view cnv-phenopacket.xml @ 0:61aad58c7b2d draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnv-phenopacket commit 022f0e712defd963f3a3480c5ee6cddf4157e81c

<tool id="cnv_phenopacket" name="CNV Phenopacket" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
    <description>Builds Phenopacket schema for the structural variants metadata from the 1000hg project</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="creators"/>
    <command detect_errors="exit_code"><![CDATA[   
        #import re
        ln -s '$input_tsv_file' ./input.tsv &&
        cnv-phenopacket
            -i ./input.tsv
            -o phenopacket.json
    ]]></command>
    <inputs>
        <param name="input_tsv_file" type="data" format="tabular" label="Metadata file" help="" />
    </inputs>
    <outputs>
        <data name="output_json" format="json" label="${tool.name} on ${on_string}: CNV Metadata JSON File" from_work_dir="phenopacket.json" />
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <param name="input_tsv_file" ftype="tabular" value="igsr-1000-genomes-30x-on-grch38.tsv" />
            <output name="output_json" file="phenopacket.json" />
        </test>
    </tests>
    <help><![CDATA[
         The tool extracts the metadata for the variants from the TSV file and and converts them into JSON file as a preprocessing step to import the data into Beacon2 MongoDB protocol
    ]]></help>
    <expand macro="citations"/>
</tool>