Mercurial > repos > artbio > snvtocnv
diff sequenza_index.xml @ 0:b77d7a0a45e8 draft
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit 10ad3a0ca7cd23ad1e0940844147e1d1b3d069f0"
author | artbio |
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date | Sun, 07 Mar 2021 23:19:59 +0000 |
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children | e0724d649885 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/sequenza_index.xml Sun Mar 07 23:19:59 2021 +0000 @@ -0,0 +1,63 @@ +<tool id="sequenzaindex" name="create GC_wiggle of reference genome" version="0.7.0"> + <description> + </description> + <macros> + <import>macro.xml</import> + </macros> + <requirements> + <requirement type="package" version="3.0.0">sequenza-utils</requirement> + </requirements> + <stdio> + <exit_code range="1:" level="fatal" description="Error occured" /> + </stdio> + <command detect_errors="exit_code"><![CDATA[ + @pipefail@ + sequenza-utils gc_wiggle --fasta $reference -o $refwig -w $window + ]]></command> + <inputs> + <param name="reference" type="data" format="fasta" label="Genome in fasta format" + help="the fasta genome whose GC content will be indexed"/> + <param name="window" type="integer" value="50" label="window size" help="The size of the wiggle for GC content calculation" /> + </inputs> + <outputs> + <data name="refwig" format="txt" label="reference_wig" /> + </outputs> + <tests> + <test> + <param name="window" value="100" ftype="vcf" /> + <param name="reference" value="hg19_chr22.fa.gz" /> + <output name="refwig" file="hg19.GCref.txt" ftype="txt" /> + </test> + <test> + <param name="window" value="100" ftype="vcf" /> + <param name="reference" value="hg38_chr22.fa.gz" /> + <output name="refwig" file="hg38.GCref.txt" ftype="txt" /> + </test> + + </tests> + <help> + +snvtocnv +============================ + +Analyzes genomic sequencing data from paired normal-tumor samples, including +cellularity and ploidy estimation; mutation and copy number (allele-specific and total +copy number) detection, quantification and visualization. + +This tools builds the GC wigle index of the reference genome required to perform analysis +of the somatic single nucleotide variations using the tool "Infer CNVs from SNVs" + + +Inputs +-------- + +The reference genome in a fasta format + +*Warning* the genome fasta must be sorted according to the chromosomes +(e.g. chr1, chr2, .. chr21, chr22) + + </help> + <citations> + <citation type="doi">10.1093/annonc/mdu479</citation> + </citations> +</tool>