Mercurial > repos > iuc > cnvkit_export_bed

comparison bed.xml @ 0:b14f1b2f6196 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit 51995527835d18a4a3a498b140382ce433f19a71
author iuc
date Mon, 20 Jan 2025 16:28:47 +0000
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children dad30a23fcd6
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-1:000000000000 0:b14f1b2f6196
1 <tool id="cnvkit_export_bed" name="CNVkit Export BED" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
2 <description>Converts the Segmented copy ratio data file (*.cns) file into BED 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 cnvkit.py export bed
12 ./sample.cns
13 $advanced_settings.label_genes
14 #if $advanced_settings.sample_id
15 --sample-id '$advanced_settings.sample_id'
16 #end if
17 #if $advanced_settings.ploidy
18 --ploidy $advanced_settings.ploidy
19 #end if
20 #if str($advanced_settings.sample_sex) and $advanced_settings.sample_sex != ""
21 --sample-sex '$advanced_settings.sample_sex'
22 #end if
23 $advanced_settings.male_reference
24 --output sample.cnv.bed
25 #if $advanced_settings.diploid_parx_genome
26 --diploid-parx-genome '$advanced_settings.diploid_parx_genome'
27 #end if
28 ]]></command>
29 <inputs>
30 <param name="input_segmented_file" type="data" format="tabular" label="Segmented Copy Ratio Data File (cns file)" help="" />
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" />
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" />
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"/>
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'" />
38 </section>
39 </inputs>
40 <outputs>
41 <data name="CNVs_BED" format="bed" label="${tool.name} on ${on_string}: CNVs BED file" from_work_dir="sample.cnv.bed" />
42 </outputs>
43 <tests>
44 <test expect_num_outputs="1">
45 <param name="input_segmented_file" ftype="tabular" value="sample.cns" />
46 <param name="sample_id" value="SampleID" />
47 <param name="sample_sex" value="Female" />
48 <output name="CNVs_BED" file="sample.cnv.bed" />
49 </test>
50 </tests>
51 <help><![CDATA[
52 Export the segmented copy number data (from a .cns file) to BED format.
53 The resulting BED file describes copy number gains and losses across each segment.
54 ]]></help>
55 <expand macro="citations" />
56 </tool>
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