annotate trinityrnaseq_protocol/align_and_estimate_abundance.xml @ 3:87c03e2aeba3 draft default tip

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<tool id="RSEM_abundance_estimation" name="RSEM_abundance_estimation" version="0.0.1">

    <description>run RSEM to estimate transcript abundances</description>
    <requirements>
        <requirement type="package">trinity</requirement>
    </requirements>
    <command interpreter="python">

        trinityToolWrapper.py util/align_and_estimate_abundance.pl --transcripts $transcripts --est_method RSEM --aln_method bowtie --trinity_mode --prep_reference

        ## Inputs.
        #if str($inputs.paired_or_single) == "paired":
            --left $inputs.left_input --right $inputs.right_input
            #if  $inputs.left_input.ext == 'fa':
                --seqType fa
            #else:
                --seqType fq
            #end if
            #if str($inputs.library_type) != "None":
                --SS_lib_type $inputs.library_type
            #end if
            
        #else:
            --single $inputs.input
            #if  str($inputs.input.ext) == 'fa':
                --seqType fa
            #else:
                --seqType fq
            #end if
            #if str($inputs.library_type) != "None":
                --SS_lib_type $inputs.library_type
            #end if
        #end if


    </command>
    <inputs>
		<param format="fasta" name="transcripts" type="data" label="transcripts_fasta" help="Fasta sequences for which reads are aligned."  />

		<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>

            </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>

	
    </inputs>
    <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
    </help>
</tool>