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comparison wgmlst_sequence.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_sequence_wrapper" name="Sequences 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 sequence
12 #if str($genes)
13 -f '${genes}'
14 #end if
15 #if $reference
16 --reference
17 #end if
18 '${database}' > '${sequence}'
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="reference" type="boolean" checked="false"
33 label="Report the number of gene found for each strain" />
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="sequence" format="fasta" label="Sequence 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="reference" value="true" />
49 <output name="sequence" ftype="fasta" file="wgmlst_ecoli.db.sequence" />
50 </test>
51 </tests>
52 <help>
53 **What it does**
54
55 Extract sequences from a wgMLST DATABASE.
56
57 **Options**
58
59 -f, --file FILENAME File containing list of coregenes to extract
60 (default:all coregenes).
61 --reference Return sequence of the reference instead of
62 strains allele
63
64 **License and citation**
65
66 This Galaxy tool is Copyright © 2022 `B. Valot` and is released under the `GPL3 license`.
67 </help>
68 <citations>
69 </citations>
70 </tool>