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comparison bed.xml @ 1:dad30a23fcd6 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 11:48:59 +0000
parents b14f1b2f6196
children
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0:b14f1b2f6196 1:dad30a23fcd6
25 #if $advanced_settings.diploid_parx_genome 25 #if $advanced_settings.diploid_parx_genome
26 --diploid-parx-genome '$advanced_settings.diploid_parx_genome' 26 --diploid-parx-genome '$advanced_settings.diploid_parx_genome'
27 #end if 27 #end if
28 ]]></command> 28 ]]></command>
29 <inputs> 29 <inputs>
30 <param name="input_segmented_file" type="data" format="tabular" label="Segmented Copy Ratio Data File (cns file)" help="" /> 30 <param name="input_segmented_file" type="data" format="cns" label="Segmented Copy Ratio Data File (cns file)" help="" />
31 <section name="advanced_settings" title="Advanced settings" expanded="false"> 31 <section name="advanced_settings" title="Advanced settings" expanded="false">
32 <param argument="--label-genes" type="boolean" checked="false" truevalue="--label-genes" falsevalue="" label="Label Genes" help="Show gene names in the 4th column of the BED file" /> 32 <param argument="--label-genes" type="boolean" checked="false" truevalue="--label-genes" falsevalue="" label="Label Genes" help="Show gene names in the 4th column of the BED file" />
33 <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" /> 33 <param argument="--sample-id" type="text" label="Sample ID" help="Sample name to write in the genotype field of the output VCF file" />
34 <param argument="--ploidy" optional="true" type="integer" label="Ploidy" min="1" value="2" help="Ploidy of the sample cells. [Default: 2]" /> 34 <param argument="--ploidy" optional="true" type="integer" label="Ploidy" min="1" value="2" help="Ploidy of the sample cells. [Default: 2]" />
35 <expand macro="sample_sex"/> 35 <expand macro="sample_sex"/>
36 <param argument="--male-reference" type="boolean" checked="false" truevalue="--male-reference" falsevalue="" label="Male Reference" help="Assume inputs were normalized to a male reference" /> 36 <param argument="--male-reference" type="boolean" checked="false" truevalue="--male-reference" falsevalue="" label="Male Reference" help="Assume inputs were normalized to a male reference" />
37 <param argument="--diploid-parx-genome" optional="true" type="text" label="Diploid Parx Genome" value="" help="Considers the given human genome's PAR of chromosome X as autosomal. Example: 'grch38'" /> 37 <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'" />
38 </section> 38 </section>
39 </inputs> 39 </inputs>
40 <outputs> 40 <outputs>
41 <data name="CNVs_BED" format="bed" label="${tool.name} on ${on_string}: CNVs BED file" from_work_dir="sample.cnv.bed" /> 41 <data name="CNVs_BED" format="bed" label="${tool.name} on ${on_string}: CNVs BED file" from_work_dir="sample.cnv.bed" />
42 </outputs> 42 </outputs>
43 <tests> 43 <tests>
44 <test expect_num_outputs="1"> 44 <test expect_num_outputs="1">
45 <param name="input_segmented_file" ftype="tabular" value="sample.cns" /> 45 <param name="input_segmented_file" ftype="cns" value="sample.cns" />
46 <param name="sample_id" value="SampleID" /> 46 <param name="sample_id" value="SampleID" />
47 <param name="sample_sex" value="Female" /> 47 <param name="sample_sex" value="Female" />
48 <output name="CNVs_BED" file="sample.cnv.bed" /> 48 <output name="CNVs_BED" file="sample.cnv.bed" />
49 </test> 49 </test>
50 </tests> 50 </tests>
51 <help><![CDATA[ 51 <help><![CDATA[
52 Export the segmented copy number data (from a .cns file) to BED format. 52
53 The resulting BED file describes copy number gains and losses across each segment. 53 Export the segmented copy number data (from a .cns file) to BED format.
54 The resulting BED file describes copy number gains and losses across each segment.
55 -----
56
57 **Segmented log2 ratios (.cns)**
58
59 Tabular file with smoothed, merged segments of stable copy number, derived from the .cnr file. Represents final CNV calls.
60
61 .. csv-table::
62 :header-rows: 0
63
64 "chromosome","start, end: Genomic coordinates of the segment"
65 "gene","Gene(s) overlapping the segment."
66 "log2","Mean log2 ratio of the segment."
67 "probes","Mean log2 ratio of the segment."
68 "depth","Average read depth."
69 "weight","Reliability weight."
70 "p_value","Statistical confidence (lower = more significant)."
71
72
54 ]]></help> 73 ]]></help>
55 <expand macro="citations" /> 74 <expand macro="citations" />
56 </tool> 75 </tool>
57 76
58 77