Mercurial > repos > mvdbeek > bam_readtagger
comparison bam_readtagger.xml @ 22:42fefb316c95 draft
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 16f35b0e373f4cbd33f1bc6aef4a13b7fd2eca12-dirty
author | mvdbeek |
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date | Sun, 23 Apr 2017 15:58:53 -0400 |
parents | 1c91108a80d5 |
children | 1323ffbc8785 |
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21:1c91108a80d5 | 22:42fefb316c95 |
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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"> |