Mercurial > repos > iuc > data_manager_mapseq
annotate mapseq_db_fetcher.xml @ 0:dbf2735e8480 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/ commit 66e797aaa79b92c282a8127260cdfd5702207e35
author | iuc |
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date | Wed, 13 Sep 2023 19:54:19 +0000 |
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dbf2735e8480
planemo upload for repository https://github.com/galaxyproject/tools-iuc/ commit 66e797aaa79b92c282a8127260cdfd5702207e35
iuc
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1 <?xml version="1.0"?> |
dbf2735e8480
planemo upload for repository https://github.com/galaxyproject/tools-iuc/ commit 66e797aaa79b92c282a8127260cdfd5702207e35
iuc
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2 <tool id="mapseq_db_fetcher" name="Mapseq DB fetcher" tool_type="manage_data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> |
dbf2735e8480
planemo upload for repository https://github.com/galaxyproject/tools-iuc/ commit 66e797aaa79b92c282a8127260cdfd5702207e35
iuc
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3 <description>Fetches the DB required for mapseq</description> |
dbf2735e8480
planemo upload for repository https://github.com/galaxyproject/tools-iuc/ commit 66e797aaa79b92c282a8127260cdfd5702207e35
iuc
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4 <macros> |
dbf2735e8480
planemo upload for repository https://github.com/galaxyproject/tools-iuc/ commit 66e797aaa79b92c282a8127260cdfd5702207e35
iuc
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5 <import>macros.xml</import> |
dbf2735e8480
planemo upload for repository https://github.com/galaxyproject/tools-iuc/ commit 66e797aaa79b92c282a8127260cdfd5702207e35
iuc
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6 </macros> |
dbf2735e8480
planemo upload for repository https://github.com/galaxyproject/tools-iuc/ commit 66e797aaa79b92c282a8127260cdfd5702207e35
iuc
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7 <expand macro="requirements" /> |
dbf2735e8480
planemo upload for repository https://github.com/galaxyproject/tools-iuc/ commit 66e797aaa79b92c282a8127260cdfd5702207e35
iuc
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8 <expand macro="version" /> |
dbf2735e8480
planemo upload for repository https://github.com/galaxyproject/tools-iuc/ commit 66e797aaa79b92c282a8127260cdfd5702207e35
iuc
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9 <command detect_errors="exit_code"> |
dbf2735e8480
planemo upload for repository https://github.com/galaxyproject/tools-iuc/ commit 66e797aaa79b92c282a8127260cdfd5702207e35
iuc
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10 <![CDATA[ |
dbf2735e8480
planemo upload for repository https://github.com/galaxyproject/tools-iuc/ commit 66e797aaa79b92c282a8127260cdfd5702207e35
iuc
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11 python '$__tool_directory__/data_manager_fetch_mapseq_db.py' |
dbf2735e8480
planemo upload for repository https://github.com/galaxyproject/tools-iuc/ commit 66e797aaa79b92c282a8127260cdfd5702207e35
iuc
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12 --out '${out_file}' |
dbf2735e8480
planemo upload for repository https://github.com/galaxyproject/tools-iuc/ commit 66e797aaa79b92c282a8127260cdfd5702207e35
iuc
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13 --version '${version}' |
dbf2735e8480
planemo upload for repository https://github.com/galaxyproject/tools-iuc/ commit 66e797aaa79b92c282a8127260cdfd5702207e35
iuc
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14 --database-type '${database_type}' |
dbf2735e8480
planemo upload for repository https://github.com/galaxyproject/tools-iuc/ commit 66e797aaa79b92c282a8127260cdfd5702207e35
iuc
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15 $test_data_manager |
dbf2735e8480
planemo upload for repository https://github.com/galaxyproject/tools-iuc/ commit 66e797aaa79b92c282a8127260cdfd5702207e35
iuc
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16 ]]> |
dbf2735e8480
planemo upload for repository https://github.com/galaxyproject/tools-iuc/ commit 66e797aaa79b92c282a8127260cdfd5702207e35
iuc
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17 </command> |
dbf2735e8480
planemo upload for repository https://github.com/galaxyproject/tools-iuc/ commit 66e797aaa79b92c282a8127260cdfd5702207e35
iuc
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18 <inputs> |
dbf2735e8480
planemo upload for repository https://github.com/galaxyproject/tools-iuc/ commit 66e797aaa79b92c282a8127260cdfd5702207e35
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19 <!-- <param name="test_data_manager" type="hidden" /> --> |
dbf2735e8480
planemo upload for repository https://github.com/galaxyproject/tools-iuc/ commit 66e797aaa79b92c282a8127260cdfd5702207e35
iuc
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20 <param name="test_data_manager" type="boolean" truevalue="--test" falsevalue="" checked="False" label="Download minimal test DB and create mock data table entry." /> |
dbf2735e8480
planemo upload for repository https://github.com/galaxyproject/tools-iuc/ commit 66e797aaa79b92c282a8127260cdfd5702207e35
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21 |
dbf2735e8480
planemo upload for repository https://github.com/galaxyproject/tools-iuc/ commit 66e797aaa79b92c282a8127260cdfd5702207e35
iuc
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22 <param name="database_type" type="select" multiple="false" label="Database Type"> |
dbf2735e8480
planemo upload for repository https://github.com/galaxyproject/tools-iuc/ commit 66e797aaa79b92c282a8127260cdfd5702207e35
iuc
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23 <option value="mgnify_lsu">MGnify LSU (v5.0.7)</option> |
dbf2735e8480
planemo upload for repository https://github.com/galaxyproject/tools-iuc/ commit 66e797aaa79b92c282a8127260cdfd5702207e35
iuc
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24 <option value="mgnify_ssu">MGnify SSU (v5.0.7)</option> |
dbf2735e8480
planemo upload for repository https://github.com/galaxyproject/tools-iuc/ commit 66e797aaa79b92c282a8127260cdfd5702207e35
iuc
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25 <option value="mgnify_its_itsonedb">MGnify ITS ITSonedb (v5.0.7)</option> |
dbf2735e8480
planemo upload for repository https://github.com/galaxyproject/tools-iuc/ commit 66e797aaa79b92c282a8127260cdfd5702207e35
iuc
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26 <option value="mgnify_its_unite">MGnify ITS UNITE (v5.0.7)</option> |
dbf2735e8480
planemo upload for repository https://github.com/galaxyproject/tools-iuc/ commit 66e797aaa79b92c282a8127260cdfd5702207e35
iuc
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27 </param> |
dbf2735e8480
planemo upload for repository https://github.com/galaxyproject/tools-iuc/ commit 66e797aaa79b92c282a8127260cdfd5702207e35
iuc
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28 |
dbf2735e8480
planemo upload for repository https://github.com/galaxyproject/tools-iuc/ commit 66e797aaa79b92c282a8127260cdfd5702207e35
iuc
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29 <!-- <param name="test_data_manager" type="text" value=""/> --> |
dbf2735e8480
planemo upload for repository https://github.com/galaxyproject/tools-iuc/ commit 66e797aaa79b92c282a8127260cdfd5702207e35
iuc
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30 <param argument="--version" type="text" value="5.0.7" help="Check MGnify GitHub (https://github.com/EBI-Metagenomics/pipeline-v5/releases) for the version."/> |
dbf2735e8480
planemo upload for repository https://github.com/galaxyproject/tools-iuc/ commit 66e797aaa79b92c282a8127260cdfd5702207e35
iuc
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31 </inputs> |
dbf2735e8480
planemo upload for repository https://github.com/galaxyproject/tools-iuc/ commit 66e797aaa79b92c282a8127260cdfd5702207e35
iuc
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32 <outputs> |
dbf2735e8480
planemo upload for repository https://github.com/galaxyproject/tools-iuc/ commit 66e797aaa79b92c282a8127260cdfd5702207e35
iuc
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33 <data format="data_manager_json" name="out_file" /> |
dbf2735e8480
planemo upload for repository https://github.com/galaxyproject/tools-iuc/ commit 66e797aaa79b92c282a8127260cdfd5702207e35
iuc
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34 </outputs> |
dbf2735e8480
planemo upload for repository https://github.com/galaxyproject/tools-iuc/ commit 66e797aaa79b92c282a8127260cdfd5702207e35
iuc
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35 <tests> |
dbf2735e8480
planemo upload for repository https://github.com/galaxyproject/tools-iuc/ commit 66e797aaa79b92c282a8127260cdfd5702207e35
iuc
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36 <test expect_num_outputs="1"> |
dbf2735e8480
planemo upload for repository https://github.com/galaxyproject/tools-iuc/ commit 66e797aaa79b92c282a8127260cdfd5702207e35
iuc
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37 <param name="test_data_manager" value="--test"/> |
dbf2735e8480
planemo upload for repository https://github.com/galaxyproject/tools-iuc/ commit 66e797aaa79b92c282a8127260cdfd5702207e35
iuc
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38 <param name="version" value="5.0.7"/> |
dbf2735e8480
planemo upload for repository https://github.com/galaxyproject/tools-iuc/ commit 66e797aaa79b92c282a8127260cdfd5702207e35
iuc
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39 <param name="database_type" value="mgnify_lsu"/> |
dbf2735e8480
planemo upload for repository https://github.com/galaxyproject/tools-iuc/ commit 66e797aaa79b92c282a8127260cdfd5702207e35
iuc
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40 <output name="out_file"> |
dbf2735e8480
planemo upload for repository https://github.com/galaxyproject/tools-iuc/ commit 66e797aaa79b92c282a8127260cdfd5702207e35
iuc
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41 <assert_contents> |
dbf2735e8480
planemo upload for repository https://github.com/galaxyproject/tools-iuc/ commit 66e797aaa79b92c282a8127260cdfd5702207e35
iuc
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42 <has_text text="mgnify_lsu"/> |
dbf2735e8480
planemo upload for repository https://github.com/galaxyproject/tools-iuc/ commit 66e797aaa79b92c282a8127260cdfd5702207e35
iuc
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43 <has_text text="5.0.7"/> |
dbf2735e8480
planemo upload for repository https://github.com/galaxyproject/tools-iuc/ commit 66e797aaa79b92c282a8127260cdfd5702207e35
iuc
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44 </assert_contents> |
dbf2735e8480
planemo upload for repository https://github.com/galaxyproject/tools-iuc/ commit 66e797aaa79b92c282a8127260cdfd5702207e35
iuc
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45 </output> |
dbf2735e8480
planemo upload for repository https://github.com/galaxyproject/tools-iuc/ commit 66e797aaa79b92c282a8127260cdfd5702207e35
iuc
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46 </test> |
dbf2735e8480
planemo upload for repository https://github.com/galaxyproject/tools-iuc/ commit 66e797aaa79b92c282a8127260cdfd5702207e35
iuc
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47 </tests> |
dbf2735e8480
planemo upload for repository https://github.com/galaxyproject/tools-iuc/ commit 66e797aaa79b92c282a8127260cdfd5702207e35
iuc
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48 <help> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/ commit 66e797aaa79b92c282a8127260cdfd5702207e35
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49 Downloads preformatted DBs form MGnify that can be used for mapseq. |
dbf2735e8480
planemo upload for repository https://github.com/galaxyproject/tools-iuc/ commit 66e797aaa79b92c282a8127260cdfd5702207e35
iuc
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50 The download paths were taken from: https://github.com/EBI-Metagenomics/pipeline-v5/ |
dbf2735e8480
planemo upload for repository https://github.com/galaxyproject/tools-iuc/ commit 66e797aaa79b92c282a8127260cdfd5702207e35
iuc
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51 </help> |
dbf2735e8480
planemo upload for repository https://github.com/galaxyproject/tools-iuc/ commit 66e797aaa79b92c282a8127260cdfd5702207e35
iuc
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52 <expand macro="citations" /> |
dbf2735e8480
planemo upload for repository https://github.com/galaxyproject/tools-iuc/ commit 66e797aaa79b92c282a8127260cdfd5702207e35
iuc
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53 <expand macro="creator" /> |
dbf2735e8480
planemo upload for repository https://github.com/galaxyproject/tools-iuc/ commit 66e797aaa79b92c282a8127260cdfd5702207e35
iuc
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54 </tool> |