annotate transcriptsToOrfs.xml @ 15:6b72a97471c6 draft

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<tool id="transcriptsToOrfs" name="transcriptsToOrfs" version="0.0.1">
	
    <description>Trinity Transcripts to Candidate Peptides</description>
    <requirements>
        <requirement type="package">trinity</requirement>
    </requirements>
    <command interpreter="python">
        trinityToolWrapper.py Analysis/Coding/transcripts_to_best_scoring_ORFs.pl 

		-t $transcripts 
		-m $min_prot_length 
		--CPU $CPU
		--search_pfam "${ filter( lambda x: str( x[0] ) == str( $pfam_db ), $__app__.tool_data_tables[ 'pfam_databases' ].get_fields() )[0][-1] }"

		#if str($strand_specificity) == 'SS':
			-S
		#end if
		                
        ## direct to output
        > output 
 
    </command>
    <inputs>

		<param format="fasta" name="transcripts" type="data" label="Transcripts sequences in fastA format" help="" />

		<param name="min_prot_length"  type="integer" label="Minimum peptide length (in amino acids)" value="100" min="50" help="" />
		
		<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="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" />

    </inputs>
    <outputs>
        <data format="txt" name="trinity_pep_pfam" label="${tool.name} on ${on_string}: Pfam matches to Candidate Peptide Sequences" from_work_dir="longest_orfs.pep.pfam.dat"/>
        <data format="fasta" name="trinity_pep_seqs" label="${tool.name} on ${on_string}: Candidate Peptide Sequences" from_work_dir="best_candidates.eclipsed_orfs_removed.pep"/>
		<data format="bed" name="trinity_pep_coords" label = "${tool.name} on ${on_string} Candidate Peptide Coordinates" from_work_dir="best_candidates.eclipsed_orfs_removed.bed" />
    </outputs>
    <tests>
    </tests>
    <help>
        Trinity is a de novo transcript assembler that uses RNA-seq data as input. This tool runs all Trinity_ commands--Inchworm, Chrysalis, and Butterfly--in a single pass.
        
        .. _Trinity: http://trinityrnaseq.sourceforge.net
    </help>
</tool>