Mercurial > repos > fubar > rg_gsea

diff rgGSEA/test-data/gentestdata.sh~ @ 4:89e89b70a867 draft default tip

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author fubar
date Sun, 09 Jun 2013 23:09:34 -0400
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rgGSEA/test-data/gentestdata.sh~	Sun Jun 09 23:09:34 2013 -0400
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+#!/bin/bash
+# generate test data for rgGSEA
+# ross lazarus June 2013 
+# adjust gseajar_path !
+GSEAJAR_PATH=/home/rlazarus/galaxy-central/tool_dependency_dir/gsea_jar/2.0.12/fubar/rg_gsea_test/8e291f464aa0/jars/gsea2-2.0.12.jar
+python ../rgGSEA.py --input_tab "gsea_test_DGE.xls"  --adjpvalcol "5" --signcol "2" --idcol "1" --outhtml "gseatestout.html" --input_name "gsea_test" --setMax "500" --setMin "15" --nPerm "10" --plotTop "20" --gsea_jar "$GSEAJAR_PATH" --output_dir "gseatestout" --mode "Max_probe" --title "GSEA test" --builtin_gmt "gseatestdata.gmt"
+
+