Mercurial > repos > nml > mykrobe_parser

annotate mykrobe_parser.xml @ 3:0dcfdec76c3c draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 44e99120db3fc06ca9302bc52687b00424e8b478
author nml
date Fri, 26 Oct 2018 16:57:34 -0400
parents f2608dccd3e0
children 8529045f0fdf
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
3
0dcfdec76c3c planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 44e99120db3fc06ca9302bc52687b00424e8b478
nml
parents: 2
diff changeset
1 <tool id="mykrobe_parseR" name="mykrobe_parseR" version="0.1.3">
0
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
2 <requirements>
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
3 <requirement type="package" version="3.4.1">r-base</requirement>
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
4 <requirement type="package" version="1.5.0">r-jsonlite</requirement>
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
5 <requirement type="package" version="0.1.0">r-here</requirement>
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
6 <requirement type="package" version="0.7.6">r-dplyr</requirement>
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
7 <requirement type="package" version="0.2.5">r-purrr</requirement>
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
8 <requirement type="package" version="0.8.1">r-tidyr</requirement>
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
9 <requirement type="package" version="1.6.0">r-optparse</requirement>
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
10 <requirement type="package" version="1.3.0">r-stringr</requirement>
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
11 </requirements>
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
12 <command detect_errors="exit_code"><![CDATA[
3
0dcfdec76c3c planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 44e99120db3fc06ca9302bc52687b00424e8b478
nml
parents: 2
diff changeset
13
0dcfdec76c3c planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 44e99120db3fc06ca9302bc52687b00424e8b478
nml
parents: 2
diff changeset
14 mkdir collection_files &&
0dcfdec76c3c planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 44e99120db3fc06ca9302bc52687b00424e8b478
nml
parents: 2
diff changeset
15
0dcfdec76c3c planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 44e99120db3fc06ca9302bc52687b00424e8b478
nml
parents: 2
diff changeset
16 #for $file in $input
0dcfdec76c3c planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 44e99120db3fc06ca9302bc52687b00424e8b478
nml
parents: 2
diff changeset
17 ln -s "$file" collection_files/"$file.element_identifier".json &&
0dcfdec76c3c planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 44e99120db3fc06ca9302bc52687b00424e8b478
nml
parents: 2
diff changeset
18 #end for
0
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
19
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
20 Rscript "$__tool_directory__/mykrobe_parser.R"
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
21
3
0dcfdec76c3c planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 44e99120db3fc06ca9302bc52687b00424e8b478
nml
parents: 2
diff changeset
22 -d "collection_files"
0
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
23
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
24 #if $version
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
25 -v "$version"
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
26 #end if
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
27 #if $depth
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
28 -D "$depth"
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
29 #end if
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
30 #if $confidence
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
31 -c "$confidence"
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
32 #end if
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
33 #if $run_name
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
34 -n "$run_name"
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
35 #end if
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
36
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
37 ]]></command>
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
38 <inputs>
3
0dcfdec76c3c planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 44e99120db3fc06ca9302bc52687b00424e8b478
nml
parents: 2
diff changeset
39 <param name="input"
0dcfdec76c3c planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 44e99120db3fc06ca9302bc52687b00424e8b478
nml
parents: 2
diff changeset
40 type="data" format="json,txt"
0dcfdec76c3c planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 44e99120db3fc06ca9302bc52687b00424e8b478
nml
parents: 2
diff changeset
41 optional="false"
0dcfdec76c3c planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 44e99120db3fc06ca9302bc52687b00424e8b478
nml
parents: 2
diff changeset
42 multiple="true"
0dcfdec76c3c planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 44e99120db3fc06ca9302bc52687b00424e8b478
nml
parents: 2
diff changeset
43 label="JSON File(s) (.JSON or .TXT)"/>
0
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
44 <param name="version" type="text"
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
45 argument="-v"
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
46 optional="true"
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
47 label="Mykrobe Workflow Version"/>
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
48 <param name="depth" type="integer"
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
49 argument="-D"
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
50 optional="true"
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
51 label="Minimum depth of coverage"
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
52 help="Enter integer values only. Default is 5"/>
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
53 <param name="confidence" type="integer"
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
54 argument="-c"
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
55 optional="true"
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
56 label="Confidence"
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
57 help="Minimum genotype confidence for variant genotyping. Enter integer values only. Default is 10"/>
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
58 <param name="run_name" type="text"
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
59 argument="-n"
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
60 optional="true"
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
61 label="Name of Run"/>
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
62 </inputs>
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
63 <outputs>
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
64 <data name="output-jsondata" from_work_dir="output-jsondata.csv" format="csv" label="jsondata"/>
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
65 <data name="output-report" from_work_dir="output-report.csv" format="csv" label="report"/>
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
66 </outputs>
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
67 <tests>
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
68 <test>
3
0dcfdec76c3c planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 44e99120db3fc06ca9302bc52687b00424e8b478
nml
parents: 2
diff changeset
69 <param name="input" value="test-data.json"/>
0dcfdec76c3c planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 44e99120db3fc06ca9302bc52687b00424e8b478
nml
parents: 2
diff changeset
70 <output name="output-jsondata" ftype="csv" value="output-jsondata.csv" compare="sim_size"/>
0dcfdec76c3c planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 44e99120db3fc06ca9302bc52687b00424e8b478
nml
parents: 2
diff changeset
71 <output name="output-report" ftype="csv" value="output-report.csv" compare="sim_size"/>
0
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
72 </test>
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
73 </tests>
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
74 <help><![CDATA[
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
75 ==============
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
76 Mykrobe Parser
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
77 ==============
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
78
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
79 R Script to parse the results of mykrobe predictor and present them in a LIMS compatible format.
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
80
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
81 =====
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
82 Legal
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
83 =====
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
84
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
85 Copyright Government of Canada 2018
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
86
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
87 Written by: National Microbiology Laboratory, Public Health Agency of Canada
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
88
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
89 Licensed under the Apache License, Version 2.0 (the "License"); you may not use
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
90 this work except in compliance with the License. You may obtain a copy of the
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
91 License at:
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
92
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
93 http://www.apache.org/licenses/LICENSE-2.0
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
94
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
95 Unless required by applicable law or agreed to in writing, software distributed
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
96 under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
97 CONDITIONS OF ANY KIND, either express or implied. See the License for the
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
98 specific language governing permissions and limitations under the License.
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
99
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
100 =======
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
101 Contact
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
102 =======
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
103
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
104 **Gary van Domselaar**: gary.vandomselaar@canada.ca
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
105
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
106 ]]></help>
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
107 <citations>
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
108 <citation type="bibtex">@ARTICLE{a1,
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
109 title = {R Script to parse the results of mykrobe predictor and present them in a LIMS compatible format.},
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
110 author = {Adrian Zetner},
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
111 url = {https://github.com/phac-nml/mykrobe-parser}
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
112 }
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
113 }</citation>
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
114 </citations>
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
115 </tool>