Mercurial > repos > cpt > cpt_wig_bigwig
comparison cpt_wig_bigwig/wigToBigWig.xml @ 0:4939ae73e79b draft
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| author | cpt |
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| date | Fri, 13 May 2022 05:42:27 +0000 |
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| -1:000000000000 | 0:4939ae73e79b |
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| 1 <tool id="edu.tamu.cpt.util.wigToBigWig" name="Wig to BigWig" version="19.1.0.0" profile="16.04"> | |
| 2 <description>CPT version accepts fasta input for genome lengths.</description> | |
| 3 <macros> | |
| 4 <import>macros.xml</import> | |
| 5 <import>cpt-macros.xml</import> | |
| 6 </macros> | |
| 7 <expand macro="requirements"> | |
| 8 <requirement type="package" version="377">ucsc-wigtobigwig</requirement> | |
| 9 </expand> | |
| 10 <command detect_errors="aggressive"><![CDATA[ | |
| 11 python $__tool_directory__/fasta_len.py '$genomes' > 'chrom.len'; | |
| 12 | |
| 13 grep -v "^track" '$wigFile' | | |
| 14 wigToBigWig -clip stdin chrom.len '$bigwig' | |
| 15 ]]></command> | |
| 16 <inputs> | |
| 17 <param name="wigFile" type="data" format="wig" label="Wig File"/> | |
| 18 <param name="genomes" type="data" format="fasta" label="Fasta File" | |
| 19 help="File containing fasta sequences referenced by wig file"/> | |
| 20 </inputs> | |
| 21 <outputs> | |
| 22 <data format="bigwig" name="bigwig" /> | |
| 23 </outputs> | |
| 24 <tests> | |
| 25 <test> | |
| 26 <param name="wigFile" value="T7_BW_I_REBASE.wig" /> | |
| 27 <param name="genomes" value="T7_CLEAN.fasta" /> | |
| 28 <output name="bigwig" value="T7_BW_I_REBASE.bigwig" /> | |
| 29 </test> | |
| 30 </tests> | |
| 31 <help><![CDATA[ | |
| 32 **What it does** | |
| 33 | |
| 34 Convert wig to bigWig | |
| 35 ]]></help> | |
| 36 <expand macro="citations"> | |
| 37 <citation type="doi">10.1093/bioinformatics/btq351</citation> | |
| 38 </expand> | |
| 39 | |
| 40 </tool> |