# HG changeset patch
# User nanette
# Date 1377083154 14400
# Node ID a303f3ffa15302f27e4b6f0ce2d81e3942ee4329
# Parent  b41fc3e15949574876803a63b9f1c87bf30989bd
Uploaded

diff -r b41fc3e15949 -r a303f3ffa153 test_script_path.py
--- a/test_script_path.py	Wed Aug 21 05:56:49 2013 -0400
+++ b/test_script_path.py	Wed Aug 21 07:05:54 2013 -0400
@@ -20,8 +20,11 @@
                       help="genes")
     parser.add_option("-o", "--output1", default=None, dest="output1", 
                       help="star genes")
+    parser.add_option("-p", "--output2", default=None, dest="output2", 
+                      help="plot")
     parser.add_option("-m", "--myflag", default=None, dest="myflag", 
                       help="star genes")
+    
     (options, args) = parser.parse_args()
 
     try:
@@ -47,6 +50,31 @@
     outfile.write("--- TEST ---" + "\n")
     outfile.close()
     
+    ##########################################################
+    
+    # Create temp direcotry
+    tempdir = tempfile.mkdtemp()
+    fixdir = options.myflag
+
+    # copy INPUT file to the temp directory
+    # create R script => save in temp directory
+    # generate new header 
+    new_script = open(tempdir+"/new_script.r","w")
+    header = "setwd(\"%s\")" %tempdir
+    new_script.write(header+"\n")
+    
+    # add script body
+    script = open(fixdir+"/r_plot.r","r")
+    for line in script:
+        new_script.write(line.strip()+"\n")
+    new_script.close()
+    
+    # run R script from temp directory
+    s = "R CMD BATCH %s/new_script.r out.txt" %tempdir
+    subprocess.call(s, shell=True)
+    
+    os.system("mv %s/plot.pdf %s" %(tempdir,options.output2))
+       
     ##############################################
     
 if __name__=="__main__": 
diff -r b41fc3e15949 -r a303f3ffa153 test_script_path.xml
--- a/test_script_path.xml	Wed Aug 21 05:56:49 2013 -0400
+++ b/test_script_path.xml	Wed Aug 21 07:05:54 2013 -0400
@@ -5,7 +5,7 @@
 		<requirement type="set_environment">SCRIPT_PATH</requirement>
 	</requirements>
 	<command interpreter="python">
-		test_script_path.py --input1 $input1 --output1 $output1 --myflag \$SCRIPT_PATH
+		test_script_path.py --input1 $input1 --output1 $output1 --output2 $output2 --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>
@@ -13,6 +13,7 @@
         </inputs>
 	<outputs>
 		<data format="tabular" name="output1" />
+		<data format="pdf" name="output2" />
 	</outputs>
 	<requirements>
 	</requirements>