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comparison sequenza_index.xml @ 0:b77d7a0a45e8 draft

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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit 10ad3a0ca7cd23ad1e0940844147e1d1b3d069f0"
author artbio
date Sun, 07 Mar 2021 23:19:59 +0000
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1 <tool id="sequenzaindex" name="create GC_wiggle of reference genome" version="0.7.0">
2 <description>
3 </description>
4 <macros>
5 <import>macro.xml</import>
6 </macros>
7 <requirements>
8 <requirement type="package" version="3.0.0">sequenza-utils</requirement>
9 </requirements>
10 <stdio>
11 <exit_code range="1:" level="fatal" description="Error occured" />
12 </stdio>
13 <command detect_errors="exit_code"><![CDATA[
14 @pipefail@
15 sequenza-utils gc_wiggle --fasta $reference -o $refwig -w $window
16 ]]></command>
17 <inputs>
18 <param name="reference" type="data" format="fasta" label="Genome in fasta format"
19 help="the fasta genome whose GC content will be indexed"/>
20 <param name="window" type="integer" value="50" label="window size" help="The size of the wiggle for GC content calculation" />
21 </inputs>
22 <outputs>
23 <data name="refwig" format="txt" label="reference_wig" />
24 </outputs>
25 <tests>
26 <test>
27 <param name="window" value="100" ftype="vcf" />
28 <param name="reference" value="hg19_chr22.fa.gz" />
29 <output name="refwig" file="hg19.GCref.txt" ftype="txt" />
30 </test>
31 <test>
32 <param name="window" value="100" ftype="vcf" />
33 <param name="reference" value="hg38_chr22.fa.gz" />
34 <output name="refwig" file="hg38.GCref.txt" ftype="txt" />
35 </test>
36
37 </tests>
38 <help>
39
40 snvtocnv
41 ============================
42
43 Analyzes genomic sequencing data from paired normal-tumor samples, including
44 cellularity and ploidy estimation; mutation and copy number (allele-specific and total
45 copy number) detection, quantification and visualization.
46
47 This tools builds the GC wigle index of the reference genome required to perform analysis
48 of the somatic single nucleotide variations using the tool "Infer CNVs from SNVs"
49
50
51 Inputs
52 --------
53
54 The reference genome in a fasta format
55
56 *Warning* the genome fasta must be sorted according to the chromosomes
57 (e.g. chr1, chr2, .. chr21, chr22)
58
59 </help>
60 <citations>
61 <citation type="doi">10.1093/annonc/mdu479</citation>
62 </citations>
63 </tool>