Mercurial > repos > brad-chapman > bam_to_bigwig

comparison bam_to_bigwig.xml @ 6:9163e1db4c16 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/lparsons/galaxy_tools/tree/master/tools/bam_to_bigwig/ commit b5c3df21127fc27f66a97761173c07e161f2fa8e
author lparsons
date Thu, 12 May 2016 11:39:13 -0400
parents
children
comparison
equal deleted inserted replaced
5:52bcd04ee0d6 6:9163e1db4c16
1 <tool id="bam_to_bigwig" name="BAM to BigWig" version="0.2.0">
2
3 <description>Calculates coverage from a BAM alignment file</description>
4
5 <requirements>
6 <requirement type="package" version="0.8.3">pysam</requirement>
7 <requirement type="package" version="2.24">bedtools</requirement>
8 <requirement type="package" version="312">ucsc_tools</requirement>
9 </requirements>
10
11 <command detect_errors="aggressive" interpreter="python"><![CDATA[
12 bam_to_bigwig.py $align --outfile=$out --split
13 ]]></command>
14
15 <inputs>
16 <param format="bam" name="align" type="data" label="BAM alignment file"/>
17 </inputs>
18
19 <outputs>
20 <data format="bigwig" name="out" />
21 </outputs>
22
23 <tests>
24 <test>
25 <param name="align" value="bam_to_bigwig_test.bam"/>
26 <output name="out" file="bam_to_bigwig_test.bigwig"/>
27 </test>
28 </tests>
29
30 <help><![CDATA[
31 **What it does**
32
33 Creates a coverage file in BigWig format, given a BAM alignment file.
34
35 Gaps or skips (CIGAR D or N operators) are not counted towards the coverage
36 calculation, which is important when mapping RNA Seq reads to genes with
37 introns.
38
39 **Input**
40
41 A BAM alignment file. This needs to have the genome database build used in
42 alignment annotated. If your file has '?' for the database build, click on the
43 pencil icon to edit the alignment attributes, and specify the organism used to
44 align against.
45
46 **Output**
47
48 BigWig files can be loaded directly from Galaxy into the UCSC browser. They can
49 be loaded incrementally by UCSC, so a single file can be used to represent the
50 entire genome without having to upload the entire thing as a custom track.
51
52 ]]></help>
53
54 <citations>
55 <citation type="doi">10.1093/bioinformatics/btp352</citation>
56 <citation type="doi">10.1093/bioinformatics/btq033</citation>
57 </citations>
58 </tool>