Mercurial > repos > iuc > data_manager_qiime_database_downloader
diff data_manager/data_manager_qiime_download.xml @ 0:f8608fddfb23 draft
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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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/data_manager_qiime_download.xml Mon May 15 11:08:43 2017 -0400 @@ -0,0 +1,95 @@ +<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> \ No newline at end of file