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annotate macros.xml @ 0:77ca66b1f5e9 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
author devteam
date Thu, 23 Jul 2015 10:56:31 -0400
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children 475284b74179
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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
devteam
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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>
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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3 <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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4 <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 <requirement type="package" version="0.10.5">kraken</requirement>
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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6 </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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7 </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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8 <xml name="stdio">
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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9 <stdio>
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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10 <exit_code description="Tool exception" level="fatal" range="1:" />
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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11 </stdio>
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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12 </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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13 <xml name="version_command">
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 <version_command>export LC_ALL=C &amp;&amp; kraken --version</version_command>
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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15 </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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16 <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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17 <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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18 <options from_data_table="kraken_databases">
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 <validator message="No databases are available built-in" type="no_options" />
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 </options>
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 </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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22 </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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23 <xml name="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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24 <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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25 <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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26 </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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27 </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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28 <token name="@INPUT_DATABASE@">--db ${kraken_database.fields.name}</token>
77ca66b1f5e9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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29 <token name="@SET_DATABASE_PATH@">export KRAKEN_DB_PATH="${kraken_database.fields.path}"</token>
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 </macros>