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author jjohnson
date Tue, 26 Nov 2019 16:11:24 -0500
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1 <tool id="data_manager_cat" name="CAT DB" version="@VERSION@.0" tool_type="manage_data">
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2 <description>Install a new CAT database</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <expand macro="version_command" />
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8 <command detect_errors="exit_code"><![CDATA[
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9 #import json, os
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10 #set params = json.loads(open(str($out_file)).read())
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11 #set install_path = $params['output_data'][0]['extra_files_path'].encode('ascii', 'replace')
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12 mkdir -p $install_path &&
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13 python '${__tool_directory__}/data_manager_cat.py' --config_file '$out_file' --install_path '$install_path'
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14 #if $db.src == 'download'
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15 --db_url '$db_url'
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16 #end if
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17 ]]></command>
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18 <inputs>
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19 <conditional name="db">
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20 <param name="src" type="select" label="Download or Build DBs">
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21 <option value="download">download</option>
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22 <option value="build">build</option>
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23 </param>
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24 <when value="download">
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25 <param name="db_url" type="text" label="DB rul at https://tbb.bio.uu.nl/bastiaan/CAT_prepare/"
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26 help="example: https://tbb.bio.uu.nl/bastiaan/CAT_prepare/CAT_prepare_20190719.tar.gz">
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27 </param>
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28 </when>
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29 <when value="build">
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30 </when>
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31 </conditional>
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32 </inputs>
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33 <outputs>
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34 <data name="out_file" format="data_manager_json" label="${tool.name}"/>
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35 </outputs>
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36 <tests>
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37 </tests>
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38 <help><![CDATA[
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39 This tool prepares reference data for CAT, the Contig Annotation Tool.
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40 It can either download prebuilt reference data from https://tbb.bio.uu.nl/bastiaan/CAT_prepare/
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41 or build new reference data using the CAT prepare application.
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42 ]]></help>
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43 <expand macro="citations" />
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44 </tool>