Mercurial > repos > mvdbeek > bam_readtagger

diff bam_readtagger.xml @ 43:c2104094afd3 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 ae40519a953219ec4cc8ef4d586fc06cad88fb01
author mvdbeek
date Mon, 14 Jan 2019 13:17:50 -0500
parents fbfd1082de71
children f178b9698b66
line wrap: on
line diff
--- a/bam_readtagger.xml	Fri Oct 26 06:10:14 2018 -0400
+++ b/bam_readtagger.xml	Mon Jan 14 13:17:50 2019 -0500
@@ -1,31 +1,31 @@
-<tool id="bam_readtagger" name="Tag alignment files" version="0.4.12">
+<tool id="bam_readtagger" name="Tag alignment files" version="0.4.13">
     <description>from multiple bam files</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <requirements>
-        <requirement type="package" version="0.4.12">readtagger</requirement>
+        <requirement type="package" version="0.4.13">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="qname_sorted.bam,bam"/>
+        <param name="tag_file" argument="--tag_file" type="data" format="bam"/>
         <repeat name="alignment_series" title="Alignments">
-            <param name="annotate_with" argument="--annotate_with" type="data" format="qname_sorted.bam,bam"/>
+            <param name="annotate_with" argument="--annotate_with" type="data" format="bam"/>
             <param type="select" name="r_tag" label="First letter to use for read tag" value="A">
                 <expand macro="tag_options"/>
             </param>