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comparison mlst_list.xml @ 0:735872ff8222 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst commit 659da38ca2b6ce2a699a263bdf6f513775e3ac21-dirty
author iuc
date Mon, 12 Dec 2016 15:07:38 -0500
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children 8e8dc9a1e3e5
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-1:000000000000 0:735872ff8222
1 <tool id="mlst_list" name="MLST List" version="0.1.0">
2 <requirements>
3 <requirement type="package" version="2.6">mlst</requirement>
4 </requirements>
5
6 <version_command>mlst --version</version_command>
7
8 <command detect_errors="exit_code"><![CDATA[
9 mlst $list_type > "$report"
10 ]]></command>
11
12 <inputs>
13 <param name="list_type" type="boolean" label="Output allele information" truevalue="--longlist" falsevalue="--list"
14 help="Selecting 'Yes' will provide the alleles for all MLST schemes" optional="false" />
15 </inputs>
16
17 <outputs>
18 <data format="txt" name="report" label="${tool.name} - list of schemes"/>
19 </outputs>
20
21 <tests>
22 <!-- Test the longlist option -->
23 <test>
24 <param name="list_type" value="true" />
25 <output name="report" ftype="txt" file="output_longlist.txt" />
26 </test>
27
28 <!-- Test the list option -->
29 <test>
30 <param name="list_type" value="false" />
31 <output name="report" ftype="txt" file="output_list.txt" />
32 </test>
33 </tests>
34
35 <help><![CDATA[
36 **What it does**
37
38 MLST List will list all the scheme names used by MLST. Selecting the long list option will also provide the alleles for all MLST schemes.
39
40 ]]></help>
41
42 <citations>
43 <citation type="bibtex">
44 @UNPUBLISHED{Seemann2016,
45 author = "Seemann T",
46 title = "ABRicate: mass screening of contigs for antiobiotic resistance genes",
47 year = "2016",
48 note = "https://github.com/tseemann/abricate"}
49 </citation>
50 </citations>
51 </tool>