Mercurial > repos > iuc > data_manager_qiime_database_downloader

annotate data_manager/data_manager_qiime_download.xml @ 4:c4dba88e85ef 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 09b56ef3e09ad6c5923c88616fea5cbd77d87616
author iuc
date Mon, 18 Dec 2023 09:36:52 +0000
parents cbe065fbd038
children ed86a8f378c8
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c4dba88e85ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_qiime_database_downloader commit 09b56ef3e09ad6c5923c88616fea5cbd77d87616
iuc
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1 <tool id="data_manager_qiime_download" name="Download QIIME reference databases" version="1.9.2" tool_type="manage_data">
2
cbe065fbd038 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_qiime_database_downloader commit 4a3c9f195ba5d899b1a1ce5e80281cdf230f456a
iuc
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2 <description></description>
0
f8608fddfb23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_qiime_database_downloader commit 4934eb34300b5fa54d62d8b67e5b6e989e963ac9
iuc
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3 <requirements>
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4 <requirement type="package" version="2.13.0">requests</requirement>
f8608fddfb23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_qiime_database_downloader commit 4934eb34300b5fa54d62d8b67e5b6e989e963ac9
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5 </requirements>
f8608fddfb23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_qiime_database_downloader commit 4934eb34300b5fa54d62d8b67e5b6e989e963ac9
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6 <stdio>
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7 <exit_code range=":-1" level="fatal" description="Error: Cannot open file" />
f8608fddfb23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_qiime_database_downloader commit 4934eb34300b5fa54d62d8b67e5b6e989e963ac9
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8 <exit_code range="1:" level="fatal" description="Error" />
f8608fddfb23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_qiime_database_downloader commit 4934eb34300b5fa54d62d8b67e5b6e989e963ac9
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9 </stdio>
f8608fddfb23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_qiime_database_downloader commit 4934eb34300b5fa54d62d8b67e5b6e989e963ac9
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10 <command><![CDATA[
f8608fddfb23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_qiime_database_downloader commit 4934eb34300b5fa54d62d8b67e5b6e989e963ac9
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11 python '$__tool_directory__/data_manager_qiime_download.py'
f8608fddfb23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_qiime_database_downloader commit 4934eb34300b5fa54d62d8b67e5b6e989e963ac9
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12 --database '$db.database'
f8608fddfb23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_qiime_database_downloader commit 4934eb34300b5fa54d62d8b67e5b6e989e963ac9
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13 --version '$db.version'
f8608fddfb23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_qiime_database_downloader commit 4934eb34300b5fa54d62d8b67e5b6e989e963ac9
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14 --jsonfile '${out_file}'
f8608fddfb23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_qiime_database_downloader commit 4934eb34300b5fa54d62d8b67e5b6e989e963ac9
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15 ]]></command>
f8608fddfb23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_qiime_database_downloader commit 4934eb34300b5fa54d62d8b67e5b6e989e963ac9
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16 <inputs>
f8608fddfb23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_qiime_database_downloader commit 4934eb34300b5fa54d62d8b67e5b6e989e963ac9
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17 <conditional name="db">
f8608fddfb23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_qiime_database_downloader commit 4934eb34300b5fa54d62d8b67e5b6e989e963ac9
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18 <param name="database" type="select" label="Database to download">
f8608fddfb23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_qiime_database_downloader commit 4934eb34300b5fa54d62d8b67e5b6e989e963ac9
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19 <option value="greengenes" selected="true">Greengenes OTUs</option>
f8608fddfb23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_qiime_database_downloader commit 4934eb34300b5fa54d62d8b67e5b6e989e963ac9
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20 <option value="silva">SILVA OTUs (16S/18S)</option>
f8608fddfb23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_qiime_database_downloader commit 4934eb34300b5fa54d62d8b67e5b6e989e963ac9
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21 <option value="unite">UNITE OTUs (ITS)</option>
f8608fddfb23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_qiime_database_downloader commit 4934eb34300b5fa54d62d8b67e5b6e989e963ac9
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22 <!--<option value="img">IMG/QIIME reference protein sequences</option>-->
f8608fddfb23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_qiime_database_downloader commit 4934eb34300b5fa54d62d8b67e5b6e989e963ac9
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23 </param>
f8608fddfb23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_qiime_database_downloader commit 4934eb34300b5fa54d62d8b67e5b6e989e963ac9
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24 <when value="greengenes">
f8608fddfb23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_qiime_database_downloader commit 4934eb34300b5fa54d62d8b67e5b6e989e963ac9
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25 <param name="version" type="select" label="Version of Greengenes">
f8608fddfb23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_qiime_database_downloader commit 4934eb34300b5fa54d62d8b67e5b6e989e963ac9
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26 <option value="13_8" selected="true">13.8</option>
f8608fddfb23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_qiime_database_downloader commit 4934eb34300b5fa54d62d8b67e5b6e989e963ac9
iuc
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27 <option value="13_5">13.5</option>
f8608fddfb23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_qiime_database_downloader commit 4934eb34300b5fa54d62d8b67e5b6e989e963ac9
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28 <option value="12_10">12.10</option>
f8608fddfb23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_qiime_database_downloader commit 4934eb34300b5fa54d62d8b67e5b6e989e963ac9
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29 </param>
f8608fddfb23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_qiime_database_downloader commit 4934eb34300b5fa54d62d8b67e5b6e989e963ac9
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30 </when>
f8608fddfb23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_qiime_database_downloader commit 4934eb34300b5fa54d62d8b67e5b6e989e963ac9
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31 <when value="silva">
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32 <param name="version" type="select" label="Version of SILVA OTUs">
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33 <option value="128_release" selected="true">128</option>
f8608fddfb23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_qiime_database_downloader commit 4934eb34300b5fa54d62d8b67e5b6e989e963ac9
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34 <option value="123_release">123</option>
f8608fddfb23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_qiime_database_downloader commit 4934eb34300b5fa54d62d8b67e5b6e989e963ac9
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35 <!--<option value="119_release_aligned_rep_files">119 (aligned rep)</option>
f8608fddfb23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_qiime_database_downloader commit 4934eb34300b5fa54d62d8b67e5b6e989e963ac9
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36 <option value="119_release">119</option>
f8608fddfb23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_qiime_database_downloader commit 4934eb34300b5fa54d62d8b67e5b6e989e963ac9
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37 <option value="119_consensus_majority_taxonomy">119 (consensus majority taxonomy)</option>
f8608fddfb23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_qiime_database_downloader commit 4934eb34300b5fa54d62d8b67e5b6e989e963ac9
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38 <option value="111_release">111</option>
f8608fddfb23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_qiime_database_downloader commit 4934eb34300b5fa54d62d8b67e5b6e989e963ac9
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39 <option value="108_release">108</option>
f8608fddfb23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_qiime_database_downloader commit 4934eb34300b5fa54d62d8b67e5b6e989e963ac9
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40 <option value="108_release_curated">108 (curated)</option>
f8608fddfb23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_qiime_database_downloader commit 4934eb34300b5fa54d62d8b67e5b6e989e963ac9
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41 <option value="104_release">104</option>-->
f8608fddfb23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_qiime_database_downloader commit 4934eb34300b5fa54d62d8b67e5b6e989e963ac9
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42 </param>
f8608fddfb23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_qiime_database_downloader commit 4934eb34300b5fa54d62d8b67e5b6e989e963ac9
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43 </when>
f8608fddfb23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_qiime_database_downloader commit 4934eb34300b5fa54d62d8b67e5b6e989e963ac9
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44 <when value="unite">
f8608fddfb23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_qiime_database_downloader commit 4934eb34300b5fa54d62d8b67e5b6e989e963ac9
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45 <param name="version" type="select" label="Version of UNITE OTUs">
f8608fddfb23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_qiime_database_downloader commit 4934eb34300b5fa54d62d8b67e5b6e989e963ac9
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46 <option value="20.11.2016">7.1 (2016-11-20, with singletons set as RefS)</option>
f8608fddfb23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_qiime_database_downloader commit 4934eb34300b5fa54d62d8b67e5b6e989e963ac9
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47 <option value="s_20.11.2016">7.1 (2016-11-20, with global and 97% singletons)</option>
f8608fddfb23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_qiime_database_downloader commit 4934eb34300b5fa54d62d8b67e5b6e989e963ac9
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48 <option value="22.08.2016">7.1 (2016-08-22, with singletons set as RefS)</option>
f8608fddfb23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_qiime_database_downloader commit 4934eb34300b5fa54d62d8b67e5b6e989e963ac9
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49 <option value="s_22.08.2016">7.1 (2016-08-22, with global and 97% singletons)</option>
f8608fddfb23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_qiime_database_downloader commit 4934eb34300b5fa54d62d8b67e5b6e989e963ac9
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50 <option value="31.01.2016">7.0 (2016-01-31, with singletons set as RefS)</option>
f8608fddfb23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_qiime_database_downloader commit 4934eb34300b5fa54d62d8b67e5b6e989e963ac9
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51 <option value="s_31.01.2016">7.0 (2016-01-31, with global and 97% singletons)</option>
f8608fddfb23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_qiime_database_downloader commit 4934eb34300b5fa54d62d8b67e5b6e989e963ac9
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52 <option value="01.08.2015">7.0 (2015-08-01, with singletons set as RefS)</option>
f8608fddfb23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_qiime_database_downloader commit 4934eb34300b5fa54d62d8b67e5b6e989e963ac9
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53 <option value="s_01.08.2015">7.0 (2015-08-01, with global and 97% singletons)</option>
f8608fddfb23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_qiime_database_downloader commit 4934eb34300b5fa54d62d8b67e5b6e989e963ac9
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54 <option value="02.03.2015">7.0 (2015-03-02, with singletons set as RefS)</option>
f8608fddfb23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_qiime_database_downloader commit 4934eb34300b5fa54d62d8b67e5b6e989e963ac9
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55 <option value="s_02.03.2015">7.0 (2015-03-02, with global and 97% singletons)</option>
f8608fddfb23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_qiime_database_downloader commit 4934eb34300b5fa54d62d8b67e5b6e989e963ac9
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56 <option value="30.12.2014">6.0 (2014-12-30, with singletons set as RefS)</option>
f8608fddfb23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_qiime_database_downloader commit 4934eb34300b5fa54d62d8b67e5b6e989e963ac9
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57 <option value="s_30.12.2014">6.0 (2014-12-30, with global and 97% singletons)</option>
f8608fddfb23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_qiime_database_downloader commit 4934eb34300b5fa54d62d8b67e5b6e989e963ac9
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58 <option value="10.09.2014">6.0 (2014-09-10, with singletons set as RefS)</option>
f8608fddfb23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_qiime_database_downloader commit 4934eb34300b5fa54d62d8b67e5b6e989e963ac9
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59 <option value="s_10.09.2014">6.0 (2014-09-10, with global and 97% singletons)</option>
f8608fddfb23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_qiime_database_downloader commit 4934eb34300b5fa54d62d8b67e5b6e989e963ac9
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60 <option value="04.07.2014">6.0 (2014-07-04, with singletons set as RefS)</option>
f8608fddfb23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_qiime_database_downloader commit 4934eb34300b5fa54d62d8b67e5b6e989e963ac9
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61 <option value="s_04.07.2014">6.0 (2014-07-04, with global and 97% singletons)</option>
f8608fddfb23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_qiime_database_downloader commit 4934eb34300b5fa54d62d8b67e5b6e989e963ac9
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62 <option value="13.05.2014">6.0 (2014-05-13, with singletons set as RefS)</option>
f8608fddfb23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_qiime_database_downloader commit 4934eb34300b5fa54d62d8b67e5b6e989e963ac9
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63 <option value="s_13.05.2014">6.0 (2014-05-13, with global and 97% singletons)</option>
f8608fddfb23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_qiime_database_downloader commit 4934eb34300b5fa54d62d8b67e5b6e989e963ac9
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64 <option value="09.02.2014">6.0 (2014-02-09, with singletons set as RefS)</option>
f8608fddfb23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_qiime_database_downloader commit 4934eb34300b5fa54d62d8b67e5b6e989e963ac9
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65 <option value="s_09.02.2014">6.0 (2014-02-09, with global and 97% singletons)</option>
f8608fddfb23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_qiime_database_downloader commit 4934eb34300b5fa54d62d8b67e5b6e989e963ac9
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66 <option value="15.01.2014">6.0 (2014-01-15, with singletons set as RefS)</option>
f8608fddfb23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_qiime_database_downloader commit 4934eb34300b5fa54d62d8b67e5b6e989e963ac9
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67 <option value="s_15.01.2014">6.0 (2014-01-15, with global and 97% singletons)</option>
f8608fddfb23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_qiime_database_downloader commit 4934eb34300b5fa54d62d8b67e5b6e989e963ac9
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68 <option value="19.12.2013">6.0 (2013-12-19, with singletons set as RefS)</option>
f8608fddfb23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_qiime_database_downloader commit 4934eb34300b5fa54d62d8b67e5b6e989e963ac9
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69 <option value="s_19.12.2013">6.0 (2013-12-19, with global and 97% singletons)</option>
f8608fddfb23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_qiime_database_downloader commit 4934eb34300b5fa54d62d8b67e5b6e989e963ac9
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70 <option value="08.12.2013">6.0 (2013-12-08, with singletons set as RefS)</option>
f8608fddfb23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_qiime_database_downloader commit 4934eb34300b5fa54d62d8b67e5b6e989e963ac9
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71 <option value="s_08.12.2013">6.0 (2013-12-08, with global and 97% singletons)</option>
f8608fddfb23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_qiime_database_downloader commit 4934eb34300b5fa54d62d8b67e5b6e989e963ac9
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72 <option value="15.10.2013">5.0 (2013-10-15, with singletons set as RefS)</option>
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73 <option value="s_15.10.2013">5.0 (2013-10-15, with global and 97% singletons)</option>
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74 </param>
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75 </when>
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76 <!--<when value="img">
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77 <param name="version" type="select" label="Version of IMG/QIIME reference protein sequences">
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78 <option value="img-qiime-25oct2012" selected="true">img-qiime-25oct2012</option>
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79 </param>
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80 </when>-->
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81 </conditional>
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82 </inputs>
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83 <outputs>
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84 <data name="out_file" format="data_manager_json" label="${tool.name}"/>
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85 </outputs>
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86 <tests>
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87 </tests>
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88 <help><![CDATA[
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89 This tool downloads the reference databases for QIIME
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90 ]]></help>
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91 <citations>
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92 <citation type="doi">10.1038/nmeth.f.303</citation>
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93 </citations>
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94 </tool>