# HG changeset patch
# User nanette
# Date 1377074441 14400
# Node ID 541625ea0e428c9d62d21626598624f47844b0bf
# Parent  bfe8aba3fd1cd1dd290f227f657e290b9006d640
Deleted selected files

diff -r bfe8aba3fd1c -r 541625ea0e42 test_script_path.py
--- a/test_script_path.py	Wed Aug 21 04:24:49 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 bfe8aba3fd1c -r 541625ea0e42 test_script_path.xml
--- a/test_script_path.xml	Wed Aug 21 04:24:49 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,30 +0,0 @@
-<tool id="script_path" name="Test" version="1.0.0">
-
-	<description>script path</description>
-	<requirements>
-		<requirement type="set_environment">SCRIPT_PATH</requirement>
-	</requirements>
-	<command interpreter="python">
-		test_script_path.py --input1 $input1 --output1 $output1 --myflag \$SCRIPT_PATH
-	</command>
-        <inputs>
-            <param label="Gene Universe file" name="input1" type="data" format="tabular" help="A tabular file with the full set of genes from the study (gene universe)"></param>
-
-        </inputs>
-	<outputs>
-		<data format="tabular" name="output1" />
-	</outputs>
-	<requirements>
-	</requirements>
-	<tests>
-          <test>
-          </test>
-	</tests>
-	<help>
-		
-**What it does**
-
-This tool uses the topGO R package to determine the enriched GO terms, for one or more gene lists simultaneously. 
-
-        </help>
-</tool>
diff -r bfe8aba3fd1c -r 541625ea0e42 tool_dependencies.xml
--- a/tool_dependencies.xml	Wed Aug 21 04:24:49 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,5 +0,0 @@
-<tool_dependency>
-    <set_environment version="1.0">
-        <environment_variable name="SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>
-    </set_environment>
-</tool_dependency>