Mercurial > repos > mvdbeek > bam_readtagger

annotate update_mapq.xml @ 62:e0dbdec47f06 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 ae20b1259f1570c5117763848867d3a84b6cd111"
author mvdbeek
date Tue, 03 Sep 2019 16:36:08 -0400
parents 46c9abed6a71
children 3cea8b694492
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
62
e0dbdec47f06 "planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit ae20b1259f1570c5117763848867d3a84b6cd111"
mvdbeek
parents: 61
diff changeset
1 <tool id="update_mapq" name="Update MAPQ score" version="0.5.14">
10
3c803db023b8 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e
mvdbeek
parents:
diff changeset
2 <description>of supplementary alignments</description>
3c803db023b8 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e
mvdbeek
parents:
diff changeset
3 <requirements>
62
e0dbdec47f06 "planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit ae20b1259f1570c5117763848867d3a84b6cd111"
mvdbeek
parents: 61
diff changeset
4 <requirement type="package" version="0.5.14">readtagger</requirement>
10
3c803db023b8 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e
mvdbeek
parents:
diff changeset
5 </requirements>
3c803db023b8 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e
mvdbeek
parents:
diff changeset
6 <version_command>update_mapq --version</version_command>
3c803db023b8 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e
mvdbeek
parents:
diff changeset
7 <command detect_errors="aggressive"><![CDATA[
3c803db023b8 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e
mvdbeek
parents:
diff changeset
8 update_mapq --source_path '$source_path' --remapped_path '$remapped_path' --output_path '$output_path'
3c803db023b8 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e
mvdbeek
parents:
diff changeset
9 ]]></command>
3c803db023b8 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e
mvdbeek
parents:
diff changeset
10 <inputs>
3c803db023b8 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e
mvdbeek
parents:
diff changeset
11 <param argument="--source_path" label="Update supplementary MAPQ scores in this BAM file" type="data" format="bam"/>
12
c7ee722e48ad planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 13fe863ca4079d83d897fdf7e394a7474eea6117
mvdbeek
parents: 11
diff changeset
12 <param argument="--remapped_path" label="Extract MAPQ scores for secondary alignments from this BAM file." type="data" format="bam"/>
10
3c803db023b8 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e
mvdbeek
parents:
diff changeset
13 </inputs>
3c803db023b8 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e
mvdbeek
parents:
diff changeset
14 <outputs>
3c803db023b8 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e
mvdbeek
parents:
diff changeset
15 <data name="output_path" format="bam"/>
3c803db023b8 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e
mvdbeek
parents:
diff changeset
16 </outputs>
3c803db023b8 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e
mvdbeek
parents:
diff changeset
17 <tests>
3c803db023b8 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e
mvdbeek
parents:
diff changeset
18 <test>
3c803db023b8 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e
mvdbeek
parents:
diff changeset
19 <param name="source_path" value="supplementary.bam" ftype="bam"/>
3c803db023b8 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e
mvdbeek
parents:
diff changeset
20 <param name="remapped_path" value="remapped_supplementary.bam" ftype="bam"/>
3c803db023b8 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e
mvdbeek
parents:
diff changeset
21 <output name="output_path" file="supplementary_new_mapq.bam" ftype="bam"/>
3c803db023b8 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e
mvdbeek
parents:
diff changeset
22 </test>
3c803db023b8 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e
mvdbeek
parents:
diff changeset
23 </tests>
3c803db023b8 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e
mvdbeek
parents:
diff changeset
24 <help><![CDATA[
3c803db023b8 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e
mvdbeek
parents:
diff changeset
25 .. code-block::
3c803db023b8 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e
mvdbeek
parents:
diff changeset
26
3c803db023b8 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e
mvdbeek
parents:
diff changeset
27 Usage: update_mapq [OPTIONS]
3c803db023b8 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e
mvdbeek
parents:
diff changeset
28
3c803db023b8 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e
mvdbeek
parents:
diff changeset
29 Update supplementary read MAPQ score after remapping.
3c803db023b8 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e
mvdbeek
parents:
diff changeset
30
3c803db023b8 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e
mvdbeek
parents:
diff changeset
31 Options:
3c803db023b8 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e
mvdbeek
parents:
diff changeset
32 --source_path PATH Alignment file where supplementary reads should be
3c803db023b8 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e
mvdbeek
parents:
diff changeset
33 updated with new MAPQ scores [required]
3c803db023b8 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e
mvdbeek
parents:
diff changeset
34 --remapped_path PATH Alignment file that contains reads that have been
3c803db023b8 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e
mvdbeek
parents:
diff changeset
35 remapped and contain an updated MAPQ score [required]
3c803db023b8 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e
mvdbeek
parents:
diff changeset
36 --output_path PATH Write all alignments in original_path to this
3c803db023b8 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e
mvdbeek
parents:
diff changeset
37 location. Supplementary reads will take the MAPQ score
3c803db023b8 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e
mvdbeek
parents:
diff changeset
38 as determined by remapping to the alignment file at
3c803db023b8 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e
mvdbeek
parents:
diff changeset
39 `remapped_path` [required]
3c803db023b8 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e
mvdbeek
parents:
diff changeset
40 --version Show the version and exit.
3c803db023b8 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e
mvdbeek
parents:
diff changeset
41 --help Show this message and exit.
3c803db023b8 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e
mvdbeek
parents:
diff changeset
42
3c803db023b8 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e
mvdbeek
parents:
diff changeset
43
3c803db023b8 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e
mvdbeek
parents:
diff changeset
44 ]]></help>
3c803db023b8 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e
mvdbeek
parents:
diff changeset
45 </tool>