Mercurial > repos > iuc > cnvkit_export_vcf

comparison vcf.xml @ 0:4cf5a2dd27dd draft

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 51995527835d18a4a3a498b140382ce433f19a71
author iuc
date Mon, 20 Jan 2025 16:31:16 +0000
parents
children 974b39eb89b6
comparison
equal deleted inserted replaced
-1:000000000000 0:4cf5a2dd27dd
1 <tool id="cnvkit_export_vcf" name="CNVkit Export VCF" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
2 <description>Converts the Segmented copy ratio data file (*.cns) file into VCF file</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="xrefs"/>
7 <expand macro="creators"/>
8 <expand macro="requirements"/>
9 <command detect_errors="exit_code"><![CDATA[
10 ln -s '$input_segmented_file' ./sample.cns &&
11 ln -s '$advanced_settings.cnr' ./sample.cnr &&
12 cnvkit.py export vcf
13 ./sample.cns
14 #if $advanced_settings.cnr
15 --cnr ./sample.cnr
16 #end if
17 #if $advanced_settings.sample_id
18 --sample-id '$advanced_settings.sample_id'
19 #end if
20 #if $advanced_settings.ploidy
21 --ploidy $advanced_settings.ploidy
22 #end if
23 #if str($advanced_settings.sample_sex) and $advanced_settings.sample_sex != ""
24 --sample-sex '$advanced_settings.sample_sex'
25 #end if
26 $advanced_settings.male_reference
27 --output sample.cnv.vcf
28 #if $advanced_settings.diploid_parx_genome
29 --diploid-parx-genome '$advanced_settings.diploid_parx_genome'
30 #end if
31 ]]></command>
32 <inputs>
33 <param name="input_segmented_file" type="data" format="tabular" label="Segmented Copy Ratio Data File (cns file)" help="" />
34 <section name="advanced_settings" title="Advanced settings" expanded="false">
35 <param argument="--cnr" optional="true" type="data" format="tabular" label="Bin-level copy ratios (cnr)" help="" />
36 <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" />
37 <param argument="--ploidy" optional="true" type="integer" label="Ploidy" min="1" value="2" help="Ploidy of the sample cells. [Default: 2]" />
38 <expand macro="sample_sex"/>
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" />
40 <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'" />
41 </section>
42 </inputs>
43 <outputs>
44 <data name="CNVs_VCF" format="vcf" label="${tool.name} on ${on_string}: CNVs VCF file" from_work_dir="sample.cnv.vcf" />
45 </outputs>
46 <tests>
47 <test expect_num_outputs="1">
48 <param name="input_segmented_file" ftype="tabular" value="sample.cns" />
49 <param name="sample_id" value="SampleID" />
50 <param name="sample_sex" value="Female" />
51 <output name="CNVs_VCF" file="sample.cnv.vcf" ftype="vcf" lines_diff="2" />
52 </test>
53 </tests>
54 <help><![CDATA[
55 Export the segmented copy number data (from a .cns file) to the standard VCF 4.2 format.
56 The resulting VCF file describes copy number gains and losses across each segment and contains
57 INFO fields for breakpoints (CIPOS, CIEND) if bin-level data (.cnr) is provided.
58 ]]></help>
59 <expand macro="citations" />
60 </tool>
61
62
63
64