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annotate facets_analysis.xml @ 5:1d56a6b5739f draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 7d1b40132efd24ac3c8a4b80cc5ca063636a2a38
author artbio
date Mon, 06 Oct 2025 13:39:01 +0000
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1 <tool id="facets_analysis" name="FACETS Analysis" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>Performs allele-specific copy number analysis from a pileup file</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <expand macro="stdio"/>
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8 <command detect_errors="exit_code"><![CDATA[
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9 Rscript '${__tool_directory__}/facets_analysis.R'
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10 --pileup '$pileup'
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11 --sample_id '$pileup.name'
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12 --output_seg '$output_seg'
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13 --output_summary '$output_summary'
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14 --output_spider '$output_spider'
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15 --output_plots '$output_plots'
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16 --output_vcf '$output_vcf'
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17 --cval $cval
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18 --min_nhet $min_nhet
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19 --snp_nbhd $snp_nbhd
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20 --gbuild '$gbuild'
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21 ]]></command>
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22 <inputs>
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23 <param name="pileup" type="data" format="tabular.gz" label="FACETS Pileup File" help="Output from the 'SNP Pileup for FACETS' tool."/>
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24
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25 <param name="cval" type="float" value="150" label="Critical value for segmentation (cval)"
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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."/>
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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."/>
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29 <param name="gbuild" type="select" label="Genome Build">
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30 <option value="hg38" selected="true">Human (hg38)</option>
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31 <option value="hg19">Human (hg19)</option>
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32 <option value="hg18">Human (hg18)</option>
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33 <option value="mm10">Mouse (mm10)</option>
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34 <option value="mm9">Mouse (mm9)</option>
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35 </param>
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37 <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."/>
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38 </inputs>
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39 <outputs>
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40 <data name="output_seg" format="tsv" label="FACETS Segmentation on ${on_string}"/>
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41 <data name="output_summary" format="tabular" label="FACETS Summary on ${on_string}"/>
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42 <data name="output_plots" format="png" label="FACETS Plots on ${on_string}"/>
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43 <data name="output_spider" format="png" label="FACETS Spider Plot on ${on_string}"/>
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44 <data name="output_vcf" format="vcf" label="FACETS CNV calls (VCF) on ${on_string}"/>
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45
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46 </outputs>
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47 <tests>
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48 <test>
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49 <param name="pileup" value="Pileup.input_test_facets.csv.gz" ftype="tabular.gz"/>
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50 <output name="output_seg" file="test_sample_01.seg.tsv" ftype="tsv"/>
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51 <output name="output_summary" file="test_sample_01.summary.txt" ftype="tabular"/>
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52 <output name="output_plots" file="test_sample_01.plots.png" ftype="png" compare="sim_size" delta="20000"/>
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53 <output name="output_spider" file="test_sample_01.spider.png" ftype="png" compare="sim_size" delta="10000"/>
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54 <output name="output_vcf" file="test_sample_01.cnv.vcf" ftype="vcf" lines_diff="2" />
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55 </test>
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56 </tests>
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57 <help><![CDATA[
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58 **What it does**
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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.
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61
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62 **Outputs**
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64 - A **Segmentation file (TSV)** with the genomic coordinates of each segment and their associated copy number (TCN, LCN).
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65 - A **Summary file** with the main estimated parameters (purity, ploidy, etc.).
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66 - A **CNV calls file (VCF)** listing the detected copy number events in a standard VCF format.
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67 - A **Plots file (PNG)** with an enhanced visualization of the genome-wide results, including a legend for copy number states.
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68 - A **Spider Plot (PNG)** for diagnosing the quality of the purity/ploidy model fit.
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69 ]]></help>
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70 <expand macro="citations"/>
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71 </tool>