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comparison mykrobe_parser.xml @ 0:6eae14751768 draft

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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
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1 <tool id="mykrobe_parseR" name="mykrobe_parseR" version="0.1.0">
2 <requirements>
3 <requirement type="package" version="3.4.1">r-base</requirement>
4 <requirement type="package" version="1.5.0">r-jsonlite</requirement>
5 <requirement type="package" version="0.1.0">r-here</requirement>
6 <requirement type="package" version="0.7.6">r-dplyr</requirement>
7 <requirement type="package" version="0.2.5">r-purrr</requirement>
8 <requirement type="package" version="0.8.1">r-tidyr</requirement>
9 <requirement type="package" version="1.6.0">r-optparse</requirement>
10 <requirement type="package" version="1.3.0">r-stringr</requirement>
11 </requirements>
12 <command detect_errors="exit_code"><![CDATA[
13
14 #if $input.type == 'collection'
15 mkdir collection_files &&
16 #for $file in $input.collection
17 cp "$file" collection_files/"$file.name".json &&
18 #end for
19 #end if
20
21 Rscript "$__tool_directory__/mykrobe_parser.R"
22
23 #if $input.type =='single'
24 -f "$input.single"
25 #else
26 -d "collection_files"
27 #end if
28
29 #if $version
30 -v "$version"
31 #end if
32 #if $depth
33 -D "$depth"
34 #end if
35 #if $confidence
36 -c "$confidence"
37 #end if
38 #if $run_name
39 -n "$run_name"
40 #end if
41
42 ]]></command>
43 <inputs>
44 <conditional name="input">
45 <param name="type" type="select" label="Sequence Data Type">
46 <option value="single">Single JSON File</option>
47 <option value="collection">Collection of JSON Files</option>
48 </param>
49 <when value="single">
50 <param name="single"
51 type="data" format="json,txt"
52 optional="false"
53 label="Single JSON File (.JSON or .TXT)"
54 />
55 </when>
56 <when value="collection">
57 <param name="collection"
58 type="data_collection" format="json,txt"
59 optional="false"
60 label="Collection of JSON Files (.JSON or .TXT)"
61 />
62 </when>
63 </conditional>
64 <param name="version" type="text"
65 argument="-v"
66 optional="true"
67 label="Mykrobe Workflow Version"/>
68 <param name="depth" type="integer"
69 argument="-D"
70 optional="true"
71 label="Minimum depth of coverage"
72 help="Enter integer values only. Default is 5"/>
73 <param name="confidence" type="integer"
74 argument="-c"
75 optional="true"
76 label="Confidence"
77 help="Minimum genotype confidence for variant genotyping. Enter integer values only. Default is 10"/>
78 <param name="run_name" type="text"
79 argument="-n"
80 optional="true"
81 label="Name of Run"/>
82 </inputs>
83 <outputs>
84 <data name="output-jsondata" from_work_dir="output-jsondata.csv" format="csv" label="jsondata"/>
85 <data name="output-report" from_work_dir="output-report.csv" format="csv" label="report"/>
86 </outputs>
87 <tests>
88 <test>
89 <param name="type" value="single"/>
90 <param name="single" ftype="json" value="test-data.json"/>
91 <output name="output-jsondata" ftype="csv" value="output-jsondata.csv" compare="sim_size"/>
92 <output name="output-report" ftype="csv" value="output-report.csv" compare="sim_size"/>
93 </test>
94 </tests>
95 <help><![CDATA[
96 ==============
97 Mykrobe Parser
98 ==============
99
100 R Script to parse the results of mykrobe predictor and present them in a LIMS compatible format.
101
102 =====
103 Legal
104 =====
105
106 Copyright Government of Canada 2018
107
108 Written by: National Microbiology Laboratory, Public Health Agency of Canada
109
110 Licensed under the Apache License, Version 2.0 (the "License"); you may not use
111 this work except in compliance with the License. You may obtain a copy of the
112 License at:
113
114 http://www.apache.org/licenses/LICENSE-2.0
115
116 Unless required by applicable law or agreed to in writing, software distributed
117 under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR
118 CONDITIONS OF ANY KIND, either express or implied. See the License for the
119 specific language governing permissions and limitations under the License.
120
121 =======
122 Contact
123 =======
124
125 **Gary van Domselaar**: gary.vandomselaar@canada.ca
126
127 ]]></help>
128 <citations>
129 <citation type="bibtex">@ARTICLE{a1,
130 title = {R Script to parse the results of mykrobe predictor and present them in a LIMS compatible format.},
131 author = {Adrian Zetner},
132 url = {https://github.com/phac-nml/mykrobe-parser}
133 }
134 }</citation>
135 </citations>
136 </tool>