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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_eukcc commit ea26eabce05391af21e0919ac5309d23396960e3
author ufz
date Fri, 25 Jul 2025 10:54:08 +0000
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7f11e0da0e4f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_eukcc commit ea26eabce05391af21e0919ac5309d23396960e3
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1 <tool id="data_manager_eukcc" name="EukCC data manager" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" tool_type="manage_data" profile="20.01">
7f11e0da0e4f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_eukcc commit ea26eabce05391af21e0919ac5309d23396960e3
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2 <macros>
7f11e0da0e4f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_eukcc commit ea26eabce05391af21e0919ac5309d23396960e3
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3 <token name="@TOOL_VERSION@">2.1.3</token>
7f11e0da0e4f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_eukcc commit ea26eabce05391af21e0919ac5309d23396960e3
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4 <token name="@VERSION_SUFFIX@">0</token>
7f11e0da0e4f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_eukcc commit ea26eabce05391af21e0919ac5309d23396960e3
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5 </macros>
7f11e0da0e4f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_eukcc commit ea26eabce05391af21e0919ac5309d23396960e3
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6 <requirements>
7f11e0da0e4f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_eukcc commit ea26eabce05391af21e0919ac5309d23396960e3
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7 <requirement type="package" version="@TOOL_VERSION@">eukcc</requirement>
7f11e0da0e4f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_eukcc commit ea26eabce05391af21e0919ac5309d23396960e3
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8 </requirements>
7f11e0da0e4f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_eukcc commit ea26eabce05391af21e0919ac5309d23396960e3
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9 <version_command>eukcc --version | cut -d" " -f3</version_command>
7f11e0da0e4f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_eukcc commit ea26eabce05391af21e0919ac5309d23396960e3
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10 <command detect_errors="exit_code"><![CDATA[
7f11e0da0e4f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_eukcc commit ea26eabce05391af21e0919ac5309d23396960e3
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11 mkdir '$output_file.extra_files_path' &&
7f11e0da0e4f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_eukcc commit ea26eabce05391af21e0919ac5309d23396960e3
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12 wget http://ftp.ebi.ac.uk/pub/databases/metagenomics/eukcc/eukcc2_db_ver_${version}.tar.gz &&
7f11e0da0e4f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_eukcc commit ea26eabce05391af21e0919ac5309d23396960e3
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13 tar -xvf eukcc2_db_ver_${version}.tar.gz &&
7f11e0da0e4f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_eukcc commit ea26eabce05391af21e0919ac5309d23396960e3
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14 rm eukcc2_db_ver_${version}.tar.gz &&
7f11e0da0e4f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_eukcc commit ea26eabce05391af21e0919ac5309d23396960e3
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15 mv eukcc2_db_ver_${version}/* '$output_file.extra_files_path'/ &&
7f11e0da0e4f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_eukcc commit ea26eabce05391af21e0919ac5309d23396960e3
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16 cp '$dmjson' '$output_file'
7f11e0da0e4f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_eukcc commit ea26eabce05391af21e0919ac5309d23396960e3
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17 ]]></command>
7f11e0da0e4f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_eukcc commit ea26eabce05391af21e0919ac5309d23396960e3
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18 <configfiles>
7f11e0da0e4f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_eukcc commit ea26eabce05391af21e0919ac5309d23396960e3
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19 <configfile name="dmjson"><![CDATA[
7f11e0da0e4f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_eukcc commit ea26eabce05391af21e0919ac5309d23396960e3
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20 {
7f11e0da0e4f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_eukcc commit ea26eabce05391af21e0919ac5309d23396960e3
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21 "data_tables":{
7f11e0da0e4f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_eukcc commit ea26eabce05391af21e0919ac5309d23396960e3
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22 "eukcc":[
7f11e0da0e4f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_eukcc commit ea26eabce05391af21e0919ac5309d23396960e3
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23 {
7f11e0da0e4f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_eukcc commit ea26eabce05391af21e0919ac5309d23396960e3
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24 "value":"$version",
7f11e0da0e4f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_eukcc commit ea26eabce05391af21e0919ac5309d23396960e3
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25 "name":"EukCC DB ${version}",
7f11e0da0e4f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_eukcc commit ea26eabce05391af21e0919ac5309d23396960e3
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26 "version":"${version}",
7f11e0da0e4f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_eukcc commit ea26eabce05391af21e0919ac5309d23396960e3
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27 "path":"$output_file.extra_files_path"
7f11e0da0e4f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_eukcc commit ea26eabce05391af21e0919ac5309d23396960e3
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28 }
7f11e0da0e4f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_eukcc commit ea26eabce05391af21e0919ac5309d23396960e3
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29 ]
7f11e0da0e4f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_eukcc commit ea26eabce05391af21e0919ac5309d23396960e3
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30 }
7f11e0da0e4f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_eukcc commit ea26eabce05391af21e0919ac5309d23396960e3
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31 }]]></configfile>
7f11e0da0e4f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_eukcc commit ea26eabce05391af21e0919ac5309d23396960e3
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32 </configfiles>
7f11e0da0e4f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_eukcc commit ea26eabce05391af21e0919ac5309d23396960e3
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33 <inputs>
7f11e0da0e4f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_eukcc commit ea26eabce05391af21e0919ac5309d23396960e3
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34 <param name="version" type="select" label="DB version">
7f11e0da0e4f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_eukcc commit ea26eabce05391af21e0919ac5309d23396960e3
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35 <option value="1.2">1.2</option>
7f11e0da0e4f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_eukcc commit ea26eabce05391af21e0919ac5309d23396960e3
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36 </param>
7f11e0da0e4f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_eukcc commit ea26eabce05391af21e0919ac5309d23396960e3
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37 </inputs>
7f11e0da0e4f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_eukcc commit ea26eabce05391af21e0919ac5309d23396960e3
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38 <outputs>
7f11e0da0e4f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_eukcc commit ea26eabce05391af21e0919ac5309d23396960e3
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39 <data name="output_file" format="data_manager_json"/>
7f11e0da0e4f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_eukcc commit ea26eabce05391af21e0919ac5309d23396960e3
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40 </outputs>
7f11e0da0e4f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_eukcc commit ea26eabce05391af21e0919ac5309d23396960e3
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41 <tests>
7f11e0da0e4f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_eukcc commit ea26eabce05391af21e0919ac5309d23396960e3
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42 <!-- data to large for test in CI
7f11e0da0e4f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_eukcc commit ea26eabce05391af21e0919ac5309d23396960e3
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43 <test>
7f11e0da0e4f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_eukcc commit ea26eabce05391af21e0919ac5309d23396960e3
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44 <param name="version" value="1.2"/>
7f11e0da0e4f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_eukcc commit ea26eabce05391af21e0919ac5309d23396960e3
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45 <output name="output_file">
7f11e0da0e4f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_eukcc commit ea26eabce05391af21e0919ac5309d23396960e3
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46 <assert_contents>
7f11e0da0e4f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_eukcc commit ea26eabce05391af21e0919ac5309d23396960e3
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47 <has_text text="EukCC DB"/>
7f11e0da0e4f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_eukcc commit ea26eabce05391af21e0919ac5309d23396960e3
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48 <has_text text="1.2"/>
7f11e0da0e4f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_eukcc commit ea26eabce05391af21e0919ac5309d23396960e3
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49 <has_text text="eukcc"/>
7f11e0da0e4f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_eukcc commit ea26eabce05391af21e0919ac5309d23396960e3
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50 </assert_contents>
7f11e0da0e4f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_eukcc commit ea26eabce05391af21e0919ac5309d23396960e3
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51 </output>
7f11e0da0e4f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_eukcc commit ea26eabce05391af21e0919ac5309d23396960e3
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52 </test> -->
7f11e0da0e4f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_eukcc commit ea26eabce05391af21e0919ac5309d23396960e3
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53 </tests>
7f11e0da0e4f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_eukcc commit ea26eabce05391af21e0919ac5309d23396960e3
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54 <help><![CDATA[
7f11e0da0e4f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_eukcc commit ea26eabce05391af21e0919ac5309d23396960e3
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55 This data managers fetches EukCC reference data from http://ftp.ebi.ac.uk/pub/databases/metagenomics/eukcc/
7f11e0da0e4f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_eukcc commit ea26eabce05391af21e0919ac5309d23396960e3
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56 ]]></help>
7f11e0da0e4f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_eukcc commit ea26eabce05391af21e0919ac5309d23396960e3
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57 <citations>
7f11e0da0e4f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_eukcc commit ea26eabce05391af21e0919ac5309d23396960e3
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58 <citation type="doi">10.1186/s13059-020-02155-4</citation>
7f11e0da0e4f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_eukcc commit ea26eabce05391af21e0919ac5309d23396960e3
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59 </citations>
7f11e0da0e4f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_eukcc commit ea26eabce05391af21e0919ac5309d23396960e3
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60 </tool>