Mercurial > repos > iuc > transdecoder
diff transdecoder.xml @ 6:d0d4cef4f967 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 52d835f027b052a0a887be14a55faf9fa9e456ae"
| author | iuc |
|---|---|
| date | Mon, 01 Feb 2021 20:51:40 +0000 |
| parents | c6334cb383ff |
| children | ffd1300599a1 |
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--- a/transdecoder.xml Thu Oct 08 12:33:46 2020 +0000 +++ b/transdecoder.xml Mon Feb 01 20:51:40 2021 +0000 @@ -2,10 +2,11 @@ <description>finds coding regions within transcripts</description> <macros> <token name="@TOOL_VERSION@">5.5.0</token> - <token name="@VERSION_SUFFIX@">0</token> + <token name="@VERSION_SUFFIX@">1</token> </macros> <requirements> <requirement type="package" version="@TOOL_VERSION@">transdecoder</requirement> + <requirement type="package" version="3.0">zip</requirement> </requirements> <version_command><![CDATA[TransDecoder.LongOrfs --version 2>&1 | grep 'TransDecoder.LongOrfs' | cut -f 2 -d ' ']]></version_command> <command detect_errors="exit_code"><![CDATA[ @@ -52,6 +53,7 @@ #if 'log' in $oo.out |& tee '$out_log' #end if +&& if ls 'output/'*'.pdf' >/dev/null 2>&1; then zip 'seqlogo.zip' 'output/'*'.pdf' -q -j; fi ]]></command> <inputs> <param argument="-t" type="data" format="fasta" label="Select file with transcripts"/> @@ -84,7 +86,7 @@ <section name="lo" title="LongOrfs options" expanded="true"> <param argument="--gene_trans_map" type="data" format="tabular" optional="true" label="Select gene-to-transcript identifier mapping file" help="gene_id<tab>trans_id<return>"/> <param argument="-m" type="integer" value="100" min="1" label="Set minimum protein length"/> - <param argument="-S" type="boolean" truevalue="-S" falsevalue="" label="Activate strand-specificity?" help="Only analyse top strand."/> + <param argument="-S" type="boolean" truevalue="-S" falsevalue="" label="Activate strand-specificity?" help="Only analyse top strand?"/> </section> <section name="po" title="Predict options" expanded="true"> <!-- @@ -106,8 +108,8 @@ <param argument="--retain_long_orfs_length" type="integer" value="1000000" min="0" label="Set long ORFs length" help="Retain all ORFs found that are equal or longer than these many nucleotides even if no other evidence marks it as coding."/> </when> </conditional> - <param argument="--retain_blastp_hits" type="data" format="tabular" optional="true" label="Select BlastP result file" help="Any ORF with a blast match will be retained in the final output. (outfmt 6 format)"/> - <param argument="--retain_pfam_hits" type="data" format="tabular" optional="true" label="Select Pfam result file" help="Domain table output file from running hmmscan to search Pfam. Any ORF with a pfam domain hit will be retained in the final output. (domtblout file)"/> + <param argument="--retain_blastp_hits" type="data" format="tabular" optional="true" label="Select BlastP result file" help="Any ORF with a blast match will be retained in the final output. (tabular outfmt6 file)"/> + <param argument="--retain_pfam_hits" type="data" format="tabular" optional="true" label="Select Pfam result file" help="Domain table output file from running hmmscan to search Pfam. Any ORF with a pfam domain hit will be retained in the final output. (tabular domtblout file)"/> <param argument="--single_best_only" type="boolean" truevalue="--single_best_only" falsevalue="" label="Retain only the single best ORF per transcript?" help="Prioritized by homology than ORF length."/> <param argument="--no_refine_starts" type="boolean" truevalue="--no_refine_starts" falsevalue="" label="Start refinement that identifies potential start codons for 5' partial ORFs using a PWM?"/> <param argument="-T" type="integer" value="500" min="1" label="Set top longest ORFs to train Markov Model" help="The first (10*value) elements are selected for removing redundancies. Then number of longst ORFs of this value are selected from the non-redundant set."/> @@ -115,8 +117,8 @@ <when value="no"/> </conditional> </section> - <section name="oo" title="Output options"> - <param name="out" type="select" multiple="true" optional="false" label="Select output file(s)" help="Only shown in history if selected here and generated by the specific NOVOplasty run."> + <section name="oo" title="Output options" expanded="true"> + <param name="out" type="select" multiple="true" optional="false" label="Select output file(s)" help="Only shown in history if selected here and generated by the specific run."> <!-- LongOrfs --> <option value="lo_cds">Longest ORFs (CDS)</option> <option value="lo_gff3">Longest ORFs (GFF3)</option> @@ -126,6 +128,7 @@ <option value="cds" selected="true">Results (CDS)</option> <option value="gff3" selected="true">Results (GFF3)</option> <option value="pep" selected="true">Results (PEP)</option> + <option value="plot">Plots</option> <!-- Others --> <option value="log">Log</option> </param> @@ -155,52 +158,53 @@ <data name="out_pep" format="fasta" from_work_dir="transcripts.fasta.transdecoder.pep" label="${tool.name} on ${on_string}: Results (PEP/FASTA)"> <filter>'pep' in oo['out'] and po['predict_cond']['predict_sel'] == 'yes'</filter> </data> + <data name="out_plot" format="zip" from_work_dir="seqlogo.zip" label="${tool.name} on ${on_string}: Plots"> + <filter>'plot' in oo['out'] and po['predict_cond']['predict_sel'] == 'yes'</filter> + </data> <!-- Others --> <data name="out_log" format="txt" label="${tool.name} on ${on_string}: Log"> <filter>'log' in oo['out']</filter> </data> </outputs> <tests> - <!-- no test implemented for: gene_trans_map, retain_blastp_hits, retain_pfam_hits --> - <!-- #1 default --> <test expect_num_outputs="5"> <param name="t" value="transcripts.fasta"/> <!-- LongOrfs --> <output name="out_lo_pep"> <assert_contents> - <has_n_lines n="772"/> - <has_text_matching expression=".+comp874.+"/> + <has_n_lines n="190"/> + <has_line line=">CUFF.20.1.p2 type:3prime_partial len:205 gc:Universal CUFF.20.1:612-1(-)"/> </assert_contents> </output> <!-- Predict --> <output name="out_bed"> <assert_contents> - <has_n_lines n="337"/> - <has_text_matching expression="comp98\_c0\_seq1.+"/> + <has_n_lines n="81"/> + <has_text_matching expression="CUFF\.9\.1.+"/> </assert_contents> </output> <output name="out_cds"> <assert_contents> - <has_n_lines n="6959"/> - <has_text_matching expression=">comp98\_c0\_seq1.+"/> + <has_n_lines n="1578"/> + <has_line line=">CUFF.9.1.p1 GENE.CUFF.9.1~~CUFF.9.1.p1 ORF type:complete len:156 (+),score=36.30 CUFF.9.1:173-640(+)"/> </assert_contents> </output> <output name="out_gff3"> <assert_contents> - <has_n_lines n="2165"/> - <has_text_matching expression="comp98\_c0\_seq1.+"/> + <has_n_lines n="542"/> + <has_text_matching expression="CUFF\.9\.1.+"/> </assert_contents> </output> <output name="out_pep"> <assert_contents> - <has_n_lines n="2644"/> - <has_text_matching expression="comp98\_c0\_seq1.+"/> + <has_n_lines n="608"/> + <has_text_matching expression="CUFF\.9\.1.+"/> </assert_contents> </output> </test> <!-- #2 --> - <test expect_num_outputs="8"> + <test expect_num_outputs="9"> <param name="t" value="transcripts.fasta"/> <param name="G" value="Acetabularia"/> <section name="lo"> @@ -211,58 +215,66 @@ <conditional name="predict_cond"> <param name="predict_sel" value="yes"/> <conditional name="mode_cond"> - <param name="mode_sel" value="dynamic"/> + <param name="mode_sel" value="strict"/> + <param name="retain_long_orfs_length" value="1000001"/> </conditional> + <param name="retain_blastp_hits" value="blastp.outfmt6"/> + <param name="retain_pfam_hits" value="pfam.domtblout"/> <param name="single_best_only" value="true"/> <param name="no_refine_starts" value="true"/> <param name="T" value="501"/> </conditional> </section> <section name="oo"> - <param name="out" value="lo_pep,lo_gff3,lo_cds,bed,cds,gff3,pep,log"/> + <param name="out" value="lo_pep,lo_gff3,lo_cds,bed,cds,gff3,pep,plot,log"/> </section> <!-- LongOrfs --> <output name="out_lo_cds"> <assert_contents> - <has_n_lines n="1454"/> - <has_text_matching expression=">comp874\_c0\_seq1.+"/> + <has_n_lines n="398"/> + <has_text_matching expression="CUFF\.20\.1.+"/> </assert_contents> </output> <output name="out_lo_gff3"> <assert_contents> - <has_n_lines n="4565"/> - <has_text_matching expression="comp874\_c0\_seq1.+"/> + <has_n_lines n="1330"/> + <has_text_matching expression="CUFF\.20\.1.+"/> </assert_contents> </output> <output name="out_lo_pep"> <assert_contents> - <has_n_lines n="1454"/> - <has_text_matching expression=">comp874\_c0\_seq1.+"/> + <has_n_lines n="398"/> + <has_text_matching expression="CUFF\.20\.1.+"/> </assert_contents> </output> <!-- Predict --> <output name="out_bed"> <assert_contents> - <has_n_lines n="340"/> - <has_text_matching expression="comp98\_c0\_seq1.+"/> + <has_n_lines n="62"/> + <has_text_matching expression="CUFF\.9\.1.+"/> </assert_contents> </output> <output name="out_cds"> <assert_contents> - <has_n_lines n="7512"/> - <has_text_matching expression=">comp98\_c0\_seq1.+"/> + <has_n_lines n="1312"/> + <has_text_matching expression="CUFF\.9\.1.+"/> </assert_contents> </output> <output name="out_gff3"> <assert_contents> - <has_n_lines n="2000"/> - <has_text_matching expression="comp98\_c0\_seq1.+"/> + <has_n_lines n="395"/> + <has_text_matching expression="CUFF\.9\.1.+"/> </assert_contents> </output> <output name="out_pep"> <assert_contents> - <has_n_lines n="2833"/> - <has_text_matching expression=">comp98\_c0\_seq1.+"/> + <has_n_lines n="500"/> + <has_text_matching expression="CUFF\.9\.1.+"/> + </assert_contents> + </output> + <output name="out_plot"> + <assert_contents> + <has_size value="0"/> </assert_contents> </output> <!-- Others --> @@ -273,62 +285,61 @@ </output> </test> <!-- #3 --> - <test expect_num_outputs="8"> - <param name="t" value="transcripts.fasta"/> - <section name="po"> - <conditional name="predict_cond"> - <param name="predict_sel" value="yes"/> - <conditional name="mode_cond"> - <param name="mode_sel" value="strict"/> - <param name="retain_long_orfs_length" value="1000001"/> - </conditional> - </conditional> + <test expect_num_outputs="9"> + <param name="t" value="pasa_assemblies.fasta"/> + <section name="lo"> + <param name="gene_trans_map" value="pasa_genetransmap.txt"/> </section> <section name="oo"> - <param name="out" value="lo_pep,lo_gff3,lo_cds,bed,cds,gff3,pep,log"/> + <param name="out" value="lo_pep,lo_gff3,lo_cds,bed,cds,gff3,pep,plot,log"/> </section> <!-- LongOrfs --> <output name="out_lo_cds"> <assert_contents> - <has_n_lines n="772"/> - <has_text_matching expression=">comp874\_c0\_seq1.+"/> + <has_n_lines n="534"/> + <has_text_matching expression=">asmbl\_236\.p1.+"/> </assert_contents> </output> <output name="out_lo_gff3"> <assert_contents> - <has_n_lines n="2486"/> - <has_text_matching expression="comp874\_c0\_seq1.+"/> + <has_n_lines n="1742"/> + <has_text_matching expression="asmbl\_236.+"/> </assert_contents> </output> <output name="out_lo_pep"> <assert_contents> - <has_n_lines n="772"/> - <has_text_matching expression=">comp874\_c0\_seq1.+"/> + <has_n_lines n="534"/> + <has_text_matching expression=">asmbl\_236\.p1.+"/> </assert_contents> </output> <!-- Predict --> <output name="out_bed"> <assert_contents> - <has_n_lines n="337"/> - <has_text_matching expression="comp98\_c0\_seq1.+"/> + <has_n_lines n="204"/> + <has_text_matching expression="asmbl\_99.+"/> </assert_contents> </output> <output name="out_cds"> <assert_contents> - <has_n_lines n="6959"/> - <has_text_matching expression=">comp98\_c0\_seq1.+"/> + <has_n_lines n="3560"/> + <has_text_matching expression=">asmbl\_99\.p1.+"/> </assert_contents> </output> <output name="out_gff3"> <assert_contents> - <has_n_lines n="2165"/> - <has_text_matching expression="comp98\_c0\_seq1.+"/> + <has_n_lines n="1337"/> + <has_text_matching expression="asmbl\_99.+"/> </assert_contents> </output> <output name="out_pep"> <assert_contents> - <has_n_lines n="2644"/> - <has_text_matching expression=">comp98\_c0\_seq1.+"/> + <has_n_lines n="1391"/> + <has_text_matching expression=">asmbl\_99\.p1.+"/> + </assert_contents> + </output> + <output name="out_plot"> + <assert_contents> + <has_size value="714868" delta="1000"/> </assert_contents> </output> <!-- Others --> @@ -347,10 +358,10 @@ </conditional> </section> <!-- LongOrfs --> - <output name="out_lo_pep"> + <output name="out_pep"> <assert_contents> - <has_n_lines n="772"/> - <has_text_matching expression="c"/> + <has_n_lines n="190"/> + <has_text_matching expression="CUFF\.9\.1.+"/> </assert_contents> </output> </test> @@ -403,6 +414,7 @@ - Results (CDS/FASTA): nucleotide sequences for coding regions of the final candidate ORFs - Results (GFF3): positions within the target transcripts of the final selected ORFs - Results (BED): BED-formatted file describing ORF positions, best for viewing using GenomeView or IGV +- Plots: sequence logos and scores (compressed PDF) *Other*