Mercurial > repos > ecology > sdmpredictors_list_layers
comparison 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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1 <tool id="sdmpredictors_list_layers" name="SdmPredictors List Layers" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> | |
2 <description>from environmental predictors for species distribution modeling</description> | |
3 <macros> | |
4 <token name="@TOOL_VERSION@">0.2.15</token> | |
5 <token name="@VERSION_SUFFIX@">0</token> | |
6 </macros> | |
7 <requirements> | |
8 <requirement type="package" version="4.3.2">r-base</requirement> | |
9 <requirement type="package" version="@TOOL_VERSION@">r-sdmpredictors</requirement> | |
10 <requirement type="package" version="0.2_19">r-codetools</requirement> | |
11 </requirements> | |
12 <command detect_errors="exit_code"><![CDATA[ | |
13 | |
14 Rscript | |
15 '$__tool_directory__/sdmpredictors_list_layers.R' | |
16 #for $i, $s in enumerate($list_layers) | |
17 ${s.choose_layer.input_layer} | |
18 ${s.choose_layer.environement.terrestrial} | |
19 ${s.choose_layer.environement.marine} | |
20 ${s.choose_layer.environement.freshwater} | |
21 ${s.choose_layer.advanced_options.monthly} | |
22 ${s.choose_layer.advanced_options.version} | |
23 #if str($s.choose_layer.input_layer) == 'layers_future' | |
24 ${s.choose_layer.advanced_options.scenario} | |
25 ${s.choose_layer.advanced_options.year} | |
26 #elif str($s.choose_layer.input_layer) == 'layers_paleo' | |
27 ${s.choose_layer.advanced_options.model_name} | |
28 ${s.choose_layer.advanced_options.epoch} | |
29 ${s.choose_layer.advanced_options.years_ago} | |
30 #end if | |
31 #end for | |
32 | |
33 ]]></command> | |
34 <inputs> | |
35 <repeat name="list_layers" title="New layer list"> | |
36 <conditional name="choose_layer"> | |
37 <param name="input_layer" type="select" label="Choose Layer Timeframe"> | |
38 <option value="layers_current" selected="true">Current Layer</option> | |
39 <option value="layers_future">Future Layer</option> | |
40 <option value="layers_paleo">Paleo Layer</option> | |
41 </param> | |
42 <when value="layers_current"> | |
43 <section name="environement" title= "Environemental Datasets" expanded="true" help="Choose at least one environemental dataset to take layers from"> | |
44 <param name ="terrestrial" type="boolean" checked="true" | |
45 label="Terrestrial Data" help="When enabled (default), then datasets that only have terrestrial data (sea masked) are returned."/> | |
46 <param name ="marine" type="boolean" | |
47 label="Marine Data" help="When enabled, then datasets that only have marine data (land masked) are returned."/> | |
48 <param name ="freshwater" type="boolean" | |
49 label="Freshwater Data" help="When enabled, then datasets that only have freshwater data are returned."/> | |
50 </section> | |
51 <section name="advanced_options" title= "Advanced Option" expanded="false"> | |
52 <param name ="monthly" type="boolean" checked="true" | |
53 label="Monthly" help="When enabled, no monthly layers are returned. All annual and monthly layers are returned by default."/> | |
54 <param name ="version" type="text" value="0" optional="false" | |
55 label="Layer Version" help="When equal to 0, layers from all versions of datasets are returned (default) else layers are filtered by version number."/> | |
56 </section> | |
57 </when> | |
58 <when value="layers_future"> | |
59 <section name="environement" title= "Environemental Datasets" expanded="true" help="Choose at least one environemental dataset to take layers from"> | |
60 <param name ="terrestrial" type="boolean" checked="true" | |
61 label="Terrestrial Data" help="When enabled (default), then datasets that only have terrestrial data (sea masked) are returned."/> | |
62 <param name ="marine" type="boolean" | |
63 label="Marine Data" help="When enabled, then datasets that only have marine data (land masked) are returned."/> | |
64 <param name ="freshwater" type="boolean" | |
65 label="Freshwater Data" help="When enabled, then datasets that only have freshwater data are returned."/> | |
66 </section> | |
67 <section name="advanced_options" title= "Advanced Option" expanded="false"> | |
68 <param name ="monthly" type="boolean" checked="true" | |
69 label="Monthly" help="When enabled, no monthly layers are returned. All annual and monthly layers are returned by default."/> | |
70 <param name ="version" type="text" value="0" optional="false" | |
71 label="Layer Version" help="When equal to 0, layers from all versions of datasets are returned (default) else layers are filtered by version number."/> | |
72 <param name ="scenario" type="text" value="All" optional="false" | |
73 label="Scenario" help="Climate change scenario, e.g. 'B1', 'A1B', 'A2'. By default All scenarios are listed."/> | |
74 <param name ="year" type="text" value="0" optional="false" | |
75 label="Year" help="Year for which you want the climate change prediction, e.g. 2100,2200. When 0 all years predicted are listed."/> | |
76 </section> | |
77 </when> | |
78 <when value="layers_paleo"> | |
79 <section name="environement" title= "Environemental Datasets" expanded="true" help="Choose at least one environemental dataset to take layers from"> | |
80 <param name ="terrestrial" type="boolean" checked="true" | |
81 label="Terrestrial Data" help="When enabled (default), then datasets that only have terrestrial data (sea masked) are returned."/> | |
82 <param name ="marine" type="boolean" | |
83 label="Marine Data" help="When enabled, then datasets that only have marine data (land masked) are returned."/> | |
84 <param name ="freshwater" type="boolean" | |
85 label="Freshwater Data" help="When enabled, then datasets that only have freshwater data are returned."/> | |
86 </section> | |
87 <section name="advanced_options" title= "Advanced Option" expanded="false"> | |
88 <param name ="monthly" type="boolean" checked="true" | |
89 label="Monthly" help="When enabled, no monthly layers are returned. All annual and monthly layers are returned by default."/> | |
90 <param name ="version" type="text" value="0" optional="false" | |
91 label="Layer Version" help="When equal to 0, layers from all versions of datasets are returned (default) else layers are filtered by version number."/> | |
92 <param name ="model_name" type="text" value="All" optional="false" | |
93 label="Model Name" help="Paleo climate model name, see the model_name column in the result. By default all models are listed."/> | |
94 <param name ="epoch" type="text" value="All" optional="false" | |
95 label="Epoch" help="Epoch for which you want the paleo layer, e.g. 'mid-Holocene', 'Last Glacial Maximum'. By default all epochs are listed."/> | |
96 <param name ="years_ago" type="text" value="0" optional="false" | |
97 label="Years Ago" help="Years for which you want the paleo layer, e.g. 6000, 21000.When 0 all years are listed."/> | |
98 </section> | |
99 </when> | |
100 </conditional> | |
101 </repeat> | |
102 </inputs> | |
103 <outputs> | |
104 <collection name="datasets_output" type="list" | |
105 label="Datasets list"> | |
106 <discover_datasets pattern="__name_and_ext__" /> | |
107 </collection> | |
108 </outputs> | |
109 <tests> | |
110 <test> | |
111 <repeat name="list_layers"> | |
112 <conditional name="choose_layer"> | |
113 <param name="input_layer" value="layers_paleo"/> | |
114 <section name="environement"> | |
115 <param name="terrestrial" value="false"/> | |
116 <param name="marine" value="true"/> | |
117 <param name="freshwater" value="false"/> | |
118 </section> | |
119 <section name="advanced_options"> | |
120 <param name="monthly" value="true"/> | |
121 <param name="version" value="0"/> | |
122 <param name="model_name" value="All"/> | |
123 <param name="epoch" value="All"/> | |
124 <param name="years_ago" value="0"/> | |
125 </section> | |
126 </conditional> | |
127 </repeat> | |
128 <repeat name="list_layers"> | |
129 <conditional name="choose_layer"> | |
130 <param name="input_layer" value="layers_future"/> | |
131 <section name="environement"> | |
132 <param name="terrestrial" value="true"/> | |
133 <param name="marine" value="false"/> | |
134 <param name="freshwater" value="false"/> | |
135 </section> | |
136 <section name="advanced_options"> | |
137 <param name="monthly" value="true"/> | |
138 <param name="version" value="0"/> | |
139 <param name="scenario" value="All"/> | |
140 <param name="year" value="0"/> | |
141 </section> | |
142 </conditional> | |
143 </repeat> | |
144 <repeat name="list_layers"> | |
145 <conditional name="choose_layer"> | |
146 <param name="input_layer" value="layers_current"/> | |
147 <section name="environement"> | |
148 <param name="terrestrial" value="false"/> | |
149 <param name="marine" value="false"/> | |
150 <param name="freshwater" value="true"/> | |
151 </section> | |
152 <section name="advanced_options"> | |
153 <param name="monthly" value="true"/> | |
154 <param name="version" value="0"/> | |
155 </section> | |
156 </conditional> | |
157 </repeat> | |
158 <output_collection name="datasets_output" type="list" count="3"> | |
159 <element name="1_data_paleo" file="1_data_paleo.tabular" ftype="tabular"/> | |
160 <element name="2_data_future" file="2_data_future.tabular" ftype="tabular"/> | |
161 <element name="3_data_current" file="3_data_current.tabular" ftype="tabular"/> | |
162 </output_collection> | |
163 </test> | |
164 </tests> | |
165 <help><![CDATA[ | |
166 | |
167 .. class:: infomark | |
168 | |
169 **What it does** | |
170 | |
171 This tool helps you get one or multiple list of environemental layers from multiple sources, including : | |
172 WorldClim <https://www.worldclim.org/> | |
173 ENVIREM <https://envirem.github.io/> | |
174 Bio-ORACLE <https://bio-oracle.org/> | |
175 and MARSPEC <http://www.marspec.org/> | |
176 | |
177 ____ | |
178 | |
179 | |
180 .. class:: infomark | |
181 | |
182 **Output** | |
183 | |
184 Eatch "New layer list" request will produce a tabular file, all files will be available in a collection | |
185 | |
186 .. class:: warning | |
187 | |
188 **If no Environement are selected, or if the option specified does not exist, the tool will produce an empty file.** | |
189 | |
190 | |
191 ]]></help> | |
192 <citations> | |
193 <citation type="bibtex">@Manual{, | |
194 title = {sdmpredictors: Species Distribution Modelling Predictor Datasets}, | |
195 author = {Samuel Bosch and Salvador Fernandez}, | |
196 year = {2023}, | |
197 note = {R package version 0.2.15}, | |
198 url = {http://lifewatch.github.io/sdmpredictors/}, | |
199 } | |
200 </citation> | |
201 </citations> | |
202 </tool> |