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comparison wigToBigWig.xml @ 3:b741d86046a6 draft

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planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
author cpt
date Mon, 05 Jun 2023 02:54:00 +0000
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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" help="File containing fasta sequences referenced by wig file"/>
19 </inputs>
20 <outputs>
21 <data format="bigwig" name="bigwig"/>
22 </outputs>
23 <tests>
24 <test>
25 <param name="wigFile" value="T7_BW_I_REBASE.wig"/>
26 <param name="genomes" value="T7_CLEAN.fasta"/>
27 <output name="bigwig" value="T7_BW_I_REBASE.bigwig"/>
28 </test>
29 </tests>
30 <help><![CDATA[
31 **What it does**
32
33 Convert wig to bigWig
34 ]]></help>
35 <expand macro="citations">
36 <citation type="doi">10.1093/bioinformatics/btq351</citation>
37 </expand>
38 </tool>