<tool id="bam_to_bigwig" name="BAM to BigWig" version="0.0.1">
  <description>Calculates coverage from a BAM alignment file</description>
  <command>bam_to_wiggle.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>

<help>
**What it does**

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

**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>