diff bismark_methylation_extractor.xml @ 18:862fb59a9a25 draft

Uploaded

--- a/bismark_methylation_extractor.xml	Sun Feb 24 14:49:36 2013 -0500
+++ b/bismark_methylation_extractor.xml	Mon Apr 14 16:42:38 2014 -0400
@@ -1,11 +1,11 @@
-<tool id="bismark_methylation_extractor" name="Bismark" version="0.7.7.2">
-    <!-- Wrapper compatible with Bismark version 0.7.7 -->
-    <description>methylation extractor</description>
+<tool id="bismark_methylation_extractor" name="Bismark Meth. Extractor" version="0.10.1">
+    <!-- Wrapper compatible with Bismark version 0.10 -->
+    <description>Reports on methylation status of reads mapped by Bismark</description>
     <!--<version_command>bismark_methylation_extractor version</version_command>-->
     <requirements>
         <requirement type="set_environment">SCRIPT_PATH</requirement>
         <requirement type="package" version="0.12.8">bowtie</requirement>
-        <requirement type="package" version="2.0.0-beta7">bowtie2</requirement>
+        <requirement type="package" version="2.1.0">bowtie2</requirement>
     </requirements>
     <parallelism method="basic"></parallelism>
     <command interpreter="python">
@@ -19,7 +19,7 @@
             --single-end
         #else:
             --paired-end
-            $no_overlap
+            $singlePaired.no_overlap
         #end if
 
         #if str($ignore_bps) != "0":
@@ -81,7 +81,7 @@
     </command>
     <inputs>
         <!-- Input Parameters -->
-        <param name="input" type="data" format="sam" label="SAM file from Bismark bisulfid mapper" />
+        <param name="input" type="data" format="sam,bam" label="SAM/BAM file from Bismark bisulfite mapper" />
         <conditional name="singlePaired">
             <param name="sPaired" type="select" label="Is this library mate-paired?">
               <option value="single">Single-end</option>
@@ -92,7 +92,6 @@
                 <param name="no_overlap" type="boolean" truevalue="--no-overlap" falsevalue="" checked="False" label="This option avoids scoring overlapping methylation calls twice, in case of overlapping read one and read two" help="" />
             </when>
         </conditional>
-
        <param name="ignore_bps" type="integer" value="0" label="Ignore the first N bp when processing the methylation call string" />
        <param name="comprehensive" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Merge all four possible strand-specific methylation info
 into context-dependent output files" help="" />