Mercurial > repos > artbio > cnv_facets

comparison facets_analysis.xml @ 2:66a56502199d draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 0176d2cc4f1caf0ab948ef72efb25ccce735461e
author artbio
date Fri, 03 Oct 2025 23:59:36 +0000
parents
children d1914f4d9daf
comparison
equal deleted inserted replaced
1:8e1fb7253c1d 2:66a56502199d
1 <tool id="facets_analysis" name="FACETS Analysis" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>Performs allele-specific copy number analysis from a pileup file</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <expand macro="stdio"/>
8 <command detect_errors="exit_code"><![CDATA[
9 Rscript '${__tool_directory__}/facets_analysis.R'
10 --pileup '$pileup'
11 --sample_id '$pileup.name'
12 --output_seg '$output_seg'
13 --output_summary '$output_summary'
14 --output_plots '$output_plots'
15 --cval $cval
16 --min_nhet $min_nhet
17 --snp_nbhd $snp_nbhd
18 --gbuild '$gbuild'
19 ]]></command>
20 <inputs>
21 <param name="pileup" type="data" format="tabular.gz" label="FACETS Pileup File" help="Output from the 'SNP Pileup for FACETS' tool."/>
22
23 <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."/>
24 <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."/>
25
26 <param name="gbuild" type="select" label="Genome Build">
27 <option value="hg38" selected="true">Human (hg38)</option>
28 <option value="hg19">Human (hg19)</option>
29 <option value="hg18">Human (hg18)</option>
30 <option value="mm10">Mouse (mm10)</option>
31 <option value="mm9">Mouse (mm9)</option>
32 </param>
33
34 <param name="snp_nbhd" type="integer" value="300" label="SNP neighborhood size (snp.nbhd)" help="Should match the --pseudo-snps distance used to generate the pileup file. Default is 300."/>
35 </inputs>
36 <outputs>
37 <data name="output_seg" format="tsv" label="FACETS Segmentation on ${on_string}"/>
38 <data name="output_summary" format="tabular" label="FACETS Summary on ${on_string}"/>
39 <data name="output_plots" format="pdf" label="FACETS Plots on ${on_string}"/>
40 </outputs>
41 <tests>
42 <test>
43 <param name="pileup" value="Pileup.input_test_facets.csv.gz" ftype="tabular.gz"/>
44 <output name="output_seg" file="test_sample_01.seg.tsv" ftype="tsv"/>
45 <output name="output_summary" file="test_sample_01.summary.txt" ftype="tabular"/>
46 <output name="output_plots" file="test_sample_01.plots.pdf" ftype="pdf" compare="sim_size" delta="1000"/>
47 </test>
48 </tests>
49 <help><![CDATA[
50 **What it does**
51
52 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.
53
54 The main outputs are:
55 - A **Segmentation file (TSV)** with the genomic coordinates of each segment and their associated copy number (TCN, LCN), purity, and ploidy.
56 - A **Summary file** containing the main estimated parameters for the sample (purity, ploidy, etc.).
57 - A **Plots file (PDF)** with standard FACETS visualizations for quality control and interpretation.
58 ]]></help>
59 <expand macro="citations"/>
60 </tool>