Mercurial > repos > artbio > snvtocnv
comparison snvtocnv.xml @ 0:b77d7a0a45e8 draft
"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 |
| parents | |
| children | d2833cfb3f08 |
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| -1:000000000000 | 0:b77d7a0a45e8 |
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| 1 <tool id="snvtocnv" name="Infer CNVs from SNVs" 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 <requirement type="package" version="3.0.0">r-sequenza</requirement> | |
| 10 <requirement type="package" version="1.6.6">r-optparse</requirement> | |
| 11 <requirement type="package" version="1.24.0">bioconductor-biocparallel</requirement> | |
| 12 <requirement type="package" version="1.3.0">r-tidyverse</requirement> | |
| 13 <requirement type="package" version="2021a=he74cb21_0">tzdata</requirement> | |
| 14 </requirements> | |
| 15 <stdio> | |
| 16 <exit_code range="1:" level="fatal" description="Error occured" /> | |
| 17 </stdio> | |
| 18 <command detect_errors="exit_code"><![CDATA[ | |
| 19 @pipefail@ | |
| 20 sequenza-utils snp2seqz -v '$input_snvs' -gc $refwig -o sample.seqz.gz && | |
| 21 sequenza-utils seqz_binning --seqz sample.seqz.gz -w 50 -o '$wiggle' && | |
| 22 Rscript $__tool_directory__/segmentation_sequenza.R | |
| 23 -i '$wiggle' | |
| 24 -s sample | |
| 25 -O test && | |
| 26 Rscript $__tool_directory__/sequenza_to_hrdtools_input.R | |
| 27 -i test/sample_segments.txt | |
| 28 -s test/sample_alternative_solutions.txt | |
| 29 -o '$cnvs' | |
| 30 ]]></command> | |
| 31 <inputs> | |
| 32 <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 </inputs> | |
| 35 <outputs> | |
| 36 <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="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 </outputs> | |
| 41 <tests> | |
| 42 <test> | |
| 43 <param name="input_snvs" value="hg19_chr22.vcf" ftype="vcf" /> | |
| 44 <param name="refwig" value="hg19.GCref.txt" /> | |
| 45 <output name="cnvs" file="hg19.cnv.tab" ftype="tabular" /> | |
| 46 </test> | |
| 47 <test> | |
| 48 <param name="input_snvs" value="hg38_chr22.vcf" ftype="vcf" /> | |
| 49 <param name="refwig" value="hg38.GCref.txt" /> | |
| 50 <output name="cnvs" file="hg38.cnv.tab" ftype="tabular" /> | |
| 51 </test> | |
| 52 </tests> | |
| 53 <help> | |
| 54 | |
| 55 snvtocnv | |
| 56 ============================ | |
| 57 | |
| 58 Analyze genomic sequencing data from paired normal-tumor samples, including | |
| 59 cellularity and ploidy estimation; mutation and copy number (allele-specific and total | |
| 60 copy number) detection, quantification and visualization. | |
| 61 | |
| 62 | |
| 63 Inputs | |
| 64 -------- | |
| 65 | |
| 66 A GC wigle of genome index generated with the tool "create GC_wiggle of reference genome" | |
| 67 available from this galaxy wrapper | |
| 68 | |
| 69 A vcf file of somatic *single* nucleotide variations observed in a tumor sample | |
| 70 | |
| 71 | |
| 72 </help> | |
| 73 <citations> | |
| 74 <citation type="doi">10.1093/annonc/mdu479</citation> | |
| 75 </citations> | |
| 76 </tool> |