Mercurial > repos > artbio > mapping_quality_stats

annotate mapping_quality_stats.xml @ 2:ce2d8f611a51 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/mapping_quality_stats commit 2661225fdd0f533d4dc8e2561ea559fcc00b9128
author artbio
date Sat, 10 Feb 2024 01:32:48 +0000
parents 7883d97fa479
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
2
ce2d8f611a51 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/mapping_quality_stats commit 2661225fdd0f533d4dc8e2561ea559fcc00b9128
artbio
parents: 1
diff changeset
1 <tool id="mapqstatistics" name="Mapping Quality Stats" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
ce2d8f611a51 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/mapping_quality_stats commit 2661225fdd0f533d4dc8e2561ea559fcc00b9128
artbio
parents: 1
diff changeset
2 <description></description>
ce2d8f611a51 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/mapping_quality_stats commit 2661225fdd0f533d4dc8e2561ea559fcc00b9128
artbio
parents: 1
diff changeset
3 <macros>
ce2d8f611a51 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/mapping_quality_stats commit 2661225fdd0f533d4dc8e2561ea559fcc00b9128
artbio
parents: 1
diff changeset
4 <token name="@TOOL_VERSION@">0.22.0</token>
ce2d8f611a51 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/mapping_quality_stats commit 2661225fdd0f533d4dc8e2561ea559fcc00b9128
artbio
parents: 1
diff changeset
5 <token name="@VERSION_SUFFIX@">0</token>
ce2d8f611a51 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/mapping_quality_stats commit 2661225fdd0f533d4dc8e2561ea559fcc00b9128
artbio
parents: 1
diff changeset
6 <token name="@PROFILE@">23.0</token>
ce2d8f611a51 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/mapping_quality_stats commit 2661225fdd0f533d4dc8e2561ea559fcc00b9128
artbio
parents: 1
diff changeset
7 </macros>
ce2d8f611a51 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/mapping_quality_stats commit 2661225fdd0f533d4dc8e2561ea559fcc00b9128
artbio
parents: 1
diff changeset
8 <requirements>
ce2d8f611a51 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/mapping_quality_stats commit 2661225fdd0f533d4dc8e2561ea559fcc00b9128
artbio
parents: 1
diff changeset
9 <requirement type="package" version="1.7.4">r-optparse</requirement>
ce2d8f611a51 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/mapping_quality_stats commit 2661225fdd0f533d4dc8e2561ea559fcc00b9128
artbio
parents: 1
diff changeset
10 <requirement type="package" version="3.4.4">r-ggplot2</requirement>
ce2d8f611a51 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/mapping_quality_stats commit 2661225fdd0f533d4dc8e2561ea559fcc00b9128
artbio
parents: 1
diff changeset
11 <requirement type="package" version="@TOOL_VERSION@">pysam</requirement>
ce2d8f611a51 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/mapping_quality_stats commit 2661225fdd0f533d4dc8e2561ea559fcc00b9128
artbio
parents: 1
diff changeset
12 </requirements>
0
f00479673d47 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
artbio
parents:
diff changeset
13 <stdio>
f00479673d47 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
artbio
parents:
diff changeset
14 <exit_code range="1:" level="fatal" description="Tool exception" />
f00479673d47 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
artbio
parents:
diff changeset
15 </stdio>
f00479673d47 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
artbio
parents:
diff changeset
16 <command detect_errors="exit_code"><![CDATA[
f00479673d47 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
artbio
parents:
diff changeset
17 ln -f -s $input.metadata.bam_index input.bam.bai &&
f00479673d47 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
artbio
parents:
diff changeset
18 ln -s $input input.bam &&
f00479673d47 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
artbio
parents:
diff changeset
19 python $__tool_directory__/mapping_quality_stats.py
f00479673d47 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
artbio
parents:
diff changeset
20 -bam input.bam
f00479673d47 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
artbio
parents:
diff changeset
21 -o $table &&
f00479673d47 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
artbio
parents:
diff changeset
22 Rscript $__tool_directory__/mapping_quality_stats.r
f00479673d47 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
artbio
parents:
diff changeset
23 -i '$table'
f00479673d47 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
artbio
parents:
diff changeset
24 -o $plot
f00479673d47 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
artbio
parents:
diff changeset
25 ]]></command>
f00479673d47 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
artbio
parents:
diff changeset
26 <inputs>
f00479673d47 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
artbio
parents:
diff changeset
27 <param name="input" type="data" format="bam" label="Select a bam file to analyze"/>
f00479673d47 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
artbio
parents:
diff changeset
28 </inputs>
f00479673d47 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
artbio
parents:
diff changeset
29
f00479673d47 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
artbio
parents:
diff changeset
30 <outputs>
f00479673d47 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
artbio
parents:
diff changeset
31 <data format="tabular" name="table" label="Distribution table" />
f00479673d47 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
artbio
parents:
diff changeset
32 <data format="pdf" name="plot" label="Distribution of MAPQs" />
f00479673d47 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
artbio
parents:
diff changeset
33 </outputs>
f00479673d47 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
artbio
parents:
diff changeset
34
f00479673d47 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
artbio
parents:
diff changeset
35 <tests>
f00479673d47 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
artbio
parents:
diff changeset
36 <test>
f00479673d47 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
artbio
parents:
diff changeset
37 <param name="input" value="sample.bam" ftype="bam"/>
f00479673d47 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
artbio
parents:
diff changeset
38 <output file="distribution.tab" name="table" />
f00479673d47 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
artbio
parents:
diff changeset
39 <output file="distribution.pdf" name="plot" />
f00479673d47 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
artbio
parents:
diff changeset
40 </test>
f00479673d47 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
artbio
parents:
diff changeset
41 </tests>
f00479673d47 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
artbio
parents:
diff changeset
42
f00479673d47 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
artbio
parents:
diff changeset
43
f00479673d47 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
artbio
parents:
diff changeset
44 <help>
f00479673d47 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
artbio
parents:
diff changeset
45
f00479673d47 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
artbio
parents:
diff changeset
46 **What it does**
f00479673d47 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
artbio
parents:
diff changeset
47
f00479673d47 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
artbio
parents:
diff changeset
48 Collects the values of mapping quality (MAPQ) in a BAM files
f00479673d47 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
artbio
parents:
diff changeset
49 Shows the data as a table and a barplot
f00479673d47 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
artbio
parents:
diff changeset
50
f00479673d47 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
artbio
parents:
diff changeset
51 **Inputs**
f00479673d47 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
artbio
parents:
diff changeset
52
f00479673d47 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
artbio
parents:
diff changeset
53 A bam alignment files which must be sorted
f00479673d47 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
artbio
parents:
diff changeset
54
f00479673d47 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
artbio
parents:
diff changeset
55 **Output**
f00479673d47 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
artbio
parents:
diff changeset
56
f00479673d47 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
artbio
parents:
diff changeset
57 A data frame of MAPQ counts
f00479673d47 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
artbio
parents:
diff changeset
58
f00479673d47 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
artbio
parents:
diff changeset
59 A pdf barplot generated by R and ggplot2
f00479673d47 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
artbio
parents:
diff changeset
60
f00479673d47 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
artbio
parents:
diff changeset
61 </help>
f00479673d47 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
artbio
parents:
diff changeset
62
f00479673d47 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
artbio
parents:
diff changeset
63 <citations>
f00479673d47 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
artbio
parents:
diff changeset
64 <citation type="doi">10.1093/bioinformatics/btp352</citation>
f00479673d47 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
artbio
parents:
diff changeset
65 </citations>
f00479673d47 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
artbio
parents:
diff changeset
66 </tool>
f00479673d47 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
artbio
parents:
diff changeset
67