Mercurial > repos > pimarin > data_manager_fetch_plasmidfinder

annotate data_manager/plasmidfinder_fetch_database.xml @ 1:9ef108e34063 draft

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planemo upload commit 32f035f6404452fc8a1cf01d71be3c0b46548338
author pimarin
date Wed, 15 Feb 2023 10:35:15 +0000
parents 8ad77a9dc91d
children bd56ac4cca16
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9ef108e34063 planemo upload commit 32f035f6404452fc8a1cf01d71be3c0b46548338
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1
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2 <tool id="data_manager_fetch_plasmidfinder" name="plasmidfinder_datamanager" tool_type="manage_data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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3 <description>plasmidfinder database builder</description>
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4 <macros>
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5 <import>macro.xml</import>
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6 </macros>
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7 <expand macro="requirements"/>
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8 <command detect_errors="exit_code">
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9 <![CDATA[
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10 python '$__tool_directory__/plasmidfinder_fetch_database.py'
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11 --db_version '$database_select'
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12 '$output_file'
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13 ]]></command>
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14 <inputs>
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15 <param name="database_select" type="select" label="Database version" help="Choose a database version to download (default latest version)">
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16 <option value="latest" selected="true">Latest available version</option>
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17 <option value="2.1">V2.1_2019-08-28</option>
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18 </param>param>
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19 </inputs>
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20 <outputs>
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21 <data name="output_file" format="data_manager_json"/>
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22 </outputs>
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23 <tests>
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24 <!-- Test_1 DB latest -->
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25 <test expect_num_outputs="1">
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26 <param name="database_select" value="latest"/>
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27 <output name="output_file" value="plasmidfinder_test_data_manager_latest.json">
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28 <assert_contents>
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29 <has_text_matching expression='\{"data_tables":\ \{\"plasmidfinder_database\"\:\ \[\{\"date\"\:\ \"\d\d\d\d\w\d\d\w\d\d\", \"name\"\: \"\w\w\w\w\w\w\w\w\w\w\w\w\d\d\d\d-\d\d-\d\d\",\ \"path\"\:\ \"plasmidfinder-db\",\ \"value\"\:\ \"plasmidfinder_\w\w\w\w\w\w\w\w\w\w\w_\d\d\d\d-\d\d-\d\d\"' />
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30 </assert_contents>
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31 </output>
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32 </test>
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33 <!-- Test_2 DB 2.1 -->
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34 <test expect_num_outputs="1">
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35 <param name="database_select" value="2.1"/>
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36 <output name="output_file" value="plasmidfinder_test_data_manager_2.1.json">
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37 <assert_contents>
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38 <has_text_matching expression='"data_tables": \{"plasmidfinder_database": \[\{"date": "\d\d\d\\d-\d\d-\d\d", "name": "2\.1_\d\d\d\d-\d\d-\d\d", "path": "plasmidfinder-db", "value": "plasmidfinder_\w\w\w\w\w\w\w\w\w\w\w\w_\d\d\d\d-\d\d-\d\d"' />
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39 </assert_contents>
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40 </output>
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41 </test>
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42 </tests>
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43 <help><![CDATA[
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44 Download plasmidfinder database from the bitbucket repository
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45 ]]></help>
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46 <citations>
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47 <citation type="doi">10.1007/978-1-4939-9877-7_20</citation>
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48 </citations>
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49 </tool>