Mercurial > repos > ecology > sdmpredictors_list_layers

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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
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f20914d71c9d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
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1 <tool id="sdmpredictors_list_layers" name="SdmPredictors List Layers" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
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2 <description>from environmental predictors for species distribution modeling</description>
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3 <macros>
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4 <token name="@TOOL_VERSION@">0.2.15</token>
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5 <token name="@VERSION_SUFFIX@">0</token>
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6 </macros>
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7 <requirements>
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8 <requirement type="package" version="4.3.2">r-base</requirement>
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9 <requirement type="package" version="@TOOL_VERSION@">r-sdmpredictors</requirement>
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10 <requirement type="package" version="0.2_19">r-codetools</requirement>
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11 </requirements>
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12 <command detect_errors="exit_code"><![CDATA[
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13
f20914d71c9d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
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14 Rscript
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15 '$__tool_directory__/sdmpredictors_list_layers.R'
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16 #for $i, $s in enumerate($list_layers)
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17 ${s.choose_layer.input_layer}
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18 ${s.choose_layer.environement.terrestrial}
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19 ${s.choose_layer.environement.marine}
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20 ${s.choose_layer.environement.freshwater}
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21 ${s.choose_layer.advanced_options.monthly}
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22 ${s.choose_layer.advanced_options.version}
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23 #if str($s.choose_layer.input_layer) == 'layers_future'
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24 ${s.choose_layer.advanced_options.scenario}
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25 ${s.choose_layer.advanced_options.year}
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26 #elif str($s.choose_layer.input_layer) == 'layers_paleo'
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27 ${s.choose_layer.advanced_options.model_name}
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28 ${s.choose_layer.advanced_options.epoch}
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29 ${s.choose_layer.advanced_options.years_ago}
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30 #end if
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31 #end for
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32
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33 ]]></command>
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34 <inputs>
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35 <repeat name="list_layers" title="New layer list">
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36 <conditional name="choose_layer">
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37 <param name="input_layer" type="select" label="Choose Layer Timeframe">
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38 <option value="layers_current" selected="true">Current Layer</option>
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39 <option value="layers_future">Future Layer</option>
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40 <option value="layers_paleo">Paleo Layer</option>
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41 </param>
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42 <when value="layers_current">
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43 <section name="environement" title= "Environemental Datasets" expanded="true" help="Choose at least one environemental dataset to take layers from">
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44 <param name ="terrestrial" type="boolean" checked="true"
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45 label="Terrestrial Data" help="When enabled (default), then datasets that only have terrestrial data (sea masked) are returned."/>
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46 <param name ="marine" type="boolean"
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47 label="Marine Data" help="When enabled, then datasets that only have marine data (land masked) are returned."/>
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48 <param name ="freshwater" type="boolean"
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49 label="Freshwater Data" help="When enabled, then datasets that only have freshwater data are returned."/>
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50 </section>
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51 <section name="advanced_options" title= "Advanced Option" expanded="false">
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52 <param name ="monthly" type="boolean" checked="true"
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53 label="Monthly" help="When enabled, no monthly layers are returned. All annual and monthly layers are returned by default."/>
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54 <param name ="version" type="text" value="0" optional="false"
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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."/>
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56 </section>
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57 </when>
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58 <when value="layers_future">
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59 <section name="environement" title= "Environemental Datasets" expanded="true" help="Choose at least one environemental dataset to take layers from">
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60 <param name ="terrestrial" type="boolean" checked="true"
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61 label="Terrestrial Data" help="When enabled (default), then datasets that only have terrestrial data (sea masked) are returned."/>
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62 <param name ="marine" type="boolean"
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63 label="Marine Data" help="When enabled, then datasets that only have marine data (land masked) are returned."/>
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64 <param name ="freshwater" type="boolean"
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65 label="Freshwater Data" help="When enabled, then datasets that only have freshwater data are returned."/>
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66 </section>
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67 <section name="advanced_options" title= "Advanced Option" expanded="false">
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68 <param name ="monthly" type="boolean" checked="true"
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69 label="Monthly" help="When enabled, no monthly layers are returned. All annual and monthly layers are returned by default."/>
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70 <param name ="version" type="text" value="0" optional="false"
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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."/>
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72 <param name ="scenario" type="text" value="All" optional="false"
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73 label="Scenario" help="Climate change scenario, e.g. 'B1', 'A1B', 'A2'. By default All scenarios are listed."/>
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74 <param name ="year" type="text" value="0" optional="false"
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75 label="Year" help="Year for which you want the climate change prediction, e.g. 2100,2200. When 0 all years predicted are listed."/>
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76 </section>
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77 </when>
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78 <when value="layers_paleo">
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79 <section name="environement" title= "Environemental Datasets" expanded="true" help="Choose at least one environemental dataset to take layers from">
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80 <param name ="terrestrial" type="boolean" checked="true"
f20914d71c9d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
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81 label="Terrestrial Data" help="When enabled (default), then datasets that only have terrestrial data (sea masked) are returned."/>
f20914d71c9d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
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82 <param name ="marine" type="boolean"
f20914d71c9d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
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83 label="Marine Data" help="When enabled, then datasets that only have marine data (land masked) are returned."/>
f20914d71c9d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
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84 <param name ="freshwater" type="boolean"
f20914d71c9d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
ecology
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85 label="Freshwater Data" help="When enabled, then datasets that only have freshwater data are returned."/>
f20914d71c9d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
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86 </section>
f20914d71c9d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
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87 <section name="advanced_options" title= "Advanced Option" expanded="false">
f20914d71c9d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
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88 <param name ="monthly" type="boolean" checked="true"
f20914d71c9d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
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89 label="Monthly" help="When enabled, no monthly layers are returned. All annual and monthly layers are returned by default."/>
f20914d71c9d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
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90 <param name ="version" type="text" value="0" optional="false"
f20914d71c9d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
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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."/>
f20914d71c9d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
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92 <param name ="model_name" type="text" value="All" optional="false"
f20914d71c9d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
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93 label="Model Name" help="Paleo climate model name, see the model_name column in the result. By default all models are listed."/>
f20914d71c9d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
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94 <param name ="epoch" type="text" value="All" optional="false"
f20914d71c9d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
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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."/>
f20914d71c9d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
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96 <param name ="years_ago" type="text" value="0" optional="false"
f20914d71c9d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
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97 label="Years Ago" help="Years for which you want the paleo layer, e.g. 6000, 21000.When 0 all years are listed."/>
f20914d71c9d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
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98 </section>
f20914d71c9d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
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99 </when>
f20914d71c9d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
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100 </conditional>
f20914d71c9d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
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101 </repeat>
f20914d71c9d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
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102 </inputs>
f20914d71c9d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
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103 <outputs>
f20914d71c9d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
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104 <collection name="datasets_output" type="list"
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105 label="Datasets list">
f20914d71c9d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
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106 <discover_datasets pattern="__name_and_ext__" />
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107 </collection>
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108 </outputs>
f20914d71c9d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
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109 <tests>
f20914d71c9d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
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110 <test>
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111 <repeat name="list_layers">
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112 <conditional name="choose_layer">
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113 <param name="input_layer" value="layers_paleo"/>
f20914d71c9d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
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114 <section name="environement">
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115 <param name="terrestrial" value="false"/>
f20914d71c9d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
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116 <param name="marine" value="true"/>
f20914d71c9d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
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117 <param name="freshwater" value="false"/>
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118 </section>
f20914d71c9d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
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119 <section name="advanced_options">
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120 <param name="monthly" value="true"/>
f20914d71c9d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
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121 <param name="version" value="0"/>
f20914d71c9d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
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122 <param name="model_name" value="All"/>
f20914d71c9d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
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123 <param name="epoch" value="All"/>
f20914d71c9d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
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124 <param name="years_ago" value="0"/>
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125 </section>
f20914d71c9d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
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126 </conditional>
f20914d71c9d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
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127 </repeat>
f20914d71c9d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
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128 <repeat name="list_layers">
f20914d71c9d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
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129 <conditional name="choose_layer">
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130 <param name="input_layer" value="layers_future"/>
f20914d71c9d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
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131 <section name="environement">
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132 <param name="terrestrial" value="true"/>
f20914d71c9d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
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133 <param name="marine" value="false"/>
f20914d71c9d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
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134 <param name="freshwater" value="false"/>
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135 </section>
f20914d71c9d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
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136 <section name="advanced_options">
f20914d71c9d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
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137 <param name="monthly" value="true"/>
f20914d71c9d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
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138 <param name="version" value="0"/>
f20914d71c9d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
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139 <param name="scenario" value="All"/>
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140 <param name="year" value="0"/>
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141 </section>
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142 </conditional>
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143 </repeat>
f20914d71c9d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
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144 <repeat name="list_layers">
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145 <conditional name="choose_layer">
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146 <param name="input_layer" value="layers_current"/>
f20914d71c9d planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
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147 <section name="environement">
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148 <param name="terrestrial" value="false"/>
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149 <param name="marine" value="false"/>
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150 <param name="freshwater" value="true"/>
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151 </section>
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152 <section name="advanced_options">
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153 <param name="monthly" value="true"/>
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154 <param name="version" value="0"/>
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155 </section>
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156 </conditional>
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157 </repeat>
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158 <output_collection name="datasets_output" type="list" count="3">
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159 <element name="1_data_paleo" file="1_data_paleo.tabular" ftype="tabular"/>
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160 <element name="2_data_future" file="2_data_future.tabular" ftype="tabular"/>
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161 <element name="3_data_current" file="3_data_current.tabular" ftype="tabular"/>
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162 </output_collection>
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163 </test>
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164 </tests>
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165 <help><![CDATA[
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166
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167 .. class:: infomark
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168
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169 **What it does**
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170
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171 This tool helps you get one or multiple list of environemental layers from multiple sources, including :
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172 WorldClim <https://www.worldclim.org/>
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173 ENVIREM <https://envirem.github.io/>
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174 Bio-ORACLE <https://bio-oracle.org/>
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175 and MARSPEC <http://www.marspec.org/>
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176
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177 ____
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178
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179
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180 .. class:: infomark
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181
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182 **Output**
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183
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184 Eatch "New layer list" request will produce a tabular file, all files will be available in a collection
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185
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186 .. class:: warning
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187
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188 **If no Environement are selected, or if the option specified does not exist, the tool will produce an empty file.**
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189
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190
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191 ]]></help>
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192 <citations>
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193 <citation type="bibtex">@Manual{,
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194 title = {sdmpredictors: Species Distribution Modelling Predictor Datasets},
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195 author = {Samuel Bosch and Salvador Fernandez},
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196 year = {2023},
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197 note = {R package version 0.2.15},
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198 url = {http://lifewatch.github.io/sdmpredictors/},
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199 }
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200 </citation>
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201 </citations>
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202 </tool>