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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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1 <tool id="wgmlst_create_wrapper" name="Create cg/wgMLST 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 create --force
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14 #if $concatenate
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15 -c
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16 #end if
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17 #if $remove
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18 -r
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19 #end if
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20 '${database}' '${coregene}' &amp;> '${logfile}'
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21 </command>
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22 <inputs>
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23 <param name="coregene" type="data" format="fasta"
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24 label="Multiple fasta with GENES sequence" help="Fasta format" />
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25 <param name="concatenate" type="boolean" checked="false"
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26 label="Automatically concatenate GENES with duplicated sequences" />
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27 <param name="remove" type="boolean" checked="false"
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28 label="Automatically remove GENES with duplicated sequences" />
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29 </inputs>
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30 <outputs>
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31 <data name="logfile" format="txt" label="${tool.name} on ${coregene.name}: log" />
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32 <data name="database" format="sqlite" label="cg/wgMLST database on ${coregene.name}" />
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33 </outputs>
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34 <tests>
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35 <test expect_num_outputs="2">
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36 <param name="coregene" ftype="fasta" value="EHSB-021_gene.fasta" />
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37 <param name="remove" value="true" />
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38 <output name="logfile" ftype="txt">
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39 <assert_contents>
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40 <has_text text="Skipped invalid genes: 99" />
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41 <has_text text="Database initialized" />
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42 </assert_contents>
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43 </output>
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44 </test>
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45 </tests>
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46 <help>
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47 **What it does**
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48
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49 Create a cg/wgMLST DATABASE from a template COREGENE.
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51 Options:
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52 -c, --concatenate Automatically concatenate GENES with duplicated sequences.
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53 -r, --remove Automatically remove GENES with duplicated sequences.
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54
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55 **License and citation**
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56
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57 This Galaxy tool is Copyright © 2022 `B. Valot` and is released under the `GPL3 license`.
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58 </help>
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59 <citations>
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60 </citations>
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61 </tool>