Mercurial > repos > artbio > mapping_quality_stats
annotate mapping_quality_stats.xml @ 0:f00479673d47 draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
author | artbio |
---|---|
date | Wed, 15 Jun 2022 10:43:07 +0000 |
parents | |
children | 7883d97fa479 |
rev | line source |
---|---|
0
f00479673d47
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
artbio
parents:
diff
changeset
|
1 <tool id="mapqstatistics" name="Mapping Quality Stats" version="0.16.0.1+galaxy0"> |
f00479673d47
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
artbio
parents:
diff
changeset
|
2 <description></description> |
f00479673d47
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
artbio
parents:
diff
changeset
|
3 <requirements> |
f00479673d47
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
artbio
parents:
diff
changeset
|
4 <requirement type="package" version="1.6.4=r36h6115d3f_0">r-optparse</requirement> |
f00479673d47
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
artbio
parents:
diff
changeset
|
5 <requirement type="package" version="3.2.1=r36h6115d3f_0">r-ggplot2</requirement> |
f00479673d47
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
artbio
parents:
diff
changeset
|
6 <requirement type="package" version="0.16.0.1">pysam</requirement> |
f00479673d47
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
artbio
parents:
diff
changeset
|
7 </requirements> |
f00479673d47
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
artbio
parents:
diff
changeset
|
8 <stdio> |
f00479673d47
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
artbio
parents:
diff
changeset
|
9 <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
|
10 </stdio> |
f00479673d47
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
artbio
parents:
diff
changeset
|
11 <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
|
12 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
|
13 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
|
14 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
|
15 -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
|
16 -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
|
17 Rscript $__tool_directory__/mapping_quality_stats.r |
f00479673d47
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
artbio
parents:
diff
changeset
|
18 -i '$table' |
f00479673d47
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
artbio
parents:
diff
changeset
|
19 -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
|
20 ]]></command> |
f00479673d47
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
artbio
parents:
diff
changeset
|
21 <inputs> |
f00479673d47
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
artbio
parents:
diff
changeset
|
22 <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
|
23 </inputs> |
f00479673d47
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
artbio
parents:
diff
changeset
|
24 |
f00479673d47
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
artbio
parents:
diff
changeset
|
25 <outputs> |
f00479673d47
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
artbio
parents:
diff
changeset
|
26 <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
|
27 <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
|
28 </outputs> |
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 <tests> |
f00479673d47
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
artbio
parents:
diff
changeset
|
31 <test> |
f00479673d47
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
artbio
parents:
diff
changeset
|
32 <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
|
33 <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
|
34 <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
|
35 </test> |
f00479673d47
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
artbio
parents:
diff
changeset
|
36 </tests> |
f00479673d47
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
artbio
parents:
diff
changeset
|
37 |
f00479673d47
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
artbio
parents:
diff
changeset
|
38 |
f00479673d47
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
artbio
parents:
diff
changeset
|
39 <help> |
f00479673d47
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
artbio
parents:
diff
changeset
|
40 |
f00479673d47
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
artbio
parents:
diff
changeset
|
41 **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
|
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 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
|
44 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
|
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 **Inputs** |
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 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
|
49 |
f00479673d47
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
artbio
parents:
diff
changeset
|
50 **Output** |
f00479673d47
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
artbio
parents:
diff
changeset
|
51 |
f00479673d47
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
artbio
parents:
diff
changeset
|
52 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
|
53 |
f00479673d47
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
artbio
parents:
diff
changeset
|
54 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
|
55 |
f00479673d47
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
artbio
parents:
diff
changeset
|
56 </help> |
f00479673d47
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
artbio
parents:
diff
changeset
|
57 |
f00479673d47
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
artbio
parents:
diff
changeset
|
58 <citations> |
f00479673d47
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
artbio
parents:
diff
changeset
|
59 <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
|
60 </citations> |
f00479673d47
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
artbio
parents:
diff
changeset
|
61 </tool> |
f00479673d47
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats commit e4b37874b820a2ac48732667128a08e5755b7c4b
artbio
parents:
diff
changeset
|
62 |