Mercurial > repos > trinity_ctat > ctat_analyze_differential_expression
diff ctat_analyze_differential_expression.xml @ 0:2ca97cd84ce3 draft default tip
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| author | trinity_ctat |
|---|---|
| date | Tue, 17 Jul 2018 11:49:33 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ctat_analyze_differential_expression.xml Tue Jul 17 11:49:33 2018 -0400 @@ -0,0 +1,76 @@ +<tool id="ctat_analyze_differential_expression" name="ctat_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">subprocess32</requirement> + <requirement type="package">bzip2</requirement> + <requirement type="package" version="1.3.0">rsem</requirement> + <requirement type="package" version="3">bioconductor-edger</requirement> + <requirement type="package" version="2">bioconductor-qvalue</requirement> + <requirement type="package">r-cluster</requirement> + <requirement type="package">r-fastcluster</requirement> + <requirement type="package" version="2.6.6">trinity</requirement> + </requirements> + <command detect_errors="exit_code"> + <![CDATA[ + python $__tool_directory__/ctat_analyze_differential_expression.py $EdgeRTarGz $Counts_matrix $Pvalue $Cvalue + ]]> + </command> + <inputs> + <param name="EdgeRTarGz" label="EdgeR tar gz file" type="data" format="txt"/> + <param name="Counts_matrix" label="Counts Matrix" type="data" format="tabular" /> + <param name="Pvalue" label="P-value" value="0.05" type="float" /> + <param name="Cvalue" label="C-value" value="0" type="float" /> + + </inputs> + <outputs> + <data format="data" name="diffExpr_matrix" label="${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	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>