view transcriptsToOrfs.xml @ 2:5eb99d21ef0d

Add trinityrnaseq_norm and transcriptsToOrfs tools

<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>