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planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/ commit 3a94fbf6a188ea81441ef2f654ba5a74bff56f22
author iuc
date Tue, 12 Mar 2024 16:10:55 +0000
parents 9a5be5b1a5c9
children
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77ca66b1f5e9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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1 <?xml version="1.0"?>
77ca66b1f5e9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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2 <macros>
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9a5be5b1a5c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/ commit 06345505a91f3dcfa8a37dceb6f25e95806dddc8"
iuc
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3 <token name="@WRAPPER_VERSION@">1.3.1</token>
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77ca66b1f5e9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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4 <xml name="requirements">
77ca66b1f5e9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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5 <requirements>
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9a5be5b1a5c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/ commit 06345505a91f3dcfa8a37dceb6f25e95806dddc8"
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6 <requirement type="package" version="1.1.1">kraken</requirement>
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77ca66b1f5e9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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7 </requirements>
77ca66b1f5e9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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8 </xml>
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8cebdc74a48f planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/ commit 3a94fbf6a188ea81441ef2f654ba5a74bff56f22
iuc
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9 <xml name="xrefs">
8cebdc74a48f planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/ commit 3a94fbf6a188ea81441ef2f654ba5a74bff56f22
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10 <xrefs>
8cebdc74a48f planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/ commit 3a94fbf6a188ea81441ef2f654ba5a74bff56f22
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11 <xref type="bio.tools">kraken</xref>
8cebdc74a48f planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/ commit 3a94fbf6a188ea81441ef2f654ba5a74bff56f22
iuc
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12 </xrefs>
8cebdc74a48f planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/ commit 3a94fbf6a188ea81441ef2f654ba5a74bff56f22
iuc
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13 </xml>
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77ca66b1f5e9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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14 <xml name="version_command">
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15 <version_command><![CDATA[
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16 export LC_ALL=C && kraken --version
9bdcba262627 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/kraken_translate/ commit e8fc7c9dad5f583ad6763ecb9bd8c924832abacd
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17 ]]></version_command>
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18 </xml>
77ca66b1f5e9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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19 <xml name="input_database">
77ca66b1f5e9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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20 <param label="Select a Kraken database" name="kraken_database" type="select">
77ca66b1f5e9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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21 <options from_data_table="kraken_databases">
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22 <validator message="No Kraken database is available" type="no_options" />
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77ca66b1f5e9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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23 </options>
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24 </param>
77ca66b1f5e9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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25 </xml>
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26 <xml name="citations">
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27 <citations>
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28 <citation type="doi">10.1186/gb-2014-15-3-r46</citation>
77ca66b1f5e9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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29 </citations>
77ca66b1f5e9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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30 </xml>
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9a5be5b1a5c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/ commit 06345505a91f3dcfa8a37dceb6f25e95806dddc8"
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31 <!-- See the kraken_databases.loc.sample documentation,
9a5be5b1a5c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/ commit 06345505a91f3dcfa8a37dceb6f25e95806dddc8"
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32 this if statement is for backward compatibility as early
9a5be5b1a5c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/ commit 06345505a91f3dcfa8a37dceb6f25e95806dddc8"
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33 versions of the wrapper assumed the UI facing field name
9a5be5b1a5c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/ commit 06345505a91f3dcfa8a37dceb6f25e95806dddc8"
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34 was also part of the directory path -->
9a5be5b1a5c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/ commit 06345505a91f3dcfa8a37dceb6f25e95806dddc8"
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35 <token name="@SET_DATABASE_PATH@">if [ -d '${kraken_database.fields.path}/${kraken_database.fields.name}' ]; then export KRAKEN_DEFAULT_DB='${kraken_database.fields.path}/${kraken_database.fields.name}'; else export KRAKEN_DEFAULT_DB='${kraken_database.fields.path}'; fi</token>
9a5be5b1a5c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/ commit 06345505a91f3dcfa8a37dceb6f25e95806dddc8"
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36 <token name="@INPUT_DATABASE@">--db "\$KRAKEN_DEFAULT_DB"</token>
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37 </macros>