view data_manager/interproscan.xml @ 2:7776cb18fdf8 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_interproscan commit 9282e18219e7e3ed6a5ee46839d17663c3134993"

<tool id="data_manager_interproscan" name="InterProScan data manager" version="0.0.2" tool_type="manage_data" profile="20.01">
    <requirements>
        <requirement type="package" version="5.54-87.0">interproscan</requirement>
        <requirement type="package" version="2.26.0">requests</requirement>
        <!-- Forcing an old hmmer version for indexing due to https://github.com/ebi-pf-team/interproscan/issues/232 -->
        <requirement type="package" version="3.1b2">hmmer</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
python -u '$__tool_directory__/interproscan.py'
$partial_data
--version '$version'
'interproscan'
'${output_file}'
    ]]></command>
    <inputs>
        <param name="partial_data" type="hidden" value="" help="Used for testing"/>
        <param name="version" type="text" value="" label="Version to download" help="Leave empty to download the latest version">
            <validator type="regex" message="Version must be a valid InterProScan version (e.g. 5.52-86.0)">^([0-9]+\.[0-9]+-[0-9]+\.[0-9]+)?$</validator>
        </param>
    </inputs>
    <outputs>
        <data name="output_file" format="data_manager_json"/>
    </outputs>
    <tests>
        <test>
            <param name="partial_data" value="--partial"/>
            <output name="output_file">
                <assert_contents>
                    <has_text text="InterProScan 5."/>
                    <has_text text='"interproscan_version": "5.'/>
                </assert_contents>
            </output>
            <assert_stdout>
                <has_text text="Pressed and indexed" />
                <has_text text="Completed indexing the hmm models" />
            </assert_stdout>
        </test>
        <test>
            <param name="partial_data" value="--partial"/>
            <param name="version" value="5.51-85.0"/>
            <output name="output_file">
                <assert_contents>
                    <has_text text="InterProScan 5.51-85.0"/>
                    <has_text text='"interproscan_version": "5.51-85.0'/>
                </assert_contents>
            </output>
            <assert_stdout>
                <has_text text="Pressed and indexed" />
                <has_text text="Completed indexing the hmm models" />
            </assert_stdout>
        </test>
        <test expect_failure="true">
            <param name="partial_data" value="--partial"/>
            <param name="version" value="xxxx"/>
            <assert_stderr>
                <has_text text="Version must be a valid InterProScan version" />
            </assert_stderr>
        </test>
    </tests>
    <help><![CDATA[
        This data managers fetches data from EBI FTP server for the InterProScan
        annotation tool and updates the InterProScan data table.
    ]]></help>
    <citations>
        <citation type="doi">10.1093/bioinformatics/btu031</citation>
        <citation type="doi">10.7717/peerj.167</citation>
        <citation type="doi">10.1093/bioinformatics/17.9.847</citation>
        <citation type="doi">10.1093/nar/gki442</citation>
        <citation type="doi">10.1093/nar/gkn785</citation>
    </citations>
</tool>