Mercurial > repos > trinity_ctat > analyze_differential_expression
annotate analyze_diff_exp.xml @ 5:dab3b085f23d draft
Adding more debugging statements.
| author | trinity_ctat |
|---|---|
| date | Mon, 02 Oct 2017 14:39:03 -0400 |
| parents | 54f173578868 |
| children | 9b2226f8c2fe |
| rev | line source |
|---|---|
| 0 | 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 $Cvalue | |
| 11 ]]> | |
| 12 </command> | |
| 13 <inputs> | |
|
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54f173578868
Changing input formats for analyze differential expression.
trinity_ctat
parents:
0
diff
changeset
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14 <param name="EdgeRTarGz" label="EdgeR tar gz file" type="data" format="txt"/> |
|
54f173578868
Changing input formats for analyze differential expression.
trinity_ctat
parents:
0
diff
changeset
|
15 <param name="TMM_Matrix_FPKM" label="TMM Normalized FPKM matrix" type="data" format="tabular" /> |
| 0 | 16 <param name="Pvalue" label="P-value" value="0.05" type="float" /> |
| 17 <param name="Cvalue" label="C-value" value="0" type="float" /> | |
| 18 | |
| 19 </inputs> | |
| 20 <outputs> | |
| 21 <data format="data" name="diffExpr_matrix" label="${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	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> |