# HG changeset patch
# User nanette
# Date 1377074781 14400
# Node ID 6c839f8050f1c12b5d76db809a26703698b43137
# Parent 541625ea0e428c9d62d21626598624f47844b0bf
Uploaded
diff -r 541625ea0e42 -r 6c839f8050f1 test_script_path.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test_script_path.py Wed Aug 21 04:46:21 2013 -0400
@@ -0,0 +1,51 @@
+"""
+@summary: GO enrichment analysis (hotspots)
+@author: nanette.coetzer@gmail.com
+@version 5
+
+"""
+import optparse, sys
+import subprocess
+import tempfile
+import os, re
+
+def stop_err( msg ):
+ sys.stderr.write( "%s\n" % msg )
+ sys.exit()
+
+def __main__():
+ #Parse Command Line
+ parser = optparse.OptionParser()
+ parser.add_option("-i", "--input1", default=None, dest="input1",
+ help="genes")
+ parser.add_option("-o", "--output1", default=None, dest="output1",
+ help="star genes")
+ parser.add_option("-m", "--myflag", default=None, dest="myflag",
+ help="star genes")
+ (options, args) = parser.parse_args()
+
+ try:
+ open(options.input1, "r").close()
+ except TypeError, e:
+ stop_err("You need to supply the Gene Universe file:\n" + str(e))
+ except IOError, e:
+ stop_err("Can not open the Gene Universe file:\n" + str(e))
+
+
+ ##########################################################
+
+ infile = open(options.input1,"r")
+ inlist = []
+ for line in infile:
+ inlist.append(line.strip())
+ infile.close()
+ outfile = open(options.output1,"w")
+ for l in inlist:
+ outfile.write("* "+str(l)+"\n")
+ outfile.write(options.myflag + "\n")
+ outfile.close()
+
+ ##############################################
+
+if __name__=="__main__":
+ __main__()
diff -r 541625ea0e42 -r 6c839f8050f1 test_script_path.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test_script_path.xml Wed Aug 21 04:46:21 2013 -0400
@@ -0,0 +1,30 @@
+
+
+ script path
+
+ SCRIPT_PATH
+
+
+ test_script_path.py --input1 $input1 --output1 $output1 --myflag \$SCRIPT_PATH
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+**What it does**
+
+This tool uses the topGO R package to determine the enriched GO terms, for one or more gene lists simultaneously.
+
+
+
diff -r 541625ea0e42 -r 6c839f8050f1 tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Wed Aug 21 04:46:21 2013 -0400
@@ -0,0 +1,12 @@
+
+
+
+ $REPOSITORY_INSTALL_DIR
+
+
+
+
+
+ $REPOSITORY_INSTALL_DIR
+
+