Mercurial > repos > iuc > cnvkit_theta

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

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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
parents 5458a2909ed8
children
comparison
equal deleted inserted replaced
0:5458a2909ed8 1:73df332e3e7b
31 --zygosity-freq $advanced_settings.zygosity_freq 31 --zygosity-freq $advanced_settings.zygosity_freq
32 #end if 32 #end if
33 --output sample.cnv.input 33 --output sample.cnv.input
34 ]]></command> 34 ]]></command>
35 <inputs> 35 <inputs>
36 <param name="input_segmented_file" type="data" format="tabular" label="Segmented copy ratio data file (cns file)" help="" /> 36 <param name="input_segmented_file" type="data" format="cns,cnr" label="Segmented copy ratio data file (cns file)" help="" />
37 <section name="advanced_settings" title="Advanced settings" expanded="false"> 37 <section name="advanced_settings" title="Advanced settings" expanded="false">
38 <param argument="--reference" optional="true" type="data" format="tabular" 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" /> 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" />
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" /> 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" />
40 <param argument="--sample-id" optional="true" type="text" label="Sample ID" value="" help="Sample name to write in the genotype field of the output VCF file" /> 40 <param argument="--sample-id" type="text" label="Sample ID" help="Sample name to write in the genotype field of the output VCF file" />
41 <param argument="--normal-id" optional="true" type="text" label="Normal Id" value="" help="Corresponding normal sample ID in the input VCF" /> 41 <param argument="--normal-id" type="text" label="Normal Id" help="Corresponding normal sample ID in the input VCF" />
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]" /> 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]" />
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]" /> 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]" />
44 44
45 </section> 45 </section>
46 </inputs> 46 </inputs>
47 <outputs> 47 <outputs>
48 <data name="CNVs_Theta" format="tabular" label="${tool.name} on ${on_string}: CNVs theta file" from_work_dir="sample.cnv.input" /> 48 <data name="CNVs_Theta" format="tabular" label="${tool.name} on ${on_string}: CNVs theta file" from_work_dir="sample.cnv.input" />
49 </outputs> 49 </outputs>
50 <tests> 50 <tests>
51 <test expect_num_outputs="1"> 51 <test expect_num_outputs="1">
52 <param name="input_segmented_file" ftype="tabular" value="tumor.cns" /> 52 <param name="input_segmented_file" ftype="cns" value="tumor.cns" />
53 <output name="CNVs_Theta" file="sample.cnv.input" /> 53 <output name="CNVs_Theta" file="sample.cnv.input" />
54 </test> 54 </test>
55 </tests> 55 </tests>
56 <help><![CDATA[ 56 <help><![CDATA[
57 Export the segmented copy number data (from a *.cns file) to THetA2 input file format (*.input). 57
58 Export the segmented copy number data (from a *.cns file) to THetA2 input file format (*.input).
59
60 -----
61
62 **Copy Number Reference Profile (.cnn)**
63
64 Tabular file defining the reference baseline built from control samples (e.g., normal samples). Used to normalize test samples.
65
66 .. csv-table::
67 :header-rows: 0
68
69 "chromosome","Genomic chromosome (e.g., chr1, chrX)."
70 "start","Start position of the bin."
71 "end","End position of the bin."
72 "gene","Gene name(s) (if applicable)."
73 "log2","Reference log2 ratio (typically 0 for diploid regions)."
74 "depth","Average read depth across control samples."
75 "spread","Variability (standard deviation) of coverage in controls."
76
77 -----
78
79 **Segmented log2 ratios (.cns)**
80
81 Tabular file with smoothed, merged segments of stable copy number, derived from the .cnr file. Represents final CNV calls.
82
83 .. csv-table::
84 :header-rows: 0
85
86 "chromosome","start, end: Genomic coordinates of the segment"
87 "gene","Gene(s) overlapping the segment."
88 "log2","Mean log2 ratio of the segment."
89 "probes","Mean log2 ratio of the segment."
90 "depth","Average read depth."
91 "weight","Reliability weight."
92 "p_value","Statistical confidence (lower = more significant)."
93
58 ]]></help> 94 ]]></help>
59 <expand macro="citations" /> 95 <expand macro="citations" />
60 </tool> 96 </tool>
61 97
62 98