view trinityrnaseq_protocol/diffExpress_edgeR.xml @ 3:87c03e2aeba3 draft default tip

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

    <description>Identify Differentially Expressed Transcripts Using EdgeR</description>
    <requirements>
        <requirement type="package">edgeR</requirement>
    </requirements>
    <command interpreter="python">

 		trinityToolWrapper.py Analysis/DifferentialExpression/run_EdgeR.pl 
			--matrix $counts_matrix 
			--transcripts $transcripts_fasta_file
			--output edgeR_results
			--dispersion $dispersion

		> stdout.txt


    </command>
    <inputs>
		
		<param type="data" format="txt" name="counts_matrix" label="Matrix of RNA-Seq fragment counts for transcripts per condition" />
		<param type="data" format="fasta" name="transcripts_fasta_file" label="Transcripts fasta file corresponding to matrix" />
		<param type="float" name="dispersion" value="0.1" min="0" label="dispersion value" help="Dispersion value to be used in the negative binomial" />
	
    </inputs>
    <outputs>
        
        <data format="txt" name="diff_expressed_edgeR_results"  label="${tool.name} on ${on_string}: differentially expressed transcripts per pair of conditions"  from_work_dir="edgeR_results/all_diff_expression_results.txt" />

        <data format="txt" name="matrix_FPKM" label="${tool.name} on ${on_string}: matrix.TMM_normalized.FPKM" from_work_dir="edgeR_results/matrix.TMM_normalized.FPKM" />

		<data format="txt" name="TMM_info" label="${tool.name} on ${on_string}: TMM library size estimates" from_work_dir="edgeR_results/TMM_info.txt" />
	
	</outputs>
    <tests>

		<test>
			<param name="myname" value="This is just a simple test" />

        </test>
	

    </tests>
    <help>
         help info here.
    </help>
</tool>