Mercurial > repos > dktanwar > test_fgsea_1

changeset 1:91eed1b5c009 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author dktanwar
date Tue, 12 Dec 2017 21:19:55 -0500
parents b75ceb945966
children 9e75d29c2409
files 16_fgsea/GSEA.xml
diffstat 1 files changed, 10 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- a/16_fgsea/GSEA.xml	Mon Dec 11 09:52:26 2017 -0500
+++ b/16_fgsea/GSEA.xml	Tue Dec 12 21:19:55 2017 -0500
@@ -1,6 +1,14 @@
 <tool id="GSEA" name="Gene Set Enrichment Analysis" version="0.1.0">
-  <command detect_errors="exit_code"><![CDATA[
-        Rscript $__tool_directory__/GSEA.R --input1 $Ranked_list --input2 $Pathway_database --output $output
+  
+<requirements>
+  <requirement type="package" version="1.4.0">bioconductor-fgsea</requirement>
+  <requirement type="package" version="1.20.0">r-getopt</requirement>
+  <!-- required for alpha function used with plotMD -->
+  <requirement type="package" version="0.12.13">r-rcpp</requirement>
+</requirements>
+
+<command detect_errors="exit_code"><![CDATA[
+        Rscript '$__tool_directory__/GSEA.R' --input1 '$Ranked_list' --input2 '$Pathway_database' --output '$output'
     ]]></command>
   <inputs>
     <param type="data" name="Ranked_list" format="txt" />