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