Mercurial > repos > devteam > data_manager_build_kraken_database

annotate data_manager/kraken_database_builder.xml @ 5:0a9ff888a4e2 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken_database/ commit 02d5f5241444bf471d3f89a6e0aeb4d9f4075811"
author iuc
date Tue, 18 Aug 2020 11:36:13 -0400
parents 6d7aef331be9
children 4269aa2e0125
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c3276afba416 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_build_kraken_database/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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1 <?xml version="1.0"?>
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0a9ff888a4e2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken_database/ commit 02d5f5241444bf471d3f89a6e0aeb4d9f4075811"
iuc
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2 <tool id="kraken_database_builder" name="Kraken" tool_type="manage_data" version="1.1.1">
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c3276afba416 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_build_kraken_database/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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3 <description>database builder</description>
c3276afba416 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_build_kraken_database/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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4 <requirements>
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0a9ff888a4e2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken_database/ commit 02d5f5241444bf471d3f89a6e0aeb4d9f4075811"
iuc
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5 <requirement type="package" version="1.1.1">kraken</requirement>
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c3276afba416 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_build_kraken_database/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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6 </requirements>
c3276afba416 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_build_kraken_database/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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7 <version_command>kraken -version | awk '{print $NF}'</version_command>
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065d8a4d74f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken_database/ commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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8 <command detect_errors="exit_code">
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c3276afba416 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_build_kraken_database/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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9 <![CDATA[
c3276afba416 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_build_kraken_database/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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10 #set $library_list = str($libraries).split(',')
c3276afba416 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_build_kraken_database/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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11 mkdir kraken-database && cd kraken-database &&
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065d8a4d74f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken_database/ commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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12 kraken-build --threads \${GALAXY_SLOTS:-1} --download-taxonomy --db '${database_name}' &&
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c3276afba416 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_build_kraken_database/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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13 #for $library in $library_list:
c3276afba416 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_build_kraken_database/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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14 #if str($library) != 'None':
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065d8a4d74f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken_database/ commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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15 kraken-build --threads \${GALAXY_SLOTS:-1} --download-library $library --db '${database_name}' &&
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c3276afba416 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_build_kraken_database/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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16 #end if
c3276afba416 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_build_kraken_database/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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17 #end for
c3276afba416 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_build_kraken_database/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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18 #for $fasta in $input_fasta:
c3276afba416 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_build_kraken_database/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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19 #if str($fasta) != 'None':
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065d8a4d74f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken_database/ commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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20 kraken-build --threads \${GALAXY_SLOTS:-1} --db '${database_name}' --add-to-library '$fasta' &&
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c3276afba416 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_build_kraken_database/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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21 #end if
c3276afba416 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_build_kraken_database/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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22 #end for
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065d8a4d74f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken_database/ commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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23 kraken-build --threads \${GALAXY_SLOTS:-1} --db '${database_name}' --build --kmer-len ${kmer_len} --minimizer-len ${minimizer_len} &&
065d8a4d74f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken_database/ commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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24 cd .. &&
065d8a4d74f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken_database/ commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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25 python '$__tool_directory__/make_json.py' --db '${database_name}' --out '${out_file}'
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c3276afba416 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_build_kraken_database/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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26 ]]>
c3276afba416 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_build_kraken_database/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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27 </command>
c3276afba416 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_build_kraken_database/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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28 <inputs>
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29 <param name="database_name" type="text" label="Name for this database" />
065d8a4d74f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken_database/ commit 8652f36a3a3838dca989426961561e81432acf4f
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30 <param name="libraries" type="select" multiple="true" label="Select partial library to download">
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c3276afba416 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_build_kraken_database/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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31 <option value="bacteria">Bacteria</option>
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32 <option value="archaea">Archaea</option>
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33 <option value="plasmid">Plasmid</option>
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34 <option value="viral">Viral</option>
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35 <option value="human">Human</option>
c3276afba416 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_build_kraken_database/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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36 </param>
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37 <param name="input_fasta" type="data" format="fasta" multiple="True" optional="true" label="Select history item" />
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38 <param name="kmer_len" type="integer" value="31" label="K-mer length in BP" />
065d8a4d74f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken_database/ commit 8652f36a3a3838dca989426961561e81432acf4f
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39 <param name="minimizer_len" type="integer" value="15" label="Minimizer length" />
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40 </inputs>
c3276afba416 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_build_kraken_database/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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41 <outputs>
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42 <data name="out_file" format="data_manager_json" />
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43 </outputs>
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44 <help>
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45 </help>
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46 <citations>
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47 <citation type="doi">10.1186/gb-2014-15-3-r46</citation>
c3276afba416 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_build_kraken_database/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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48 </citations>
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49 </tool>