Mercurial > repos > yating-l > bamtobigwig

comparison bam_to_bigwig.xml @ 1:2e812b4f91ce draft default tip

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planemo upload commit 250051c3d660df43da92c76913552767ce142a45-dirty
author yating-l
date Tue, 30 May 2017 18:18:20 -0400
parents 61f39c77b13d
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0:61f39c77b13d 1:2e812b4f91ce
7 <exit_code range="1:" /> 7 <exit_code range="1:" />
8 </stdio> 8 </stdio>
9 <command><![CDATA[ 9 <command><![CDATA[
10 faToTwoBit $input_reference_fasta two_bit.2bit; 10 faToTwoBit $input_reference_fasta two_bit.2bit;
11 twoBitInfo two_bit.2bit stdout | sort -k2nr > chrom.sizes; 11 twoBitInfo two_bit.2bit stdout | sort -k2nr > chrom.sizes;
12 bedtools genomecov -bg -split -ibam $input_bam -g chrom.sizes > temp.bg; 12 bedtools genomecov -bg -split -ibam $input_bam -g chrom.sizes
13 | LC_COLLATE=C sort -k1,1 -k2,2n
14 > temp.bg &&
13 bedGraphToBigWig temp.bg chrom.sizes $output_bigwig; 15 bedGraphToBigWig temp.bg chrom.sizes $output_bigwig;
14 ]]></command> 16 ]]></command>
15 <inputs> 17 <inputs>
16 <param format="bam" name="input_bam" type="data" label="Choose BAM file" /> 18 <param format="bam" name="input_bam" type="data" label="Choose BAM file" />
17 <param format="fasta" name="input_reference_fasta" 19 <param format="fasta" name="input_reference_fasta"