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comparison 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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41:29734dbad6de 42:fbfd1082de71
1 <tool id="bam_readtagger" name="Tag alignment files" version="0.4.10"> 1 <tool id="bam_readtagger" name="Tag alignment files" version="0.4.12">
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="0.4.10">readtagger</requirement> 7 <requirement type="package" version="0.4.12">readtagger</requirement>
8 </requirements> 8 </requirements>
9 <command detect_errors="aggressive"><![CDATA[ 9 <command detect_errors="aggressive"><![CDATA[
10 readtagger -t '$tag_file' -s 10 readtagger -t '$tag_file' -s
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
13 #end for 13 #end for
14 #if $reference_fasta: 14 #if $reference_fasta:
15 --reference_fasta '$reference_fasta' 15 --reference_fasta '$reference_fasta'
16 #end if 16 #end if
17 $allow_dovetailing 17 $allow_dovetailing
18 $discard_suboptimal 18 $discard_suboptimal
19 $discarded 19 $discarded
20 $verified 20 $verified
21 $discard_proper_pairs 21 $discard_proper_pairs
22 --cores "\${GALAXY_SLOTS:-2}" 22 --cores "\${GALAXY_SLOTS:-2}"
23 -o '$tagged_file' 23 -o '$tagged_file'
24 ]]></command> 24 ]]></command>
25 <inputs> 25 <inputs>
26 <param name="tag_file" argument="--tag_file" type="data" format="bam"/> 26 <param name="tag_file" argument="--tag_file" type="data" format="qname_sorted.bam,bam"/>
27 <repeat name="alignment_series" title="Alignments"> 27 <repeat name="alignment_series" title="Alignments">
28 <param name="annotate_with" argument="--annotate_with" type="data" format="bam"/> 28 <param name="annotate_with" argument="--annotate_with" type="data" format="qname_sorted.bam,bam"/>
29 <param type="select" name="r_tag" label="First letter to use for read tag" value="A"> 29 <param type="select" name="r_tag" label="First letter to use for read tag" value="A">
30 <expand macro="tag_options"/> 30 <expand macro="tag_options"/>
31 </param> 31 </param>
32 <param type="select" name="m_tag" label="First letter to use for mate tag" value="B"> 32 <param type="select" name="m_tag" label="First letter to use for mate tag" value="B">
33 <expand macro="tag_options"/> 33 <expand macro="tag_options"/>