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annotate mykrobe_parser.xml @ 4:8529045f0fdf draft

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planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 34d9c47b9451e5f7843028dba22b96d125fb09f5
author nml
date Thu, 25 Apr 2019 10:13:46 -0400
parents 0dcfdec76c3c
children deebc6410d13
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1 <tool id="mykrobe_parseR" name="mykrobe_parseR" version="0.1.4">
0
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2 <requirements>
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3 <requirement type="package" version="3.4.1">r-base</requirement>
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4 <requirement type="package" version="1.5.0">r-jsonlite</requirement>
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5 <requirement type="package" version="0.1.0">r-here</requirement>
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6 <requirement type="package" version="0.7.6">r-dplyr</requirement>
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7 <requirement type="package" version="0.2.5">r-purrr</requirement>
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8 <requirement type="package" version="0.8.1">r-tidyr</requirement>
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9 <requirement type="package" version="1.6.0">r-optparse</requirement>
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10 <requirement type="package" version="1.3.0">r-stringr</requirement>
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11 </requirements>
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12 <command detect_errors="exit_code"><![CDATA[
3
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14 mkdir collection_files &&
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16 #for $file in $input
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17 ln -s "$file" collection_files/"$file.element_identifier".json &&
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18 #end for
0
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19
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20 Rscript "$__tool_directory__/mykrobe_parser.R"
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21
3
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22 -d "collection_files"
0
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23
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24 #if $version
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25 -v "$version"
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26 #end if
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27 #if $depth
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28 -D "$depth"
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29 #end if
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30 #if $confidence
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31 -c "$confidence"
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32 #end if
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33 #if $run_name
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34 -n "$run_name"
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35 #end if
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36
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37 ]]></command>
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38 <inputs>
3
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39 <param name="input"
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40 type="data" format="json,txt"
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41 optional="false"
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42 multiple="true"
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43 label="JSON File(s) (.JSON or .TXT)"/>
0
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44 <param name="version" type="text"
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45 argument="-v"
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46 optional="true"
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47 label="Mykrobe Workflow Version"/>
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48 <param name="depth" type="integer"
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49 argument="-D"
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50 optional="true"
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51 label="Minimum depth of coverage"
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52 help="Enter integer values only. Default is 5"/>
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53 <param name="confidence" type="integer"
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54 argument="-c"
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55 optional="true"
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56 label="Confidence"
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57 help="Minimum genotype confidence for variant genotyping. Enter integer values only. Default is 10"/>
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58 <param name="run_name" type="text"
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59 argument="-n"
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60 optional="true"
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61 label="Name of Run"/>
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62 </inputs>
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63 <outputs>
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64 <data name="output-jsondata" from_work_dir="output-jsondata.csv" format="csv" label="jsondata"/>
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65 <data name="output-report" from_work_dir="output-report.csv" format="csv" label="report"/>
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66 </outputs>
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67 <tests>
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68 <test>
3
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69 <param name="input" value="test-data.json"/>
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70 <output name="output-jsondata" ftype="csv" value="output-jsondata.csv" compare="sim_size"/>
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71 <output name="output-report" ftype="csv" value="output-report.csv" compare="sim_size"/>
0
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72 </test>
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73 </tests>
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74 <help><![CDATA[
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75 ==============
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76 Mykrobe Parser
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77 ==============
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78
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79 R Script to parse the results of mykrobe predictor and present them in a LIMS compatible format.
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80
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81 =====
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82 Legal
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83 =====
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84
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85 Copyright Government of Canada 2018
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86
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87 Written by: National Microbiology Laboratory, Public Health Agency of Canada
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88
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89 Licensed under the Apache License, Version 2.0 (the "License"); you may not use
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90 this work except in compliance with the License. You may obtain a copy of the
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91 License at:
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92
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93 http://www.apache.org/licenses/LICENSE-2.0
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94
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95 Unless required by applicable law or agreed to in writing, software distributed
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96 under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR
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97 CONDITIONS OF ANY KIND, either express or implied. See the License for the
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98 specific language governing permissions and limitations under the License.
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99
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100 =======
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101 Contact
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102 =======
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103
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104 **Gary van Domselaar**: gary.vandomselaar@canada.ca
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105
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106 ]]></help>
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107 <citations>
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108 <citation type="bibtex">@ARTICLE{a1,
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109 title = {R Script to parse the results of mykrobe predictor and present them in a LIMS compatible format.},
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110 author = {Adrian Zetner},
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111 url = {https://github.com/phac-nml/mykrobe-parser}
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112 }
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113 }</citation>
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114 </citations>
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115 </tool>