Mercurial > repos > mvdbeek > bam_readtagger

diff bam_readtagger.xml @ 42:fbfd1082de71 draft

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planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 7ee4c1dd4e13a4d634b0e80efdd2309289a29a1c
author mvdbeek
date Fri, 26 Oct 2018 06:10:14 -0400
parents 29734dbad6de
children c2104094afd3
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line diff
--- a/bam_readtagger.xml	Sun Apr 01 03:38:16 2018 -0400
+++ b/bam_readtagger.xml	Fri Oct 26 06:10:14 2018 -0400
@@ -1,31 +1,31 @@
-<tool id="bam_readtagger" name="Tag alignment files" version="0.4.10">
+<tool id="bam_readtagger" name="Tag alignment files" version="0.4.12">
     <description>from multiple bam files</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <requirements>
-        <requirement type="package" version="0.4.10">readtagger</requirement>
+        <requirement type="package" version="0.4.12">readtagger</requirement>
     </requirements>
     <command detect_errors="aggressive"><![CDATA[
-        readtagger -t '$tag_file' -s
-        #for $element in $alignment_series
-            '$element.annotate_with':$element.r_tag:$element.m_tag
-        #end for
-        #if $reference_fasta:
-            --reference_fasta '$reference_fasta'
-        #end if
-        $allow_dovetailing
-        $discard_suboptimal
-        $discarded
-        $verified
-        $discard_proper_pairs
-        --cores "\${GALAXY_SLOTS:-2}"
-        -o '$tagged_file'
+readtagger -t '$tag_file' -s
+#for $element in $alignment_series
+    '$element.annotate_with':$element.r_tag:$element.m_tag
+#end for
+#if $reference_fasta:
+    --reference_fasta '$reference_fasta'
+#end if
+$allow_dovetailing
+$discard_suboptimal
+$discarded
+$verified
+$discard_proper_pairs
+--cores "\${GALAXY_SLOTS:-2}"
+-o '$tagged_file'
     ]]></command>
     <inputs>
-        <param name="tag_file" argument="--tag_file" type="data" format="bam"/>
+        <param name="tag_file" argument="--tag_file" type="data" format="qname_sorted.bam,bam"/>
         <repeat name="alignment_series" title="Alignments">
-            <param name="annotate_with" argument="--annotate_with" type="data" format="bam"/>
+            <param name="annotate_with" argument="--annotate_with" type="data" format="qname_sorted.bam,bam"/>
             <param type="select" name="r_tag" label="First letter to use for read tag" value="A">
                 <expand macro="tag_options"/>
             </param>