annotate tools/ngs_rna/trinity_all.xml @ 0:9071e359b9a3

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<tool id="trinity_all" name="Trinity" version="0.0.1">
    <!-- Run all steps of Trinity-Inchworm, Chrysalis, and Butterfly-in a single step. Wrapper status is alpha. -->
    <description>De novo assembly of RNA-Seq data</description>
    <requirements>
        <requirement type="package">trinity</requirement>
    </requirements>
    <command>
        Trinity.pl 
        
        ## Additional parameters.
        #if $additional_params.use_additional == "yes":
            --min_contig_length $additional_params.min_contig_length
        #end if
        
        ## Inputs.
        #if $inputs.paired_or_single == "paired":
            --left $inputs.left_input --right $inputs.right_input
            #if  $inputs.left_input.ext == 'fa':
                --seqType fa
            #else:
                --seqType fq
            #end if
            #if $inputs.library_type != 'None':
                --SS_lib_type $inputs.library_type
            #end if
        #else:
            --single $inputs.input
            #if  $inputs.input.ext == 'fa':
                --seqType fa
            #else:
                --seqType fq
            #end if
            #if $inputs.library_type != 'None':
                --SS_lib_type $inputs.library_type
            #end if
        #end if
        
        ## CPU and butterfly options.
        --CPU 4 --run_butterfly --bfly_opts "-V 10 --stderr" > $trinity_log 2>&amp;1 
    </command>
    <inputs>
        <conditional name="inputs">
            <param name="paired_or_single" type="select" label="Paired or Single-end data?">
                <option value="paired">Paired</option>
                <option value="single">Single</option>
            </param>
            <when value="paired">
                <param format="fasta,fastq" name="left_input" type="data" label="Left/Forward strand reads" help=""/>
                <param format="fasta,fastq" name="right_input" type="data" label="Right/Reverse strand reads" help=""/>
                <param name="library_type" type="select" label="Strand-specific Library Type">
                    <option value="None">None</option>
                    <option value="FR">FR</option>
                    <option value="RF">RF</option>
                </param>
                <param name="paired_fragment_length" type="integer" value="300" min="1" label="Paired Fragment Length" help="Maximum length expected between fragment pairs"/>
            </when>
            <when value="single">
                <param format="fasta,fastq" name="input" type="data" label="Single-end reads" help=""/>
                <param name="library_type" type="select" label="Strand-specific Library Type">
                    <option value="None">None</option>
                    <option value="F">F</option>
                    <option value="R">R</option>
                </param>
            </when>
        </conditional>
        <conditional name="additional_params">
            <param name="use_additional" type="select" label="Use Additional Params?">
                <option value="no">No</option>
                <option value="yes">Yes</option>
            </param>
            <when value="no">
            </when>
            <when value="yes">            
                <param name="min_contig_length" type="integer" value="200" min="1" label="Minimum Contig Length" help=""/>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data format="txt" name="trinity_log" label="${tool.name} on ${on_string}: log" />
        <data format="fasta" name="assembled_transcripts" label="${tool.name} on ${on_string}: Assembled Transcripts" from_work_dir="trinity_out_dir/Trinity.fasta"/>
    </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>