="top/test.fa.transdecoder.gff3" compare="sim_size" /> <output name="transdecoder_bed" file="top/test.fa.transdecoder.bed" compare="sim_size" /> <output name="transdecoder_cds" file="top/test.fa.transdecoder.cds" compare="sim_size" /> - <output name="transdecoder_mRNA" file="top/test.fa.transdecoder.mRNA" compare="sim_size" /> <output name="transdecoder_pep" file="top/test.fa.transdecoder.pep" compare="sim_size" /> </test> <test> @@ -131,7 +98,6 @@ <output name="transdecoder_gff3" file="gencode/test.fa.transdecoder.gff3" compare="sim_size" /> <output name="transdecoder_bed" file="gencode/test.fa.transdecoder.bed" compare="sim_size" /> <output name="transdecoder_cds" file="gencode/test.fa.transdecoder.cds" compare="sim_size" /> - <output name="transdecoder_mRNA" file="gencode/test.fa.transdecoder.mRNA" compare="sim_size" /> <output name="transdecoder_pep" file="gencode/test.fa.transdecoder.pep" compare="sim_size" /> </test> <test> @@ -140,12 +106,10 @@ <output name="transdecoder_gff3" file="strand/test.fa.transdecoder.gff3" compare="sim_size" /> <output name="transdecoder_bed" file="strand/test.fa.transdecoder.bed" compare="sim_size" /> <output name="transdecoder_cds" file="strand/test.fa.transdecoder.cds" compare="sim_size" /> - <output name="transdecoder_mRNA" file="strand/test.fa.transdecoder.mRNA" compare="sim_size" /> <output name="transdecoder_pep" file="strand/test.fa.transdecoder.pep" compare="sim_size" /> </test> </tests> <help> - **What it does** TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks. @@ -163,9 +127,8 @@ - optional the putative peptide has a match to a Pfam domain above the noise cutoff score. The software is primarily maintained by Brian Haas at the Broad Institute and Alexie Papanicolaou at the Commonwealth Scientific and Industrial Research Organisation (CSIRO). It is integrated into other related software such as Trinity, PASA, EVidenceModeler, and Trinotate. - </help> - <citations> + <citations> <citation type="doi">10.1038/nprot.2013.084</citation> </citations> </tool>