# HG changeset patch
# User bgruening
# Date 1384520268 18000
# Node ID a22ccc261bb3a0ade58559322e0cdb9f63e5a90e
# Parent  d957e25e18a321e6a891bbd8ea10c59f4e18f35c
Uploaded

diff -r d957e25e18a3 -r a22ccc261bb3 bamCorrelate.xml
--- a/bamCorrelate.xml	Thu Nov 14 16:39:18 2013 -0500
+++ b/bamCorrelate.xml	Fri Nov 15 07:57:48 2013 -0500
@@ -33,7 +33,7 @@
 
         #if $mode.modeOpt == "bins":
             --binSize '$mode.binSize'
-            --numberOfSamples '$modenumberOfSamples'
+            --numberOfSamples '$mode.numberOfSamples'
         #else:
             --BED $mode.region_file
         #end if
diff -r d957e25e18a3 -r a22ccc261bb3 bigwigCompare.xml
--- a/bigwigCompare.xml	Thu Nov 14 16:39:18 2013 -0500
+++ b/bigwigCompare.xml	Fri Nov 15 07:57:48 2013 -0500
@@ -29,6 +29,12 @@
 
         #end if
     </command>
+    <stdio>
+        <exit_code range="1:" />
+        <exit_code range=":-1" />
+        <regex match="Error:" />
+        <regex match="EXception:" />
+    </stdio>
     <inputs>
         <param name="bigwigFile1" format="bigwig" type="data" label="Treatment bigwig file" />
         <param name="bigwigFile2" format="bigwig" type="data" label="Input bigwig file" />
diff -r d957e25e18a3 -r a22ccc261bb3 deepTools_macros.xml
--- a/deepTools_macros.xml	Thu Nov 14 16:39:18 2013 -0500
+++ b/deepTools_macros.xml	Fri Nov 15 07:57:48 2013 -0500
@@ -40,7 +40,7 @@
     <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
     <macro name="requirements">
         <requirements>
-            <requirement type="package" version="1.5.1_91b873c095bb4ca44da99e57d8b49784508aa98b">deepTools</requirement>
+            <requirement type="package" version="1.5.1_323fa6bf083c9d40e5092a6364a4ab8fee57507a">deepTools</requirement>
             <requirement type="package" version="0.1">ucsc_tools</requirement>
             <requirement type="package" version="1.7.1">numpy</requirement>
             <requirement type="package" version="0.7.6">pysam</requirement>
diff -r d957e25e18a3 -r a22ccc261bb3 tool_dependencies.xml
--- a/tool_dependencies.xml	Thu Nov 14 16:39:18 2013 -0500
+++ b/tool_dependencies.xml	Fri Nov 15 07:57:48 2013 -0500
@@ -54,7 +54,7 @@
          <readme>The tools downloaded by this dependency definition are free for academic use. TODO: UCSC tools are only available with their latest version. That is not good for reproducibility.</readme>
      </package>
 
-    <package name="deepTools" version="1.5.1_91b873c095bb4ca44da99e57d8b49784508aa98b">
+    <package name="deepTools" version="1.5.1_323fa6bf083c9d40e5092a6364a4ab8fee57507a">
         <install version="1.0">
             <actions>
                 <!-- populate the environment variables from the dependend repos -->
@@ -64,7 +64,7 @@
                     </repository>
                 </action>
                 <action type="shell_command">git clone --recursive https://github.com/fidelram/deepTools.git</action>
-                <action type="shell_command">git reset --hard 91b873c095bb4ca44da99e57d8b49784508aa98b</action>
+                <action type="shell_command">git reset --hard 323fa6bf083c9d40e5092a6364a4ab8fee57507a</action>
                 <action type="make_directory">$INSTALL_DIR/lib/python</action>
                 <action type="shell_command">
                     export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp;