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comparison lissero/lissero.xml @ 10:412d55f09755 draft

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date Thu, 08 Feb 2024 18:18:47 +0000
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1 <tool id="lissero" name="lissero" version="1.0.0+galaxy0" python_template_version="3.5" profile="21.05">
2 <requirements>
3 <requirement type="package">lissero</requirement>
4 </requirements>
5 <command detect_errors="exit_code"><![CDATA[
6 lissero
7 #if $settings.advanced == "advanced"
8 --min_id $settings.min_id
9 --min_cov $settings.min_cov
10 #end if
11 '$input1' > output1;
12 python $__tool_directory__/variant4b.py output1 output2.txt;
13 ]]></command>
14 <inputs>
15 <param type="data" name="input1" format="fasta" />
16 <conditional name="settings">
17 <param name="advanced" type="select" label="Specify advanced parameters">
18 <option value="simple" selected="true">No, use program defaults.</option>
19 <option value="advanced">Yes, see full parameter list.</option>
20 </param>
21 <when value="simple">
22 </when>
23 <when value="advanced">
24 <param name="min_id" type="float" label="Minimum percent identity to accept a match" value="95.0" min="0" max="100" />
25 <param name="min_cov" type="float" label="Minimum coverage of a gene to accept a match" value="95.0" min="0" max="100" />
26 </when>
27 </conditional>
28 </inputs>
29 <outputs>
30 <data format="tabular" name="lissero.tsv" label="${tool.name} on ${on_string}: LisSero" from_work_dir="*.txt"/>
31 </outputs>
32 <help><![CDATA[
33 Usage: lissero [OPTIONS] FASTA...
34
35 In silico serogroup prediction for L. monocytogenes. Alleles: lmo1118,
36 lmo0737, ORF2819, ORF2110, Prs
37
38 References:
39
40 Doumith et al. Differentiation of the major Listeria monocytogenes
41 serovars by multiplex PCR. J Clin Microbiol, 2004; 42:8; 3819-22
42
43 Options:
44 -h, --help Show this message and exit.
45 --min_id FLOAT Minimum percent identity to accept a match. [0-100][default=95.0]
46 --min_cov FLOAT Minimum coverage of the gene to accept a match. [0-100][default=95.0]
47
48 ]]></help>
49 <citations>
50 <citation type="doi">10.1128/JCM.42.8.3819-3822.2004</citation>
51 </citations>
52 </tool>