annotate mykrobe_parser.xml @ 0:6eae14751768 draft

planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
author nml
date Fri, 28 Sep 2018 16:01:47 -0400
parents
children 05ca0dbc9f46
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
1 <tool id="mykrobe_parseR" name="mykrobe_parseR" version="0.1.0">
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[
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
13
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
14 #if $input.type == 'collection'
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
15 mkdir collection_files &&
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
16 #for $file in $input.collection
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
17 cp "$file" collection_files/"$file.name".json &&
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
18 #end for
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
19 #end if
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
20
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
21 Rscript "$__tool_directory__/mykrobe_parser.R"
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
22
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
23 #if $input.type =='single'
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
24 -f "$input.single"
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
25 #else
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
26 -d "collection_files"
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
27 #end if
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
28
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
29 #if $version
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
30 -v "$version"
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
31 #end if
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
32 #if $depth
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
33 -D "$depth"
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
34 #end if
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
35 #if $confidence
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
36 -c "$confidence"
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
37 #end if
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
38 #if $run_name
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
39 -n "$run_name"
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
40 #end if
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
41
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
42 ]]></command>
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
43 <inputs>
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
44 <conditional name="input">
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
45 <param name="type" type="select" label="Sequence Data Type">
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
46 <option value="single">Single JSON File</option>
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
47 <option value="collection">Collection of JSON Files</option>
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
48 </param>
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
49 <when value="single">
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
50 <param name="single"
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
51 type="data" format="json,txt"
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
52 optional="false"
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
53 label="Single JSON File (.JSON or .TXT)"
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
54 />
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
55 </when>
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
56 <when value="collection">
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
57 <param name="collection"
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
58 type="data_collection" format="json,txt"
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
59 optional="false"
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
60 label="Collection of JSON Files (.JSON or .TXT)"
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
61 />
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
62 </when>
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
63 </conditional>
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
64 <param name="version" type="text"
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
65 argument="-v"
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
66 optional="true"
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
67 label="Mykrobe Workflow Version"/>
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
68 <param name="depth" type="integer"
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
69 argument="-D"
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
70 optional="true"
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
71 label="Minimum depth of coverage"
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
72 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
73 <param name="confidence" type="integer"
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
74 argument="-c"
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
75 optional="true"
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
76 label="Confidence"
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
77 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
78 <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
79 argument="-n"
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
80 optional="true"
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
81 label="Name of Run"/>
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
82 </inputs>
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
83 <outputs>
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
84 <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
85 <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
86 </outputs>
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
87 <tests>
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
88 <test>
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
89 <param name="type" value="single"/>
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
90 <param name="single" ftype="json" value="test-data.json"/>
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
91 <output name="output-jsondata" ftype="csv" value="output-jsondata.csv" compare="sim_size"/>
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
92 <output name="output-report" ftype="csv" value="output-report.csv" compare="sim_size"/>
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
93 </test>
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
94 </tests>
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
95 <help><![CDATA[
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
96 ==============
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
97 Mykrobe Parser
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
98 ==============
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 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
101
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 Legal
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
104 =====
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 Copyright Government of Canada 2018
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
107
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
108 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
109
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
110 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
111 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
112 License at:
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
113
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
114 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
115
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
116 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
117 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
118 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
119 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
120
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
121 =======
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
122 Contact
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
123 =======
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
124
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
125 **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
126
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
127 ]]></help>
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
128 <citations>
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
129 <citation type="bibtex">@ARTICLE{a1,
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
130 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
131 author = {Adrian Zetner},
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
132 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
133 }
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
134 }</citation>
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
135 </citations>
6eae14751768 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty
nml
parents:
diff changeset
136 </tool>