Mercurial > repos > trinity_ctat > analyze_differential_expression
annotate analyze_diff_exp.xml @ 9:c556f5136cf2 draft
Adding requirement to analyze_diff_exp.
| author | trinity_ctat |
|---|---|
| date | Fri, 06 Oct 2017 13:59:16 -0400 |
| parents | f51625f25d56 |
| children | da02ebc6a91c |
| rev | line source |
|---|---|
|
7
f51625f25d56
Adding profile info and exit code behavior. Making version numbers consistent. Upping test number.
trinity_ctat
parents:
6
diff
changeset
|
1 <tool id="Analyze_Diff_Exp" name="Analyze_Differential_Expression" version="1.0.0" profile="17.05"> |
| 0 | 2 |
| 3 <description>Analyze differential expression</description> | |
| 4 <requirements> | |
| 5 <requirement type="package" version="2.7">python</requirement> | |
| 6 | 6 <requirement type="package" version="1.3.0">rsem</requirement> |
| 9 | 7 <requirement type="package" version="3">bioconductor-edger</requirement> |
| 0 | 8 <requirement type="package">trinity</requirement> |
| 9 </requirements> | |
|
7
f51625f25d56
Adding profile info and exit code behavior. Making version numbers consistent. Upping test number.
trinity_ctat
parents:
6
diff
changeset
|
10 <command detect_errors="exit_code"> |
| 0 | 11 <![CDATA[ |
| 12 python $__tool_directory__/analyze_diff_exp_wrapper.py $EdgeRTarGz $TMM_Matrix_FPKM $Pvalue $Cvalue | |
| 13 ]]> | |
| 14 </command> | |
| 15 <inputs> | |
|
1
54f173578868
Changing input formats for analyze differential expression.
trinity_ctat
parents:
0
diff
changeset
|
16 <param name="EdgeRTarGz" label="EdgeR tar gz file" type="data" format="txt"/> |
|
54f173578868
Changing input formats for analyze differential expression.
trinity_ctat
parents:
0
diff
changeset
|
17 <param name="TMM_Matrix_FPKM" label="TMM Normalized FPKM matrix" type="data" format="tabular" /> |
| 0 | 18 <param name="Pvalue" label="P-value" value="0.05" type="float" /> |
| 19 <param name="Cvalue" label="C-value" value="0" type="float" /> | |
| 20 | |
| 21 </inputs> | |
| 22 <outputs> | |
| 23 <data format="data" name="diffExpr_matrix" label="${tool.name} on ${on_string}: Matrix" from_work_dir="diffExpr.matrix"/> | |
| 24 <data format="data" name="diffExpr_correlation_matrix" label="${tool.name} on ${on_string}: Sample_Correlation_Matrix" from_work_dir="diffExpr.matrix.log2.sample_cor.dat"/> | |
| 25 <data format="data" name="diffExpr_correlation_matrix_pdf" label="${tool.name} on ${on_string}: Sample_Correlation_Matrix_PDF" from_work_dir="diffExpr.matrix.log2.sample_cor_matrix.pdf"/> | |
| 26 <data format="data" name="Heatmap" label="${tool.name} on ${on_string}: Heatmap" from_work_dir="diffExpr.matrix.log2.centered.genes_vs_samples_heatmap.pdf"/> | |
| 27 </outputs> | |
| 28 <tests> | |
| 29 <test> | |
| 30 <param name="EdgeRTarGz" value="Sp.edgeR.tar.gz" ftype="tar" /> | |
| 31 <param name="TMM_Matrix_FPKM" value="Sp.TMM.EXPR.matrix" /> | |
| 32 <param name="Pvalue" value="0.05" /> | |
| 33 <param name="Cvalue" value="0.0" /> | |
| 34 | |
| 35 <output name="diffExpr_matrix" > | |
| 36 <assert_contents> | |
| 37 <has_line_matching expression=".+" /> | |
| 38 <has_line line="Sp_ds	Sp_hs" /> | |
| 39 <has_line_matching expression="TRINITY_DN.+" /> | |
| 40 </assert_contents> | |
| 41 </output> | |
| 42 <output name="diffExpr_correlation_matrix" file="Sp.diffExpr.matrix.log2.sample_cor.dat" /> | |
| 43 <output name="diffExpr_correlation_matrix_pdf" > | |
| 44 <assert_contents> | |
| 45 <has_line_matching expression=".+" /> | |
| 46 </assert_contents> | |
| 47 </output> | |
| 48 <output name="Heatmap" > | |
| 49 <assert_contents> | |
| 50 <has_line_matching expression=".+" /> | |
| 51 </assert_contents> | |
| 52 </output> | |
| 53 | |
| 54 </test> | |
| 55 </tests> | |
| 56 <help> | |
| 57 .. class:: infomark | |
| 58 | |
| 59 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). | |
| 60 | |
| 61 If you are following the Trinity RNA-seq protocol please go here_ for a galaxy tool walk through or the Nature Protocols paper_. | |
| 62 | |
| 63 .. _here: https://github.com/trinityrnaseq/GalaxyTrinityProtocol/wiki | |
| 64 .. _paper: http://www.nature.com/nprot/journal/v8/n8/full/nprot.2013.084.html | |
| 65 </help> | |
| 66 | |
| 67 <citations> | |
| 68 <citation type="doi">10.1038/nbt.1883</citation> | |
| 69 </citations> | |
| 70 | |
| 71 </tool> |