view data_manager/data_manager_gemini_download.xml @ 9:27a6a256cd23 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gemini_database_downloader commit 275b7863ff4f8b0dff9cd7ea6c4b635694f0168d

<tool id="data_manager_gemini_download" name="GEMINI Download" version="@VERSION@+galaxy1" tool_type="manage_data" profile="18.09">
    <description>the annotation files required by the GEMINI suite of tools</description>
    <macros>
        <token name="@VERSION@">0.20.1</token>
        <token name="@DB_VERSION@">200</token>
    </macros>
    <requirements>
        <requirement type="package" version="@VERSION@">gemini</requirement>
    </requirements>
    <command detect_errors="exit_code">
        python '$__tool_directory__/data_manager_gemini_download.py' '$out_file'
    </command>
    <inputs>
        <param name="cadd" type="boolean" truevalue="cadd" falsevalue="" checked="True"
            label="Download CADD scores for GEMINI database annotation" help="(--extra cadd_score)"/>
        <param name="gerp_bp" type="boolean" truevalue="gerp_bp" falsevalue="" checked="True"
            label="Download GERP for GEMINI database annotation" help="(--extra gerp_bp)"/>
        <param name="gemini_db_version" type="hidden" value="@DB_VERSION@"/>
        <param name="test_data_manager" type="hidden" value=""/>
    </inputs>
    <outputs>
        <data name="out_file" format="data_manager_json" label="${tool.name}"/>
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <param name="test_data_manager" value="--test" />
            <param name="cadd" value="false" />
            <param name="gerp_bp" value="false" />
            <output name="out_file" file="test.json" compare="re_match" />
        </test>
        <!-- Test 2 with the latest option -->
        <test expect_num_outputs="1">
            <param name="test_data_manager" value="--test" />
            <output name="out_file">
                <assert_contents>
                    <has_text text="&quot;name&quot;: &quot;GEMINI annotations w/ GERP &amp; CADD" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help>
This tool downloads the GEMINI annotation files and makes them available to
corresponding versions of the GEMINI suite of tools. Downloading the (very large) CADD_ scores and GERP_ annotation files is optional.

Please visit http://gemini.readthedocs.io for details about GEMINI.

.. _GERP: http://mendel.stanford.edu/SidowLab/downloads/gerp/index.html
.. _CADD: https://cadd.gs.washington.edu/
    </help>
    <citations>
        <citation type="doi">10.1371/journal.pcbi.1003153</citation>
    </citations>
</tool>