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view data_manager/data_manager_qiime_download.xml @ 0:f8608fddfb23 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_qiime_database_downloader commit 4934eb34300b5fa54d62d8b67e5b6e989e963ac9
author iuc
date Mon, 15 May 2017 11:08:43 -0400
parents
children cbe065fbd038
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<tool id="data_manager_qiime_download" name="Download QIIME" version="1.9.1" tool_type="manage_data">
    <description>reference databases</description>
    <requirements>
        <requirement type="package" version="2.13.0">requests</requirement>
    </requirements>
    <stdio>
        <exit_code range=":-1" level="fatal" description="Error: Cannot open file" />
        <exit_code range="1:" level="fatal" description="Error" />
    </stdio>
    <command><![CDATA[
        python '$__tool_directory__/data_manager_qiime_download.py'
            --database '$db.database'
            --version '$db.version'
            --jsonfile '${out_file}'
    ]]></command>
    <inputs>
        <conditional name="db">
            <param name="database" type="select" label="Database to download">
                <option value="greengenes" selected="true">Greengenes OTUs</option>
                <option value="silva">SILVA OTUs (16S/18S)</option>
                <option value="unite">UNITE OTUs (ITS)</option>
                <!--<option value="img">IMG/QIIME reference protein sequences</option>-->
            </param>
            <when value="greengenes">
                <param name="version" type="select" label="Version of Greengenes">
                    <option value="13_8" selected="true">13.8</option>
                    <option value="13_5">13.5</option>
                    <option value="12_10">12.10</option>
                </param>
            </when>
            <when value="silva">
                <param name="version" type="select" label="Version of SILVA OTUs">
                    <option value="128_release" selected="true">128</option>
                    <option value="123_release">123</option>
                    <!--<option value="119_release_aligned_rep_files">119 (aligned rep)</option>
                    <option value="119_release">119</option>
                    <option value="119_consensus_majority_taxonomy">119 (consensus majority taxonomy)</option>
                    <option value="111_release">111</option>
                    <option value="108_release">108</option>
                    <option value="108_release_curated">108 (curated)</option>
                    <option value="104_release">104</option>-->
                </param>
            </when>
            <when value="unite">
                <param name="version" type="select" label="Version of UNITE OTUs">
                    <option value="20.11.2016">7.1 (2016-11-20, with singletons set as RefS)</option>
                    <option value="s_20.11.2016">7.1 (2016-11-20, with global and 97% singletons)</option>
                    <option value="22.08.2016">7.1 (2016-08-22, with singletons set as RefS)</option>
                    <option value="s_22.08.2016">7.1 (2016-08-22, with global and 97% singletons)</option>
                    <option value="31.01.2016">7.0 (2016-01-31, with singletons set as RefS)</option> 
                    <option value="s_31.01.2016">7.0 (2016-01-31, with global and 97% singletons)</option> 
                    <option value="01.08.2015">7.0 (2015-08-01, with singletons set as RefS)</option>
                    <option value="s_01.08.2015">7.0 (2015-08-01, with global and 97% singletons)</option>
                    <option value="02.03.2015">7.0 (2015-03-02, with singletons set as RefS)</option>
                    <option value="s_02.03.2015">7.0 (2015-03-02, with global and 97% singletons)</option>
                    <option value="30.12.2014">6.0 (2014-12-30, with singletons set as RefS)</option>
                    <option value="s_30.12.2014">6.0 (2014-12-30, with global and 97% singletons)</option>
                    <option value="10.09.2014">6.0 (2014-09-10, with singletons set as RefS)</option>
                    <option value="s_10.09.2014">6.0 (2014-09-10, with global and 97% singletons)</option>
                    <option value="04.07.2014">6.0 (2014-07-04, with singletons set as RefS)</option>
                    <option value="s_04.07.2014">6.0 (2014-07-04, with global and 97% singletons)</option>
                    <option value="13.05.2014">6.0 (2014-05-13, with singletons set as RefS)</option> 
                    <option value="s_13.05.2014">6.0 (2014-05-13, with global and 97% singletons)</option>
                    <option value="09.02.2014">6.0 (2014-02-09, with singletons set as RefS)</option>
                    <option value="s_09.02.2014">6.0 (2014-02-09, with global and 97% singletons)</option>
                    <option value="15.01.2014">6.0 (2014-01-15, with singletons set as RefS)</option>
                    <option value="s_15.01.2014">6.0 (2014-01-15, with global and 97% singletons)</option>
                    <option value="19.12.2013">6.0 (2013-12-19, with singletons set as RefS)</option>
                    <option value="s_19.12.2013">6.0 (2013-12-19, with global and 97% singletons)</option>
                    <option value="08.12.2013">6.0 (2013-12-08, with singletons set as RefS)</option>
                    <option value="s_08.12.2013">6.0 (2013-12-08, with global and 97% singletons)</option>
                    <option value="15.10.2013">5.0 (2013-10-15, with singletons set as RefS)</option>   
                    <option value="s_15.10.2013">5.0 (2013-10-15, with global and 97% singletons)</option>
                </param>
            </when>
            <!--<when value="img">
                <param name="version" type="select" label="Version of IMG/QIIME reference protein sequences">
                    <option value="img-qiime-25oct2012" selected="true">img-qiime-25oct2012</option>
                </param>
            </when>-->
        </conditional>
    </inputs>
    <outputs>
           <data name="out_file" format="data_manager_json" label="${tool.name}"/>
    </outputs>
    <tests>
    </tests>
    <help><![CDATA[
This tool downloads the reference databases for QIIME
    ]]></help>
    <citations>
        <citation type="doi">10.1038/nmeth.f.303</citation>
        <yield />
    </citations>
</tool>