# HG changeset patch
# User yhoogstrate
# Date 1447362514 18000
# Node ID 9a3254bb8c4eeab0772be7a53ec8a54b366c9ffe
# Parent  c8fbdbd346ea22d343916bf928a40cd684604bd7
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 2a0f8a26551929e52f6aea1d109b8a3bda81af8b-dirty

diff -r c8fbdbd346ea -r 9a3254bb8c4e crossmap.xml
--- a/crossmap.xml	Thu Nov 12 15:55:37 2015 -0500
+++ b/crossmap.xml	Thu Nov 12 16:08:34 2015 -0500
@@ -14,7 +14,8 @@
     
     <version_command>python $CROSSMAP_ROOT_DIR/bin/CrossMap.py 2&gt;&amp;1 | head -n 1 | grep -E --only-matching 'CrossMap.*'</version_command>
     
-    <command><!-- First line of CrossMap has hardcoded "#!/usr/bin/python". This makes use of Galaxy's python: -->
+    <!-- First line of CrossMap has hardcoded "#!/usr/bin/python". This makes use of Galaxy's python: -->
+    <command><![CDATA[
         python \$CROSSMAP_ROOT_DIR/bin/CrossMap.py
             ${multiple.input_format.replace("sam","bam")}
             
@@ -53,7 +54,7 @@
                 && mv "${output}.bw" "$output"
                 && mv "${output}.sorted.bgr" "$output2"
             #end if
-    </command>
+    ]]></command>
 
     <inputs>
         <conditional name="multiple">