Mercurial > repos > iuc > data_manager_metaphlan_database_downloader

annotate data_manager/data_manager_metaphlan_download.xml @ 3:4ba60cb14cb0 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_metaphlan_database_downloader commit f5c02de49bb33445667dd359bc7ce5801140b207
author iuc
date Wed, 05 Apr 2023 15:01:49 +0000
parents 5fe20c915fa6
children 0cb27ea69dc1
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5fe20c915fa6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_metaphlan_database_downloader commit 57df6e8a0ffd145e560f7c7e20cfedbbe2ce01d2
iuc
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1 <tool id="data_manager_metaphlan_download" name="Download and build MetaPhlAn database" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" tool_type="manage_data" profile="22.05">
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169b08c9713c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_metaphlan_database_downloader commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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2 <description></description>
169b08c9713c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_metaphlan_database_downloader commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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3 <requirements>
169b08c9713c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_metaphlan_database_downloader commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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4 <requirement type="package" version="@TOOL_VERSION@">metaphlan</requirement>
169b08c9713c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_metaphlan_database_downloader commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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5 </requirements>
169b08c9713c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_metaphlan_database_downloader commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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6 <macros>
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5fe20c915fa6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_metaphlan_database_downloader commit 57df6e8a0ffd145e560f7c7e20cfedbbe2ce01d2
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7 <token name="@TOOL_VERSION@">4.0.6</token>
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4ba60cb14cb0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_metaphlan_database_downloader commit f5c02de49bb33445667dd359bc7ce5801140b207
iuc
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8 <token name="@VERSION_SUFFIX@">1</token>
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169b08c9713c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_metaphlan_database_downloader commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
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9 </macros>
169b08c9713c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_metaphlan_database_downloader commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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10 <stdio>
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5fe20c915fa6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_metaphlan_database_downloader commit 57df6e8a0ffd145e560f7c7e20cfedbbe2ce01d2
iuc
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11 <exit_code range=":-1" level="fatal" description="Error: Cannot open file"/>
5fe20c915fa6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_metaphlan_database_downloader commit 57df6e8a0ffd145e560f7c7e20cfedbbe2ce01d2
iuc
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12 <exit_code range="1:" level="fatal" description="Error"/>
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169b08c9713c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_metaphlan_database_downloader commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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13 </stdio>
169b08c9713c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_metaphlan_database_downloader commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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14 <command><![CDATA[
169b08c9713c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_metaphlan_database_downloader commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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15 python '$__tool_directory__/data_manager_metaphlan_download.py'
169b08c9713c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_metaphlan_database_downloader commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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16 --index '$index'
169b08c9713c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_metaphlan_database_downloader commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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17 --json '$out_file'
169b08c9713c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_metaphlan_database_downloader commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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18 ]]></command>
169b08c9713c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_metaphlan_database_downloader commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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19 <inputs>
169b08c9713c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_metaphlan_database_downloader commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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20 <param name="index" type="select" label="Version">
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4ba60cb14cb0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_metaphlan_database_downloader commit f5c02de49bb33445667dd359bc7ce5801140b207
iuc
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21 <option value="mpa_vOct22_CHOCOPhlAnSGB_202212" selected="true">FULL: mpa_vOct22_CHOCOPhlAnSGB_202212</option>
4ba60cb14cb0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_metaphlan_database_downloader commit f5c02de49bb33445667dd359bc7ce5801140b207
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22 <option value="mpa_vJan21_CHOCOPhlAnSGB_202103">FULL: mpa_vJan21_CHOCOPhlAnSGB_202103</option>
4ba60cb14cb0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_metaphlan_database_downloader commit f5c02de49bb33445667dd359bc7ce5801140b207
iuc
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23 <option value="mpa_vJan21_TOY_CHOCOPhlAnSGB_202103">DEMO: mpa_vJan21_TOY_CHOCOPhlAnSGB_202103</option>
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169b08c9713c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_metaphlan_database_downloader commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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24 </param>
169b08c9713c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_metaphlan_database_downloader commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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25 </inputs>
169b08c9713c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_metaphlan_database_downloader commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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26 <outputs>
169b08c9713c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_metaphlan_database_downloader commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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27 <data name="out_file" format="data_manager_json" label="${tool.name}"/>
169b08c9713c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_metaphlan_database_downloader commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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28 </outputs>
169b08c9713c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_metaphlan_database_downloader commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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29 <tests>
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5fe20c915fa6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_metaphlan_database_downloader commit 57df6e8a0ffd145e560f7c7e20cfedbbe2ce01d2
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30 <test expect_num_outputs="1">
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4ba60cb14cb0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_metaphlan_database_downloader commit f5c02de49bb33445667dd359bc7ce5801140b207
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31 <param name="index" value="mpa_vJan21_TOY_CHOCOPhlAnSGB_202103"/>
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5fe20c915fa6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_metaphlan_database_downloader commit 57df6e8a0ffd145e560f7c7e20cfedbbe2ce01d2
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32 <output name="out_file">
5fe20c915fa6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_metaphlan_database_downloader commit 57df6e8a0ffd145e560f7c7e20cfedbbe2ce01d2
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33 <assert_contents>
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4ba60cb14cb0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_metaphlan_database_downloader commit f5c02de49bb33445667dd359bc7ce5801140b207
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34 <has_text text="mpa_vJan21_TOY_CHOCOPhlAnSGB_202103"/>
4ba60cb14cb0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_metaphlan_database_downloader commit f5c02de49bb33445667dd359bc7ce5801140b207
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35 <has_text text="MetaPhlAn clade-specific marker genes (mpa_vJan21_TOY_CHOCOPhlAnSGB_202103)"/>
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5fe20c915fa6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_metaphlan_database_downloader commit 57df6e8a0ffd145e560f7c7e20cfedbbe2ce01d2
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36 </assert_contents>
5fe20c915fa6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_metaphlan_database_downloader commit 57df6e8a0ffd145e560f7c7e20cfedbbe2ce01d2
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37 </output>
5fe20c915fa6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_metaphlan_database_downloader commit 57df6e8a0ffd145e560f7c7e20cfedbbe2ce01d2
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38 </test>
0
169b08c9713c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_metaphlan_database_downloader commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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39 </tests>
169b08c9713c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_metaphlan_database_downloader commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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40 <help><![CDATA[
169b08c9713c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_metaphlan_database_downloader commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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41 This tool downloads and builds the MetaPhlAn databases.
169b08c9713c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_metaphlan_database_downloader commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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42 ]]></help>
169b08c9713c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_metaphlan_database_downloader commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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43 <citations>
169b08c9713c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_metaphlan_database_downloader commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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44 <citation type="doi">1101/2020.11.19.388223</citation>
169b08c9713c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_metaphlan_database_downloader commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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45 <yield />
169b08c9713c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_metaphlan_database_downloader commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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46 </citations>
169b08c9713c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_metaphlan_database_downloader commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
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47 </tool>