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view data_manager/plasmidfinder_fetch_database.xml @ 3:5ffc68b4ec04 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_plasmidfinder commit 5c04f6f49deca3735a752e5ac29027ba9d5ff000-dirty
author pimarin
date Fri, 17 Feb 2023 14:03:19 +0000
parents bd56ac4cca16
children 60cfd33bc2fb
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<tool id="data_manager_fetch_plasmidfinder" name="plasmidfinder_datamanager" tool_type="manage_data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>plasmidfinder database builder</description>
    <macros>
        <import>macro.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="exit_code">
      <![CDATA[
        python '$__tool_directory__/plasmidfinder_fetch_database.py'
        --db_version '$database_select'
        '$output_file'
      ]]></command>
    <inputs>
        <param name="database_select" type="select" label="Database version" help="Choose a database version to download (default latest version)">
            <option value="latest" selected="true">Latest available version</option>
            <option value="2.1">V2.1_2019-08-28</option>
        </param>param>
    </inputs>
    <outputs>
        <data name="output_file" format="data_manager_json"/>
    </outputs>
    <tests>
        <!-- Test_1 DB latest -->
        <test expect_num_outputs="1">
            <param name="database_select" value="latest"/>
            <output name="output_file" value="plasmidfinder_test_data_manager_latest.json">
                <assert_contents>
                    <has_text_matching expression="\{&quot;data_tables&quot;\:\ {&quot;plasmidfinder_database&quot;\:\ \[\{&quot;date&quot;\:\ &quot;\d\d\d\d-\d\d-\d\d&quot;,\ &quot;name&quot;\:\ &quot;\w\w\w\w\w\w\w\w\w\w\w\w_\d\d\d\d-\d\d-\d\d&quot;,\ &quot;path&quot;\:\ &quot;plasmidfinder_database&quot;,\ &quot;value&quot;\:\ &quot;plasmidfinder_\w\w\w\w\w\w\w\w\w\w\w\w_\d\d\d\d-\d\d-\d\d&quot;\}\]\}\}"/>
                </assert_contents>
            </output>
        </test>
         <!-- Test_2 DB 2.1 -->
        <test expect_num_outputs="1">
            <param name="database_select" value="2.1"/>
            <output name="output_file" value="plasmidfinder_test_data_manager_2.1.json">
                <assert_contents>
                    <has_text_matching expression="\{&quot;data_tables&quot;\:\ {&quot;plasmidfinder_database&quot;:\ \[\{&quot;date&quot;\:\ &quot;\d\d\d\d-\d\d-\d\d&quot;,\ &quot;name&quot;\:\ &quot;2.1_\d\d\d\d-\d\d-\d\d&quot;,\ &quot;path&quot;\:\ &quot;plasmidfinder_database&quot;,\ &quot;value&quot;\:\ &quot;plasmidfinder_1307168b1ce7_\d\d\d\d-\d\d-\d\d&quot;\}\]\}\}"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
        Download plasmidfinder database from the bitbucket repository
    ]]></help>
    <citations>
        <citation type="doi">10.1007/978-1-4939-9877-7_20</citation>
    </citations>
</tool>