changeset 6:066c5504de31 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test_script_path.py	Wed Aug 21 04:51:37 2013 -0400
@@ -0,0 +1,51 @@
+"""
+@summary: GO enrichment analysis (hotspots)
+@author: [e-mail]
+@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__()

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test_script_path.xml	Wed Aug 21 04:51:37 2013 -0400
@@ -0,0 +1,30 @@
+<tool id="script_path" name="nanettetest3" 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>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Wed Aug 21 04:51:37 2013 -0400
@@ -0,0 +1,5 @@
+<tool_dependency>
+     <set_environment version="1.0">
+        <environment_variable name="SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>
+    </set_environment>
+</tool_dependency>