# HG changeset patch
# User alenail
# Date 1460670312 14400
# Node ID d7baa700a9306cb22cba515aead0f141e8ac83fd
# Parent  01748da366c35a32da4ed7a28243c218087c1542
Uploaded

diff -r 01748da366c3 -r d7baa700a930 pieplot_macs/pieplots_macs.py
--- a/pieplot_macs/pieplots_macs.py	Thu Apr 14 17:40:18 2016 -0400
+++ b/pieplot_macs/pieplots_macs.py	Thu Apr 14 17:45:12 2016 -0400
@@ -41,7 +41,16 @@
         chrom = words[2]
 
 
-        if not macsFlag:
+        if macsFlag:
+            print "MacsFlag off"
+            start = int(words[3])-1
+            dist = abs(int(words[12]))
+            maptype = words[14]
+            if maptype == 'gene':
+                maptype = words[15]
+
+        else:
+            print "macsFlag on"
             try:
                 start = int(words[3])
                 dist = abs(int(words[15]))
@@ -51,13 +60,8 @@
             except:
                 pass
 
-        else:
-            start = int(words[3])-1
-            dist = abs(int(words[12]))
-            maptype = words[14]
-            if maptype == 'gene':
-                maptype = words[15]
-
+        print "dist:"
+        print dist
 
         if chrom not in peaks:
             #new chrom
@@ -120,6 +124,8 @@
 
     args=parser.parse_args()
 
+    print args.MACS
+
     map_peaks(args.genefile, args.peakfile, args.outfile, args.MACS)
 
 
diff -r 01748da366c3 -r d7baa700a930 pieplot_macs/pieplots_macs.xml
--- a/pieplot_macs/pieplots_macs.xml	Thu Apr 14 17:40:18 2016 -0400
+++ b/pieplot_macs/pieplots_macs.xml	Thu Apr 14 17:45:12 2016 -0400
@@ -18,5 +18,5 @@
   <outputs>
     <data name="out" format="pdf" hidden="false" />
   </outputs>
-  <help>help</help>
+  <help></help>
 </tool>