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annotate facets_analysis.xml @ 7:86bcdc94b008 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/facets commit 2da49e9385ddce5c74e077c81a52ff1ea4131b81
author artbio
date Wed, 08 Oct 2025 17:41:18 +0000
parents 625038b7d764
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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 --vcf_min_nhet $filtering.vcf_min_nhet
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27 --vcf_min_num_mark $filtering.vcf_min_num_mark
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28 ]]></command>
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29 <inputs>
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30 <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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31
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32 <param name="cval" type="float" value="150" label="Critical value for segmentation (cval)"
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33 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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34 <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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36 <param name="gbuild" type="select" label="Genome Build">
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37 <option value="hg38" selected="true">Human (hg38)</option>
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38 <option value="hg19">Human (hg19)</option>
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39 <option value="hg18">Human (hg18)</option>
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40 <option value="mm10">Mouse (mm10)</option>
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41 <option value="mm9">Mouse (mm9)</option>
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42 </param>
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43 <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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44 <conditional name="merging">
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45 <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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46 <option value="no" selected="true">No</option>
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47 <option value="yes">Yes</option>
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48 </param>
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49 <when value="no"/>
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50 <when value="yes">
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51 <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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52 <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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53 </when>
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54 </conditional>
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55 <section name="filtering" title="VCF Output Filtering" expanded="false">
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56 <param name="vcf_min_nhet" type="integer" value="2" label="Minimum heterozygous SNPs for VCF output" help="Post-filter to remove final segments with fewer than this many heterozygous SNPs."/>
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57 <param name="vcf_min_num_mark" type="integer" value="3" label="Minimum total markers for VCF output" help="Post-filter to remove final segments with fewer than this many total markers (SNPs). Helps remove SVLEN=0 artifacts."/>
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58 </section>
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59 </inputs>
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60 <outputs>
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61 <data name="output_seg" format="tsv" label="FACETS Segmentation on ${on_string}"/>
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62 <data name="output_summary" format="tabular" label="FACETS Summary on ${on_string}"/>
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63 <data name="output_plots" format="png" label="FACETS Plots on ${on_string}"/>
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64 <data name="output_spider" format="png" label="FACETS Spider Plot on ${on_string}"/>
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65 <data name="output_vcf" format="vcf" label="FACETS CNV calls (VCF) on ${on_string}"/>
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66
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67 </outputs>
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68 <tests>
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69 <test>
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70 <param name="pileup" value="Pileup.input_test_facets.csv.gz" ftype="tabular.gz"/>
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71 <output name="output_seg" file="test_sample_01.seg.tsv" ftype="tsv"/>
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72 <output name="output_summary" file="test_sample_01.summary.txt" ftype="tabular"/>
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73 <output name="output_plots" file="test_sample_01.plots.png" ftype="png" compare="sim_size" delta="20000"/>
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74 <output name="output_spider" file="test_sample_01.spider.png" ftype="png" compare="sim_size" delta="10000"/>
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75 <output name="output_vcf" file="test_sample_01.cnv.vcf" ftype="vcf" lines_diff="2" />
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76 </test>
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77 </tests>
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78 <help><![CDATA[
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79 **What it does**
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81 This tool runs the `FACETS` R package to perform allele-specific copy number
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82 and clonal heterogeneity analysis. It takes the compressed pileup file
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83 generated by the "SNP Pileup for FACETS" tool as its primary input and
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84 produces a set of standard FACETS outputs.
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86 ---
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87
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88 **Primary Parameters**
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89
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90 These parameters control the core of the FACETS segmentation algorithm.
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91
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92 - **Critical value for segmentation (cval):** This is the most important
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93 parameter for controlling the sensitivity. A *higher* value (e.g., 200-800)
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94 results in fewer segments (less sensitive) and is recommended for
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95 high-density data (WGS). A *lower* value (e.g., 50-150) increases
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96 sensitivity and is more suitable for sparser data (WES).
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97
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98 - **Minimum number of heterozygous SNPs (min.nhet):** This is a quality
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99 filter. Segments supported by fewer heterozygous SNPs than this
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100 threshold will be discarded during the initial segmentation pass.
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101
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102 - **SNP neighbourhood size (snp.nbhd):** Defines the genomic window (in bp)
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103 around a SNP used for local read depth normalization.
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104
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105 ---
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106
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107 **Advanced VCF Post-processing**
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108
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109 You can optionally enable post-processing steps to refine the final VCF.
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110
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111 - **Merging Segments:** This option merges adjacent CNV segments that likely
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112 represent a single biological event, providing a cleaner and more
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113 biologically accurate output.
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114
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115 - **Filtering Segments:** This option removes low-quality or artefactual
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116 segments based on the number of SNPs supporting them. This is recommended
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117 as FACETS can sometimes report micro-segments that are not biologically
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118 relevant.
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119
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120 ---
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121
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122 **Outputs**
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123
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124 - **Segmentation file (TSV):** The raw segment data with genomic coordinates
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125 and their associated copy number (TCN, LCN).
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126 - **Summary file:** The main estimated parameters like purity, ploidy, etc.
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127 - **Plots file (PNG):** A genome-wide visualization of the copy number and
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128 allelic imbalance results across all chromosomes.
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129 - **Spider Plot (PNG):** The most important **diagnostic plot** for assessing
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130 the quality of the FACETS fit. See detailed explanation below.
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131 - **CNV calls file (VCF):** A summary of the detected copy number events in
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132 a standard VCF format for structural variants. The `ALT` column contains
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133 symbolic alleles (`<DEL>`, `<DUP>`). All FACETS-specific details are in
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134 the `INFO` field:
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135
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136 ``SVTYPE``
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137 Type of variant (e.g., DEL, DUP).
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138 ``EVENT``
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139 FACETS classification (e.g., HOMOZYG_DEL, CN_LOH).
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140 ``TCN``
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141 Total Copy Number.
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142 ``LCN``
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143 Lesser Copy Number.
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144 ``NUM_MARK``
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145 Total number of SNPs in the segment.
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146 ``NHET``
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147 Number of heterozygous SNPs in the segment.
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148
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149 **Interpreting the Spider Plot**
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150
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151 On this plot (generated by the `logRlogORspider` function), each
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152 **circle** is a genomic segment from your data. The **curves** (labeled
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153 `2-1`, `1-0`, etc.) represent the theoretical positions for integer copy
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154 number states. A high-confidence result is achieved when your data (the
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155 circles) align closely with these curves. For details, refer to the
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156 original FACETS publication: Shen and Seshan, *NAR*, 2016.
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157
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158 ]]></help>
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159 <expand macro="citations"/>
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160 </tool>