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annotate wormsmeasurements.xml @ 0:4da00cf02719 draft default tip

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planemo upload for repository https://github.com/jeanlecras/tools-ecology/tree/master/tools/WormsMeasurements commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
author ecology
date Wed, 28 May 2025 10:12:16 +0000
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4da00cf02719 planemo upload for repository https://github.com/jeanlecras/tools-ecology/tree/master/tools/WormsMeasurements commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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1 <tool id="WormsMeasurements" name="Enrich dataset with WoRMS" version="0.1.2" profile="23.2">
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2 <description>Enrich dataset with measurement type data from WoRMS</description>
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3
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4 <requirements>
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5 <requirement type="package" version="4.3.3">r-base</requirement>
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6 <requirement type="package" version="0.4.3">r-worrms</requirement>
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7 <requirement type="package" version="1.1.4">r-dplyr</requirement>
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8 <requirement type="package" version="2.0.0">r-tidyverse</requirement>
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9 <requirement type="package" version="1.7.5">r-fastDummies</requirement>
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10 </requirements>
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11
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12 <command detect_errors="exit_code"><![CDATA[
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13 Rscript '$__tool_directory__/wormsmeasurements.R'
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14 '$data'
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15 '$measurement_types'
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16 '$scientic_name'
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17 '$include_inherited'
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18 '$pivot_wider'
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19 '$exclude_NA'
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20 '$output'
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21 ]]></command>
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22
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23 <inputs>
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24 <param name="data" type="data" format="tabular" label="occurrence data"/>
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25 <param name="measurement_types" type="text" format="txt" label="list of measurement types">
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26 </param>
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27 <param name="scientic_name" type="text" format="txt" label="scientific names column name" value="scientificName" optional="false">
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28 <validator type="regex" message="this field can't be empty">.+</validator>
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29 </param>
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30 <param name="include_inherited" type="boolean" label="include attributes inherited from parent taxon" checked="false"/>
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31 <param name="pivot_wider" type="boolean" label="one hot encoding on the measurement types" checked="false"/>
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32 <param name="exclude_NA" type="boolean" label="exclude lines with missing values (NA)" checked="false"/>
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33 </inputs>
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34
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35 <outputs>
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36 <data name="output" from_work_dir="enriched_data.tabular" format="tabular" label="dataset enriched with measurments"/>
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37 </outputs>
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38
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39 <tests>
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40 <test>
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41 <param name="data" value="sample.tabular"/>
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42 <param name="measurement_types" value="Development,Fecundity"/>
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43 <param name="scientic_name" value="scientificName"/>
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44 <param name="include_inherited" value="true"/>
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45 <param name="pivot_wider" value="false"/>
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46 <param name="exclude_NA" value="false"/>
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47 <output name="output" file="enriched_data_inherited.tabular"/>
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48 </test>
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49 <test>
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50 <param name="data" value="sample.tabular"/>
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51 <param name="measurement_types" value="Development,Fecundity"/>
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52 <param name="scientic_name" value="scientificName"/>
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53 <param name="include_inherited" value="false"/>
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54 <param name="pivot_wider" value="false"/>
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55 <param name="exclude_NA" value="false"/>
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56 <output name="output" file="enriched_data.tabular"/>
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57 </test>
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58 <test>
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59 <param name="data" value="sample.tabular"/>
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60 <param name="measurement_types" value="Development,Fecundity"/>
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61 <param name="include_inherited" value="true"/>
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62 <param name="scientic_name" value="scientificName"/>
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63 <param name="pivot_wider" value="true"/>
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64 <param name="exclude_NA" value="false"/>
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65 <output name="output" file="enriched_data_inherited_ohe.tabular"/>
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66 </test>
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67 </tests>
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68
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69 <help><![CDATA[
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70 ==================
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71 **What it does ?**
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72 ==================
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73
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74 This tool requests WoRMS (World Register of Marine Species) to get data about a specific by accessing the entry returned by an its scientific name, it looks for the measurementType(s) requested by the user and select the associated measurement value to add it to a dataset.
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75
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76 ===================
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77 **How to use it ?**
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78 ===================
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79
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80 ## Parameters:
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81
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82 - **data**: a dataset containing a variable of scientific names.
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83 - **list of measurement types**: a list of measurements types present in WoRMS (ex: Development, Fecundity, Size ...) separated by ','.
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84 - **scientific names column name**: the name of column in the dataset containing scientific names.
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85 - **include attributes inherited from parent taxon**: usefull when the data you are looking for are incomplete.
4da00cf02719 planemo upload for repository https://github.com/jeanlecras/tools-ecology/tree/master/tools/WormsMeasurements commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
ecology
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86 - **one hot encoding on the measurement types**: each possible values of a measurementType becomes a column encoded in 0/1
4da00cf02719 planemo upload for repository https://github.com/jeanlecras/tools-ecology/tree/master/tools/WormsMeasurements commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
ecology
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87 - **exclude_NA**: exclude lines with missing measurement value
4da00cf02719 planemo upload for repository https://github.com/jeanlecras/tools-ecology/tree/master/tools/WormsMeasurements commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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88
4da00cf02719 planemo upload for repository https://github.com/jeanlecras/tools-ecology/tree/master/tools/WormsMeasurements commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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89 ## Outputs:
4da00cf02719 planemo upload for repository https://github.com/jeanlecras/tools-ecology/tree/master/tools/WormsMeasurements commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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90
4da00cf02719 planemo upload for repository https://github.com/jeanlecras/tools-ecology/tree/master/tools/WormsMeasurements commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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91 The inputed dataset with columns of measurement types or measurements
4da00cf02719 planemo upload for repository https://github.com/jeanlecras/tools-ecology/tree/master/tools/WormsMeasurements commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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92
4da00cf02719 planemo upload for repository https://github.com/jeanlecras/tools-ecology/tree/master/tools/WormsMeasurements commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
ecology
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93 **Example of input data :**
4da00cf02719 planemo upload for repository https://github.com/jeanlecras/tools-ecology/tree/master/tools/WormsMeasurements commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
ecology
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94 "decimalLatitude" "decimalLongitude" "scientificName"
4da00cf02719 planemo upload for repository https://github.com/jeanlecras/tools-ecology/tree/master/tools/WormsMeasurements commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
ecology
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95 -49.355 70.215 "Abatus cordatus" "planktotrophic" NA
4da00cf02719 planemo upload for repository https://github.com/jeanlecras/tools-ecology/tree/master/tools/WormsMeasurements commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
ecology
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96 -66.963303 163.223297 "Ctenocidaris spinosa"
4da00cf02719 planemo upload for repository https://github.com/jeanlecras/tools-ecology/tree/master/tools/WormsMeasurements commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
ecology
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97 -42.45 -74.75833333 "Loxechinus albus"
4da00cf02719 planemo upload for repository https://github.com/jeanlecras/tools-ecology/tree/master/tools/WormsMeasurements commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
ecology
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98 -37.606167 176.705167 "Ogmocidaris benhami"
4da00cf02719 planemo upload for repository https://github.com/jeanlecras/tools-ecology/tree/master/tools/WormsMeasurements commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
ecology
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99 -36.201698 175.834198 "Peronella hinemoae"
4da00cf02719 planemo upload for repository https://github.com/jeanlecras/tools-ecology/tree/master/tools/WormsMeasurements commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
ecology
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100 -37.494667 176.672501 "Phormosoma bursarium"
4da00cf02719 planemo upload for repository https://github.com/jeanlecras/tools-ecology/tree/master/tools/WormsMeasurements commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
ecology
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101 -43.469 173.572 "Pseudechinus huttoni"
4da00cf02719 planemo upload for repository https://github.com/jeanlecras/tools-ecology/tree/master/tools/WormsMeasurements commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
ecology
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102 -47.7 179.45 "Pseudechinus novaezealandiae"
4da00cf02719 planemo upload for repository https://github.com/jeanlecras/tools-ecology/tree/master/tools/WormsMeasurements commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
ecology
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103 -74.72 164.2183333 "Sterechinus neumayeri"
4da00cf02719 planemo upload for repository https://github.com/jeanlecras/tools-ecology/tree/master/tools/WormsMeasurements commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
ecology
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104 -70.51166667 -8.801 "Sterechinus sp"
4da00cf02719 planemo upload for repository https://github.com/jeanlecras/tools-ecology/tree/master/tools/WormsMeasurements commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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105
4da00cf02719 planemo upload for repository https://github.com/jeanlecras/tools-ecology/tree/master/tools/WormsMeasurements commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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106 **Example of output data :**
4da00cf02719 planemo upload for repository https://github.com/jeanlecras/tools-ecology/tree/master/tools/WormsMeasurements commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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107 "decimalLatitude" "decimalLongitude" "scientificName" "Development" " Fecundity"
4da00cf02719 planemo upload for repository https://github.com/jeanlecras/tools-ecology/tree/master/tools/WormsMeasurements commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
ecology
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108 -49.355 70.215 "Abatus cordatus" "planktotrophic" NA
4da00cf02719 planemo upload for repository https://github.com/jeanlecras/tools-ecology/tree/master/tools/WormsMeasurements commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
ecology
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109 -66.963303 163.223297 "Ctenocidaris spinosa" "direct development" NA
4da00cf02719 planemo upload for repository https://github.com/jeanlecras/tools-ecology/tree/master/tools/WormsMeasurements commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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110 -42.45 -74.75833333 "Loxechinus albus" "planktotrophic" NA
4da00cf02719 planemo upload for repository https://github.com/jeanlecras/tools-ecology/tree/master/tools/WormsMeasurements commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
ecology
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111 -37.606167 176.705167 "Ogmocidaris benhami" "planktotrophic" NA
4da00cf02719 planemo upload for repository https://github.com/jeanlecras/tools-ecology/tree/master/tools/WormsMeasurements commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
ecology
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112 -36.201698 175.834198 "Peronella hinemoae" "planktotrophic" NA
4da00cf02719 planemo upload for repository https://github.com/jeanlecras/tools-ecology/tree/master/tools/WormsMeasurements commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
ecology
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113 -37.494667 176.672501 "Phormosoma bursarium" "planktotrophic" NA
4da00cf02719 planemo upload for repository https://github.com/jeanlecras/tools-ecology/tree/master/tools/WormsMeasurements commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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114 -43.469 173.572 "Pseudechinus huttoni" "planktotrophic" NA
4da00cf02719 planemo upload for repository https://github.com/jeanlecras/tools-ecology/tree/master/tools/WormsMeasurements commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
ecology
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115 -47.7 179.45 "Pseudechinus novaezealandiae" "planktotrophic" NA
4da00cf02719 planemo upload for repository https://github.com/jeanlecras/tools-ecology/tree/master/tools/WormsMeasurements commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
ecology
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116 -74.72 164.2183333 "Sterechinus neumayeri" "planktotrophic" NA
4da00cf02719 planemo upload for repository https://github.com/jeanlecras/tools-ecology/tree/master/tools/WormsMeasurements commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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117 -70.51166667 -8.801 "Sterechinus sp" NA NA
4da00cf02719 planemo upload for repository https://github.com/jeanlecras/tools-ecology/tree/master/tools/WormsMeasurements commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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118
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119 ]]></help>
4da00cf02719 planemo upload for repository https://github.com/jeanlecras/tools-ecology/tree/master/tools/WormsMeasurements commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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120
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121 <citations>
4da00cf02719 planemo upload for repository https://github.com/jeanlecras/tools-ecology/tree/master/tools/WormsMeasurements commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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122 <citation type="doi">10.32614/CRAN.package.dplyr</citation>
4da00cf02719 planemo upload for repository https://github.com/jeanlecras/tools-ecology/tree/master/tools/WormsMeasurements commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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123 <citation type="doi">10.32614/CRAN.package.tidyverse</citation>
4da00cf02719 planemo upload for repository https://github.com/jeanlecras/tools-ecology/tree/master/tools/WormsMeasurements commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
ecology
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124 <citation type="doi">10.32614/CRAN.package.worrms</citation>
4da00cf02719 planemo upload for repository https://github.com/jeanlecras/tools-ecology/tree/master/tools/WormsMeasurements commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
ecology
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125 <citation type="doi">10.32614/CRAN.package.fastDummies</citation>
4da00cf02719 planemo upload for repository https://github.com/jeanlecras/tools-ecology/tree/master/tools/WormsMeasurements commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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126 </citations>
4da00cf02719 planemo upload for repository https://github.com/jeanlecras/tools-ecology/tree/master/tools/WormsMeasurements commit ced658540f05bb07e1e687af30a3fa4ea8e4803c
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127 </tool>