Mercurial > repos > mvdbeek > bam_readtagger

diff bam_readtagger.xml @ 20:03415763c62c draft

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planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 62ae1272b167d6bc411f95fb324df9f6286f8450-dirty
author mvdbeek
date Wed, 19 Apr 2017 16:23:12 -0400
parents 97c1b92dbd28
children 1c91108a80d5
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line diff
--- a/bam_readtagger.xml	Wed Apr 05 17:34:55 2017 -0400
+++ b/bam_readtagger.xml	Wed Apr 19 16:23:12 2017 -0400
@@ -1,10 +1,10 @@
-<tool id="bam_readtagger" name="Tag alignment files" version="0.3.13">
+<tool id="bam_readtagger" name="Tag alignment files" version="0.3.14">
     <description>from multiple bam files</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <requirements>
-        <requirement type="package" version="0.3.13">readtagger</requirement>
+        <requirement type="package" version="0.3.14">readtagger</requirement>
     </requirements>
     <command detect_errors="aggressive"><![CDATA[
         readtagger -t '$tag_file' -a
@@ -54,9 +54,9 @@
             </repeat>
             <param name="discarded" value="True"/>
             <param name="verified" value="True"/>
-            <output name="tagged_file" file="dm6_tagged_with_a_pasteurianus.bam" ftype="bam" lines_diff="5"/>
-            <output name="verified_file" file="dm6_tagged_with_a_pasteurianus_verified.bam" ftype="bam" lines_diff="5"/>
-            <output name="discarded_file" file="dm6_tagged_with_a_pasteurianus_discarded.bam" ftype="bam" lines_diff="5"/>
+            <output name="tagged_file" file="dm6_tagged_with_a_pasteurianus.bam" ftype="bam" lines_diff="7"/>
+            <output name="verified_file" file="dm6_tagged_with_a_pasteurianus_verified.bam" ftype="bam" lines_diff="7"/>
+            <output name="discarded_file" file="dm6_tagged_with_a_pasteurianus_discarded.bam" ftype="bam" lines_diff="7"/>
         </test>
         <test> <!-- test that a single read originating from a pasteurianus is annotated in pasteurianus.bam as having homology with dm6, but marked as discarded (should end in discarded bam file) -->
             <param name="tag_file" value="pasteurianus.bam" ftype="bam"/>
@@ -67,9 +67,9 @@
             </repeat>
             <param name="discarded" value="True"/>
             <param name="verified" value="True"/>
-            <output name="tagged_file" file="a_pasteurianus_tagged_with_dm6.bam" ftype="bam" lines_diff="5" />
-            <output name="verified_file" file="a_pasteurianus_tagged_with_dm6_verified.bam" ftype="bam" lines_diff="5"/>
-            <output name="discarded_file" file="a_pasteurianus_tagged_with_dm6_discarded.bam" ftype="bam" lines_diff="5"/>
+            <output name="tagged_file" file="a_pasteurianus_tagged_with_dm6.bam" ftype="bam" lines_diff="7" />
+            <output name="verified_file" file="a_pasteurianus_tagged_with_dm6_verified.bam" ftype="bam" lines_diff="7"/>
+            <output name="discarded_file" file="a_pasteurianus_tagged_with_dm6_discarded.bam" ftype="bam" lines_diff="7"/>
         </test>
         <test> <!-- test that a pair with homology to a TE insertion is discarded, because it is a proper pair -->
             <param name="tag_file" value="proper_pair_discard.bam" ftype="bam"/>
@@ -82,9 +82,9 @@
             <param name="keep_suboptimal" value="True"/>
             <param name="discard_proper_pairs" value="True"/>
             <param name="verified" value="True"/>
-            <output name="tagged_file" file="proper_pair_out_suboptimal_tags.bam" ftype="bam" lines_diff="5" />
-            <output name="verified_file" file="proper_pair_discard_verified_empty.bam" ftype="bam" lines_diff="5"/>
-            <output name="discarded_file" file="proper_pair_discard_out.bam" ftype="bam" lines_diff="5"/>
+            <output name="tagged_file" file="proper_pair_out_suboptimal_tags.bam" ftype="bam" lines_diff="7" />
+            <output name="verified_file" file="proper_pair_discard_verified_empty.bam" ftype="bam" lines_diff="7"/>
+            <output name="discarded_file" file="proper_pair_discard_out.bam" ftype="bam" lines_diff="7"/>
         </test>
     </tests>
     <help><![CDATA[