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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
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1 <tool id="clamlst_import_wrapper" name="Import MLST 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>claMLST -v</version_command>
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12 <command>
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13 claMLST import --force --no-prompt
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14 #if $mlst
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15 -m $mlst
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16 #end if
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17 $database '$search' &amp;> $logfile
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18 </command>
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19 <inputs>
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20 <param name="search" type="text" value="" optional="false" size="50"
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21 label="Species name to import"
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22 help="Bacterial species to download from pubMLST database" />
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23 <param name="mlst" type="text" value="" optional="true" size="50"
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24 label="MLST shema"
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25 help="Precise mlst shema if multiple exists for the " />
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26 </inputs>
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27 <outputs>
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28 <data name="logfile" format="txt" label="${tool.name} import on ${search}: log" />
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29 <data name="database" format="sqlite" label="claMLST database on ${search}" />
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30 </outputs>
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31 <tests>
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32 <test expect_num_outputs="2">
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33 <param name="search" value="Escherichia spp" />
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34 <param name="mlst" value="achtman" />
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35 <output name="logfile" ftype="txt">
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36 <assert_contents>
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37 <has_text text="One element found : escherichia spp" />
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38 <has_text text="One element found : mlst (achtman)" />
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39 <has_text text="Database initialized" />
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40 </assert_contents>
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41 </output>
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42 </test>
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43 </tests>
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44 <help>
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45 **What it does**
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46
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47 Import a classical MLST database from pubMLST
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48 Example :
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49 - Pseudomonas aeruginosa
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50 - Escherichia spp (mlst=achtman)
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51
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52 **License and citation**
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53
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54 This Galaxy tool is Copyright © 2022 `B. Valot` and is released under the `GPL3 license`.
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55 </help>
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56 <citations>
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57 </citations>
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58 </tool>