Mercurial > repos > lldelisle > revertr2orientationinbam

changeset 1:21ddefab2e4f draft default tip

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planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/revertR2orientationInBam commit 49a42d0e75d6ae7faa3ce399524157c35546fbaa
author lldelisle
date Thu, 20 Oct 2022 10:51:18 +0000
parents 05aa21d39189
children
files revertR2orientationInBam.xml
diffstat 1 files changed, 6 insertions(+), 4 deletions(-) [+]
line wrap: on
line diff
--- a/revertR2orientationInBam.xml	Wed Oct 19 08:50:18 2022 +0000
+++ b/revertR2orientationInBam.xml	Thu Oct 20 10:51:18 2022 +0000
@@ -1,7 +1,8 @@
-<tool id="revertR2orientationInBam" name="revertR2orientationInBam" version="0.0.1" profile="16.04">
+<tool id="revertR2orientationInBam" name="revertR2orientationInBam" version="0.0.2" profile="16.04">
   <description> Revert the mapped orientation of R2 mates in a bam.</description>
   <requirements>
-    <requirement type="package" version="1.9">samtools</requirement>
+    <requirement type="package" version="1.16.1">samtools</requirement>
+    <requirement type="package" version="5.1.0">gawk</requirement>
   </requirements>
   <stdio>
     <!-- Anything other than zero is an error -->
@@ -13,7 +14,8 @@
   </stdio>
   <command>
 <![CDATA[
-        bash $__tool_directory__/revertR2orientationInBam.sh $input $output
+        set -o pipefail;
+        bash $__tool_directory__/revertR2orientationInBam.sh '$input' '$output'
 ]]>
   </command>
   <inputs>
@@ -27,7 +29,7 @@
   <tests>
     <test>
       <param name="input" value="input.sam"/>
-      <output name="output" file="output.bam" ftype="bam"/>
+      <output name="output" file="output.bam" ftype="bam" lines_diff="2"/>
     </test>
   </tests>  
   <help>