# HG changeset patch
# User nanette
# Date 1377075076 14400
# Node ID 94b0fd035fec3397e24e45d2d4f0ca4bf8a132e9
# Parent a99218bd868fe3645c11cf459ea0748ede146e20
Deleted selected files
diff -r a99218bd868f -r 94b0fd035fec test_script_path.py
--- a/test_script_path.py Wed Aug 21 04:48:54 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,51 +0,0 @@
-"""
-@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 a99218bd868f -r 94b0fd035fec test_script_path.xml
--- a/test_script_path.xml Wed Aug 21 04:48:54 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,30 +0,0 @@
-
-
- script path
-
- SCRIPT_PATH
-
-
- test_script_path.py --input1 $input1 --output1 $output1 --myflag \$SCRIPT_PATH
-
-
-
-
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-
-
-
-
-
-
-**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 a99218bd868f -r 94b0fd035fec tool_dependencies.xml
--- a/tool_dependencies.xml Wed Aug 21 04:48:54 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,9 +0,0 @@
-
-
-
- $REPOSITORY_INSTALL_DIR
-
-
-
-
-