annotate sdmpredictors_list_layers.xml @ 0:f20914d71c9d draft default tip

planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0

<tool id="sdmpredictors_list_layers" name="SdmPredictors List Layers" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
    <description>from environmental predictors for species distribution modeling</description>
    <macros>
        <token name="@TOOL_VERSION@">0.2.15</token> 
        <token name="@VERSION_SUFFIX@">0</token>
    </macros>
    <requirements> 
        <requirement type="package" version="4.3.2">r-base</requirement>
        <requirement type="package" version="@TOOL_VERSION@">r-sdmpredictors</requirement>
        <requirement type="package" version="0.2_19">r-codetools</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        
        Rscript
         '$__tool_directory__/sdmpredictors_list_layers.R'
         #for $i, $s in enumerate($list_layers)
            ${s.choose_layer.input_layer}
            ${s.choose_layer.environement.terrestrial}
            ${s.choose_layer.environement.marine}
            ${s.choose_layer.environement.freshwater}
            ${s.choose_layer.advanced_options.monthly}
            ${s.choose_layer.advanced_options.version}
            #if str($s.choose_layer.input_layer) == 'layers_future'
                ${s.choose_layer.advanced_options.scenario}
                ${s.choose_layer.advanced_options.year}
            #elif str($s.choose_layer.input_layer) == 'layers_paleo'
                ${s.choose_layer.advanced_options.model_name}
                ${s.choose_layer.advanced_options.epoch}
                ${s.choose_layer.advanced_options.years_ago}
            #end if            
         #end for

         ]]></command>
    <inputs>
        <repeat name="list_layers" title="New layer list">
            <conditional name="choose_layer">
                <param name="input_layer" type="select" label="Choose Layer Timeframe">
                    <option value="layers_current" selected="true">Current Layer</option>
                    <option value="layers_future">Future Layer</option>
                    <option value="layers_paleo">Paleo Layer</option>
                </param>
                <when value="layers_current">
                    <section name="environement" title= "Environemental Datasets" expanded="true" help="Choose at least one environemental dataset to take layers from">
                        <param name ="terrestrial" type="boolean" checked="true"
                               label="Terrestrial Data" help="When enabled (default), then datasets that only have terrestrial data (sea masked) are returned."/>
                        <param name ="marine" type="boolean" 
                               label="Marine Data" help="When enabled, then datasets that only have marine data (land masked) are returned."/>
                        <param name ="freshwater" type="boolean" 
                               label="Freshwater Data" help="When enabled, then datasets that only have freshwater data are returned."/>
                    </section>
                    <section name="advanced_options" title= "Advanced Option" expanded="false">
                        <param name ="monthly" type="boolean" checked="true" 
                               label="Monthly" help="When enabled, no monthly layers are returned. All annual and monthly layers are returned by default."/>
                        <param name ="version" type="text" value="0" optional="false"
                               label="Layer Version" help="When equal to 0, layers from all versions of datasets are returned (default) else layers are filtered by version number."/>
                    </section>
                </when>
                <when value="layers_future">
                    <section name="environement" title= "Environemental Datasets" expanded="true" help="Choose at least one environemental dataset to take layers from">
                        <param name ="terrestrial" type="boolean" checked="true"
                               label="Terrestrial Data" help="When enabled (default), then datasets that only have terrestrial data (sea masked) are returned."/>
                        <param name ="marine" type="boolean" 
                               label="Marine Data" help="When enabled, then datasets that only have marine data (land masked) are returned."/>
                        <param name ="freshwater" type="boolean" 
                               label="Freshwater Data" help="When enabled, then datasets that only have freshwater data are returned."/>
                    </section>
                    <section name="advanced_options" title= "Advanced Option" expanded="false">
                        <param name ="monthly" type="boolean" checked="true" 
                               label="Monthly" help="When enabled, no monthly layers are returned. All annual and monthly layers are returned by default."/>
                        <param name ="version" type="text" value="0" optional="false"
                               label="Layer Version" help="When equal to 0, layers from all versions of datasets are returned (default) else layers are filtered by version number."/>
                        <param name ="scenario" type="text" value="All" optional="false"
                               label="Scenario" help="Climate change scenario, e.g. 'B1', 'A1B', 'A2'. By default All scenarios are listed."/>
                        <param name ="year" type="text" value="0" optional="false"
                               label="Year" help="Year for which you want the climate change prediction, e.g. 2100,2200. When 0 all years predicted are listed."/>
                    </section>
                </when>
                <when value="layers_paleo">
                    <section name="environement" title= "Environemental Datasets" expanded="true" help="Choose at least one environemental dataset to take layers from">
                        <param name ="terrestrial" type="boolean" checked="true"
                               label="Terrestrial Data" help="When enabled (default), then datasets that only have terrestrial data (sea masked) are returned."/>
                        <param name ="marine" type="boolean" 
                               label="Marine Data" help="When enabled, then datasets that only have marine data (land masked) are returned."/>
                        <param name ="freshwater" type="boolean" 
                               label="Freshwater Data" help="When enabled, then datasets that only have freshwater data are returned."/>
                     </section>
                    <section name="advanced_options" title= "Advanced Option" expanded="false">
                        <param name ="monthly" type="boolean" checked="true" 
                               label="Monthly" help="When enabled, no monthly layers are returned. All annual and monthly layers are returned by default."/>
                        <param name ="version" type="text" value="0" optional="false"
                               label="Layer Version" help="When equal to 0, layers from all versions of datasets are returned (default) else layers are filtered by version number."/>
                        <param name ="model_name" type="text" value="All" optional="false"
                               label="Model Name" help="Paleo climate model name, see the model_name column in the result. By default all models are listed."/>
                        <param name ="epoch" type="text" value="All" optional="false"
                               label="Epoch" help="Epoch for which you want the paleo layer, e.g. 'mid-Holocene', 'Last Glacial Maximum'. By default all epochs are listed."/>
                        <param name ="years_ago" type="text" value="0" optional="false"
                               label="Years Ago" help="Years for which you want the paleo layer, e.g. 6000, 21000.When 0 all years are listed."/>
                   </section>
                </when>
            </conditional>
        </repeat>
    </inputs>
    <outputs>
        <collection name="datasets_output" type="list"
            label="Datasets list">
        <discover_datasets pattern="__name_and_ext__" />
        </collection>
    </outputs>
    <tests>
        <test>
            <repeat name="list_layers">
                <conditional name="choose_layer">
                    <param name="input_layer" value="layers_paleo"/>
                    <section name="environement">
                        <param name="terrestrial" value="false"/>
                        <param name="marine" value="true"/>
                        <param name="freshwater" value="false"/>
                    </section>
                    <section name="advanced_options">
                        <param name="monthly" value="true"/>
                        <param name="version" value="0"/>
                        <param name="model_name" value="All"/>
                        <param name="epoch" value="All"/>
                        <param name="years_ago" value="0"/>
                    </section>
                </conditional>
            </repeat>
            <repeat name="list_layers">
                <conditional name="choose_layer">
                    <param name="input_layer" value="layers_future"/>
                    <section name="environement">
                        <param name="terrestrial" value="true"/>
                        <param name="marine" value="false"/>
                        <param name="freshwater" value="false"/>
                    </section>
                    <section name="advanced_options">
                        <param name="monthly" value="true"/>
                        <param name="version" value="0"/>
                        <param name="scenario" value="All"/>
                        <param name="year" value="0"/>
                    </section>
                </conditional>
            </repeat>
            <repeat name="list_layers">
                <conditional name="choose_layer">
                    <param name="input_layer" value="layers_current"/>
                    <section name="environement">
                        <param name="terrestrial" value="false"/>
                        <param name="marine" value="false"/>
                        <param name="freshwater" value="true"/>
                    </section>
                    <section name="advanced_options">
                        <param name="monthly" value="true"/>
                        <param name="version" value="0"/>
                    </section>
                </conditional>
            </repeat>
            <output_collection name="datasets_output" type="list" count="3">
                <element name="1_data_paleo" file="1_data_paleo.tabular" ftype="tabular"/>
                <element name="2_data_future" file="2_data_future.tabular" ftype="tabular"/>
                <element name="3_data_current" file="3_data_current.tabular" ftype="tabular"/>
            </output_collection>
        </test>
    </tests>
    <help><![CDATA[ 

.. class:: infomark

**What it does**

This tool helps you get one or multiple list of environemental layers from multiple sources, including :
WorldClim <https://www.worldclim.org/>
ENVIREM <https://envirem.github.io/> 
Bio-ORACLE <https://bio-oracle.org/> 
and MARSPEC <http://www.marspec.org/> 

____


.. class:: infomark

**Output**

Eatch "New layer list" request will produce a tabular file, all files will be available in a collection

.. class:: warning

**If no Environement are selected, or if the option specified does not exist, the tool will produce an empty file.**


    ]]></help>
    <citations>
        <citation type="bibtex">@Manual{,
  title = {sdmpredictors: Species Distribution Modelling Predictor Datasets},
  author = {Samuel Bosch and Salvador Fernandez},
  year = {2023},
  note = {R package version 0.2.15},
  url = {http://lifewatch.github.io/sdmpredictors/},
}        
        </citation>
    </citations>
</tool>