Mercurial > repos > trinity_ctat > ctat_analyze_differential_expression

comparison ctat_analyze_differential_expression.xml @ 4:b37d57c8ce7e draft

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author trinity_ctat
date Fri, 29 Jun 2018 14:54:40 -0400
parents 68c6c52d2ced
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3:68c6c52d2ced 4:b37d57c8ce7e
12 <requirement type="package">r-fastcluster</requirement> 12 <requirement type="package">r-fastcluster</requirement>
13 <requirement type="package" version="2.6.6">trinity</requirement> 13 <requirement type="package" version="2.6.6">trinity</requirement>
14 </requirements> 14 </requirements>
15 <command detect_errors="exit_code"> 15 <command detect_errors="exit_code">
16 <![CDATA[ 16 <![CDATA[
17 python $__tool_directory__/ctat_analyze_differential_expression.py $Counts_matrix $TMM_Matrix_FPKM $Pvalue $Cvalue 17 python $__tool_directory__/ctat_analyze_differential_expression.py $EdgeRTarGz $Counts_matrix $Pvalue $Cvalue
18 ]]> 18 ]]>
19 </command> 19 </command>
20 <inputs> 20 <inputs>
21 <param name="EdgeRTarGz" label="EdgeR tar gz file" type="data" format="txt"/> 21 <param name="EdgeRTarGz" label="EdgeR tar gz file" type="data" format="txt"/>
22 <param name="Counts_matrix" label="Counts Matrix" type="data" format="tabular" /> 22 <param name="Counts_matrix" label="Counts Matrix" type="data" format="tabular" />
23 <param name="Pvalue" label="P-value" value="0.05" type="float" /> 23 <param name="Pvalue" label="P-value" value="0.05" type="float" />
24 <param name="Cvalue" label="C-value" value="0" type="float" /> 24 <param name="Cvalue" label="C-value" value="0" type="float" />
25 25
26 </inputs> 26 </inputs>
27 <outputs> 27 <outputs>
28 <data format="data" name="diffExpr_matrix" label="${tool.name} on ${on_string}: Matrix" from_work_dir="diffExpr.matrix"/> 28 <data format="data" name="diffExpr_matrix" label="${tool.name} on ${on_string}: Matrix" from_work_dir="diffExpr.matrix"/>
29 <data format="data" name="diffExpr_correlation_matrix" label="${tool.name} on ${on_string}: Sample_Correlation_Matrix" from_work_dir="diffExpr.matrix.log2.sample_cor.dat"/> 29 <data format="data" name="diffExpr_correlation_matrix" label="${tool.name} on ${on_string}: Sample_Correlation_Matrix" from_work_dir="diffExpr.matrix.log2.sample_cor.dat"/>
30 <data format="data" name="diffExpr_correlation_matrix_pdf" label="${tool.name} on ${on_string}: Sample_Correlation_Matrix_PDF" from_work_dir="diffExpr.matrix.log2.sample_cor_matrix.pdf"/> 30 <data format="data" name="diffExpr_correlation_matrix_pdf" label="${tool.name} on ${on_string}: Sample_Correlation_Matrix_PDF" from_work_dir="diffExpr.matrix.log2.sample_cor_matrix.pdf"/>
31 <data format="data" name="Heatmap" label="${tool.name} on ${on_string}: Heatmap" from_work_dir="diffExpr.matrix.log2.centered.genes_vs_samples_heatmap.pdf"/> 31 <data format="data" name="Heatmap" label="${tool.name} on ${on_string}: Heatmap" from_work_dir="diffExpr.matrix.log2.centered.genes_vs_samples_heatmap.pdf"/>
32 </outputs> 32 </outputs>
33 <tests> 33 <tests>
34 <test> 34 <test>
35 <param name="EdgeRTarGz" value="Sp.edgeR.tar.gz" ftype="tar" /> 35 <param name="EdgeRTarGz" value="Sp.edgeR.tar.gz" ftype="tar" />
36 <param name="TMM_Matrix_FPKM" value="Sp.TMM.EXPR.matrix" /> 36 <param name="TMM_Matrix_FPKM" value="Sp.TMM.EXPR.matrix" />
37 <param name="Pvalue" value="0.05" /> 37 <param name="Pvalue" value="0.05" />
38 <param name="Cvalue" value="0.0" /> 38 <param name="Cvalue" value="0.0" />
39 39
40 <output name="diffExpr_matrix" > 40 <output name="diffExpr_matrix" >
41 <assert_contents> 41 <assert_contents>
42 <has_line_matching expression=".+" /> 42 <has_line_matching expression=".+" />
43 <has_line line="Sp_ds&#009;Sp_hs" /> 43 <has_line line="Sp_ds&#009;Sp_hs" />
44 <has_line_matching expression="TRINITY_DN.+" /> 44 <has_line_matching expression="TRINITY_DN.+" />
45 </assert_contents> 45 </assert_contents>
46 </output> 46 </output>
47 <output name="diffExpr_correlation_matrix" file="Sp.diffExpr.matrix.log2.sample_cor.dat" /> 47 <output name="diffExpr_correlation_matrix" file="Sp.diffExpr.matrix.log2.sample_cor.dat" />
48 <output name="diffExpr_correlation_matrix_pdf" > 48 <output name="diffExpr_correlation_matrix_pdf" >
49 <assert_contents> 49 <assert_contents>
50 <has_line_matching expression=".+" /> 50 <has_line_matching expression=".+" />
51 </assert_contents> 51 </assert_contents>
52 </output> 52 </output>
53 <output name="Heatmap" > 53 <output name="Heatmap" >
54 <assert_contents> 54 <assert_contents>
55 <has_line_matching expression=".+" /> 55 <has_line_matching expression=".+" />
56 </assert_contents> 56 </assert_contents>
57 </output> 57 </output>
58 58