Mercurial > repos > iuc > data_manager_build_bracken_database

annotate data_manager/bracken_build_database.xml @ 0:c2e4127fb5bf draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
author iuc
date Sun, 20 Oct 2019 09:37:21 -0400
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children 9059edc96a85
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c2e4127fb5bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
iuc
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1 <?xml version="1.0"?>
c2e4127fb5bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
iuc
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2 <tool id="bracken_build_database" name="Bracken Database Builder" tool_type="manage_data" version="2.5+galaxy0" profile="19.01">
c2e4127fb5bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
iuc
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3 <description>bracken database builder</description>
c2e4127fb5bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
iuc
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4 <requirements>
c2e4127fb5bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
iuc
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5 <requirement type="package" version="2.5">bracken</requirement>
c2e4127fb5bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
iuc
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6 <requirement type="package" version="2.0.8_beta">kraken2</requirement>
c2e4127fb5bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
iuc
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7 </requirements>
c2e4127fb5bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
iuc
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8 <command>
c2e4127fb5bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
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9 <![CDATA[
c2e4127fb5bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
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10 python '$__tool_directory__/bracken_build_database.py'
c2e4127fb5bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
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11 '${out_file}'
c2e4127fb5bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
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12 --kraken-db '${kraken_db.fields.path}'
c2e4127fb5bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
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13 --threads \${GALAXY_SLOTS:-1}
c2e4127fb5bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
iuc
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14 --kmer-len ${kmer_len}
c2e4127fb5bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
iuc
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15 --read-len ${read_len}
c2e4127fb5bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
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16 --database-name '${database_name}'
c2e4127fb5bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
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17 ]]>
c2e4127fb5bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
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18 </command>
c2e4127fb5bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
iuc
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19 <inputs>
c2e4127fb5bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
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20 <param name="kraken_db" type="select">
c2e4127fb5bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
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21 <options from_data_table="kraken2_databases">
c2e4127fb5bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
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22 <validator type="no_options" message="No Kraken2 databases are available" />
c2e4127fb5bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
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23 </options>
c2e4127fb5bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
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24 </param>
c2e4127fb5bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
iuc
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25 <param name="kmer_len" type="integer" min="8" max="256" value="35" label="K-mer length" />
c2e4127fb5bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
iuc
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26 <param name="read_len" type="integer" min="8" max="1000" value="100" label="Read length" />
c2e4127fb5bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
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27 <param name="database_name" type="text" label="Database Name" />
c2e4127fb5bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
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28 </inputs>
c2e4127fb5bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
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29 <outputs>
c2e4127fb5bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
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30 <data name="out_file" format="data_manager_json" />
c2e4127fb5bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
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31 </outputs>
c2e4127fb5bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
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32 <tests>
c2e4127fb5bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
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33 <test>
c2e4127fb5bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
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34 <param name="kraken_db" value="test_entry" />
c2e4127fb5bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
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35 <param name="database_name" value="database" />
c2e4127fb5bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
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36 <output name="out_file">
c2e4127fb5bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
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37 <assert_contents>
c2e4127fb5bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
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38 <has_text text="test_db/database100mers.kmer_distrib" />
c2e4127fb5bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
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39 </assert_contents>
c2e4127fb5bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
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40 </output>
c2e4127fb5bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
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41 </test>
c2e4127fb5bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
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42 </tests>
c2e4127fb5bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
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43 <help>
c2e4127fb5bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
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44 </help>
c2e4127fb5bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
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45 <citations>
c2e4127fb5bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
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46 <citation type="doi">10.7717/peerj-cs.104</citation>
c2e4127fb5bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
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47 </citations>
c2e4127fb5bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
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48 </tool>