Mercurial > repos > trinity_ctat > ctat_analyze_differential_expression
changeset 4:b37d57c8ce7e draft
Uploaded
author | trinity_ctat |
---|---|
date | Fri, 29 Jun 2018 14:54:40 -0400 |
parents | 68c6c52d2ced |
children | 57bdc1772c5b |
files | ctat_analyze_differential_expression.xml |
diffstat | 1 files changed, 15 insertions(+), 15 deletions(-) [+] |
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--- a/ctat_analyze_differential_expression.xml Thu Jun 28 22:45:26 2018 -0400 +++ b/ctat_analyze_differential_expression.xml Fri Jun 29 14:54:40 2018 -0400 @@ -14,43 +14,43 @@ </requirements> <command detect_errors="exit_code"> <![CDATA[ - python $__tool_directory__/ctat_analyze_differential_expression.py $Counts_matrix $TMM_Matrix_FPKM $Pvalue $Cvalue + python $__tool_directory__/ctat_analyze_differential_expression.py $EdgeRTarGz $Counts_matrix $Pvalue $Cvalue ]]> </command> <inputs> <param name="EdgeRTarGz" label="EdgeR tar gz file" type="data" format="txt"/> <param name="Counts_matrix" label="Counts Matrix" type="data" format="tabular" /> - <param name="Pvalue" label="P-value" value="0.05" type="float" /> - <param name="Cvalue" label="C-value" value="0" type="float" /> + <param name="Pvalue" label="P-value" value="0.05" type="float" /> + <param name="Cvalue" label="C-value" value="0" type="float" /> </inputs> <outputs> <data format="data" name="diffExpr_matrix" label="${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 ${on_string}: Heatmap" from_work_dir="diffExpr.matrix.log2.centered.genes_vs_samples_heatmap.pdf"/> + <data format="data" name="diffExpr_correlation_matrix" label="${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" /> +<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" > +<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" > +<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" > +<output name="Heatmap" > <assert_contents> <has_line_matching expression=".+" /> </assert_contents>