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annotate data_manager/mapseq_db_fetcher.xml @ 0:f99c1cc0b190 draft

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author galaxytrakr
date Thu, 26 Mar 2026 20:22:36 +0000
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1 <tool id="mapseq_db_fetcher" name="Mapseq DB fetcher" tool_type="manage_data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>Fetches the DB required for mapseq</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <expand macro="version" />
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8 <command detect_errors="exit_code">
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9 <![CDATA[
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10 python '$__tool_directory__/data_manager_fetch_mapseq_db.py'
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11 --out '${out_file}'
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12 --version '${select_version.version}'
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13 --database-type '${database_type}'
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14 ]]>
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15 </command>
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16 <inputs>
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17 <conditional name="select_version">
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18 <param argument="--version" type="select" label="Select MGnify version">
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19 <option value="5.0">v5.0</option>
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20 <option value="6.0">v6.0</option>
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21 </param>
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22 <when value="5.0">
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23 <param name="database_type" type="select" multiple="false" label="Database Type">
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24 <option value="mgnify_v5_lsu">MGnify LSU (v5.0.7)</option>
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25 <option value="mgnify_v5_ssu">MGnify SSU (v5.0.7)</option>
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26 <option value="mgnify_v5_its_itsonedb">MGnify ITS ITSonedb (v5.0.7)</option>
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27 <option value="mgnify_v5_its_unite">MGnify ITS UNITE (v5.0.7)</option>
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28 </param>
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29 </when>
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30 <when value="6.0">
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31 <param name="database_type" type="select" multiple="false" label="Database Type">
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32 <option value="mgnify_v6_lsu">MGnify LSU (v6.0)</option>
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33 <option value="mgnify_v6_ssu">MGnify SSU (v6.0)</option>
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34 <option value="mgnify_v6_its_itsonedb">MGnify ITS ITSonedb (v6.0)</option>
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35 <option value="mgnify_v6_its_unite">MGnify ITS UNITE (v6.0)</option>
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36 <option value="mgnify_v6_pr2">MGnify PR2 (v6.0)</option>
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37 </param>
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38 </when>
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39 </conditional>
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40 </inputs>
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41 <outputs>
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42 <data format="data_manager_json" name="out_file" />
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43 </outputs>
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44 <tests>
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45 </tests>
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46 <help>
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47 Downloads preformatted DBs form MGnify that can be used for mapseq.
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48 The download paths were taken from: https://github.com/EBI-Metagenomics/pipeline-v5/
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49 </help>
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50 <expand macro="citations" />
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51 <expand macro="creator" />
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52 </tool>