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planemo upload commit 09b56ef3e09ad6c5923c88616fea5cbd77d87616
author iuc
date Mon, 18 Dec 2023 09:36:10 +0000
parents cffd8e2382cf
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472dabcb03bf 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>