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