view data_manager/install_packaged_annotation_data.xml @ 0:bd26448ea6bc draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_packaged_annotation_data commit 339a6c16fb6d944d4e147b5192cbeb0ebd26d18e"

<tool id="data_manager_packaged_annotation_data" name="Download and install packaged collections of genome annotation data" version="0.1" tool_type="manage_data" profile="20.05">
    <description>fetching</description>
    <requirements>
        <requirement type="package" version="3.9">python</requirement>
        <requirement type="package" version="6.0">pyyaml</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
python '$__tool_directory__/install_packaged_annotation_data.py'
  --target-directory '${out_file.extra_files_path}'
  -o '$out_file'
  --dbkey '$dbkey'
  '$metadata'
    ]]></command>
    <inputs>
        <param name="dbkey" type="genomebuild"
        label="DBKEY of genome that the annotation data is for"
        help="Take a look at the refgenome value from the metadata file to guide you in your selection." />
        <param name="metadata" type="data" format="txt" label="Metadata describing the package and its contents" />
    </inputs>
    <outputs>
        <data name="out_file" format="data_manager_json" />
    </outputs>
    <tests>
        <!-- TODO: need some way to test that new entry was added to data table -->
        <test>
            <param name="dbkey" value="hg19"/>
            <param name="metadata" value="test-meta.yml"/>
            <output name="out_file" file="from_test-meta.data_manager.json"/>
        </test>
    </tests>
    <help>
**What it does**

This tool fetches and installs packages of genome annotation datasets that are
not tightly bound to specific tools, but generic enough to be of use for many
different tools.

It populates the "packaged_annotation_data" data table.
    </help>
</tool>