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comparison count_mapped_reads.xml @ 0:90d81e551420 draft

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planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 54eef6140a5086e3373b2406efb2e18dbfae1336-dirty
author jvolkening
date Sat, 02 Mar 2024 07:42:45 +0000
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1 <tool id="b2b_count_mapped_reads" name="Count mapped reads" version="0.001">
2
3 <description>Count reads uniquely mapped to each reference sequence</description>
4
5 <!-- ***************************************************************** -->
6
7 <requirements>
8 <!-- ncurses needs to be explicitly pulled from conda-forge for samtools to work -->
9 <requirement type="package" version="6.1">ncurses</requirement>
10 <requirement type="package" version="1.9">samtools</requirement>
11 </requirements>
12
13 <!-- ***************************************************************** -->
14
15 <version_command>echo "0.001"</version_command>
16
17 <!-- ***************************************************************** -->
18
19 <command detect_errors="aggressive">
20 <![CDATA[
21
22 #if $uniq:
23 samtools view -F 0x04 -F 0x100 -F 0x800 $in
24 #else
25 samtools view -F 0x04 $in
26 #end if
27 | cut -f3
28 | sort
29 | uniq -c
30 | awk -v OFS='\t' '{print $2,$1}'
31 > $out
32
33 ]]>
34 </command>
35
36 <!-- ***************************************************************** -->
37
38 <inputs>
39 <param name="in" type="data" format="bam" label="Read mapping" help="BAM format" />
40 <param name="uniq" type="boolean" checked="True" label="Exclude ambiguous mappings" />
41 </inputs>
42
43 <!-- ***************************************************************** -->
44
45 <outputs>
46 <data name="out" format="tabular" label="Read counts" />
47 </outputs>
48
49 <!-- ***************************************************************** -->
50
51 <tests>
52 <test>
53 <param name="in" value="b2c.bam" ftype="bam" />
54 <output name="out" file="b2c.counts" compare="diff" />
55 </test>
56 </tests>
57
58 <!-- ***************************************************************** -->
59
60 <help>
61
62 `count_mapped_reads` is a Galaxy-only utility from BASE2BIO that simply
63 reports the number of reads mapped to each sequence from a BAM input file.
64
65 </help>
66
67 <!-- ***************************************************************** -->
68
69 <citations>
70 </citations>
71
72 </tool>