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planemo upload commit 1b7d98a104f966bbc5edbbee79160b8994b57081
author rhpvorderman
date Wed, 13 Dec 2023 15:41:00 +0000
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1 <tool id="updio" name="UPDio" version="1.1.0+galaxy3" python_template_version="3.5" profile="21.05">
2 <requirements>
3 <requirement type="package" version="1.1.0">updio</requirement>
4 <container type="docker">quay.io/biocontainers/updio:1.1.0--hdfd78af_0</container>
5 </requirements>
6 <command detect_errors="exit_code"><![CDATA[
7 #if str($input_type.input_type_selector) == "file"
8 #from pathlib import Path
9 #set $child_id = Path(str($input_type.child_id_file)).read_text().strip()
10 #set $mother_id = Path(str($input_type.mother_id_file)).read_text().strip()
11 #set $father_id = Path(str($input_type.father_id_file)).read_text().strip()
12 #end if
13 ln -s $multisample_vcf input.vcf.gz &&
14 updio --multisample_vcf input.vcf.gz
15 --childID $child_id
16 --momID $mother_id
17 --dadID $father_id &&
18 mv output_dir/${child_id}.table ${updio_table} &&
19 mv output_dir/${child_id}.upd ${updio_verdict}
20 ]]></command>
21 <inputs>
22 <param name="multisample_vcf" type="data" format="vcf_bgzip"
23 label="multisample VCF file" />
24 <param name="output_label" type="text"
25 label="Analysis name, to distinguish the output." />
26 <conditional name="input_type">
27 <param name="input_type_selector" type="select" label="Sample IDs submitted by:">
28 <option value="text" selected="true">Text</option>
29 <option value="file">Files (for easier workflow integration)</option>
30 </param>
31 <when value="text">
32 <param name="child_id" type="text"
33 label="child sample ID in the VCF file" />
34 <param name="mother_id" type="text"
35 label="Mother sample ID in the VCF file" />
36 <param name="father_id" type="text"
37 label="Father sample ID in the VCF file" />
38 </when>
39 <when value="file">
40 <param name="child_id_file" type="data"
41 label="Child sample ID in the VCF file. Provided as a single line file."/>
42 <param name="mother_id_file" type="data"
43 label="Mother sample ID in the VCF file. Provided as a single line file."/>
44 <param name="father_id_file" type="data"
45 label="Father sample ID in the VCF file. Provided as a single line file."/>
46 </when>
47 </conditional>
48 </inputs>
49 <outputs>
50 <data format="tsv" name="updio_table" label="${tool.name} on ${output_label}: table"/>
51 <data format="tsv" name="updio_verdict" label="${tool.name} on ${output_label}: verdict"/>
52 </outputs>
53 <help><![CDATA[
54 UPDio is designed to detect UPD events in probands from vcf trio data.
55 ]]></help>
56 </tool>