view cpt_wig_bigwig/wigToBigWig.xml @ 0:4939ae73e79b draft

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<tool id="edu.tamu.cpt.util.wigToBigWig" name="Wig to BigWig" version="19.1.0.0" profile="16.04">
	<description>CPT version accepts fasta input for genome lengths.</description>
	<macros>
		<import>macros.xml</import>
		<import>cpt-macros.xml</import>
	</macros>
	<expand macro="requirements">
		<requirement type="package" version="377">ucsc-wigtobigwig</requirement>
	</expand>
	<command detect_errors="aggressive"><![CDATA[
python $__tool_directory__/fasta_len.py '$genomes' > 'chrom.len';

grep -v "^track" '$wigFile' |
wigToBigWig -clip stdin chrom.len '$bigwig'
]]></command>
	<inputs>
		<param name="wigFile" type="data" format="wig" label="Wig File"/>
		<param name="genomes" type="data" format="fasta" label="Fasta File"
			help="File containing fasta sequences referenced by wig file"/>
	</inputs>
	<outputs>
		<data format="bigwig" name="bigwig" />
	</outputs>
        <tests>
          <test>
            <param name="wigFile" value="T7_BW_I_REBASE.wig" />
            <param name="genomes" value="T7_CLEAN.fasta" />
            <output name="bigwig" value="T7_BW_I_REBASE.bigwig" />
          </test>
        </tests>
	<help><![CDATA[
**What it does**

Convert wig to bigWig
]]></help>
	<expand macro="citations">
		<citation type="doi">10.1093/bioinformatics/btq351</citation>
	</expand>
	
</tool>