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comparison snvtocnv.xml @ 1:d2833cfb3f08 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/snvtocnv commit aa1b68e64cbbdcdd9167134ec2ea61a151333688
author artbio
date Thu, 19 May 2022 20:35:24 +0000
parents b77d7a0a45e8
children e0724d649885
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0:b77d7a0a45e8 1:d2833cfb3f08
1 <tool id="snvtocnv" name="Infer CNVs from SNVs" version="0.7.0"> 1 <tool id="snvtocnv" name="Infer CNVs from SNVs" version="3.0.0+galaxy0">
2 <description> 2 <description>
3 </description> 3 </description>
4 <macros> 4 <macros>
5 <import>macro.xml</import> 5 <import>macro.xml</import>
6 </macros> 6 </macros>
24 -s sample 24 -s sample
25 -O test && 25 -O test &&
26 Rscript $__tool_directory__/sequenza_to_hrdtools_input.R 26 Rscript $__tool_directory__/sequenza_to_hrdtools_input.R
27 -i test/sample_segments.txt 27 -i test/sample_segments.txt
28 -s test/sample_alternative_solutions.txt 28 -s test/sample_alternative_solutions.txt
29 -o '$cnvs' 29 -o '$cnvs' &&
30 ls test
30 ]]></command> 31 ]]></command>
31 <inputs> 32 <inputs>
32 <param name="refwig" type="data" format="txt" label="GC wigle of reference genome"/> 33 <param name="refwig" type="data" format="txt" label="GC wigle of reference genome"/>
33 <param name="input_snvs" type="data" format="vcf" label="SNVs to process in a vcf file"/> 34 <param name="input_snvs" type="data" format="vcf" label="SNVs to process in a vcf file"/>
34 </inputs> 35 </inputs>
35 <outputs> 36 <outputs>
36 <data name="wiggle" format="txt" label="binned wiggle" /> 37 <data name="wiggle" format="txt" label="binned wiggle" />
37 <data name="sample_segment" format="txt" label="sample segments" from_work_dir="test/sample_segments.txt" /> 38 <data name="sample_segment" format="txt" label="sample segments" from_work_dir="test/sample_segments.txt" />
38 <data name="alt_solutions" format="txt" label="alternate solutions" from_work_dir="test/sample_alternative_solutions.txt" /> 39 <data name="alt_solutions" format="txt" label="alternate solutions" from_work_dir="test/sample_alternative_solutions.txt" />
39 <data name="cnvs" format="tabular" label="Annotated CNVs" /> 40 <data name="cnvs" format="tabular" label="Annotated CNVs" />
41 <data name="chrom_depths" format="pdf" label="Chromosomes sequencing depth" from_work_dir="test/sample_chromosome_depths.pdf"/>
42 <data name="chrom_view" format="pdf" label="Chromosomes views" from_work_dir="test/sample_chromosome_view.pdf"/>
43 <data name="genome_view" format="pdf" label="Genome view" from_work_dir="test/sample_genome_view.pdf"/>
44 <data name="model_fit" format="pdf" label="Cellularity and Diploidy model" from_work_dir="test/sample_model_fit.pdf"/>
45 <data name="CN_histo" format="pdf" label="Copy Numbers histogram" from_work_dir="test/sample_CN_bars.pdf"/>
40 </outputs> 46 </outputs>
41 <tests> 47 <tests>
42 <test> 48 <test>
43 <param name="input_snvs" value="hg19_chr22.vcf" ftype="vcf" /> 49 <param name="input_snvs" value="hg19_chr22.vcf" ftype="vcf" />
44 <param name="refwig" value="hg19.GCref.txt" /> 50 <param name="refwig" value="hg19.GCref.txt" />
45 <output name="cnvs" file="hg19.cnv.tab" ftype="tabular" /> 51 <output name="cnvs" file="hg19.cnv.tab" ftype="tabular" />
52 <output name="chrom_depths" ftype="pdf" file="hg19_chrom_depths.pdf"/>
53 <output name="chrom_view" ftype="pdf" file="hg19_chrom_view.pdf"/>
54 <output name="genome_view" ftype="pdf" file="hg19_genome_view.pdf"/>
55 <output name="model_fit" ftype="pdf" file="hg19_model.pdf"/>
56 <output name="CN_histo" ftype="pdf" file="hg19_CN_histo.pdf"/>
46 </test> 57 </test>
47 <test> 58 <test>
48 <param name="input_snvs" value="hg38_chr22.vcf" ftype="vcf" /> 59 <param name="input_snvs" value="hg38_chr22.vcf" ftype="vcf" />
49 <param name="refwig" value="hg38.GCref.txt" /> 60 <param name="refwig" value="hg38.GCref.txt" />
50 <output name="cnvs" file="hg38.cnv.tab" ftype="tabular" /> 61 <output name="cnvs" file="hg38.cnv.tab" ftype="tabular" />
62 <output name="chrom_depths" ftype="pdf" file="hg38_chrom_depths.pdf"/>
63 <output name="chrom_view" ftype="pdf" file="hg38_chrom_view.pdf"/>
64 <output name="genome_view" ftype="pdf" file="hg38_genome_view.pdf"/>
65 <output name="model_fit" ftype="pdf" file="hg38_model.pdf"/>
66 <output name="CN_histo" ftype="pdf" file="hg38_CN_histo.pdf"/>
51 </test> 67 </test>
52 </tests> 68 </tests>
53 <help> 69 <help>
54 70
55 snvtocnv 71 snvtocnv