Mercurial > repos > cpt > cpt_wig_bigwig
diff cpt_wig_bigwig/wigToBigWig.xml @ 0:4939ae73e79b draft
Uploaded
| author | cpt |
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| date | Fri, 13 May 2022 05:42:27 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cpt_wig_bigwig/wigToBigWig.xml Fri May 13 05:42:27 2022 +0000 @@ -0,0 +1,40 @@ +<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>