Mercurial > repos > mvdbeek > bam_readtagger

annotate add_matesequence.xml @ 34:5b08a7a4caa9 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36
author mvdbeek
date Wed, 21 Jun 2017 09:38:09 -0400
parents 5c32fb616d95
children e19ff7992765
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
34
5b08a7a4caa9 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36
mvdbeek
parents: 31
diff changeset
1 <tool id="add_matesequence" name="Add matesequence" version="0.3.25">
4
e0b1919b6bd8 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c
mvdbeek
parents:
diff changeset
2 <description>into tag field</description>
e0b1919b6bd8 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c
mvdbeek
parents:
diff changeset
3 <requirements>
34
5b08a7a4caa9 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36
mvdbeek
parents: 31
diff changeset
4 <requirement type="package" version="0.3.25">readtagger</requirement>
4
e0b1919b6bd8 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c
mvdbeek
parents:
diff changeset
5 </requirements>
e0b1919b6bd8 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c
mvdbeek
parents:
diff changeset
6 <version_command>add_matesequence --version</version_command>
e0b1919b6bd8 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c
mvdbeek
parents:
diff changeset
7 <command detect_errors="aggressive"><![CDATA[
29
4be52149b343 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9b9334bf4c0364e3e06e64a9b3e532d0b10f93ba
mvdbeek
parents: 28
diff changeset
8 add_matesequence --target '$file_to_annotate' --source '$annotate_source' --output_path '$output'
4
e0b1919b6bd8 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c
mvdbeek
parents:
diff changeset
9 ]]></command>
e0b1919b6bd8 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c
mvdbeek
parents:
diff changeset
10 <inputs>
e0b1919b6bd8 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c
mvdbeek
parents:
diff changeset
11 <param name="file_to_annotate" argument="--file_to_annotate" label="Annotate reads in this file with their mate sequence" type="data" format="bam"/>
e0b1919b6bd8 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c
mvdbeek
parents:
diff changeset
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"/>
e0b1919b6bd8 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c
mvdbeek
parents:
diff changeset
13 <param name="mate_sequence_tag" type="text" value="MS"/>
e0b1919b6bd8 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c
mvdbeek
parents:
diff changeset
14 </inputs>
e0b1919b6bd8 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c
mvdbeek
parents:
diff changeset
15 <outputs>
e0b1919b6bd8 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c
mvdbeek
parents:
diff changeset
16 <data name="output" format="bam" label="Add matesequence on $on_string"/>
e0b1919b6bd8 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c
mvdbeek
parents:
diff changeset
17 </outputs>
e0b1919b6bd8 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c
mvdbeek
parents:
diff changeset
18 <tests>
e0b1919b6bd8 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c
mvdbeek
parents:
diff changeset
19 <test>
e0b1919b6bd8 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c
mvdbeek
parents:
diff changeset
20 <param name="file_to_annotate" value="dm6.bam" ftype="bam"/>
e0b1919b6bd8 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c
mvdbeek
parents:
diff changeset
21 <param name="annotate_source" value="dm6.bam" ftype="bam"/>
e0b1919b6bd8 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c
mvdbeek
parents:
diff changeset
22 <output name="output" file="dm6_mate_annotated.bam" ftype="bam" lines_diff="2"/>
e0b1919b6bd8 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c
mvdbeek
parents:
diff changeset
23 </test>
e0b1919b6bd8 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c
mvdbeek
parents:
diff changeset
24 </tests>
e0b1919b6bd8 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c
mvdbeek
parents:
diff changeset
25 <help><![CDATA[
e0b1919b6bd8 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c
mvdbeek
parents:
diff changeset
26 .. code-block::
e0b1919b6bd8 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c
mvdbeek
parents:
diff changeset
27
e0b1919b6bd8 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c
mvdbeek
parents:
diff changeset
28 usage: add_matesequence [-h] -a FILE_TO_ANNOTATE -s ANNOTATE_SOURE -o
e0b1919b6bd8 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c
mvdbeek
parents:
diff changeset
29 OUTPUT_PATH [--version]
e0b1919b6bd8 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c
mvdbeek
parents:
diff changeset
30
e0b1919b6bd8 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c
mvdbeek
parents:
diff changeset
31 Annotate reads with Mate Sequence in tag field
e0b1919b6bd8 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c
mvdbeek
parents:
diff changeset
32
e0b1919b6bd8 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c
mvdbeek
parents:
diff changeset
33 optional arguments:
e0b1919b6bd8 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c
mvdbeek
parents:
diff changeset
34 -h, --help show this help message and exit
e0b1919b6bd8 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c
mvdbeek
parents:
diff changeset
35 -a FILE_TO_ANNOTATE, --file_to_annotate FILE_TO_ANNOTATE
e0b1919b6bd8 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c
mvdbeek
parents:
diff changeset
36 Annotate reads in this file with their mate sequence
e0b1919b6bd8 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c
mvdbeek
parents:
diff changeset
37 -s ANNOTATE_SOURE, --annotate_soure ANNOTATE_SOURE
e0b1919b6bd8 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c
mvdbeek
parents:
diff changeset
38 Use this file to find the mate sequence (can be same
e0b1919b6bd8 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c
mvdbeek
parents:
diff changeset
39 file as file_to_annotate)
e0b1919b6bd8 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c
mvdbeek
parents:
diff changeset
40 -o OUTPUT_PATH, --output_path OUTPUT_PATH
e0b1919b6bd8 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c
mvdbeek
parents:
diff changeset
41 Write resulting BAM file to this path
e0b1919b6bd8 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c
mvdbeek
parents:
diff changeset
42 --version show program's version number and exit
e0b1919b6bd8 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c
mvdbeek
parents:
diff changeset
43
e0b1919b6bd8 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c
mvdbeek
parents:
diff changeset
44 ]]></help>
e0b1919b6bd8 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c
mvdbeek
parents:
diff changeset
45 </tool>