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planemo upload for repository https://github.com/bvalot/pyMLST commit 142042a3856f8886031cacaa4fb28743a1bcd540
author bvalot
date Wed, 15 Nov 2023 12:22:07 +0000
parents 5b2c48fa0175
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5b2c48fa0175 planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b
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1 <tool id="wgmlst_import_wrapper" name="Import cgMLST database"
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2 version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
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3 <description></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 <stdio>
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9 <exit_code range="1:" level="fatal" />
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10 </stdio>
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11 <version_command>wgMLST -v</version_command>
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12 <command>
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13 wgMLST import --force --no-prompt
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14 '${database}' '$search' &amp;> '${logfile}'
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15 </command>
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16 <inputs>
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17 <param name="search" type="text" value="" optional="false" size="50"
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18 label="Species name to import"
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19 help="Bacterial species to download from cgMLST.org database" />
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20 </inputs>
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21 <outputs>
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22 <data name="logfile" format="txt" label="${tool.name} import on ${search}: log" />
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23 <data name="database" format="sqlite" label="cgMLST database on ${search}" />
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24 </outputs>
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25 <tests>
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26 <test expect_num_outputs="2">
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27 <param name="search" value="Escherichia" />
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28 <output name="logfile" ftype="txt">
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29 <assert_contents>
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30 <has_text text="One element found : Escherichia coli" />
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31 <has_text text="Downloading the core genome..." />
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32 <has_text text="Reverse-complemented genes: 1294" />
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33 <has_text text="Database initialized" />
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34 </assert_contents>
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35 </output>
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36 </test>
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37 </tests>
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38 <help>
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39 **What it does**
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41 Import a cgMLST database from cgmlst.org
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43 Example :
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44 - Pseudomonas aeruginosa
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45 - Escherichia
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47 **License and citation**
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49 This Galaxy tool is Copyright © 2022 `B. Valot` and is released under the `GPL3 license`.
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50 </help>
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51 <citations>
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52 </citations>
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53 </tool>