Mercurial > repos > ecology > sdmpredictors_list_layers
annotate 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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f20914d71c9d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
ecology
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1 <tool id="sdmpredictors_list_layers" name="SdmPredictors List Layers" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> |
f20914d71c9d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
ecology
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2 <description>from environmental predictors for species distribution modeling</description> |
f20914d71c9d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
ecology
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3 <macros> |
f20914d71c9d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
ecology
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4 <token name="@TOOL_VERSION@">0.2.15</token> |
f20914d71c9d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
ecology
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5 <token name="@VERSION_SUFFIX@">0</token> |
f20914d71c9d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
ecology
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6 </macros> |
f20914d71c9d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
ecology
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7 <requirements> |
f20914d71c9d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
ecology
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8 <requirement type="package" version="4.3.2">r-base</requirement> |
f20914d71c9d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
ecology
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9 <requirement type="package" version="@TOOL_VERSION@">r-sdmpredictors</requirement> |
f20914d71c9d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
ecology
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10 <requirement type="package" version="0.2_19">r-codetools</requirement> |
f20914d71c9d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
ecology
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11 </requirements> |
f20914d71c9d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
ecology
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12 <command detect_errors="exit_code"><![CDATA[ |
f20914d71c9d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
ecology
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13 |
f20914d71c9d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
ecology
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14 Rscript |
f20914d71c9d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
ecology
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15 '$__tool_directory__/sdmpredictors_list_layers.R' |
f20914d71c9d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
ecology
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16 #for $i, $s in enumerate($list_layers) |
f20914d71c9d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
ecology
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17 ${s.choose_layer.input_layer} |
f20914d71c9d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
ecology
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18 ${s.choose_layer.environement.terrestrial} |
f20914d71c9d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
ecology
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19 ${s.choose_layer.environement.marine} |
f20914d71c9d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
ecology
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20 ${s.choose_layer.environement.freshwater} |
f20914d71c9d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
ecology
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21 ${s.choose_layer.advanced_options.monthly} |
f20914d71c9d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
ecology
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22 ${s.choose_layer.advanced_options.version} |
f20914d71c9d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
ecology
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23 #if str($s.choose_layer.input_layer) == 'layers_future' |
f20914d71c9d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
ecology
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24 ${s.choose_layer.advanced_options.scenario} |
f20914d71c9d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
ecology
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25 ${s.choose_layer.advanced_options.year} |
f20914d71c9d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
ecology
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26 #elif str($s.choose_layer.input_layer) == 'layers_paleo' |
f20914d71c9d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
ecology
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27 ${s.choose_layer.advanced_options.model_name} |
f20914d71c9d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
ecology
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28 ${s.choose_layer.advanced_options.epoch} |
f20914d71c9d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
ecology
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29 ${s.choose_layer.advanced_options.years_ago} |
f20914d71c9d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
ecology
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30 #end if |
f20914d71c9d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
ecology
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31 #end for |
f20914d71c9d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
ecology
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32 |
f20914d71c9d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
ecology
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33 ]]></command> |
f20914d71c9d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
ecology
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34 <inputs> |
f20914d71c9d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
ecology
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35 <repeat name="list_layers" title="New layer list"> |
f20914d71c9d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
ecology
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36 <conditional name="choose_layer"> |
f20914d71c9d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
ecology
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37 <param name="input_layer" type="select" label="Choose Layer Timeframe"> |
f20914d71c9d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
ecology
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38 <option value="layers_current" selected="true">Current Layer</option> |
f20914d71c9d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
ecology
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39 <option value="layers_future">Future Layer</option> |
f20914d71c9d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
ecology
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40 <option value="layers_paleo">Paleo Layer</option> |
f20914d71c9d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
ecology
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41 </param> |
f20914d71c9d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
ecology
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42 <when value="layers_current"> |
f20914d71c9d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
ecology
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43 <section name="environement" title= "Environemental Datasets" expanded="true" help="Choose at least one environemental dataset to take layers from"> |
f20914d71c9d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
ecology
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44 <param name ="terrestrial" type="boolean" checked="true" |
f20914d71c9d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
ecology
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45 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
ecology
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46 <param name ="marine" type="boolean" |
f20914d71c9d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
ecology
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47 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
ecology
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48 <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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49 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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50 </section> |
f20914d71c9d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
ecology
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51 <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
ecology
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52 <param name ="monthly" type="boolean" checked="true" |
f20914d71c9d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
ecology
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53 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
ecology
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54 <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
ecology
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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."/> |
f20914d71c9d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
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56 </section> |
f20914d71c9d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
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57 </when> |
f20914d71c9d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
ecology
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58 <when value="layers_future"> |
f20914d71c9d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
ecology
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59 <section name="environement" title= "Environemental Datasets" expanded="true" help="Choose at least one environemental dataset to take layers from"> |
f20914d71c9d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
ecology
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60 <param name ="terrestrial" type="boolean" checked="true" |
f20914d71c9d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
ecology
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61 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
ecology
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62 <param name ="marine" type="boolean" |
f20914d71c9d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
ecology
parents:
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63 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
ecology
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64 <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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65 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
ecology
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66 </section> |
f20914d71c9d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
ecology
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67 <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
ecology
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68 <param name ="monthly" type="boolean" checked="true" |
f20914d71c9d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
ecology
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69 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
ecology
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70 <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
ecology
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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."/> |
f20914d71c9d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
ecology
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72 <param name ="scenario" type="text" value="All" optional="false" |
f20914d71c9d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
ecology
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73 label="Scenario" help="Climate change scenario, e.g. 'B1', 'A1B', 'A2'. By default All scenarios are listed."/> |
f20914d71c9d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
ecology
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74 <param name ="year" type="text" value="0" optional="false" |
f20914d71c9d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
ecology
parents:
diff
changeset
|
75 label="Year" help="Year for which you want the climate change prediction, e.g. 2100,2200. When 0 all years predicted are listed."/> |
f20914d71c9d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
ecology
parents:
diff
changeset
|
76 </section> |
f20914d71c9d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
ecology
parents:
diff
changeset
|
77 </when> |
f20914d71c9d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
ecology
parents:
diff
changeset
|
78 <when value="layers_paleo"> |
f20914d71c9d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
ecology
parents:
diff
changeset
|
79 <section name="environement" title= "Environemental Datasets" expanded="true" help="Choose at least one environemental dataset to take layers from"> |
f20914d71c9d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
ecology
parents:
diff
changeset
|
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
ecology
parents:
diff
changeset
|
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
ecology
parents:
diff
changeset
|
82 <param name ="marine" type="boolean" |
f20914d71c9d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
ecology
parents:
diff
changeset
|
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
ecology
parents:
diff
changeset
|
84 <param name ="freshwater" type="boolean" |
f20914d71c9d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
ecology
parents:
diff
changeset
|
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
ecology
parents:
diff
changeset
|
86 </section> |
f20914d71c9d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
ecology
parents:
diff
changeset
|
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
ecology
parents:
diff
changeset
|
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
ecology
parents:
diff
changeset
|
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
ecology
parents:
diff
changeset
|
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
ecology
parents:
diff
changeset
|
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
ecology
parents:
diff
changeset
|
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
ecology
parents:
diff
changeset
|
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
ecology
parents:
diff
changeset
|
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
ecology
parents:
diff
changeset
|
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
ecology
parents:
diff
changeset
|
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
ecology
parents:
diff
changeset
|
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
ecology
parents:
diff
changeset
|
98 </section> |
f20914d71c9d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
ecology
parents:
diff
changeset
|
99 </when> |
f20914d71c9d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
ecology
parents:
diff
changeset
|
100 </conditional> |
f20914d71c9d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
ecology
parents:
diff
changeset
|
101 </repeat> |
f20914d71c9d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
ecology
parents:
diff
changeset
|
102 </inputs> |
f20914d71c9d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
ecology
parents:
diff
changeset
|
103 <outputs> |
f20914d71c9d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
ecology
parents:
diff
changeset
|
104 <collection name="datasets_output" type="list" |
f20914d71c9d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
ecology
parents:
diff
changeset
|
105 label="Datasets list"> |
f20914d71c9d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
ecology
parents:
diff
changeset
|
106 <discover_datasets pattern="__name_and_ext__" /> |
f20914d71c9d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
ecology
parents:
diff
changeset
|
107 </collection> |
f20914d71c9d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
ecology
parents:
diff
changeset
|
108 </outputs> |
f20914d71c9d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
ecology
parents:
diff
changeset
|
109 <tests> |
f20914d71c9d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
ecology
parents:
diff
changeset
|
110 <test> |
f20914d71c9d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
ecology
parents:
diff
changeset
|
111 <repeat name="list_layers"> |
f20914d71c9d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
ecology
parents:
diff
changeset
|
112 <conditional name="choose_layer"> |
f20914d71c9d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
ecology
parents:
diff
changeset
|
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
ecology
parents:
diff
changeset
|
114 <section name="environement"> |
f20914d71c9d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
ecology
parents:
diff
changeset
|
115 <param name="terrestrial" value="false"/> |
f20914d71c9d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
ecology
parents:
diff
changeset
|
116 <param name="marine" value="true"/> |
f20914d71c9d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
ecology
parents:
diff
changeset
|
117 <param name="freshwater" value="false"/> |
f20914d71c9d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
ecology
parents:
diff
changeset
|
118 </section> |
f20914d71c9d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
ecology
parents:
diff
changeset
|
119 <section name="advanced_options"> |
f20914d71c9d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
ecology
parents:
diff
changeset
|
120 <param name="monthly" value="true"/> |
f20914d71c9d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
ecology
parents:
diff
changeset
|
121 <param name="version" value="0"/> |
f20914d71c9d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
ecology
parents:
diff
changeset
|
122 <param name="model_name" value="All"/> |
f20914d71c9d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
ecology
parents:
diff
changeset
|
123 <param name="epoch" value="All"/> |
f20914d71c9d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
ecology
parents:
diff
changeset
|
124 <param name="years_ago" value="0"/> |
f20914d71c9d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
ecology
parents:
diff
changeset
|
125 </section> |
f20914d71c9d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
ecology
parents:
diff
changeset
|
126 </conditional> |
f20914d71c9d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
ecology
parents:
diff
changeset
|
127 </repeat> |
f20914d71c9d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
ecology
parents:
diff
changeset
|
128 <repeat name="list_layers"> |
f20914d71c9d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
ecology
parents:
diff
changeset
|
129 <conditional name="choose_layer"> |
f20914d71c9d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
ecology
parents:
diff
changeset
|
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
ecology
parents:
diff
changeset
|
131 <section name="environement"> |
f20914d71c9d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
ecology
parents:
diff
changeset
|
132 <param name="terrestrial" value="true"/> |
f20914d71c9d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
ecology
parents:
diff
changeset
|
133 <param name="marine" value="false"/> |
f20914d71c9d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
ecology
parents:
diff
changeset
|
134 <param name="freshwater" value="false"/> |
f20914d71c9d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
ecology
parents:
diff
changeset
|
135 </section> |
f20914d71c9d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
ecology
parents:
diff
changeset
|
136 <section name="advanced_options"> |
f20914d71c9d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
ecology
parents:
diff
changeset
|
137 <param name="monthly" value="true"/> |
f20914d71c9d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
ecology
parents:
diff
changeset
|
138 <param name="version" value="0"/> |
f20914d71c9d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
ecology
parents:
diff
changeset
|
139 <param name="scenario" value="All"/> |
f20914d71c9d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
ecology
parents:
diff
changeset
|
140 <param name="year" value="0"/> |
f20914d71c9d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
ecology
parents:
diff
changeset
|
141 </section> |
f20914d71c9d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
ecology
parents:
diff
changeset
|
142 </conditional> |
f20914d71c9d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
ecology
parents:
diff
changeset
|
143 </repeat> |
f20914d71c9d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
ecology
parents:
diff
changeset
|
144 <repeat name="list_layers"> |
f20914d71c9d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
ecology
parents:
diff
changeset
|
145 <conditional name="choose_layer"> |
f20914d71c9d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
ecology
parents:
diff
changeset
|
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
ecology
parents:
diff
changeset
|
147 <section name="environement"> |
f20914d71c9d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
ecology
parents:
diff
changeset
|
148 <param name="terrestrial" value="false"/> |
f20914d71c9d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
ecology
parents:
diff
changeset
|
149 <param name="marine" value="false"/> |
f20914d71c9d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
ecology
parents:
diff
changeset
|
150 <param name="freshwater" value="true"/> |
f20914d71c9d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
ecology
parents:
diff
changeset
|
151 </section> |
f20914d71c9d
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors commit a4635c2349750b45d47b50ff1cecc8c5fdeb58e0
ecology
parents:
diff
changeset
|
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> |