Mercurial > repos > mvdbeek > bam_readtagger

comparison add_matesequence.xml @ 4:e0b1919b6bd8 draft

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planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c
author mvdbeek
date Tue, 21 Feb 2017 04:39:17 -0500
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3:e68a225983d5 4:e0b1919b6bd8
1 <tool id="add_matesequence" name="Add matesequence" version="0.2.0">
2 <description>into tag field</description>
3 <requirements>
4 <requirement type="package" version="0.2.0">readtagger</requirement>
5 </requirements>
6 <version_command>add_matesequence --version</version_command>
7 <command detect_errors="aggressive"><![CDATA[
8 add_matesequence --file_to_annotate '$file_to_annotate' --annotate_source '$annotate_source' --output_path '$output'
9 ]]></command>
10 <inputs>
11 <param name="file_to_annotate" argument="--file_to_annotate" label="Annotate reads in this file with their mate sequence" type="data" format="bam"/>
12 <param name="annotate_source" argument="--annotate_source" label="Use this file to find the mate sequence (can be same file as file_to_annotate)" type="data" format="bam"/>
13 <param name="mate_sequence_tag" type="text" value="MS"/>
14 </inputs>
15 <outputs>
16 <data name="output" format="bam" label="Add matesequence on $on_string"/>
17 </outputs>
18 <tests>
19 <test>
20 <param name="file_to_annotate" value="dm6.bam" ftype="bam"/>
21 <param name="annotate_source" value="dm6.bam" ftype="bam"/>
22 <output name="output" file="dm6_mate_annotated.bam" ftype="bam" lines_diff="2"/>
23 </test>
24 </tests>
25 <help><![CDATA[
26 .. code-block::
27
28 usage: add_matesequence [-h] -a FILE_TO_ANNOTATE -s ANNOTATE_SOURE -o
29 OUTPUT_PATH [--version]
30
31 Annotate reads with Mate Sequence in tag field
32
33 optional arguments:
34 -h, --help show this help message and exit
35 -a FILE_TO_ANNOTATE, --file_to_annotate FILE_TO_ANNOTATE
36 Annotate reads in this file with their mate sequence
37 -s ANNOTATE_SOURE, --annotate_soure ANNOTATE_SOURE
38 Use this file to find the mate sequence (can be same
39 file as file_to_annotate)
40 -o OUTPUT_PATH, --output_path OUTPUT_PATH
41 Write resulting BAM file to this path
42 --version show program's version number and exit
43
44 ]]></help>
45 </tool>