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comparison wgmlst_msa.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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-1:000000000000 0:a3cc35af3635
1 <tool id="wgmlst_msa_wrapper" name="MSA of 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 msa
12 #if str($genes)
13 -f '${genes}'
14 #end if
15 #if $realign
16 --realign
17 #end if
18 '${database}' > '${msa}'
19 #if $log
20 2> '${logfile}'
21 #end if
22 </command>
23 <inputs>
24 <param name="database" type="data"
25 format="sqlite"
26 label="cg/wgMLST database"
27 help="Sqlite format from cg/wgMLST database" />
28 <param name="genes" type="data"
29 format="txt"
30 label="Genes list"
31 help="File containing list of genes to extract" />
32 <param name="realign" type="boolean" checked="false"
33 label="Realign genes with same length" />
34 <param name="log" type="boolean" checked="false"
35 label="Write log file" />
36 </inputs>
37 <outputs>
38 <data name="logfile" format="txt" label="Sequence of
39 ${database.name}: log">
40 <filter>log</filter>
41 </data>
42 <data name="msa" format="fasta" label="MSA of ${database.name}: fasta" />
43 </outputs>
44 <tests>
45 <test expect_num_outputs="1">
46 <param name="database" value="wgmlst_ecoli.db" />
47 <param name="genes" value="wgmlst_ecoli.db.gene" />
48 <param name="realign" value="true" />
49 <output name="msa" ftype="fasta" file="wgmlst_ecoli.db.msa" />
50 </test>
51 </tests>
52 <help>
53 **What it does**
54
55 Compute Multiple Sequence Alignment from a wgMLST DATABASE
56
57 **Options**
58
59 -f, --file FILENAME File containing list of coregenes to extract
60 (default:all coregenes).
61 -r, --realign Realign genes with same length (Default:No).
62
63 **License and citation**
64
65 This Galaxy tool is Copyright © 2022 `B. Valot` and is released under the `GPL3 license`.
66 </help>
67 <citations>
68 </citations>
69 </tool>