Mercurial > repos > iuc > cnvkit_theta

annotate theta.xml @ 1:73df332e3e7b draft default tip

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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 11:53:33 +0000
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1 <tool id="cnvkit_theta" name="CNVkit Theta" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
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2 <description>Convert segments to THetA2 input file format</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.reference' ./reference.cnn &&
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12 ln -s '$advanced_settings.vcf' ./sample.vcf &&
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13 cnvkit.py export theta
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14 ./sample.cns
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15 #if $advanced_settings.reference
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16 --reference ./reference.cnn
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17 #end if
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18 #if $advanced_settings.vcf
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19 --vcf ./sample.vcf
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20 #end if
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21 #if $advanced_settings.sample_id
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22 --sample-id '$advanced_settings.sample_id'
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23 #end if
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24 #if $advanced_settings.normal_id
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25 --normal-id '$advanced_settings.normal_id'
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26 #end if
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27 #if $advanced_settings.min_variant_depth
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28 --min-variant-depth $advanced_settings.min_variant_depth
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29 #end if
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30 #if $advanced_settings.zygosity_freq
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31 --zygosity-freq $advanced_settings.zygosity_freq
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32 #end if
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33 --output sample.cnv.input
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34 ]]></command>
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35 <inputs>
1
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36 <param name="input_segmented_file" type="data" format="cns,cnr" label="Segmented copy ratio data file (cns file)" help="" />
0
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37 <section name="advanced_settings" title="Advanced settings" expanded="false">
1
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38 <param argument="--reference" optional="true" type="data" format="cnn" label="Reference" help="Reference copy number profile (.cnn), or normal-sample bin-level log2 copy ratios (.cnr). Use if the tumor_segment input file does not contain a 'weight' column" />
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39 <param argument="--vcf" optional="true" type="data" format="vcf" label="VCF" help="VCF file containing SNVs observed in both the tumor and normal samples. Tumor sample ID should match the `tumor_segment` filename or be specified with sample ID" />
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40 <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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41 <param argument="--normal-id" type="text" label="Normal Id" help="Corresponding normal sample ID in the input VCF" />
0
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42 <param argument="--min-variant-depth" optional="true" type="integer" label="Minimum Variant Depth" min="1" value="20" help="Minimum read depth for a SNP in the VCF to be counted. [Default: 20]" />
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43 <param argument="--zygosity-freq" optional="true" type="float" label="Zygosity Frequency" min="0" value="0.25" help="Ignore VCF's genotypes (GT field) and instead infer zygosity from allele frequencies. [Default if used without a number: 0.25]" />
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44
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45 </section>
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46 </inputs>
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47 <outputs>
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48 <data name="CNVs_Theta" format="tabular" label="${tool.name} on ${on_string}: CNVs theta file" from_work_dir="sample.cnv.input" />
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49 </outputs>
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50 <tests>
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51 <test expect_num_outputs="1">
1
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52 <param name="input_segmented_file" ftype="cns" value="tumor.cns" />
0
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53 <output name="CNVs_Theta" file="sample.cnv.input" />
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54 </test>
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55 </tests>
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56 <help><![CDATA[
1
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58 Export the segmented copy number data (from a *.cns file) to THetA2 input file format (*.input).
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59
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60 -----
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62 **Copy Number Reference Profile (.cnn)**
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64 Tabular file defining the reference baseline built from control samples (e.g., normal samples). Used to normalize test samples.
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66 .. csv-table::
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67 :header-rows: 0
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69 "chromosome","Genomic chromosome (e.g., chr1, chrX)."
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70 "start","Start position of the bin."
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71 "end","End position of the bin."
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72 "gene","Gene name(s) (if applicable)."
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73 "log2","Reference log2 ratio (typically 0 for diploid regions)."
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74 "depth","Average read depth across control samples."
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75 "spread","Variability (standard deviation) of coverage in controls."
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76
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77 -----
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79 **Segmented log2 ratios (.cns)**
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81 Tabular file with smoothed, merged segments of stable copy number, derived from the .cnr file. Represents final CNV calls.
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82
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83 .. csv-table::
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84 :header-rows: 0
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85
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86 "chromosome","start, end: Genomic coordinates of the segment"
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87 "gene","Gene(s) overlapping the segment."
73df332e3e7b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
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88 "log2","Mean log2 ratio of the segment."
73df332e3e7b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
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89 "probes","Mean log2 ratio of the segment."
73df332e3e7b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
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90 "depth","Average read depth."
73df332e3e7b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
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91 "weight","Reliability weight."
73df332e3e7b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
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92 "p_value","Statistical confidence (lower = more significant)."
73df332e3e7b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit fc1282ec68b346988203ead860e9b9d6a47e9efb
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93
0
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94 ]]></help>
5458a2909ed8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
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95 <expand macro="citations" />
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96 </tool>
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97
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100