Mercurial > repos > yating-l > bamtobigwig
comparison bam_to_bigwig.xml @ 0:61f39c77b13d draft
planemo upload commit 250051c3d660df43da92c76913552767ce142a45
| author | yating-l |
|---|---|
| date | Wed, 12 Apr 2017 17:52:09 -0400 |
| parents | |
| children | 2e812b4f91ce |
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| -1:000000000000 | 0:61f39c77b13d |
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| 1 <tool id="bam_to_bigwig" name="Convert Bam to BigWig" version="0.1.0"> | |
| 2 <requirements> | |
| 3 <requirement type="package" version="1.0">ucsc_tools_340</requirement> | |
| 4 <requirement type="package" version="2.24">bedtools</requirement> | |
| 5 </requirements> | |
| 6 <stdio> | |
| 7 <exit_code range="1:" /> | |
| 8 </stdio> | |
| 9 <command><![CDATA[ | |
| 10 faToTwoBit $input_reference_fasta two_bit.2bit; | |
| 11 twoBitInfo two_bit.2bit stdout | sort -k2nr > chrom.sizes; | |
| 12 bedtools genomecov -bg -split -ibam $input_bam -g chrom.sizes > temp.bg; | |
| 13 bedGraphToBigWig temp.bg chrom.sizes $output_bigwig; | |
| 14 ]]></command> | |
| 15 <inputs> | |
| 16 <param format="bam" name="input_bam" type="data" label="Choose BAM file" /> | |
| 17 <param format="fasta" name="input_reference_fasta" | |
| 18 type="data" label="Choose Reference Genome (Fasta)" /> | |
| 19 </inputs> | |
| 20 <outputs> | |
| 21 <data format="bigwig" name="output_bigwig" /> | |
| 22 </outputs> | |
| 23 <help> | |
| 24 This tool converts a Bam file to a BigWig file. | |
| 25 | |
| 26 It needs: | |
| 27 - A Bam file | |
| 28 - The reference genome as a Fasta file | |
| 29 </help> | |
| 30 </tool> |