Mercurial > repos > fubar > differential_count_models

annotate test-data/gentestdata.sh @ 111:9f2e0ec3e826 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author fubar
date Wed, 22 Oct 2014 23:37:31 -0400
parents c0fa3dde02d9
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
25
c0fa3dde02d9 Uploaded
fubar
parents:
diff changeset
1 #!/bin/bash
c0fa3dde02d9 Uploaded
fubar
parents:
diff changeset
2 # generate test data for rgGSEA
c0fa3dde02d9 Uploaded
fubar
parents:
diff changeset
3 # ross lazarus June 2013
c0fa3dde02d9 Uploaded
fubar
parents:
diff changeset
4 # adjust gseajar_path !
c0fa3dde02d9 Uploaded
fubar
parents:
diff changeset
5 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
c0fa3dde02d9 Uploaded
fubar
parents:
diff changeset
6 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"
c0fa3dde02d9 Uploaded
fubar
parents:
diff changeset
7 --title "GSEA test" --builtin_gmt "gseatestdata.gmt"
c0fa3dde02d9 Uploaded
fubar
parents:
diff changeset
8
c0fa3dde02d9 Uploaded
fubar
parents:
diff changeset
9