Mercurial > repos > bgruening > bismark

diff bismark_methylation_extractor.xml @ 22:047eb877b6f0 draft

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Uploaded
author iuc
date Sun, 28 Jun 2015 07:23:35 -0400
parents 507901240749
children
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--- a/bismark_methylation_extractor.xml	Wed Feb 11 16:21:27 2015 -0500
+++ b/bismark_methylation_extractor.xml	Sun Jun 28 07:23:35 2015 -0400
@@ -1,11 +1,10 @@
-<tool id="bismark_methylation_extractor" name="Bismark Meth. Extractor" version="0.10.2">
+<tool id="bismark_methylation_extractor" name="Bismark Meth. Extractor" version="0.14.3">
     <!-- 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="2.1.0">bowtie2</requirement>
+        <requirement type="package" version="1.0.0">bowtie</requirement>
+        <requirement type="package" version="2.2.5">bowtie2</requirement>
     </requirements>
     <parallelism method="basic"></parallelism>
     <command interpreter="python">
@@ -14,7 +13,7 @@
 
         --infile $input
 
-        --bismark_path \$SCRIPT_PATH
+        --bismark_path $__tool_directory__
 
         #if $singlePaired.sPaired == "single":
             --single-end