Mercurial > repos > artbio > cnv_facets

annotate facets_analysis.xml @ 6:625038b7d764 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 8cced47697e5777fd60dacc60300e770bd409e9d
author artbio
date Mon, 06 Oct 2025 15:50:12 +0000
parents 1d56a6b5739f
children 86bcdc94b008
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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 #if $merging.merge_select == "yes":
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22 --enable_merging
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23 --merge_gap_abs $merging.max_gap_abs
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24 --merge_gap_rel $merging.max_gap_rel
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25 #end if
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26 ]]></command>
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27 <inputs>
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28 <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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29
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30 <param name="cval" type="float" value="150" label="Critical value for segmentation (cval)"
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31 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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32 <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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34 <param name="gbuild" type="select" label="Genome Build">
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35 <option value="hg38" selected="true">Human (hg38)</option>
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36 <option value="hg19">Human (hg19)</option>
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37 <option value="hg18">Human (hg18)</option>
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38 <option value="mm10">Mouse (mm10)</option>
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39 <option value="mm9">Mouse (mm9)</option>
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40 </param>
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41 <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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42 <conditional name="merging">
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43 <param name="merge_select" type="select" label="Post-process VCF to merge adjacent segments?" help="Optional step to merge adjacent CNV calls that likely represent a single biological event.">
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44 <option value="no" selected="true">No</option>
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45 <option value="yes">Yes</option>
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46 </param>
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47 <when value="no"/>
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48 <when value="yes">
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49 <param name="max_gap_abs" type="integer" value="1000000" label="Absolute maximum gap to merge (bp)" help="Maximum distance in base pairs allowed between two segments to consider them for merging."/>
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50 <param name="max_gap_rel" type="float" value="0.5" label="Relative maximum gap to merge (fraction)" help="Maximum relative distance, as a fraction of the average size of the two segments."/>
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51 </when>
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52 </conditional>
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53 </inputs>
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54 <outputs>
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55 <data name="output_seg" format="tsv" label="FACETS Segmentation on ${on_string}"/>
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56 <data name="output_summary" format="tabular" label="FACETS Summary on ${on_string}"/>
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57 <data name="output_plots" format="png" label="FACETS Plots on ${on_string}"/>
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58 <data name="output_spider" format="png" label="FACETS Spider Plot on ${on_string}"/>
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59 <data name="output_vcf" format="vcf" label="FACETS CNV calls (VCF) on ${on_string}"/>
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60
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61 </outputs>
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62 <tests>
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63 <test>
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64 <param name="pileup" value="Pileup.input_test_facets.csv.gz" ftype="tabular.gz"/>
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65 <output name="output_seg" file="test_sample_01.seg.tsv" ftype="tsv"/>
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66 <output name="output_summary" file="test_sample_01.summary.txt" ftype="tabular"/>
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67 <output name="output_plots" file="test_sample_01.plots.png" ftype="png" compare="sim_size" delta="20000"/>
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68 <output name="output_spider" file="test_sample_01.spider.png" ftype="png" compare="sim_size" delta="10000"/>
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69 <output name="output_vcf" file="test_sample_01.cnv.vcf" ftype="vcf" lines_diff="2" />
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70 </test>
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71 </tests>
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72 <help><![CDATA[
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73 **What it does**
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74
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75 This tool runs the `FACETS` R package to perform allele-specific copy number
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76 and clonal heterogeneity analysis. It takes the compressed pileup file
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77 generated by the "SNP Pileup for FACETS" tool as its primary input and
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78 produces a set of standard FACETS outputs, including segmentation calls,
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79 purity/ploidy estimates, plots, and a VCF file summarizing the CNV events.
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80
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81 ---
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83 **Primary Parameters**
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84
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85 These parameters control the core of the FACETS segmentation algorithm.
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86
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87 - **Critical value for segmentation (cval):** This is the most important
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88 parameter for controlling the sensitivity of the segmentation. A *higher*
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89 value (e.g., 200-800) will result in fewer segments and is generally
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90 recommended for high-density data like Whole Genome Sequencing (WGS).
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91 A *lower* value (e.g., 50-150) increases sensitivity, resulting in more
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92 segments, and is more suitable for sparser data like Whole Exome
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93 Sequencing (WES).
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94
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95 - **Minimum number of heterozygous SNPs (min.nhet):** This is a quality
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96 filter. After segmentation, any segment that is supported by fewer
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97 heterozygous SNPs than this threshold will be discarded. This helps
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98 to remove unreliable, small segments.
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99
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100 - **SNP neighbourhood size (snp.nbhd):** This parameter defines the genomic
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101 window (in bp) around a SNP used for local read depth normalization.
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102 The default value is generally appropriate.
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103
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104 ---
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105
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106 **Advanced VCF Post-processing: Merging Segments**
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107
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108 You can optionally enable a post-processing step to merge adjacent CNV
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109 segments in the output VCF.
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110
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111 *Why is this useful?*
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112 Segmentation algorithms can sometimes split a single, large biological event
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113 (e.g., a 10 Mb deletion) into several smaller, adjacent segments with the
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114 same copy number state. This feature attempts to correct this by merging
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115 these segments back together, providing a cleaner and more biologically
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116 accurate representation of the CNV landscape.
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117
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118 The merging is controlled by an algorithm using two thresholds:
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119
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120 - **Absolute maximum gap:** The maximum distance in base pairs allowed
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121 between two segments to even consider them for merging. This acts as a
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122 safeguard.
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123 - **Relative maximum gap:** The maximum distance allowed, expressed as a
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124 *fraction* of the average size of the two segments. This allows large
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125 gaps between large segments, but not between small ones, trying to mimic
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126 how a human expert would interpret the data.
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127
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128 ---
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129
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130 **Outputs**
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131
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132 - **Segmentation file (TSV):** The raw segment data with genomic coordinates
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133 and their associated copy number (TCN, LCN).
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134 - **Summary file:** The main estimated parameters like purity, ploidy, etc.
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135 - **CNV calls file (VCF):** A summary of the detected copy number events in
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136 a standard VCF format, suitable for downstream analysis.
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137 - **Plots file (PNG):** An enhanced visualization of the genome-wide results.
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138 - **Spider Plot (PNG):** This is the most important **diagnostic plot** for
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139 assessing the quality of the FACETS fit.
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140 On this plot (generated by the `logRlogORspider` function), each
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141 **circle** is a genomic segment from your data. The **curves** (labeled
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142 `2-1`, `1-0`, etc.) represent the theoretical positions for integer copy
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143 number states given the estimated purity and ploidy. A high-confidence
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144 result is achieved when your data (the circles) align closely with these
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145 theoretical curves. For a detailed interpretation, please refer to the
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146 original FACETS publication: Shen and Seshan, *NAR*, 2016.
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147 ]]></help>
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148 <expand macro="citations"/>
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149 </tool>