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comparison wormsmeasurements.xml @ 1:6f75ab89587a 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 10:13:42 +0000
parents 23b963a1284e
children
comparison
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0:23b963a1284e 1:6f75ab89587a
1 <tool id="WormsMeasurements" name="Enrich dataset with WoRMS" version="0.1.1" profile="23.2"> 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> 2 <description>Enrich dataset with measurement type data from WoRMS</description>
3 3
4 <requirements> 4 <requirements>
5 <requirement type="package" version="4.3.3">r-base</requirement> 5 <requirement type="package" version="4.3.3">r-base</requirement>
6 <requirement type="package" version="0.4.3">r-worrms</requirement> 6 <requirement type="package" version="0.4.3">r-worrms</requirement>
14 '$data' 14 '$data'
15 '$measurement_types' 15 '$measurement_types'
16 '$scientic_name' 16 '$scientic_name'
17 '$include_inherited' 17 '$include_inherited'
18 '$pivot_wider' 18 '$pivot_wider'
19 '$exclude_NA'
19 '$output' 20 '$output'
20 ]]></command> 21 ]]></command>
21 22
22 <inputs> 23 <inputs>
23 <param name="data" type="data" format="tabular" label="occurrence data"/> 24 <param name="data" type="data" format="tabular" label="occurrence data"/>
24 <param name="measurement_types" type="text" format="txt" label="list of measurement types"/> 25 <param name="measurement_types" type="text" format="txt" label="list of measurement types">
25 <param name="scientic_name" type="text" format="txt" label="scientific names column name" value="scientificName"/> 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>
26 <param name="include_inherited" type="boolean" label="include attributes inherited from parent taxon" checked="false"/> 30 <param name="include_inherited" type="boolean" label="include attributes inherited from parent taxon" checked="false"/>
27 <param name="pivot_wider" type="boolean" label="one hot encoding on the measurement types" 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"/>
28 </inputs> 33 </inputs>
29 34
30 <outputs> 35 <outputs>
31 <data name="output" from_work_dir="enriched_data.tabular" format="tabular" label="dataset enriched with measurments"/> 36 <data name="output" from_work_dir="enriched_data.tabular" format="tabular" label="dataset enriched with measurments"/>
32 </outputs> 37 </outputs>
33 38
34 <tests> 39 <tests>
35 <test> 40 <test>
36 <param name="data" value="sample.tabular"/> 41 <param name="data" value="sample.tabular"/>
37 <param name="measurement_types" value="Development, Fecundity"/> 42 <param name="measurement_types" value="Development,Fecundity"/>
38 <param name="scientic_name" value="scientificName"/> 43 <param name="scientic_name" value="scientificName"/>
39 <param name="include_inherited" value="true"/> 44 <param name="include_inherited" value="true"/>
40 <param name="pivot_wider" value="false"/> 45 <param name="pivot_wider" value="false"/>
46 <param name="exclude_NA" value="false"/>
41 <output name="output" file="enriched_data_inherited.tabular"/> 47 <output name="output" file="enriched_data_inherited.tabular"/>
42 </test> 48 </test>
43 <test> 49 <test>
44 <param name="data" value="sample.tabular"/> 50 <param name="data" value="sample.tabular"/>
45 <param name="measurement_types" value="Development, Fecundity"/> 51 <param name="measurement_types" value="Development,Fecundity"/>
46 <param name="scientic_name" value="scientificName"/> 52 <param name="scientic_name" value="scientificName"/>
47 <param name="include_inherited" value="false"/> 53 <param name="include_inherited" value="false"/>
48 <param name="pivot_wider" value="false"/> 54 <param name="pivot_wider" value="false"/>
55 <param name="exclude_NA" value="false"/>
49 <output name="output" file="enriched_data.tabular"/> 56 <output name="output" file="enriched_data.tabular"/>
50 </test> 57 </test>
51 <test> 58 <test>
52 <param name="data" value="sample.tabular"/> 59 <param name="data" value="sample.tabular"/>
53 <param name="measurement_types" value="Development, Fecundity"/> 60 <param name="measurement_types" value="Development,Fecundity"/>
54 <param name="include_inherited" value="true"/> 61 <param name="include_inherited" value="true"/>
55 <param name="scientic_name" value="scientificName"/> 62 <param name="scientic_name" value="scientificName"/>
56 <param name="pivot_wider" value="true"/> 63 <param name="pivot_wider" value="true"/>
64 <param name="exclude_NA" value="false"/>
57 <output name="output" file="enriched_data_inherited_ohe.tabular"/> 65 <output name="output" file="enriched_data_inherited_ohe.tabular"/>
58 </test> 66 </test>
59 </tests> 67 </tests>
60 68
61 <help><![CDATA[ 69 <help><![CDATA[
74 - **data**: a dataset containing a variable of scientific names. 82 - **data**: a dataset containing a variable of scientific names.
75 - **list of measurement types**: a list of measurements types present in WoRMS (ex: Development, Fecundity, Size ...) separated by ','. 83 - **list of measurement types**: a list of measurements types present in WoRMS (ex: Development, Fecundity, Size ...) separated by ','.
76 - **scientific names column name**: the name of column in the dataset containing scientific names. 84 - **scientific names column name**: the name of column in the dataset containing scientific names.
77 - **include attributes inherited from parent taxon**: usefull when the data you are looking for are incomplete. 85 - **include attributes inherited from parent taxon**: usefull when the data you are looking for are incomplete.
78 - **one hot encoding on the measurement types**: each possible values of a measurementType becomes a column encoded in 0/1 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
79 88
80 ## Outputs: 89 ## Outputs:
81 90
82 The inputed dataset with columns of measurement types or measurements 91 The inputed dataset with columns of measurement types or measurements
83 92