view bam_to_bigwig/bam_to_bigwig.xml @ 2:e2edfa478eb4

Covert to use bedGraph intermediate with bedtools. Thanks to Peter Cock and Lance Parsons for the updates

<tool id="bam_to_bigwig" name="BAM to BigWig" version="0.1.0">
  <description>Calculates coverage from a BAM alignment file</description>
  <command interpreter="python">bam_to_bigwig.py $align --outfile=$out</command>
  <inputs>
    <param format="bam" name="align" type="data" label="BAM alignment file"/>
  </inputs>
  <outputs>
    <data format="bigwig" name="out" />
  </outputs>
  <requirements>
        <requirement type="python-module">pysam</requirement>
        <requirement type="binary">genomeCoverageBed</requirement>
        <requirement type="binary">bedGraphToBigWig</requirement>
  </requirements>
<help>
**What it does**

Creates a coverage file in BigWig format, given a BAM alignment file.

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.

**Input**

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.

**Output**

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.
</help>
</tool>