<tool id="bam_to_bigwig" name="BAM to BigWig" version="0.2.0">

  <description>Calculates coverage from a BAM alignment file</description>

  <requirements>
    <requirement type="package" version="0.8.3">pysam</requirement>
    <requirement type="package" version="2.24">bedtools</requirement>
    <requirement type="package" version="312">ucsc_tools</requirement>
  </requirements>

  <command detect_errors="aggressive" interpreter="python"><![CDATA[
    bam_to_bigwig.py $align --outfile=$out --split
  ]]></command>

  <inputs>
    <param format="bam" name="align" type="data" label="BAM alignment file"/>
  </inputs>

  <outputs>
    <data format="bigwig" name="out" />
  </outputs>

  <tests>
    <test>
      <param name="align" value="bam_to_bigwig_test.bam"/>
      <output name="out" file="bam_to_bigwig_test.bigwig"/>
    </test>
  </tests>

<help><![CDATA[
**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>

  <citations>
    <citation type="doi">10.1093/bioinformatics/btp352</citation>
    <citation type="doi">10.1093/bioinformatics/btq033</citation>
  </citations>
</tool>