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

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<tool id="Analyze_Diff_Exp" name="Analyze_Differential_Expression" version="0.0.1">

    <description>Analyze differential expression</description>
    <requirements>
        <requirement type="package">trinity</requirement>
    </requirements>
    <command interpreter="python">

        analyze_diff_exp_wrapper.py $EdgeRTarGz $TMM_Matrix_FPKM $Pvalue $Cvalue 
	
    </command>
    <inputs>
              <param name="EdgeRTarGz" label="EdgeR tar gz file" type="data" format="file"/>
              <param name="TMM_Matrix_FPKM" label="TMM Normalized FPKM matrix" type="data" format="file" />
	      <param name="Pvalue" label="P-value" value="0.05" type="float" />
	      <param name="Cvalue" label="C-value" value="0" type="float" />
      
    </inputs>
    <outputs>
        <data format="data" name="diffExpr_matrix" label="${tool.name} on ${on_string}: Matrix" from_work_dir="diffExpr.matrix"/>
	<data format="data" name="diffExpr_correlation_matrix" label="${tool.name} on ${on_string}: Sample_Correlation_Matrix" from_work_dir="diffExpr.matrix.log2.sample_cor.dat"/>
	<data format="data" name="diffExpr_correlation_matrix_pdf" label="${tool.name} on ${on_string}: Sample_Correlation_Matrix_PDF" from_work_dir="diffExpr.matrix.log2.sample_cor_matrix.pdf"/>
	<data format="data" name="Heatmap" label="${tool.name} on ${on_string}: Heatmap" from_work_dir="diffExpr.matrix.log2.centered.genes_vs_samples_heatmap.pdf"/>
    </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>