Mercurial > repos > ecology > sdmpredictors_list_layers

comparison sdmpredictors_list_layers.xml @ 0:f20914d71c9d draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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
comparison
equal deleted inserted replaced
-1:000000000000 0:f20914d71c9d
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>