Mercurial > repos > nml > mykrobe_parser

annotate mykrobe_parser.xml @ 2:f2608dccd3e0 draft

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planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 1d77b6cae26ef3456ff6d469d71c61cab6a19906-dirty
author nml
date Tue, 23 Oct 2018 08:54:51 -0400
parents 05ca0dbc9f46
children 0dcfdec76c3c
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1 <tool id="mykrobe_parseR" name="mykrobe_parseR" version="0.1.2">
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[
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13
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14 #if $input.type == 'collection'
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15 mkdir collection_files &&
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16 #for $file in $input.collection
1
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17 ln -s "$file" collection_files/"$file.element_identifier".json &&
0
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18 #end for
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19 #end if
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20
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21 Rscript "$__tool_directory__/mykrobe_parser.R"
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22
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23 #if $input.type =='single'
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24 -f "$input.single"
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25 #else
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26 -d "collection_files"
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27 #end if
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28
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29 #if $version
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30 -v "$version"
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31 #end if
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32 #if $depth
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33 -D "$depth"
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34 #end if
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35 #if $confidence
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36 -c "$confidence"
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37 #end if
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38 #if $run_name
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39 -n "$run_name"
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40 #end if
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41
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42 ]]></command>
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43 <inputs>
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44 <conditional name="input">
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45 <param name="type" type="select" label="Sequence Data Type">
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46 <option value="single">Single JSON File</option>
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47 <option value="collection">Collection of JSON Files</option>
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48 </param>
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49 <when value="single">
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50 <param name="single"
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51 type="data" format="json,txt"
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52 optional="false"
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53 label="Single JSON File (.JSON or .TXT)"
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54 />
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55 </when>
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56 <when value="collection">
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57 <param name="collection"
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58 type="data_collection" format="json,txt"
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59 optional="false"
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60 label="Collection of JSON Files (.JSON or .TXT)"
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61 />
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62 </when>
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63 </conditional>
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64 <param name="version" type="text"
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65 argument="-v"
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66 optional="true"
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67 label="Mykrobe Workflow Version"/>
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68 <param name="depth" type="integer"
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69 argument="-D"
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70 optional="true"
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71 label="Minimum depth of coverage"
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72 help="Enter integer values only. Default is 5"/>
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73 <param name="confidence" type="integer"
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74 argument="-c"
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75 optional="true"
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76 label="Confidence"
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77 help="Minimum genotype confidence for variant genotyping. Enter integer values only. Default is 10"/>
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78 <param name="run_name" type="text"
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79 argument="-n"
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80 optional="true"
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81 label="Name of Run"/>
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82 </inputs>
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83 <outputs>
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84 <data name="output-jsondata" from_work_dir="output-jsondata.csv" format="csv" label="jsondata"/>
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85 <data name="output-report" from_work_dir="output-report.csv" format="csv" label="report"/>
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86 </outputs>
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87 <tests>
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88 <test>
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89 <param name="type" value="single"/>
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90 <param name="single" ftype="json" value="test-data.json"/>
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91 <output name="output-jsondata" ftype="csv" value="output-jsondata.csv" compare="sim_size"/>
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92 <output name="output-report" ftype="csv" value="output-report.csv" compare="sim_size"/>
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93 </test>
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94 </tests>
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95 <help><![CDATA[
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96 ==============
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97 Mykrobe Parser
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98 ==============
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99
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100 R Script to parse the results of mykrobe predictor and present them in a LIMS compatible format.
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101
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102 =====
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103 Legal
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104 =====
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105
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106 Copyright Government of Canada 2018
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107
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108 Written by: National Microbiology Laboratory, Public Health Agency of Canada
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109
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110 Licensed under the Apache License, Version 2.0 (the "License"); you may not use
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111 this work except in compliance with the License. You may obtain a copy of the
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112 License at:
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113
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114 http://www.apache.org/licenses/LICENSE-2.0
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115
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116 Unless required by applicable law or agreed to in writing, software distributed
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117 under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR
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118 CONDITIONS OF ANY KIND, either express or implied. See the License for the
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119 specific language governing permissions and limitations under the License.
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120
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121 =======
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122 Contact
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123 =======
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124
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125 **Gary van Domselaar**: gary.vandomselaar@canada.ca
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126
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127 ]]></help>
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128 <citations>
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129 <citation type="bibtex">@ARTICLE{a1,
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130 title = {R Script to parse the results of mykrobe predictor and present them in a LIMS compatible format.},
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131 author = {Adrian Zetner},
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132 url = {https://github.com/phac-nml/mykrobe-parser}
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133 }
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134 }</citation>
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135 </citations>
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136 </tool>