Mercurial > repos > badger > trinityrnaseq
diff transcriptsToOrfs.xml @ 14:961b5bf3fcc8 draft default tip
remove other tools
| author | Eric Badger <badger@msi.umn.edu> |
|---|---|
| date | Tue, 08 Apr 2014 13:16:06 -0500 |
| parents | 6425d1da3746 |
| children |
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--- a/transcriptsToOrfs.xml Fri Apr 04 15:30:44 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,117 +0,0 @@ -<tool id="transcriptsToOrfs" name="transcriptsToOrfs" version="0.0.2"> - <description>Trinity Transcripts to Candidate Peptides</description> - <requirements> - <requirement type="package" version="2013_08_14">trinityrnaseq</requirement> - <requirement type="package" version="3.0">hmmer</requirement> - </requirements> - <command> - \$TRINITY_HOME/trinity-plugins/transdecoder/transcripts_to_best_scoring_ORFs.pl - -t $transcripts - #if $min_prot_length: - -m $min_prot_length - #end if - #if $retain_long_orfs: - --retain_long_orfs $retain_long_orfs - #end if - #if $training_count: - -T $training_count - #end if - #if str($strand_specificity) == 'SS': - -S - #end if - #if $genetic_code.__str__ != '': - -G $genetic_code - #end if - #if $search.use_pfam == 'yes': - --search_pfam "${ filter( lambda x: str( x[0] ) == str( $search.pfam_db ), $__app__.tool_data_tables[ 'pfam_databases' ].get_fields() )[0][-1] }" - --CPU $search.CPU - #end if - </command> - <inputs> - <param format="fasta" name="transcripts" type="data" label="Transcripts sequences in fastA format" help="" /> - <param name="min_prot_length" type="integer" value="" optional="true" label="Minimum peptide length (in amino acids)" help="default: 100"> - <validator type="in_range" message="Minimum peptide length should be at least 50" min="50" /> - </param> - <param name="retain_long_orfs" type="integer" value="" optional="true" label="Retain all ORFs found that are of minimum length in nucleotides" help="default: 900" > - <validator type="in_range" message="ORF length should be at least 50" min="50" /> - </param> - <param name="training_count" type="integer" value="" optional="true" label="Number of top longest ORFs to train Markov Model (hexamer stats)" help="default: 500" > - <validator type="in_range" message="ORF count should be at least 50" min="50" /> - </param> - <param name="strand_specificity" type="select" label="Strand specificity type"> - <option value="DS">NOT strand specific, examine both strands</option> - <option value="SS">Strand specific, examine only top strand</option> - </param> - <param name="genetic_code" type="select" label="Genetic Code"> - <option value="">use default(universal)</option> - <option value="universal">universal</option> - <option value="Euplotes">Euplotes</option> - <option value="Tetrahymena">Tetrahymena</option> - <option value="Candida">Candida</option> - <option value="Acetabularia">Acetabularia</option> - </param> - <conditional name="search"> - <param name="use_pfam" type="select" label="Search PFAM database"> - <option value="no">NO</option> - <option value="yes">YES</option> - </param> - <when value="no"/> - <when value="yes"> - <param name="pfam_db" type="select" label="Pfam database"> - <options from_data_table="pfam_databases" /> - </param> - <param name="CPU" type="integer" value="2" min="1" label="CPU" help="Number of CPUs to use by hmmscan" /> - </when> - </conditional> - </inputs> - <stdio> - <exit_code range="1:" level="fatal" description="Failed" /> - <regex match="Error" - source="stderr" - level="fatal" - description="Failed" /> - </stdio> - <outputs> - <data format="txt" name="trinity_pep_pfam" label="${tool.name} on ${on_string}: Pfam matches to Candidate Peptide Sequences" from_work_dir="longest_orfs.pep.pfam.dat"> - <filter>search['use_pfam'] == 'yes'</filter> - </data> - <data format="gff3" name="trinity_pep_gff3" label="${tool.name} on ${on_string} Candidate Peptide Features" from_work_dir="best_candidates.eclipsed_orfs_removed.gff3" /> - <data format="bed" name="trinity_pep_bed" label="${tool.name} on ${on_string} Candidate Peptide Coordinates" from_work_dir="best_candidates.eclipsed_orfs_removed.bed" /> - <data format="fasta" name="trinity_pep_cds" label="${tool.name} on ${on_string}: Candidate Peptide CDS Sequences" from_work_dir="best_candidates.eclipsed_orfs_removed.cds"/> - <data format="fasta" name="trinity_pep_seqs" label="${tool.name} on ${on_string}: Candidate Peptide Sequences" from_work_dir="best_candidates.eclipsed_orfs_removed.pep"/> - </outputs> - <tests> - <test> - <param name="transcripts" ftype="fasta" value="TrinitySingle.fasta"/> - <param name="min_prot_length" value="100"/> - <param name="use_pfam" value="no"/> - <output name="trinity_pep_seqs"> - <assert_contents> - <has_text text="WAAKAWLITARSLYPADF" /> - </assert_contents> - </output> - <output name="trinity_pep_cds"> - <assert_contents> - <has_text text="TGGGCAGCCAAGGCATGGCTGATCACGGCCCGCA" /> - </assert_contents> - </output> - <output name="trinity_pep_bed"> - <assert_contents> - <has_text text="comp10_c0_seq1" /> - </assert_contents> - </output> - <output name="trinity_pep_gff3"> - <assert_contents> - <has_text text="comp10_c0_seq1" /> - </assert_contents> - </output> - </test> - </tests> - <help> - ** transcriptsToOrfs ** - Trinity_ is a de novo transcript assembler that uses RNA-seq data as input. - This tool searches for open reading frames in the assembled transcripts. - - .. _Trinity: http://trinityrnaseq.sourceforge.net - </help> -</tool>