annotate update_mapq.xml @ 76:8c3d8d38674a draft

"planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit fee3f43c26cd13ffdb81d64a3c7809c570ba2194"
author mvdbeek
date Mon, 23 Mar 2020 12:42:34 -0400
parents 2c7f70390b7c
children 6178c24ddd5a
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
76
8c3d8d38674a "planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit fee3f43c26cd13ffdb81d64a3c7809c570ba2194"
mvdbeek
parents: 75
diff changeset
1 <tool id="update_mapq" name="Update MAPQ score" version="0.5.23">
9
53b71263e2a2 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
parents:
diff changeset
2 <description>of supplementary alignments</description>
53b71263e2a2 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
parents:
diff changeset
3 <requirements>
76
8c3d8d38674a "planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit fee3f43c26cd13ffdb81d64a3c7809c570ba2194"
mvdbeek
parents: 75
diff changeset
4 <requirement type="package" version="0.5.23">readtagger</requirement>
9
53b71263e2a2 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
parents:
diff changeset
5 </requirements>
53b71263e2a2 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
parents:
diff changeset
6 <version_command>update_mapq --version</version_command>
53b71263e2a2 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
parents:
diff changeset
7 <command detect_errors="aggressive"><![CDATA[
53b71263e2a2 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
parents:
diff changeset
8 update_mapq --source_path '$source_path' --remapped_path '$remapped_path' --output_path '$output_path'
53b71263e2a2 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
parents:
diff changeset
9 ]]></command>
53b71263e2a2 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
parents:
diff changeset
10 <inputs>
53b71263e2a2 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
parents:
diff changeset
11 <param argument="--source_path" label="Update supplementary MAPQ scores in this BAM file" type="data" format="bam"/>
11
124f7f8ee080 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 13fe863ca4079d83d897fdf7e394a7474eea6117-dirty
mvdbeek
parents: 10
diff changeset
12 <param argument="--remapped_path" label="Extract MAPQ scores for secondary alignments from this BAM file." type="data" format="bam"/>
9
53b71263e2a2 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
parents:
diff changeset
13 </inputs>
53b71263e2a2 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
parents:
diff changeset
14 <outputs>
53b71263e2a2 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
parents:
diff changeset
15 <data name="output_path" format="bam"/>
53b71263e2a2 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
parents:
diff changeset
16 </outputs>
53b71263e2a2 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
parents:
diff changeset
17 <tests>
53b71263e2a2 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
parents:
diff changeset
18 <test>
53b71263e2a2 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
parents:
diff changeset
19 <param name="source_path" value="supplementary.bam" ftype="bam"/>
53b71263e2a2 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
parents:
diff changeset
20 <param name="remapped_path" value="remapped_supplementary.bam" ftype="bam"/>
53b71263e2a2 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
parents:
diff changeset
21 <output name="output_path" file="supplementary_new_mapq.bam" ftype="bam"/>
53b71263e2a2 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
parents:
diff changeset
22 </test>
53b71263e2a2 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
parents:
diff changeset
23 </tests>
53b71263e2a2 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
parents:
diff changeset
24 <help><![CDATA[
53b71263e2a2 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
parents:
diff changeset
25 .. code-block::
53b71263e2a2 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
parents:
diff changeset
26
53b71263e2a2 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
parents:
diff changeset
27 Usage: update_mapq [OPTIONS]
53b71263e2a2 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
parents:
diff changeset
28
53b71263e2a2 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
parents:
diff changeset
29 Update supplementary read MAPQ score after remapping.
53b71263e2a2 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
parents:
diff changeset
30
53b71263e2a2 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
parents:
diff changeset
31 Options:
53b71263e2a2 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
parents:
diff changeset
32 --source_path PATH Alignment file where supplementary reads should be
53b71263e2a2 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
parents:
diff changeset
33 updated with new MAPQ scores [required]
53b71263e2a2 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
parents:
diff changeset
34 --remapped_path PATH Alignment file that contains reads that have been
53b71263e2a2 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
parents:
diff changeset
35 remapped and contain an updated MAPQ score [required]
53b71263e2a2 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
parents:
diff changeset
36 --output_path PATH Write all alignments in original_path to this
53b71263e2a2 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
parents:
diff changeset
37 location. Supplementary reads will take the MAPQ score
53b71263e2a2 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
parents:
diff changeset
38 as determined by remapping to the alignment file at
53b71263e2a2 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
parents:
diff changeset
39 `remapped_path` [required]
53b71263e2a2 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
parents:
diff changeset
40 --version Show the version and exit.
53b71263e2a2 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
parents:
diff changeset
41 --help Show this message and exit.
53b71263e2a2 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
parents:
diff changeset
42
53b71263e2a2 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
parents:
diff changeset
43
53b71263e2a2 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
parents:
diff changeset
44 ]]></help>
53b71263e2a2 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
parents:
diff changeset
45 </tool>