Mercurial > repos > yating-l > bamtobigwig

annotate bam_to_bigwig.xml @ 0:61f39c77b13d draft

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author yating-l
date Wed, 12 Apr 2017 17:52:09 -0400
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61f39c77b13d planemo upload commit 250051c3d660df43da92c76913552767ce142a45
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1 <tool id="bam_to_bigwig" name="Convert Bam to BigWig" version="0.1.0">
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2 <requirements>
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3 <requirement type="package" version="1.0">ucsc_tools_340</requirement>
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4 <requirement type="package" version="2.24">bedtools</requirement>
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5 </requirements>
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6 <stdio>
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7 <exit_code range="1:" />
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8 </stdio>
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9 <command><![CDATA[
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10 faToTwoBit $input_reference_fasta two_bit.2bit;
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11 twoBitInfo two_bit.2bit stdout | sort -k2nr > chrom.sizes;
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12 bedtools genomecov -bg -split -ibam $input_bam -g chrom.sizes > temp.bg;
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13 bedGraphToBigWig temp.bg chrom.sizes $output_bigwig;
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14 ]]></command>
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15 <inputs>
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16 <param format="bam" name="input_bam" type="data" label="Choose BAM file" />
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17 <param format="fasta" name="input_reference_fasta"
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18 type="data" label="Choose Reference Genome (Fasta)" />
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19 </inputs>
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20 <outputs>
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21 <data format="bigwig" name="output_bigwig" />
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22 </outputs>
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23 <help>
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24 This tool converts a Bam file to a BigWig file.
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25
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26 It needs:
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27 - A Bam file
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28 - The reference genome as a Fasta file
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29 </help>
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30 </tool>