Mercurial > repos > mvdbeek > bam_readtagger

diff extract_variants.xml @ 65:08a10eefc2ca draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 1bc80492c93251d0cbe39d120872869e08d8d435"
author mvdbeek
date Tue, 05 Nov 2019 05:05:32 -0500
parents 31dc40ec7067
children 9ac536101591
line wrap: on
line diff
--- a/extract_variants.xml	Thu Sep 05 10:21:59 2019 -0400
+++ b/extract_variants.xml	Tue Nov 05 05:05:32 2019 -0500
@@ -1,12 +1,13 @@
-<tool id="extract_variants" name="Extract variant fragments" version="0.5.16">
+<tool id="extract_variants" name="Extract variant fragments" version="0.5.17">
     <description>from long reads</description>
     <requirements>
-        <requirement type="package" version="0.5.16">readtagger</requirement>
+        <requirement type="package" version="0.5.17">readtagger</requirement>
     </requirements>
     <version_command>extract_variants --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
 ln -fs '$insert_reference.fields.path' reference.fa &&
-extract_variants '$input' '$output' reference.fa
+extract_variants '$input' '$output_alignment' reference.fa &&
+summarize_fragments '$output_alignment' '$output_tabular'
     ]]></command>
     <inputs>
         <param name="input" label="Select alignment for which to extract variants" type="data" format="bam,cram"/>
@@ -15,13 +16,15 @@
         </param>
     </inputs>
     <outputs>
-        <data name="output" format_source="input"/>
+        <data name="output_alignment" format_source="input" label="${tool.name} on ${on_string}: alignment"/>
+        <data name="output_tabular" format="tabular" label="${tool.name} on ${on_string}: summary"/>
     </outputs>
     <tests>
         <test>
             <param name="input" value="long_insertion.bam" ftype="bam"/>
             <param name="insert_reference" value="transposon"/>
-            <output name="output" file="long_insert_tagged.bam" ftype="bam"/>
+            <output name="output_alignment" file="long_insert_tagged.bam" ftype="bam"/>
+            <output name="output_tabular" file="long_insert_tagged.tab" ftype="tabular"/>
         </test>
     </tests>
     <help><![CDATA[