Mercurial > repos > iuc > cnvkit_export_vcf

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
author iuc
date Sat, 01 Mar 2025 11:55:26 +0000
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1 <tool id="cnvkit_export_vcf" name="CNVkit Export VCF" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
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2 <description>Converts the Segmented copy ratio data file (*.cns) file into VCF 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="xrefs"/>
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7 <expand macro="creators"/>
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8 <expand macro="requirements"/>
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9 <command detect_errors="exit_code"><![CDATA[
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10 ln -s '$input_segmented_file' ./sample.cns &&
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11 ln -s '$advanced_settings.cnr' ./sample.cnr &&
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12 cnvkit.py export vcf
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13 ./sample.cns
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14 #if $advanced_settings.cnr
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15 --cnr ./sample.cnr
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16 #end if
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17 #if $advanced_settings.sample_id
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18 --sample-id '$advanced_settings.sample_id'
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19 #end if
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20 #if $advanced_settings.ploidy
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21 --ploidy $advanced_settings.ploidy
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22 #end if
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23 #if str($advanced_settings.sample_sex) and $advanced_settings.sample_sex != ""
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24 --sample-sex '$advanced_settings.sample_sex'
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25 #end if
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26 $advanced_settings.male_reference
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27 --output sample.cnv.vcf
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28 #if $advanced_settings.diploid_parx_genome
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29 --diploid-parx-genome '$advanced_settings.diploid_parx_genome'
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30 #end if
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31 ]]></command>
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32 <inputs>
1
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33 <param name="input_segmented_file" type="data" format="cns" label="Segmented Copy Ratio Data File (cns file)" help="" />
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34 <section name="advanced_settings" title="Advanced settings" expanded="false">
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35 <param argument="--cnr" optional="true" type="data" format="cnr" label="Bin-level copy ratios (cnr)" help="" />
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36 <param argument="--sample-id" type="text" label="Sample ID" help="Sample name to write in the genotype field of the output VCF file" />
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37 <param argument="--ploidy" optional="true" type="integer" label="Ploidy" min="1" value="2" help="Ploidy of the sample cells. [Default: 2]" />
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38 <expand macro="sample_sex"/>
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39 <param argument="--male-reference" type="boolean" checked="false" truevalue="--male-reference" falsevalue="" label="MALE REFERENCE" help="Assume inputs were normalized to a male reference" />
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40 <param argument="--diploid-parx-genome" type="text" label="Diploid Parx Genome" help="Considers the given human genome's PAR of chromosome X as autosomal. Example: 'grch38'" />
0
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41 </section>
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42 </inputs>
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43 <outputs>
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44 <data name="CNVs_VCF" format="vcf" label="${tool.name} on ${on_string}: CNVs VCF file" from_work_dir="sample.cnv.vcf" />
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45 </outputs>
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46 <tests>
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47 <test expect_num_outputs="1">
1
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48 <param name="input_segmented_file" ftype="cns" value="sample.cns" />
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49 <param name="sample_id" value="SampleID" />
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50 <param name="sample_sex" value="Female" />
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51 <output name="CNVs_VCF" file="sample.cnv.vcf" ftype="vcf" lines_diff="2" />
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52 </test>
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53 </tests>
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54 <help><![CDATA[
1
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55 Export the segmented copy number data (from a .cns file) to the standard VCF 4.2 format.
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56 The resulting VCF file describes copy number gains and losses across each segment and contains
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57 INFO fields for breakpoints (CIPOS, CIEND) if bin-level data (.cnr) is provided.
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58
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59 -----
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61 **Bin-level log2 ratios (.cnr)**
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63 Tabular file containing normalized log2 ratios for small genomic bins (divided regions of the genome). Used to detect raw copy number variations (CNVs) before segmentation.
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64
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65 .. csv-table::
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66 :header-rows: 0
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67
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68 "chromosome","Genomic chromosome (e.g., chr1, chrX)"
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69 "start","Start position of the bin."
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70 "end","End position of the bin."
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71 "gene","Gene name(s) overlapping the bin (if applicable)."
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72 "log2","Normalized log2 ratio (sample coverage / reference coverage)."
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73 "depth","Average read depth in the bin."
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74 "weight","Reliability weight of the bin (higher = more reliable)."
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75
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76 -----
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78 **Segmented log2 ratios (.cns)**
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80 Tabular file with smoothed, merged segments of stable copy number, derived from the .cnr file. Represents final CNV calls.
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81
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82 .. csv-table::
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83 :header-rows: 0
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84
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85 "chromosome","start, end: Genomic coordinates of the segment"
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86 "gene","Gene(s) overlapping the segment."
974b39eb89b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
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87 "log2","Mean log2 ratio of the segment."
974b39eb89b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
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88 "probes","Mean log2 ratio of the segment."
974b39eb89b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
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89 "depth","Average read depth."
974b39eb89b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
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90 "weight","Reliability weight."
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91 "p_value","Statistical confidence (lower = more significant)."
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92
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93
0
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94 ]]></help>
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95 <expand macro="citations" />
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96 </tool>
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97
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98
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99
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100