<tool id="WormsMeasurements" name="Enrich dataset with WoRMS" version="0.1.2" profile="23.2">
    <description>Enrich dataset with measurement type data from WoRMS</description>

    <requirements>
        <requirement type="package" version="4.3.3">r-base</requirement>
        <requirement type="package" version="0.4.3">r-worrms</requirement>
        <requirement type="package" version="1.1.4">r-dplyr</requirement>
        <requirement type="package" version="2.0.0">r-tidyverse</requirement>
        <requirement type="package" version="1.7.5">r-fastDummies</requirement>
    </requirements>

    <command detect_errors="exit_code"><![CDATA[
Rscript '$__tool_directory__/wormsmeasurements.R'
    '$data'
    '$measurement_types'
    '$scientic_name'
    '$include_inherited'
    '$pivot_wider'
    '$exclude_NA'
    '$output'
    ]]></command>

    <inputs>
        <param name="data" type="data" format="tabular" label="occurrence data"/>
        <param name="measurement_types" type="text" format="txt" label="list of measurement types">
        </param>
        <param name="scientic_name" type="text" format="txt" label="scientific names column name" value="scientificName" optional="false">
            <validator type="regex" message="this field can't be empty">.+</validator>
        </param>
        <param name="include_inherited" type="boolean" label="include attributes inherited from parent taxon" checked="false"/>        
        <param name="pivot_wider" type="boolean" label="one hot encoding on the measurement types" checked="false"/>
        <param name="exclude_NA" type="boolean" label="exclude lines with missing values (NA)" checked="false"/>
    </inputs>

    <outputs>
        <data name="output" from_work_dir="enriched_data.tabular" format="tabular" label="dataset enriched with measurments"/>
    </outputs>

    <tests>
        <test>
            <param name="data" value="sample.tabular"/>
            <param name="measurement_types" value="Development,Fecundity"/>
            <param name="scientic_name" value="scientificName"/>
            <param name="include_inherited" value="true"/>
            <param name="pivot_wider" value="false"/>
            <param name="exclude_NA" value="false"/>
            <output name="output" file="enriched_data_inherited.tabular"/>
        </test>
        <test>
            <param name="data" value="sample.tabular"/>
            <param name="measurement_types" value="Development,Fecundity"/>
            <param name="scientic_name" value="scientificName"/>
            <param name="include_inherited" value="false"/>
            <param name="pivot_wider" value="false"/>
            <param name="exclude_NA" value="false"/>
            <output name="output" file="enriched_data.tabular"/>
        </test>
        <test>
            <param name="data" value="sample.tabular"/>
            <param name="measurement_types" value="Development,Fecundity"/>
            <param name="include_inherited" value="true"/>
            <param name="scientic_name" value="scientificName"/>
            <param name="pivot_wider" value="true"/>
            <param name="exclude_NA" value="false"/>
            <output name="output" file="enriched_data_inherited_ohe.tabular"/>
        </test>
    </tests>

    <help><![CDATA[
==================    
**What it does ?**
==================

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.

===================         
**How to use it ?**
===================

## Parameters:

- **data**: a dataset containing a variable of scientific names.
- **list of measurement types**: a list of measurements types present in WoRMS (ex: Development, Fecundity, Size ...) separated by ','.
- **scientific names column name**: the name of column in the dataset containing scientific names.
- **include attributes inherited from parent taxon**: usefull when the data you are looking for are incomplete.
- **one hot encoding on the measurement types**: each possible values of a measurementType becomes a column encoded in 0/1
- **exclude_NA**: exclude lines with missing measurement value

## Outputs:

The inputed dataset with columns of measurement types or measurements

**Example of input data :**
"decimalLatitude"	"decimalLongitude"	"scientificName"
-49.355	70.215	"Abatus cordatus"	"planktotrophic"	NA
-66.963303	163.223297	"Ctenocidaris spinosa"
-42.45	-74.75833333	"Loxechinus albus"
-37.606167	176.705167	"Ogmocidaris benhami"
-36.201698	175.834198	"Peronella hinemoae"
-37.494667	176.672501	"Phormosoma bursarium"
-43.469	173.572	"Pseudechinus huttoni"
-47.7	179.45	"Pseudechinus novaezealandiae"
-74.72	164.2183333	"Sterechinus neumayeri"
-70.51166667	-8.801	"Sterechinus sp"

**Example of output data :**
"decimalLatitude"	"decimalLongitude"	"scientificName"	"Development"	" Fecundity"
-49.355	70.215	"Abatus cordatus"	"planktotrophic"	NA
-66.963303	163.223297	"Ctenocidaris spinosa"	"direct development"	NA
-42.45	-74.75833333	"Loxechinus albus"	"planktotrophic"	NA
-37.606167	176.705167	"Ogmocidaris benhami"	"planktotrophic"	NA
-36.201698	175.834198	"Peronella hinemoae"	"planktotrophic"	NA
-37.494667	176.672501	"Phormosoma bursarium"	"planktotrophic"	NA
-43.469	173.572	"Pseudechinus huttoni"	"planktotrophic"	NA
-47.7	179.45	"Pseudechinus novaezealandiae"	"planktotrophic"	NA
-74.72	164.2183333	"Sterechinus neumayeri"	"planktotrophic"	NA
-70.51166667	-8.801	"Sterechinus sp"	NA	NA

]]></help>

    <citations>
        <citation type="doi">10.32614/CRAN.package.dplyr</citation>
        <citation type="doi">10.32614/CRAN.package.tidyverse</citation>
        <citation type="doi">10.32614/CRAN.package.worrms</citation>
        <citation type="doi">10.32614/CRAN.package.fastDummies</citation>
    </citations>
</tool>