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planemo upload commit e12eb56d1744da8f7af8ca1819e2617c83fb17a8
author estrain
date Fri, 13 Mar 2026 12:01:17 +0000
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1 <tool id="lissero" name="lissero" version="1.0.1+galaxy2" python_template_version="3.5" profile="21.05">
2 <requirements>
3 <requirement type="package" version="0.4.9">lissero</requirement>
4
5 </requirements>
6 <command detect_errors="exit_code"><![CDATA[
7 lissero
8 #if $settings.advanced == "advanced"
9 --min_id $settings.min_id
10 --min_cov $settings.min_cov
11 #end if
12 '$input1' > output1;
13 python $__tool_directory__/variant4b.py output1 output2.txt ${input1.element_identifier};
14 ]]></command>
15 <inputs>
16 <param type="data" name="input1" format="fasta" />
17 <conditional name="settings">
18 <param name="advanced" type="select" label="Specify advanced parameters">
19 <option value="simple" selected="true">No, use program defaults.</option>
20 <option value="advanced">Yes, see full parameter list.</option>
21 </param>
22 <when value="simple">
23 </when>
24 <when value="advanced">
25 <param name="min_id" type="float" label="Minimum percent identity to accept a match" value="95.0" min="0" max="100" />
26 <param name="min_cov" type="float" label="Minimum coverage of a gene to accept a match" value="95.0" min="0" max="100" />
27 </when>
28 </conditional>
29 </inputs>
30 <outputs>
31 <data format="tabular" name="lissero.tsv" label="${tool.name} on ${on_string}: LisSero" from_work_dir="*.txt"/>
32 </outputs>
33 <help><![CDATA[
34 Usage: lissero [OPTIONS] FASTA...
35
36 In silico serogroup prediction for L. monocytogenes. Alleles: lmo1118,
37 lmo0737, ORF2819, ORF2110, Prs
38
39 References:
40
41 Doumith et al. Differentiation of the major Listeria monocytogenes
42 serovars by multiplex PCR. J Clin Microbiol, 2004; 42:8; 3819-22
43
44 Options:
45 -h, --help Show this message and exit.
46 --min_id FLOAT Minimum percent identity to accept a match. [0-100][default=95.0]
47 --min_cov FLOAT Minimum coverage of the gene to accept a match. [0-100][default=95.0]
48
49 ]]></help>
50 <citations>
51 <citation type="doi">10.1128/JCM.42.8.3819-3822.2004</citation>
52 </citations>
53 </tool>