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comparison cnv-vcf2json.xml @ 1:6763389420f5 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnv-vcf2json commit fc1282ec68b346988203ead860e9b9d6a47e9efb
author iuc
date Sat, 01 Mar 2025 11:47:41 +0000
parents 9be5490bb681
children
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0:9be5490bb681 1:6763389420f5
1 <tool id="cnv_vcf2json" name="CNV VCF2JSON" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> 1 <tool id="cnv_vcf2json" name="CNV VCF2JSON" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
2 <description>Converts 1000hg structural variants VCF file to JSON</description> 2 <description>Converts the CNVkit structural variants VCF file to JSON</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <expand macro="creators"/> 7 <expand macro="creators"/>
8 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
9 #import re 9 #import re
10 ln -s '$input_vcf_file' ./input.vcf && 10 ln -s '$input_vcf_file' ./input.vcf &&
11 cnv-vcf2json 11 cnv-vcf2json
12 -i ./input.vcf 12 ./input.vcf
13 #if $advanced_settings.assembly
14 --assembly '$advanced_settings.assembly'
15 #end if
16 #if $advanced_settings.analysis
17 --analysis '$advanced_settings.analysis'
18 #end if
19 #if $advanced_settings.individual
20 --individual '$advanced_settings.individual'
21 #end if
22 #if $advanced_settings.sequence
23 --sequence '$advanced_settings.sequence'
24 #end if
25 #if $advanced_settings.reference
26 --reference '$advanced_settings.reference'
27 #end if
28 #if $advanced_settings.fusion
29 --fusion '$advanced_settings.fusion'
30 #end if
13 -o output.json 31 -o output.json
14 ]]></command> 32 ]]></command>
15 <inputs> 33 <inputs>
16 <param name="input_vcf_file" type="data" format="vcf" label="CNV VCF file" help="" /> 34 <param name="input_vcf_file" type="data" format="vcf" label="CNVkit VCF file" help="The file Generated from CNVkit Export" />
35 <section name="advanced_settings" title="Advanced settings" expanded="false">
36 <param argument="--assembly" type="text" optional="true" label="Assembly Identifier" help="For example: GRCh37" >
37 <validator type="regex">^[0-9a-zA-Z_ .-]+$</validator>
38 </param>
39 <param argument="--analysis" type="text" optional="true" label="Analysis Identifier" help="" >
40 <validator type="regex">^[0-9a-zA-Z_,: .-]+$</validator>
41 </param>
42 <param argument="--individual" type="text" optional="true" label="Individual Identifier" help="" >
43 <validator type="regex">^[0-9a-zA-Z_,: .-]+$</validator>
44 </param>
45 <param argument="--sequence" type="text" optional="true" label="Variant Sequence" help="" >
46 <validator type="regex">^[0-9a-zA-Z_,: .-]+$</validator>
47 </param>
48 <param argument="--reference" type="text" optional="true" label="Reference Sequence" help="" >
49 <validator type="regex">^[0-9a-zA-Z_,: .-]+$</validator>
50 </param>
51 <param argument="--fusion" type="text" optional="true" label="Fusion Identifier" help="" >
52 <validator type="regex">^[0-9a-zA-Z_,: .-]+$</validator>
53 </param>
54 </section>
17 </inputs> 55 </inputs>
18 <outputs> 56 <outputs>
19 <data name="output_json" format="json" label="${tool.name} on ${on_string}: CNV JSON File" from_work_dir="output.json" /> 57 <data name="output_json" format="json" label="${tool.name} on ${on_string}: CNV JSON File" from_work_dir="output.json" />
20 </outputs> 58 </outputs>
21 <tests> 59 <tests>
22 <test expect_num_outputs="1"> 60 <test expect_num_outputs="1">
23 <param name="input_vcf_file" ftype="vcf" value="HG00096.cnv.vcf" /> 61 <param name="input_vcf_file" ftype="vcf" value="input.vcf" />
24 <output name="output_json" file="output.json" ftype="json" compare="sim_size" > 62 <param name="assembly" value="GRCh37" />
25 <assert_contents><has_size value="356000" delta="20000" /></assert_contents> 63 <output name="output_json">
64 <assert_contents>
65 <has_json_property_with_text property="biosampleId" text="SampleID" />
66 </assert_contents>
26 </output> 67 </output>
27 </test> 68 </test>
28 </tests> 69 </tests>
29 <help><![CDATA[ 70 <help><![CDATA[
30 The tool converts the structural variants VCF file into JSON file as a preprocessing step to import the data into Beacon2 MongoDB protocol 71 The tool converts the structural variants VCF file generated from the CNVkit export subcommand into JSON file as a preprocessing step to import the data into Beacon2 MongoDB protocol
31 ]]></help> 72 ]]></help>
32 <expand macro="citations"/> 73 <expand macro="citations"/>
33 </tool> 74 </tool>