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Adding analyze differential expression.
author trinity_ctat
date Fri, 29 Sep 2017 14:36:11 -0400
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children 54f173578868
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-1:000000000000 0:5bbc80dbfb5f
1 <tool id="Analyze_Diff_Exp" name="Analyze_Differential_Expression" version="0.0.1">
2
3 <description>Analyze differential expression</description>
4 <requirements>
5 <requirement type="package" version="2.7">python</requirement>
6 <requirement type="package">trinity</requirement>
7 </requirements>
8 <command>
9 <![CDATA[
10 python $__tool_directory__/analyze_diff_exp_wrapper.py $EdgeRTarGz $TMM_Matrix_FPKM $Pvalue $Cvalue
11 ]]>
12 </command>
13 <inputs>
14 <param name="EdgeRTarGz" label="EdgeR tar gz file" type="data" format="file"/>
15 <param name="TMM_Matrix_FPKM" label="TMM Normalized FPKM matrix" type="data" format="file" />
16 <param name="Pvalue" label="P-value" value="0.05" type="float" />
17 <param name="Cvalue" label="C-value" value="0" type="float" />
18
19 </inputs>
20 <outputs>
21 <data format="data" name="diffExpr_matrix" label="${tool.name} on ${on_string}: Matrix" from_work_dir="diffExpr.matrix"/>
22 <data format="data" name="diffExpr_correlation_matrix" label="${tool.name} on ${on_string}: Sample_Correlation_Matrix" from_work_dir="diffExpr.matrix.log2.sample_cor.dat"/>
23 <data format="data" name="diffExpr_correlation_matrix_pdf" label="${tool.name} on ${on_string}: Sample_Correlation_Matrix_PDF" from_work_dir="diffExpr.matrix.log2.sample_cor_matrix.pdf"/>
24 <data format="data" name="Heatmap" label="${tool.name} on ${on_string}: Heatmap" from_work_dir="diffExpr.matrix.log2.centered.genes_vs_samples_heatmap.pdf"/>
25 </outputs>
26 <tests>
27 <test>
28 <param name="EdgeRTarGz" value="Sp.edgeR.tar.gz" ftype="tar" />
29 <param name="TMM_Matrix_FPKM" value="Sp.TMM.EXPR.matrix" />
30 <param name="Pvalue" value="0.05" />
31 <param name="Cvalue" value="0.0" />
32
33 <output name="diffExpr_matrix" >
34 <assert_contents>
35 <has_line_matching expression=".+" />
36 <has_line line="Sp_ds&#009;Sp_hs" />
37 <has_line_matching expression="TRINITY_DN.+" />
38 </assert_contents>
39 </output>
40 <output name="diffExpr_correlation_matrix" file="Sp.diffExpr.matrix.log2.sample_cor.dat" />
41 <output name="diffExpr_correlation_matrix_pdf" >
42 <assert_contents>
43 <has_line_matching expression=".+" />
44 </assert_contents>
45 </output>
46 <output name="Heatmap" >
47 <assert_contents>
48 <has_line_matching expression=".+" />
49 </assert_contents>
50 </output>
51
52 </test>
53 </tests>
54 <help>
55 .. class:: infomark
56
57 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).
58
59 If you are following the Trinity RNA-seq protocol please go here_ for a galaxy tool walk through or the Nature Protocols paper_.
60
61 .. _here: https://github.com/trinityrnaseq/GalaxyTrinityProtocol/wiki
62 .. _paper: http://www.nature.com/nprot/journal/v8/n8/full/nprot.2013.084.html
63 </help>
64
65 <citations>
66 <citation type="doi">10.1038/nbt.1883</citation>
67 </citations>
68
69 </tool>