Mercurial > repos > mvdbeek > bam_readtagger

comparison bam_readtagger.xml @ 23:2981ab2c7217 draft

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planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 16f35b0e373f4cbd33f1bc6aef4a13b7fd2eca12
author mvdbeek
date Sun, 23 Apr 2017 15:58:38 -0400
parents 32e191f572e1
children 4f28f8cc8cf4
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22:32e191f572e1 23:2981ab2c7217
1 <tool id="bam_readtagger" name="Tag alignment files" version="0.3.15"> 1 <tool id="bam_readtagger" name="Tag alignment files" version="0.3.16">
2 <description>from multiple bam files</description> 2 <description>from multiple bam files</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <requirements> 6 <requirements>
7 <requirement type="package" version="0.3.15">readtagger</requirement> 7 <requirement type="package" version="0.3.16">readtagger</requirement>
8 </requirements> 8 </requirements>
9 <command detect_errors="aggressive"><![CDATA[ 9 <command detect_errors="aggressive"><![CDATA[
10 readtagger -t '$tag_file' -a 10 readtagger -t '$tag_file' -a
11 #for $element in $alignment_series 11 #for $element in $alignment_series
12 '$element.annotate_with':$element.r_tag:$element.m_tag 12 '$element.annotate_with':$element.r_tag:$element.m_tag
14 $allow_dovetailing 14 $allow_dovetailing
15 $keep_suboptimal 15 $keep_suboptimal
16 $discarded 16 $discarded
17 $verified 17 $verified
18 $discard_proper_pairs 18 $discard_proper_pairs
19 --cores "\${GALAXY_SLOTS:-2}"
19 -o '$tagged_file' 20 -o '$tagged_file'
20 ]]></command> 21 ]]></command>
21 <inputs> 22 <inputs>
22 <param name="tag_file" argument="--tag_file" type="data" format="bam"/> 23 <param name="tag_file" argument="--tag_file" type="data" format="bam"/>
23 <repeat name="alignment_series" title="Alignments"> 24 <repeat name="alignment_series" title="Alignments">