view vcf2bff.xml @ 1:ef90043ba759 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit eecd43b81a8c9f2175c50a71ae85ce9185a9d3a7

<tool id="beacon2_vcf2bff" name="Beacon2 VCF2BFF" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
    <description>converting annotated VCF files to Beacon v2 format</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="xrefs"/>
    <expand macro="requirements"/>
    <expand macro="creators"/>
    <command detect_errors="exit_code"><![CDATA[   
        ln -s '$input' ./sample.vcf.gz &&
        vcf2bff.pl
            --input ./sample.vcf.gz
            --format '$format'
            --project-dir ./
            --dataset-id '$dataset_id'
            --genome '$genome'
        && gunzip ./genomicVariationsVcf.json.gz
    ]]></command>
    <inputs>
        <param argument="--input" type="data" format="tabular.gz" label="Annotated vcf file" help="The output genomic variations VCF file of bcftools, snpeff, snpsift" />
        <param argument="--format" type="select" label="Output format" help="">
            <option value="bff" selected="True">BFF</option>
            <option value="hash">hash</option>
            <option value="json">json</option>
        </param>
        <param argument="--dataset-id" type="text" label="Dataset ID" value="" help="Give an ID for the created genomicVariations dataset" />
        <param argument="--genome" type="text" label="Reference genome" value="" help="Select the reference genome used the annotate the data to create the genomicVariations dataset examples for reference genomes are hs37, hg37 and hg38" />
    </inputs>
    <outputs>
        <data name="genomicVariationsVcf" format="json" label="${tool.name} on ${on_string}: genomicVariationsVcf file" from_work_dir="genomicVariationsVcf.json" />
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <param name="input" ftype="tabular.gz" value="test.vcf.gz" />
            <param name="format" value="bff"/>
            <param name="dataset_id" value="beacon"/>
            <param name="genome" value="hg19"/>
            <output name="genomicVariationsVcf" file="genomicVariationsVcf.json" ftype="json" compare="sim_size">
                <assert_contents><has_size value="730000" delta="90000" /></assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
          The tool Creates genomicVariations file from annotated genomic variations VCF file. The VCF file is annotated by using the
          workflow of those tools bcftools -> snpeff -> snpsift.
          The tool converts the annotated VCF file into genomicVariations entry type and serializes it as a JSON file also called Beacon Friendly Format (BFF).
          The generated file will be ready to be stored on the MongoDB instance as MongoDB works directly with JSON files.
    ]]></help>
    <expand macro="citations" />
</tool>