Mercurial > repos > brad-chapman > bam_to_bigwig
annotate bam_to_bigwig/bam_to_bigwig.xml @ 4:14e5258d1b39
v0.1.1: Add the forgotten --split argument in XML and moves to using the new bedtools. Thanks to David Leader
author | Brad Chapman <chapmanb@50mail.com> |
---|---|
date | Tue, 11 Feb 2014 15:55:22 -0500 |
parents | e2edfa478eb4 |
children |
rev | line source |
---|---|
4
14e5258d1b39
v0.1.1: Add the forgotten --split argument in XML and moves to using the new bedtools. Thanks to David Leader
Brad Chapman <chapmanb@50mail.com>
parents:
2
diff
changeset
|
1 <tool id="bam_to_bigwig" name="BAM to BigWig" version="0.1.1"> |
0
d2c1af657010
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
brad-chapman
parents:
diff
changeset
|
2 <description>Calculates coverage from a BAM alignment file</description> |
4
14e5258d1b39
v0.1.1: Add the forgotten --split argument in XML and moves to using the new bedtools. Thanks to David Leader
Brad Chapman <chapmanb@50mail.com>
parents:
2
diff
changeset
|
3 <command interpreter="python">bam_to_bigwig.py $align --outfile=$out --split</command> |
0
d2c1af657010
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
brad-chapman
parents:
diff
changeset
|
4 <inputs> |
d2c1af657010
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
brad-chapman
parents:
diff
changeset
|
5 <param format="bam" name="align" type="data" label="BAM alignment file"/> |
d2c1af657010
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
brad-chapman
parents:
diff
changeset
|
6 </inputs> |
d2c1af657010
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
brad-chapman
parents:
diff
changeset
|
7 <outputs> |
d2c1af657010
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
brad-chapman
parents:
diff
changeset
|
8 <data format="bigwig" name="out" /> |
d2c1af657010
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
brad-chapman
parents:
diff
changeset
|
9 </outputs> |
2
e2edfa478eb4
Covert to use bedGraph intermediate with bedtools. Thanks to Peter Cock and Lance Parsons for the updates
Brad Chapman <chapmanb@50mail.com>
parents:
1
diff
changeset
|
10 <requirements> |
e2edfa478eb4
Covert to use bedGraph intermediate with bedtools. Thanks to Peter Cock and Lance Parsons for the updates
Brad Chapman <chapmanb@50mail.com>
parents:
1
diff
changeset
|
11 <requirement type="python-module">pysam</requirement> |
e2edfa478eb4
Covert to use bedGraph intermediate with bedtools. Thanks to Peter Cock and Lance Parsons for the updates
Brad Chapman <chapmanb@50mail.com>
parents:
1
diff
changeset
|
12 <requirement type="binary">genomeCoverageBed</requirement> |
e2edfa478eb4
Covert to use bedGraph intermediate with bedtools. Thanks to Peter Cock and Lance Parsons for the updates
Brad Chapman <chapmanb@50mail.com>
parents:
1
diff
changeset
|
13 <requirement type="binary">bedGraphToBigWig</requirement> |
e2edfa478eb4
Covert to use bedGraph intermediate with bedtools. Thanks to Peter Cock and Lance Parsons for the updates
Brad Chapman <chapmanb@50mail.com>
parents:
1
diff
changeset
|
14 </requirements> |
0
d2c1af657010
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
brad-chapman
parents:
diff
changeset
|
15 <help> |
d2c1af657010
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
brad-chapman
parents:
diff
changeset
|
16 **What it does** |
d2c1af657010
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
brad-chapman
parents:
diff
changeset
|
17 |
2
e2edfa478eb4
Covert to use bedGraph intermediate with bedtools. Thanks to Peter Cock and Lance Parsons for the updates
Brad Chapman <chapmanb@50mail.com>
parents:
1
diff
changeset
|
18 Creates a coverage file in BigWig format, given a BAM alignment file. |
e2edfa478eb4
Covert to use bedGraph intermediate with bedtools. Thanks to Peter Cock and Lance Parsons for the updates
Brad Chapman <chapmanb@50mail.com>
parents:
1
diff
changeset
|
19 |
e2edfa478eb4
Covert to use bedGraph intermediate with bedtools. Thanks to Peter Cock and Lance Parsons for the updates
Brad Chapman <chapmanb@50mail.com>
parents:
1
diff
changeset
|
20 Gaps or skips (CIGAR D or N operators) are not counted towards the coverage calculation, which is important when mapping RNA Seq reads to genes with introns. |
0
d2c1af657010
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
brad-chapman
parents:
diff
changeset
|
21 |
d2c1af657010
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
brad-chapman
parents:
diff
changeset
|
22 **Input** |
d2c1af657010
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
brad-chapman
parents:
diff
changeset
|
23 |
d2c1af657010
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
brad-chapman
parents:
diff
changeset
|
24 A BAM alignment file. This needs to have the genome database build used in alignment annotated. If your file has '?' for the database build, click on the pencil icon to edit the alignment attributes, and specify the organism used to align against. |
d2c1af657010
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
brad-chapman
parents:
diff
changeset
|
25 |
d2c1af657010
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
brad-chapman
parents:
diff
changeset
|
26 **Output** |
d2c1af657010
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
brad-chapman
parents:
diff
changeset
|
27 |
d2c1af657010
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
brad-chapman
parents:
diff
changeset
|
28 BigWig files can be loaded directly from Galaxy into the UCSC browser. They can be loaded incrementally by UCSC, so a single file can be used to represent the entire genome without having to upload the entire thing as a custom track. |
d2c1af657010
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
brad-chapman
parents:
diff
changeset
|
29 </help> |
d2c1af657010
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
brad-chapman
parents:
diff
changeset
|
30 </tool> |