Mercurial > repos > iuc > trinity_run_de_analysis
diff run_de_analysis.xml @ 9:0f5bfda8f46c draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
| author | iuc |
|---|---|
| date | Thu, 14 Jun 2018 03:10:09 -0400 |
| parents | 2a30d7dfe8de |
| children | 118308b20d2c |
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--- a/run_de_analysis.xml Mon Jan 22 11:25:10 2018 -0500 +++ b/run_de_analysis.xml Thu Jun 14 03:10:09 2018 -0400 @@ -1,16 +1,16 @@ -<tool id="trinity_run_de_analysis" name="Differential expression analysis" version="@WRAPPER_VERSION@.0"> +<tool id="trinity_run_de_analysis" name="Differential expression analysis" version="@WRAPPER_VERSION@"> <description>using a Trinity assembly</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"> - <requirement type="package" version="3.16.5">bioconductor-edger</requirement> - <requirement type="package" version="3.30.13">bioconductor-limma</requirement> - <requirement type="package" version="1.14.1">bioconductor-deseq2</requirement> + <requirement type="package" version="3.20.7">bioconductor-edger</requirement> + <requirement type="package" version="3.34.9">bioconductor-limma</requirement> + <requirement type="package" version="1.18.1">bioconductor-deseq2</requirement> </expand> <command detect_errors="aggressive"><![CDATA[ - ln -f -s "${matrix}" "input.matrix" + ln -f -s '${matrix}' "input.matrix" && @@ -18,7 +18,7 @@ --matrix "input.matrix" - --samples_file "${samples}" + --samples_file '${samples}' --method ${method_choice.method} @@ -103,7 +103,7 @@ </output_collection> <output_collection name="PDF_results"> <element name="input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.MA_n_Volcano" compare="sim_size" delta="100" file="count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.MA_n_Volcano.pdf"/> - <element name="input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.MA_n_Volcano" compare="sim_size" delta="100" file="count/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.MA_n_Volcano.pdf"/> + <element name="input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.MA_n_Volcano" compare="sim_size" delta="200" file="count/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.MA_n_Volcano.pdf"/> <element name="input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.MA_n_Volcano" compare="sim_size" delta="100" file="count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.MA_n_Volcano.pdf"/> </output_collection> </test>