view data_manager/install_packaged_annotation_data.xml @ 0:632d33df6758 draft

"planemo upload commit 3dc5291eccd1fb516be67694c18a27bda5f69f91"

<tool id="data_manager_packaged_annotation_data" name="Download and install packaged collections of genome annotation data" version="0.0.1" tool_type="manage_data" profile="19.01">
    <description>fetching</description>
    <requirements>
        <requirement type="package" version="3.7">python</requirement>
        <requirement type="package" version="5.1.1">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>