view cnv-vcf2json.xml @ 1:7d2d2e3b9891 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnv-vcf2json commit 7b5c842d3c006d2afd00aff1ef833f236a45dd3d

<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>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="creators"/>
    <command detect_errors="exit_code"><![CDATA[   
        #import re
        ln -s '$input_vcf_file' ./input.vcf &&
        cnv-vcf2json
            -i ./input.vcf
            -o output.json
    ]]></command>
    <inputs>
        <param name="input_vcf_file" type="data" format="vcf" label="CNV VCF file" help="" />
    </inputs>
    <outputs>
        <data name="output_json" format="json" label="${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>
            </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
    ]]></help>
    <expand macro="citations"/>
</tool>