Mercurial > repos > iuc > data_manager_cat
annotate data_manager/data_manager_cat.xml @ 2:472dabcb03bf draft default tip
planemo upload commit 09b56ef3e09ad6c5923c88616fea5cbd77d87616
author | iuc |
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date | Mon, 18 Dec 2023 09:36:10 +0000 |
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planemo upload commit 09b56ef3e09ad6c5923c88616fea5cbd77d87616
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1 <tool id="data_manager_cat" name="CAT DB" version="5.0.3.1" tool_type="manage_data" profile="18.09"> |
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2 <description>Install a new CAT database</description> |
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3 <requirements> |
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4 <requirement type="package" version="5.0.3">cat</requirement> |
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5 </requirements> |
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6 <version_command><![CDATA[ CAT --version ]]></version_command> |
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7 <command detect_errors="exit_code"><![CDATA[ |
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8 mkdir -p '$out_file.extra_files_path' && |
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9 python '${__tool_directory__}/data_manager_cat.py' |
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10 --config_file '$out_file' |
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11 --install_path '$out_file.extra_files_path' |
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12 #if $db.src == 'download' |
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13 --db_url '$db.db_url' |
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14 #end if |
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15 ]]></command> |
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16 <inputs> |
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17 <conditional name="db"> |
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18 <param name="src" type="select" label="Download or Build DBs"> |
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19 <option value="download">download</option> |
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20 <option value="build">build</option> |
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21 </param> |
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22 <when value="download"> |
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23 <param name="db_url" type="text" label="DB URL at https://tbb.bio.uu.nl/bastiaan/CAT_prepare/" |
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24 help="example: https://tbb.bio.uu.nl/bastiaan/CAT_prepare/CAT_prepare_20190719.tar.gz"> |
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25 </param> |
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26 </when> |
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27 <when value="build"> |
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28 </when> |
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29 </conditional> |
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30 </inputs> |
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31 <outputs> |
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32 <data name="out_file" format="data_manager_json" label="${tool.name}"/> |
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33 </outputs> |
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34 <tests> |
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35 <test> |
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36 <conditional name="db"> |
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37 <param name="src" value="download"/> |
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38 <param name="db_url" value="https://github.com/galaxyproject/tools-iuc/blob/ce82f787f1f035debfc86de09a271a9ec8d27e0e/data_managers/data_manager_cat/test-data/CAT_prepare_test.tar.gz?raw=true"/> |
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39 </conditional> |
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40 <output name="out_file"> |
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41 <assert_contents> |
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42 <has_text text="CAT_prepare_test/taxonomy" /> |
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43 </assert_contents> |
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44 </output> |
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45 </test> |
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46 </tests> |
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47 <help><![CDATA[ |
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48 This tool prepares reference data for CAT, the Contig Annotation Tool. |
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49 It can either download prebuilt reference data from https://tbb.bio.uu.nl/bastiaan/CAT_prepare/ |
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50 or build new reference data using the CAT prepare application. |
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51 |
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52 This requires at least 100GB of RAM, 250GB of disk space, and 24 hours. |
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53 ]]></help> |
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54 <citations> |
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55 <citation type="doi">https://doi.org/10.1101/072868</citation> |
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56 <citation type="doi">https://doi.org/10.1186/s13059-019-1817-x</citation> |
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57 <citation type="doi">https://doi.org/10.1038/nmeth.3176</citation> |
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58 <citation type="doi">https://doi.org/10.1186/1471-2105-11-119</citation> |
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59 </citations> |
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60 </tool> |