Mercurial > repos > cpt > cpt_wig_bigwig

annotate wigToBigWig.xml @ 3:b741d86046a6 draft

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