Mercurial > repos > devteam > data_manager_build_kraken_database
annotate data_manager/kraken_database_builder.xml @ 8:4269aa2e0125 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken_database/ commit a54e50916ebdb0858b049cdc549a43df801e1a71
author | iuc |
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date | Tue, 21 May 2024 07:35:43 +0000 |
parents | 0a9ff888a4e2 |
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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
devteam
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1 <?xml version="1.0"?> |
8
4269aa2e0125
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken_database/ commit a54e50916ebdb0858b049cdc549a43df801e1a71
iuc
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2 <tool id="kraken_database_builder" name="Kraken" tool_type="manage_data" version="1.1.2" profile="23.0"> |
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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
devteam
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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
devteam
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4 <requirements> |
5
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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4269aa2e0125
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken_database/ commit a54e50916ebdb0858b049cdc549a43df801e1a71
iuc
parents:
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6 <requirement type="package" version="3.8.3">python</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
devteam
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7 </requirements> |
c3276afba416
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_build_kraken_database/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
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8 <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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9 <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
devteam
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10 <![CDATA[ |
c3276afba416
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_build_kraken_database/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
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11 #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
devteam
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12 mkdir kraken-database && cd kraken-database && |
2
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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13 kraken-build --threads \${GALAXY_SLOTS:-1} --download-taxonomy --db '${database_name}' && |
0
c3276afba416
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_build_kraken_database/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
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14 #for $library in $library_list: |
c3276afba416
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_build_kraken_database/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
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15 #if str($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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16 kraken-build --threads \${GALAXY_SLOTS:-1} --download-library $library --db '${database_name}' && |
0
c3276afba416
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_build_kraken_database/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
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17 #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
devteam
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18 #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
devteam
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19 #for $fasta in $input_fasta: |
c3276afba416
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_build_kraken_database/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
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20 #if str($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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changeset
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21 kraken-build --threads \${GALAXY_SLOTS:-1} --db '${database_name}' --add-to-library '$fasta' && |
0
c3276afba416
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_build_kraken_database/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
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22 #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
devteam
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23 #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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changeset
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24 kraken-build --threads \${GALAXY_SLOTS:-1} --db '${database_name}' --build --kmer-len ${kmer_len} --minimizer-len ${minimizer_len} && |
065d8a4d74f4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken_database/ commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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25 cd .. && |
065d8a4d74f4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken_database/ commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents:
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26 python '$__tool_directory__/make_json.py' --db '${database_name}' --out '${out_file}' |
0
c3276afba416
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_build_kraken_database/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
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27 ]]> |
c3276afba416
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_build_kraken_database/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
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28 </command> |
c3276afba416
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_build_kraken_database/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
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29 <inputs> |
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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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30 <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
iuc
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31 <param name="libraries" type="select" multiple="true" label="Select partial library to download"> |
0
c3276afba416
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_build_kraken_database/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
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32 <option value="bacteria">Bacteria</option> |
4
6d7aef331be9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken_database/ commit 20cfde679c4064cea8a0b64763ddd5e092af7eab
iuc
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33 <option value="archaea">Archaea</option> |
6d7aef331be9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken_database/ commit 20cfde679c4064cea8a0b64763ddd5e092af7eab
iuc
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34 <option value="plasmid">Plasmid</option> |
6d7aef331be9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken_database/ commit 20cfde679c4064cea8a0b64763ddd5e092af7eab
iuc
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35 <option value="viral">Viral</option> |
0
c3276afba416
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_build_kraken_database/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
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36 <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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37 </param> |
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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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38 <param name="input_fasta" type="data" format="fasta" multiple="True" optional="true" label="Select history item" /> |
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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39 <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
iuc
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40 <param name="minimizer_len" type="integer" value="15" label="Minimizer length" /> |
0
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 </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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42 <outputs> |
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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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43 <data name="out_file" format="data_manager_json" /> |
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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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44 </outputs> |
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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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45 <help> |
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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46 </help> |
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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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47 <citations> |
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 <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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49 </citations> |
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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50 </tool> |