Mercurial > repos > brad-chapman > bam_to_bigwig

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