view RSEM_abundance_estimation.xml @ 6:8d546ef8cfea

Add RSEM_abundance_estimation

<tool id="RSEM_abundance_estimation" name="RSEM abundance estimation" version="0.0.2">
    <description>run RSEM to estimate transcript abundances</description>
    <requirements>
        <requirement type="package" version="2013_08_14">trinityrnaseq</requirement>
        <requirement type="package" version="1.1.17">rsem</requirement>
    </requirements>
    <command>
        \$TRINITY_HOME/util/RSEM_util/run_RSEM_align_n_estimate.pl  --transcripts $transcripts 
        ## Inputs.
        #if str($read_type.paired_or_single) == "single":
            #if  $read_type.single_reads.extension.startswith( "fastq"):
                --seqType fq
            #else
                --seqType fa
            #end if
            --single $read_type.single_reads
        #else
            #if  $read_type.left_reads.extension.startswith( "fastq"):
                --seqType fq
            #else
                --seqType fa
            #end if
            --left $read_type.left_reads
            --right $read_type.right_reads
        #end if
        #if $transcript.source == "other":
            --no_group_by_component
            --gene_trans_map $transcript.gene_trans_map
        #end if         
    </command>
    <inputs>
        <param name="transcripts" type="data" format="fasta" label="transcripts_fasta" help="Fasta sequences for which reads are aligned."  />
        <conditional name="read_type">
            <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 name="left_reads" type="data" format="fasta,fastq" label="left reads" help=""  />
                <param name="right_reads" type="data" format="fasta,fastq" label="right reads" help=""  />
                <param name="ss_lib_type" type="select" label="strand-specific library type">
                    <option value="RF">RF</option>
                    <option value="FR">FR</option>
                </param>
            </when>
            <when value="single">
                <param name="single_reads" type="data" format="fasta,fastq" label="single reads" help=""  />
                <param name="ss_lib_type" type="select" label="strand-specific library type">
                    <option value="F">F</option>
                    <option value="R">R</option>
                </param>
            </when>
        </conditional>
        <conditional name="transcript">
            <param name="source" type="select" label="Transcripts Source">
                <option value="trinity">Trinity</option>
                <option value="other">NOT trinity</option>
            </param>
            <when value="trinity"/>
            <when value="other">
                <param name="gene_trans_map" type="data" format="tabular" optional="true" label="Map of gene ids to transcript (isoform) ids" >
                  <help>
                    Each line of should be of the form: gene_id transcript_id ( with the two fields separated by a tab character )
                  </help>
                </param>
            </when>
        </conditional>
    </inputs>
    <stdio>
        <exit_code range="1:"  level="fatal" description="Error Running RSEM" />
    </stdio>
    <outputs>
        <data format="text" name="transcript_counts" label="${tool.name} on ${on_string}: Isoform Counts" from_work_dir="RSEM.isoforms.results"/>
        <data format="text" name="gene_counts" label="${tool.name} on ${on_string}: Gene counts" from_work_dir="RSEM.genes.results"/>
    </outputs>
    <tests>
        <test>
            <param name="target" value="trinity/Trinity.fasta" />
            <param name="aligner" value="bowtie" />
            <param name="paired_or_single" value="single" />
            <param name="library_type" value="None" />
            <param name="input" value="trinity/reads.left.fq" />
        </test>
    </tests>
    <help>
        .. _Trinity: http://trinityrnaseq.sourceforge.net

        $TRINITY_HOME/util/RSEM_util/run_RSEM_align_n_estimate.pl --transcripts Trinity.fasta \
        --seqType fq --left left.reads.fq --right right.reads.fq
    </help>
</tool>