Mercurial > repos > ecology > wormsmeasurements

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

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:4da00cf02719
1 <tool id="WormsMeasurements" name="Enrich dataset with WoRMS" version="0.1.2" profile="23.2">
2 <description>Enrich dataset with measurement type data from WoRMS</description>
3
4 <requirements>
5 <requirement type="package" version="4.3.3">r-base</requirement>
6 <requirement type="package" version="0.4.3">r-worrms</requirement>
7 <requirement type="package" version="1.1.4">r-dplyr</requirement>
8 <requirement type="package" version="2.0.0">r-tidyverse</requirement>
9 <requirement type="package" version="1.7.5">r-fastDummies</requirement>
10 </requirements>
11
12 <command detect_errors="exit_code"><![CDATA[
13 Rscript '$__tool_directory__/wormsmeasurements.R'
14 '$data'
15 '$measurement_types'
16 '$scientic_name'
17 '$include_inherited'
18 '$pivot_wider'
19 '$exclude_NA'
20 '$output'
21 ]]></command>
22
23 <inputs>
24 <param name="data" type="data" format="tabular" label="occurrence data"/>
25 <param name="measurement_types" type="text" format="txt" label="list of measurement types">
26 </param>
27 <param name="scientic_name" type="text" format="txt" label="scientific names column name" value="scientificName" optional="false">
28 <validator type="regex" message="this field can't be empty">.+</validator>
29 </param>
30 <param name="include_inherited" type="boolean" label="include attributes inherited from parent taxon" checked="false"/>
31 <param name="pivot_wider" type="boolean" label="one hot encoding on the measurement types" checked="false"/>
32 <param name="exclude_NA" type="boolean" label="exclude lines with missing values (NA)" checked="false"/>
33 </inputs>
34
35 <outputs>
36 <data name="output" from_work_dir="enriched_data.tabular" format="tabular" label="dataset enriched with measurments"/>
37 </outputs>
38
39 <tests>
40 <test>
41 <param name="data" value="sample.tabular"/>
42 <param name="measurement_types" value="Development,Fecundity"/>
43 <param name="scientic_name" value="scientificName"/>
44 <param name="include_inherited" value="true"/>
45 <param name="pivot_wider" value="false"/>
46 <param name="exclude_NA" value="false"/>
47 <output name="output" file="enriched_data_inherited.tabular"/>
48 </test>
49 <test>
50 <param name="data" value="sample.tabular"/>
51 <param name="measurement_types" value="Development,Fecundity"/>
52 <param name="scientic_name" value="scientificName"/>
53 <param name="include_inherited" value="false"/>
54 <param name="pivot_wider" value="false"/>
55 <param name="exclude_NA" value="false"/>
56 <output name="output" file="enriched_data.tabular"/>
57 </test>
58 <test>
59 <param name="data" value="sample.tabular"/>
60 <param name="measurement_types" value="Development,Fecundity"/>
61 <param name="include_inherited" value="true"/>
62 <param name="scientic_name" value="scientificName"/>
63 <param name="pivot_wider" value="true"/>
64 <param name="exclude_NA" value="false"/>
65 <output name="output" file="enriched_data_inherited_ohe.tabular"/>
66 </test>
67 </tests>
68
69 <help><![CDATA[
70 ==================
71 **What it does ?**
72 ==================
73
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.
75
76 ===================
77 **How to use it ?**
78 ===================
79
80 ## Parameters:
81
82 - **data**: a dataset containing a variable of scientific names.
83 - **list of measurement types**: a list of measurements types present in WoRMS (ex: Development, Fecundity, Size ...) separated by ','.
84 - **scientific names column name**: the name of column in the dataset containing scientific names.
85 - **include attributes inherited from parent taxon**: usefull when the data you are looking for are incomplete.
86 - **one hot encoding on the measurement types**: each possible values of a measurementType becomes a column encoded in 0/1
87 - **exclude_NA**: exclude lines with missing measurement value
88
89 ## Outputs:
90
91 The inputed dataset with columns of measurement types or measurements
92
93 **Example of input data :**
94 "decimalLatitude" "decimalLongitude" "scientificName"
95 -49.355 70.215 "Abatus cordatus" "planktotrophic" NA
96 -66.963303 163.223297 "Ctenocidaris spinosa"
97 -42.45 -74.75833333 "Loxechinus albus"
98 -37.606167 176.705167 "Ogmocidaris benhami"
99 -36.201698 175.834198 "Peronella hinemoae"
100 -37.494667 176.672501 "Phormosoma bursarium"
101 -43.469 173.572 "Pseudechinus huttoni"
102 -47.7 179.45 "Pseudechinus novaezealandiae"
103 -74.72 164.2183333 "Sterechinus neumayeri"
104 -70.51166667 -8.801 "Sterechinus sp"
105
106 **Example of output data :**
107 "decimalLatitude" "decimalLongitude" "scientificName" "Development" " Fecundity"
108 -49.355 70.215 "Abatus cordatus" "planktotrophic" NA
109 -66.963303 163.223297 "Ctenocidaris spinosa" "direct development" NA
110 -42.45 -74.75833333 "Loxechinus albus" "planktotrophic" NA
111 -37.606167 176.705167 "Ogmocidaris benhami" "planktotrophic" NA
112 -36.201698 175.834198 "Peronella hinemoae" "planktotrophic" NA
113 -37.494667 176.672501 "Phormosoma bursarium" "planktotrophic" NA
114 -43.469 173.572 "Pseudechinus huttoni" "planktotrophic" NA
115 -47.7 179.45 "Pseudechinus novaezealandiae" "planktotrophic" NA
116 -74.72 164.2183333 "Sterechinus neumayeri" "planktotrophic" NA
117 -70.51166667 -8.801 "Sterechinus sp" NA NA
118
119 ]]></help>
120
121 <citations>
122 <citation type="doi">10.32614/CRAN.package.dplyr</citation>
123 <citation type="doi">10.32614/CRAN.package.tidyverse</citation>
124 <citation type="doi">10.32614/CRAN.package.worrms</citation>
125 <citation type="doi">10.32614/CRAN.package.fastDummies</citation>
126 </citations>
127 </tool>