Mercurial > repos > jjjjia > cpo_prediction

comparison cpo_mlst.xml @ 1:fea89c4d5227 draft

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author jjjjia
date Thu, 16 Aug 2018 19:27:05 -0400
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children 698579246d0d
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0:917a05a03ac9 1:fea89c4d5227
1 <tool id="mlst" name="MLST" version="2.11">
2 <requirements>
3 <requirement type="package" version="2.11">mlst</requirement>
4 </requirements>
5
6 <version_command>mlst --version</version_command>
7
8 <command detect_errors="exit_code"><![CDATA[
9 mlst "$input_file" --nopath > "$report"
10 ]]></command>
11
12 <inputs>
13 <param type="data" name="input_file" format="fasta,genbank" />
14 <conditional name="settings">
15 <param name="advanced" type="select" label="Specify advanced parameters">
16 <option value="simple" selected="true">No, use program defaults.</option>
17 <option value="advanced">Yes, see full parameter list.</option>
18 </param>
19 <when value="simple">
20 </when>
21 <when value="advanced">
22 <param name="min_dna_id" type="integer" label="Minimum DNA identity" value="95" min="0" max="100" help="Minimum DNA identity of full allelle to consider 'similar' (default 95, must be between 0-100)" optional="true" />
23 <param name="min_dna_cov" type="integer" label="Minimum DNA coverage" value="10" help="Minimum DNA coverage to report partial allele at all (default 10)" optional="true" />
24 <param name="scheme" type="text" area="false" label="PubMLST Scheme" help="Turn off auto-detection and only use this scheme" optional="true" />
25 </when>
26 </conditional>
27 </inputs>
28
29 <outputs>
30 <data name="report" format="tabular" />
31 </outputs>
32
33 <tests>
34 <!-- Basic test - will produce no results. -->
35 <test>
36 <param name="input_file" value="Acetobacter.fna"/>
37 <param name="advanced" value="simple"/>
38 <output name="report" ftype="tabular" file="output_noresults.txt" compare="contains"/>
39 </test>
40
41 <!-- Basic test - will produce results. -->
42 <test>
43 <param name="input_file" value="MRSA0252_trimmed.fna"/>
44 <param name="advanced" value="simple"/>
45 <output name="report" ftype="tabular" file="output_mrsa.txt" compare="contains"/>
46 </test>
47
48 <!-- Advanced test - Min DNA Coverage 100 -->
49 <test>
50 <param name="input_file" value="MRSA0252_trimmed.fna"/>
51 <param name="advanced" value="advanced"/>
52 <param name="min_dna_cov" value="100"/>
53 <output name="report" ftype="tabular" file="output_mincov100.txt" compare="contains"/>
54 </test>
55
56 <!-- Advanced test - Min DNA ID 100 -->
57 <test>
58 <param name="input_file" value="MRSA0252_trimmed.fna"/>
59 <param name="advanced" value="advanced"/>
60 <param name="min_dna_id" value="100"/>
61 <output name="report" ftype="tabular" file="output_minid100.txt" compare="contains"/>
62 </test>
63 </tests>
64
65 <help>performs mlst</help>
66
67 <citations>
68 <citation type="bibtex">
69 @UNPUBLISHED{Seemann2016,
70 author = "Seemann T",
71 title = "MLST: Scan contig files against PubMLST typing schemes",
72 year = "2016",
73 note = "https://github.com/tseemann/mlst"}
74 </citation>
75 </citations>
76 </tool>