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comparison update_mapq.xml @ 9:53b71263e2a2 draft

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planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
author mvdbeek
date Wed, 08 Mar 2017 05:14:25 -0500
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children c179d081b6ba
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8:bf8ffb337cbe 9:53b71263e2a2
1 <tool id="update_mapq" name="Update MAPQ score" version="0.3.5">
2 <description>of supplementary alignments</description>
3 <requirements>
4 <requirement type="package" version="0.3.5">readtagger</requirement>
5 </requirements>
6 <version_command>update_mapq --version</version_command>
7 <command detect_errors="aggressive"><![CDATA[
8 update_mapq --source_path '$source_path' --remapped_path '$remapped_path' --output_path '$output_path'
9 ]]></command>
10 <inputs>
11 <param argument="--source_path" label="Update supplementary MAPQ scores in this BAM file" type="data" format="bam"/>
12 <param argument="--remapped_path" label="Extarct MAPQ scores for secondary alignments from this BAM file." type="data" format="bam"/>
13 </inputs>
14 <outputs>
15 <data name="output_path" format="bam"/>
16 </outputs>
17 <tests>
18 <test>
19 <param name="source_path" value="supplementary.bam" ftype="bam"/>
20 <param name="remapped_path" value="remapped_supplementary.bam" ftype="bam"/>
21 <output name="output_path" file="supplementary_new_mapq.bam" ftype="bam"/>
22 </test>
23 </tests>
24 <help><![CDATA[
25 .. code-block::
26
27 Usage: update_mapq [OPTIONS]
28
29 Update supplementary read MAPQ score after remapping.
30
31 Options:
32 --source_path PATH Alignment file where supplementary reads should be
33 updated with new MAPQ scores [required]
34 --remapped_path PATH Alignment file that contains reads that have been
35 remapped and contain an updated MAPQ score [required]
36 --output_path PATH Write all alignments in original_path to this
37 location. Supplementary reads will take the MAPQ score
38 as determined by remapping to the alignment file at
39 `remapped_path` [required]
40 --version Show the version and exit.
41 --help Show this message and exit.
42
43
44 ]]></help>
45 </tool>