Mercurial > repos > ecology > sdmpredictors_list_layers
diff 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 |
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| date | Mon, 08 Apr 2024 16:33:11 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/sdmpredictors_list_layers.xml Mon Apr 08 16:33:11 2024 +0000 @@ -0,0 +1,202 @@ +<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>