diff bismark_methylation_extractor.xml @ 4:243e8f9fb75b draft

Uploaded

--- a/bismark_methylation_extractor.xml	Mon Apr 14 16:43:14 2014 -0400
+++ b/bismark_methylation_extractor.xml	Mon Feb 09 18:24:41 2015 -0500
@@ -9,11 +9,12 @@
     </requirements>
     <parallelism method="basic"></parallelism>
     <command interpreter="python">
+<![CDATA[
         bismark_methylation_extractor.py
 
         --infile $input
 
-        --bismark_path \$SCRIPT_PATH
+        #--bismark_path \$SCRIPT_PATH
 
         #if $singlePaired.sPaired == "single":
             --single-end
@@ -78,6 +79,7 @@
         ## end compress
         #end if
 
+]]>
     </command>
     <inputs>
         <!-- Input Parameters -->
@@ -187,11 +189,12 @@
     </tests>
 
     <help>
+<![CDATA[
 
 **What it does**
 
 The following is a brief description of all options to control the Bismark_
-methylation extractor. The script reads in a bisulfite read alignment results file 
+methylation extractor. The script reads in a bisulfite read alignment results file
 produced by the Bismark bisulfite mapper and extracts the methylation information
 for individual cytosines. This information is found in the methylation call field
 which can contain the following characters:
@@ -285,8 +288,8 @@
 
 Output::
 
-  --comprehensive          Specifying this option will merge all four possible strand-specific 
-                           methylation info into context-dependent output files. The default 
+  --comprehensive          Specifying this option will merge all four possible strand-specific
+                           methylation info into context-dependent output files. The default
                            contexts are:
                             - CpG context
                             - CHG context
@@ -301,5 +304,6 @@
                            this script.
 
 
+]]>
   </help>
 </tool>