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annotate wgmlst_import.xml @ 0:a3cc35af3635 draft

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planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
author bvalot
date Thu, 16 Jun 2022 12:32:28 +0000
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a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
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1 <tool id="wgmlst_import_wrapper" name="Import cgMLST database" version="2.1.3">
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2 <description></description>
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3 <requirements>
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4 <requirement type="package" version="2.1.3">pymlst</requirement>
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5 </requirements>
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6 <stdio>
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7 <exit_code range="1:" level="fatal" />
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8 </stdio>
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9 <version_command>wgMLST -v</version_command>
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10 <command>
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11 wgMLST import --force --no-prompt
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12 '${database}' '$search' &amp;> '${logfile}'
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
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13 </command>
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14 <inputs>
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15 <param name="search" type="text" value="" optional="false" size="50"
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16 label="Species name to import"
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17 help="Bacterial species to download from cgMLST.org database" />
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
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18 </inputs>
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19 <outputs>
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20 <data name="logfile" format="txt" label="${tool.name} import on ${search}: log" />
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21 <data name="database" format="sqlite" label="cgMLST database on ${search}" />
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22 </outputs>
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23 <tests>
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24 <test expect_num_outputs="2">
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25 <param name="search" value="Escherichia" />
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26 <output name="logfile" ftype="txt">
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27 <assert_contents>
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28 <has_text text="One element found : Escherichia coli" />
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29 <has_text text="Downloading the core genome..." />
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30 <has_text text="Reverse-complemented genes: 1294" />
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31 <has_text text="Database initialized" />
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32 </assert_contents>
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33 </output>
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34 </test>
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35 </tests>
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36 <help>
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37 **What it does**
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38
a3cc35af3635 planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
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39 Import a cgMLST database from cgmlst.org
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40
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41 Example :
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42 - Pseudomonas aeruginosa
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43 - Escherichia
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44
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45 **License and citation**
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46
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47 This Galaxy tool is Copyright © 2022 `B. Valot` and is released under the `GPL3 license`.
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48 </help>
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49 <citations>
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50 </citations>
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51 </tool>