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Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
author brad-chapman
date Tue, 07 Jun 2011 16:25:46 -0400
parents
children 0ff100a057ef
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d2c1af657010 Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
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1 <tool id="bam_to_bigwig" name="BAM to BigWig" version="0.0.1">
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2 <description>Calculates coverage from a BAM alignment file</description>
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3 <command>bam_to_wiggle.py $align --outfile=$out</command>
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4 <inputs>
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5 <param format="bam" name="align" type="data" label="BAM alignment file"/>
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6 </inputs>
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7 <outputs>
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8 <data format="bigwig" name="out" />
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9 </outputs>
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10
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11 <help>
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12 **What it does**
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14 Creates a coverage file in BigWig format, given a BAM alignment file.
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15
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16 **Input**
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18 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.
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19
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20 **Output**
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22 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.
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23 </help>
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25 </tool>