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comparison facets_analysis.xml @ 4:3f62267c4be7 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit e47e0ed100904318ef4aae661b763e049c358edf
author artbio
date Sun, 05 Oct 2025 18:42:30 +0000
parents d1914f4d9daf
children 1d56a6b5739f
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3:d1914f4d9daf 4:3f62267c4be7
11 --sample_id '$pileup.name' 11 --sample_id '$pileup.name'
12 --output_seg '$output_seg' 12 --output_seg '$output_seg'
13 --output_summary '$output_summary' 13 --output_summary '$output_summary'
14 --output_spider '$output_spider' 14 --output_spider '$output_spider'
15 --output_plots '$output_plots' 15 --output_plots '$output_plots'
16 --output_vcf '$output_vcf'
16 --cval $cval 17 --cval $cval
17 --min_nhet $min_nhet 18 --min_nhet $min_nhet
18 --snp_nbhd $snp_nbhd 19 --snp_nbhd $snp_nbhd
19 --gbuild '$gbuild' 20 --gbuild '$gbuild'
20 ]]></command> 21 ]]></command>
21 <inputs> 22 <inputs>
22 <param name="pileup" type="data" format="tabular.gz" label="FACETS Pileup File" help="Output from the 'SNP Pileup for FACETS' tool."/> 23 <param name="pileup" type="data" format="tabular.gz" label="FACETS Pileup File" help="Output from the 'SNP Pileup for FACETS' tool."/>
23 24
24 <param name="cval" type="float" value="150" label="Critical value for segmentation (cval)" help="Higher values lead to fewer segments (less sensitive). Lower values are more sensitive."/> 25 <param name="cval" type="float" value="150" label="Critical value for segmentation (cval)"
26 help="Higher values lead to fewer segments (less sensitive). Lower values are more sensitive. For dense data (e.g., from WGS), higher values like 400-800 are recommended."/>
25 <param name="min_nhet" type="integer" value="25" label="Minimum number of heterozygous SNPs per segment" help="Ensures that segments are supported by sufficient allelic information."/> 27 <param name="min_nhet" type="integer" value="25" label="Minimum number of heterozygous SNPs per segment" help="Ensures that segments are supported by sufficient allelic information."/>
26 28
27 <param name="gbuild" type="select" label="Genome Build"> 29 <param name="gbuild" type="select" label="Genome Build">
28 <option value="hg38" selected="true">Human (hg38)</option> 30 <option value="hg38" selected="true">Human (hg38)</option>
29 <option value="hg19">Human (hg19)</option> 31 <option value="hg19">Human (hg19)</option>
37 <outputs> 39 <outputs>
38 <data name="output_seg" format="tsv" label="FACETS Segmentation on ${on_string}"/> 40 <data name="output_seg" format="tsv" label="FACETS Segmentation on ${on_string}"/>
39 <data name="output_summary" format="tabular" label="FACETS Summary on ${on_string}"/> 41 <data name="output_summary" format="tabular" label="FACETS Summary on ${on_string}"/>
40 <data name="output_plots" format="png" label="FACETS Plots on ${on_string}"/> 42 <data name="output_plots" format="png" label="FACETS Plots on ${on_string}"/>
41 <data name="output_spider" format="png" label="FACETS Spider Plot on ${on_string}"/> 43 <data name="output_spider" format="png" label="FACETS Spider Plot on ${on_string}"/>
44 <data name="output_vcf" format="vcf" label="FACETS CNV calls (VCF) on ${on_string}"/>
42 45
43 </outputs> 46 </outputs>
44 <tests> 47 <tests>
45 <test> 48 <test>
46 <param name="pileup" value="Pileup.input_test_facets.csv.gz" ftype="tabular.gz"/> 49 <param name="pileup" value="Pileup.input_test_facets.csv.gz" ftype="tabular.gz"/>
47 <output name="output_seg" file="test_sample_01.seg.tsv" ftype="tsv"/> 50 <output name="output_seg" file="test_sample_01.seg.tsv" ftype="tsv"/>
48 <output name="output_summary" file="test_sample_01.summary.txt" ftype="tabular"/> 51 <output name="output_summary" file="test_sample_01.summary.txt" ftype="tabular"/>
49 <output name="output_plots" file="test_sample_01.plots.png" ftype="png" compare="sim_size" delta="20000"/> 52 <output name="output_plots" file="test_sample_01.plots.png" ftype="png" compare="sim_size" delta="20000"/>
50 <output name="output_spider" file="test_sample_01.spider.png" ftype="png" compare="sim_size" delta="10000"/> 53 <output name="output_spider" file="test_sample_01.spider.png" ftype="png" compare="sim_size" delta="10000"/>
54 <output name="output_vcf" file="test_sample_01.cnv.vcf" ftype="vcf" />
51 </test> 55 </test>
52 </tests> 56 </tests>
53 <help><![CDATA[ 57 <help><![CDATA[
54 **What it does** 58 **What it does**
55 59
56 This tool runs the `FACETS` R package to perform allele-specific copy number and clonal heterogeneity analysis. It takes the compressed pileup file generated by the "SNP Pileup for FACETS" tool as its primary input. 60 This tool runs the `FACETS` R package to perform allele-specific copy number and clonal heterogeneity analysis. It takes the compressed pileup file generated by the "SNP Pileup for FACETS" tool as its primary input.
57 61
58 The main outputs are: 62 **Outputs**
59 - A **Segmentation file (TSV)** with the genomic coordinates of each segment and their associated copy number (TCN, LCN), purity, and ploidy. 63
60 - A **Summary file** containing the main estimated parameters for the sample (purity, ploidy, etc.). 64 - A **Segmentation file (TSV)** with the genomic coordinates of each segment and their associated copy number (TCN, LCN).
61 - A **Plots file (PDF)** with standard FACETS visualizations for quality control and interpretation. 65 - A **Summary file** with the main estimated parameters (purity, ploidy, etc.).
66 - A **CNV calls file (VCF)** listing the detected copy number events in a standard VCF format.
67 - A **Plots file (PNG)** with an enhanced visualization of the genome-wide results, including a legend for copy number states.
68 - A **Spider Plot (PNG)** for diagnosing the quality of the purity/ploidy model fit.
62 ]]></help> 69 ]]></help>
63 <expand macro="citations"/> 70 <expand macro="citations"/>
64 </tool> 71 </tool>