Mercurial > repos > iuc > cnv_vcf2json
diff cnv-vcf2json.xml @ 1:6763389420f5 draft default tip
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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--- a/cnv-vcf2json.xml Wed Jul 24 12:53:58 2024 +0000 +++ b/cnv-vcf2json.xml Sat Mar 01 11:47:41 2025 +0000 @@ -1,5 +1,5 @@ <tool id="cnv_vcf2json" name="CNV VCF2JSON" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> - <description>Converts 1000hg structural variants VCF file to JSON</description> + <description>Converts the CNVkit structural variants VCF file to JSON</description> <macros> <import>macros.xml</import> </macros> @@ -9,25 +9,66 @@ #import re ln -s '$input_vcf_file' ./input.vcf && cnv-vcf2json - -i ./input.vcf + ./input.vcf + #if $advanced_settings.assembly + --assembly '$advanced_settings.assembly' + #end if + #if $advanced_settings.analysis + --analysis '$advanced_settings.analysis' + #end if + #if $advanced_settings.individual + --individual '$advanced_settings.individual' + #end if + #if $advanced_settings.sequence + --sequence '$advanced_settings.sequence' + #end if + #if $advanced_settings.reference + --reference '$advanced_settings.reference' + #end if + #if $advanced_settings.fusion + --fusion '$advanced_settings.fusion' + #end if -o output.json ]]></command> <inputs> - <param name="input_vcf_file" type="data" format="vcf" label="CNV VCF file" help="" /> + <param name="input_vcf_file" type="data" format="vcf" label="CNVkit VCF file" help="The file Generated from CNVkit Export" /> + <section name="advanced_settings" title="Advanced settings" expanded="false"> + <param argument="--assembly" type="text" optional="true" label="Assembly Identifier" help="For example: GRCh37" > + <validator type="regex">^[0-9a-zA-Z_ .-]+$</validator> + </param> + <param argument="--analysis" type="text" optional="true" label="Analysis Identifier" help="" > + <validator type="regex">^[0-9a-zA-Z_,: .-]+$</validator> + </param> + <param argument="--individual" type="text" optional="true" label="Individual Identifier" help="" > + <validator type="regex">^[0-9a-zA-Z_,: .-]+$</validator> + </param> + <param argument="--sequence" type="text" optional="true" label="Variant Sequence" help="" > + <validator type="regex">^[0-9a-zA-Z_,: .-]+$</validator> + </param> + <param argument="--reference" type="text" optional="true" label="Reference Sequence" help="" > + <validator type="regex">^[0-9a-zA-Z_,: .-]+$</validator> + </param> + <param argument="--fusion" type="text" optional="true" label="Fusion Identifier" help="" > + <validator type="regex">^[0-9a-zA-Z_,: .-]+$</validator> + </param> + </section> </inputs> <outputs> <data name="output_json" format="json" label="${tool.name} on ${on_string}: CNV JSON File" from_work_dir="output.json" /> </outputs> <tests> <test expect_num_outputs="1"> - <param name="input_vcf_file" ftype="vcf" value="HG00096.cnv.vcf" /> - <output name="output_json" file="output.json" ftype="json" compare="sim_size" > - <assert_contents><has_size value="356000" delta="20000" /></assert_contents> + <param name="input_vcf_file" ftype="vcf" value="input.vcf" /> + <param name="assembly" value="GRCh37" /> + <output name="output_json"> + <assert_contents> + <has_json_property_with_text property="biosampleId" text="SampleID" /> + </assert_contents> </output> </test> </tests> <help><![CDATA[ - The tool converts the structural variants VCF file into JSON file as a preprocessing step to import the data into Beacon2 MongoDB protocol + 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 ]]></help> <expand macro="citations"/> </tool>