Mercurial > repos > ecology > sdmpredictors_list_layers
view 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
author | ecology |
---|---|
date | Mon, 08 Apr 2024 16:33:11 +0000 |
parents | |
children |
line wrap: on
line source
<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>