annotate cpo_mlst.xml @ 16:1642e3d402f8 draft

planemo upload
author jjjjia
date Sun, 26 Aug 2018 22:00:43 -0400
parents 698579246d0d
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
5
698579246d0d planemo upload
jjjjia
parents: 1
diff changeset
1 <tool id="cpo_mlst" name="cpo_mlst" version="2.11">
698579246d0d planemo upload
jjjjia
parents: 1
diff changeset
2 <description>Modified MLST v2.11 to support for the cpo_prediction workflow</description>
698579246d0d planemo upload
jjjjia
parents: 1
diff changeset
3 <requirements>
1
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
4 <requirement type="package" version="2.11">mlst</requirement>
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
5 </requirements>
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
6
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
7 <version_command>mlst --version</version_command>
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
8
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
9 <command detect_errors="exit_code"><![CDATA[
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
10 mlst "$input_file" --nopath > "$report"
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
11 ]]></command>
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
12
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
13 <inputs>
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
14 <param type="data" name="input_file" format="fasta,genbank" />
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
15 <conditional name="settings">
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
16 <param name="advanced" type="select" label="Specify advanced parameters">
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
17 <option value="simple" selected="true">No, use program defaults.</option>
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
18 <option value="advanced">Yes, see full parameter list.</option>
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
19 </param>
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
20 <when value="simple">
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
21 </when>
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
22 <when value="advanced">
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
23 <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" />
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
24 <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" />
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
25 <param name="scheme" type="text" area="false" label="PubMLST Scheme" help="Turn off auto-detection and only use this scheme" optional="true" />
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
26 </when>
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
27 </conditional>
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
28 </inputs>
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
29
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
30 <outputs>
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
31 <data name="report" format="tabular" />
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
32 </outputs>
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
33
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
34 <tests>
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
35 <!-- Basic test - will produce no results. -->
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
36 <test>
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
37 <param name="input_file" value="Acetobacter.fna"/>
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
38 <param name="advanced" value="simple"/>
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
39 <output name="report" ftype="tabular" file="output_noresults.txt" compare="contains"/>
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
40 </test>
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
41
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
42 <!-- Basic test - will produce results. -->
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
43 <test>
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
44 <param name="input_file" value="MRSA0252_trimmed.fna"/>
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
45 <param name="advanced" value="simple"/>
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
46 <output name="report" ftype="tabular" file="output_mrsa.txt" compare="contains"/>
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
47 </test>
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
48
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
49 <!-- Advanced test - Min DNA Coverage 100 -->
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
50 <test>
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
51 <param name="input_file" value="MRSA0252_trimmed.fna"/>
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
52 <param name="advanced" value="advanced"/>
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
53 <param name="min_dna_cov" value="100"/>
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
54 <output name="report" ftype="tabular" file="output_mincov100.txt" compare="contains"/>
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
55 </test>
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
56
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
57 <!-- Advanced test - Min DNA ID 100 -->
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
58 <test>
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
59 <param name="input_file" value="MRSA0252_trimmed.fna"/>
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
60 <param name="advanced" value="advanced"/>
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
61 <param name="min_dna_id" value="100"/>
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
62 <output name="report" ftype="tabular" file="output_minid100.txt" compare="contains"/>
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
63 </test>
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
64 </tests>
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
65
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
66 <help>performs mlst</help>
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
67
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
68 <citations>
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
69 <citation type="bibtex">
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
70 @UNPUBLISHED{Seemann2016,
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
71 author = "Seemann T",
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
72 title = "MLST: Scan contig files against PubMLST typing schemes",
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
73 year = "2016",
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
74 note = "https://github.com/tseemann/mlst"}
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
75 </citation>
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
76 </citations>
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
77 </tool>