view analyze_diff_exp.xml @ 7:f51625f25d56 draft

Adding profile info and exit code behavior. Making version numbers consistent. Upping test number.

<tool id="Analyze_Diff_Exp" name="Analyze_Differential_Expression" version="1.0.0" profile="17.05">

    <description>Analyze differential expression</description>
    <requirements>
        <requirement type="package" version="2.7">python</requirement>
        <requirement type="package" version="1.3.0">rsem</requirement>
        <requirement type="package">trinity</requirement>
    </requirements>
    <command detect_errors="exit_code">
        <![CDATA[
        python $__tool_directory__/analyze_diff_exp_wrapper.py $EdgeRTarGz $TMM_Matrix_FPKM $Pvalue $Cvalue 
        ]]>
    </command>
    <inputs>
          <param name="EdgeRTarGz" label="EdgeR tar gz file" type="data" format="txt"/>
          <param name="TMM_Matrix_FPKM" label="TMM Normalized FPKM matrix" type="data" format="tabular" />
	      <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="EdgeRTarGz" value="Sp.edgeR.tar.gz" ftype="tar" />
		<param name="TMM_Matrix_FPKM" value="Sp.TMM.EXPR.matrix" />
		<param name="Pvalue" value="0.05" />
		<param name="Cvalue" value="0.0" />

		<output name="diffExpr_matrix" >
                    <assert_contents>
                        <has_line_matching expression=".+" />
                        <has_line line="Sp_ds&#009;Sp_hs" />
                        <has_line_matching expression="TRINITY_DN.+" />
                    </assert_contents>
                </output>
		<output name="diffExpr_correlation_matrix" file="Sp.diffExpr.matrix.log2.sample_cor.dat" />
		<output name="diffExpr_correlation_matrix_pdf" >
                    <assert_contents>
                        <has_line_matching expression=".+" />
                    </assert_contents>
                </output>
		<output name="Heatmap" >
                    <assert_contents>
                        <has_line_matching expression=".+" />
                    </assert_contents>
                </output>

        </test>
    </tests>
    <help>
.. class:: infomark 

This tool filters differentially expressed transcripts derived from edgeR using a minimum fold change (C-value) which will be log2 transformed before use and a required significance (P-value) in the pairwise sample comparisons (after false discovery rate correction). 

If you are following the Trinity RNA-seq protocol please go here_ for a galaxy tool walk through or the Nature Protocols paper_.

.. _here: https://github.com/trinityrnaseq/GalaxyTrinityProtocol/wiki
.. _paper: http://www.nature.com/nprot/journal/v8/n8/full/nprot.2013.084.html
    </help>

    <citations>
        <citation type="doi">10.1038/nbt.1883</citation>
    </citations>

</tool>