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annotate macros.xml @ 2:b9971bca4b01 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit c5dd035dbee6021f3555755cf4c814e760cecd09
author devteam
date Wed, 23 Mar 2016 11:02:57 -0400
parents 475284b74179
children 9bdcba262627
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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>
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>
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475284b74179 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit 3abfc7eb2999fa588862b84c453012c811fa8350
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5 <requirement type="package" version="0.10.6_eaf8fb68">kraken</requirement>
475284b74179 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit 3abfc7eb2999fa588862b84c453012c811fa8350
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6 <requirement type="package" version="0.10.6-eaf8fb68">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>
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 <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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10 <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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11 <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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12 </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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13 </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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14 <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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15 <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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16 </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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17 <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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18 <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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19 <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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20 <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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21 </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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22 </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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23 </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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24 <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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25 <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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26 <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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27 </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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28 </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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29 <token name="@INPUT_DATABASE@">--db ${kraken_database.fields.name}</token>
77ca66b1f5e9 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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30 <token name="@SET_DATABASE_PATH@">export KRAKEN_DB_PATH="${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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31 </macros>