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annotate mykrobe_parser.xml @ 6:8e7e5a660942 draft

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planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
author nml
date Fri, 22 Sep 2023 17:24:02 +0000
parents deebc6410d13
children 12b397ad8687
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1 <tool id="mykrobe_parseR" name="mykrobe_parseR" version="@VERSION@+galaxy1" profile="16.04">
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2 <macros>
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3 <token name="@VERSION@">0.1.4.1</token>
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4 </macros>
0
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5 <requirements>
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6 <requirement type="package" version="3.4.1">r-base</requirement>
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7 <requirement type="package" version="1.5.0">r-jsonlite</requirement>
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8 <requirement type="package" version="0.1.0">r-here</requirement>
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9 <requirement type="package" version="0.7.6">r-dplyr</requirement>
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10 <requirement type="package" version="0.2.5">r-purrr</requirement>
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11 <requirement type="package" version="0.8.1">r-tidyr</requirement>
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12 <requirement type="package" version="1.6.0">r-optparse</requirement>
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13 <requirement type="package" version="1.3.0">r-stringr</requirement>
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14 </requirements>
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15 <command detect_errors="exit_code"><![CDATA[
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17 mkdir collection_files &&
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19 #for $file in $input
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20 ln -s "$file" collection_files/"$file.element_identifier".json &&
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21 #end for
0
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23 Rscript "$__tool_directory__/mykrobe_parser.R"
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24
3
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25 -d "collection_files"
0
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27 #if $version
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28 -v "$version"
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29 #end if
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30 #if $depth
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31 -D "$depth"
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32 #end if
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33 #if $confidence
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34 -c "$confidence"
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35 #end if
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36 #if $panel
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37 -p "$panel"
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38 #end if
0
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39 #if $run_name
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40 -n "$run_name"
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41 #end if
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42
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43 ]]></command>
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44 <inputs>
3
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45 <param name="input"
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46 type="data" format="json,txt"
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47 optional="false"
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48 multiple="true"
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49 label="JSON File(s) (.JSON or .TXT)"/>
0
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50 <param name="version" type="text"
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51 argument="-v"
0
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52 optional="true"
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53 label="Mykrobe Workflow Version"/>
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54 <param name="panel" type="select" label="Mykrobe Panel Version" multiple="false">
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55 <option value="2019">2019</option>
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56 <option value="2020">2020</option>
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57 </param>
0
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58 <param name="depth" type="integer"
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59 argument="-D"
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60 optional="true"
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61 label="Minimum depth of coverage"
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62 help="Enter integer values only. Default is 5"/>
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63 <param name="confidence" type="integer"
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64 argument="-c"
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65 optional="true"
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66 label="Confidence"
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67 help="Minimum genotype confidence for variant genotyping. Enter integer values only. Default is 10"/>
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68 <param name="run_name" type="text"
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69 argument="-n"
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70 optional="true"
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71 label="Name of Run"/>
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72 </inputs>
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73 <outputs>
6
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74 <data name="output_jsondata" from_work_dir="output-jsondata.csv" format="csv" label="jsondata"/>
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75 <data name="output_report" from_work_dir="output-report.csv" format="csv" label="report"/>
0
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76 </outputs>
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77 <tests>
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78 <test>
6
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79 <param name="input" value="prediction_2019/data/ERR031480_L6.json,prediction_2019/data/ERR125628_MBOV.json,prediction_2019/data/ERR181314_L9.json,prediction_2019/data/ERR234162_L3.json,prediction_2019/data/ERR2659153.json,prediction_2019/data/ERR266106_MCAN.json,prediction_2019/data/ERR2704812_L5.json,prediction_2019/data/ERR3335753_L1.json,prediction_2019/data/ERR4143897_MPIN.json,prediction_2019/data/ERR756348_L7.json,prediction_2019/data/ERR841495_L5.json,prediction_2019/data/SRR17089001.json,prediction_2019/data/SRR1710097_L2.json,prediction_2019/data/SRR3500411_MMUN.json,prediction_2019/data/SRR9157804.json"/>
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80 <param name="panel" value="2019"/>
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81 <output name="output_jsondata" ftype="csv" value="prediction_2019/output-jsondata.csv"/>
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82 <output name="output_report" ftype="csv" value="prediction_2019/output-report.csv"/>
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83 </test>
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84 <test>
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85 <param name="input" value="prediction_2020/data/ERR031480_L6.json,prediction_2020/data/ERR125628_MBOV.json,prediction_2020/data/ERR181314_L9.json,prediction_2020/data/ERR234162_L3.json,prediction_2020/data/ERR2659153.json,prediction_2020/data/ERR266106_MCAN.json,prediction_2020/data/ERR2704812_L5.json,prediction_2020/data/ERR3335753_L1.json,prediction_2020/data/ERR4143897_MPIN.json,prediction_2020/data/ERR756348_L7.json,prediction_2020/data/ERR841495_L5.json,prediction_2020/data/SRR17089001.json,prediction_2020/data/SRR1710097_L2.json,prediction_2020/data/SRR3500411_MMUN.json,prediction_2020/data/SRR9157804.json"/>
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86 <param name="panel" value="2020"/>
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87 <output name="output_jsondata" ftype="csv" value="prediction_2020/output-jsondata.csv"/>
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88 <output name="output_report" ftype="csv" value="prediction_2020/output-report.csv"/>
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89 </test>
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90 <test>
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91 <param name="input" value="single_2019/single2019.json"/>
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92 <param name="panel" value="2019"/>
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93 <output name="output_jsondata" ftype="csv" value="single_2019/output-jsondata.csv"/>
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94 <output name="output_report" ftype="csv" value="single_2019/output-report.csv"/>
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95 </test>
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96 <test>
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97 <param name="input" value="single_2020/single2020.json"/>
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98 <param name="panel" value="2020"/>
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99 <output name="output_jsondata" ftype="csv" value="single_2020/output-jsondata.csv"/>
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100 <output name="output_report" ftype="csv" value="single_2020/output-report.csv"/>
0
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101 </test>
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102 </tests>
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103 <help><![CDATA[
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104 ==============
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105 Mykrobe Parser
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106 ==============
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107
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108 R Script to parse the results of mykrobe predictor and present them in a LIMS compatible format.
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109
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110 =====
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111 Legal
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112 =====
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113
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114 Copyright Government of Canada 2018
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115
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116 Written by: National Microbiology Laboratory, Public Health Agency of Canada
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117
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118 Licensed under the Apache License, Version 2.0 (the "License"); you may not use
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119 this work except in compliance with the License. You may obtain a copy of the
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120 License at:
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121
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122 http://www.apache.org/licenses/LICENSE-2.0
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123
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124 Unless required by applicable law or agreed to in writing, software distributed
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125 under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR
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126 CONDITIONS OF ANY KIND, either express or implied. See the License for the
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127 specific language governing permissions and limitations under the License.
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128
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129 =======
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130 Contact
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131 =======
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132
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133 **Gary van Domselaar**: gary.vandomselaar@canada.ca
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134
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135 ]]></help>
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136 <citations>
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137 <citation type="bibtex">@ARTICLE{a1,
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138 title = {R Script to parse the results of mykrobe predictor and present them in a LIMS compatible format.},
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139 author = {Adrian Zetner},
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140 url = {https://github.com/phac-nml/mykrobe-parser}
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141 }
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142 }</citation>
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143 </citations>
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144 </tool>