Mercurial > repos > ecology > map_shp

annotate Map_shp.xml @ 0:ce9979488ebb draft default tip

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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
author ecology
date Sat, 25 Nov 2023 15:18:33 +0000
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ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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1 <tool id="Map_shp" name="Make a map with a shapefile" version="0.1.0+galaxy0">
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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2 <requirements>
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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3 <requirement type="package" version="4.3.2">r-base</requirement>
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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4 <requirement type="package" version="3.4.4">r-ggplot2</requirement>
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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5 <requirement type="package" version="1.0_14">r-sf</requirement>
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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6 <requirement type="package" version="1.1.9">r-ggspatial</requirement>
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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7 <requirement type="package" version="1.1.3">r-dplyr</requirement>
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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8 <requirement type="package" version="1.1_3">r-rcolorbrewer</requirement>
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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9 </requirements>
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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10 <command detect_errors="exit_code"><![CDATA[
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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11 Rscript
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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12 "$__tool_directory__/Map_shp.R"
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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13 #if $input1.is_of_type("shp")
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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14 ${os.path.join( $input1.extra_files_path, "shapefile.shp" )}
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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15 #else
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16 "$input1"
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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17 #end if
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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18 "$input2"
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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19 "$input3"
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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20 "$input4"
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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21 "$input5"
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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22 "$output"
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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23
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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24 ]]></command>
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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25 <inputs>
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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26 <param name="input1" type="data" format="shp" label="Shapefile"/>
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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27 <param name="input2" type="data" format="tabular" label="Data to represent"/>
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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28 <param name="input3" type="text" label="What is the title of your map ?">
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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29 <sanitizer invalid_char="">
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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30 <valid initial="string.printable">
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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31 <add value="é"/>
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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32 <add value="è"/>
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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33 </valid>
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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34 </sanitizer>
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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35 </param>
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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36 <param name="input4" type="text" label="What is the legend of your map ?">
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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37 <sanitizer invalid_char="">
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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38 <valid initial="string.printable">
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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39 <add value="é"/>
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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40 <add value="è"/>
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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41 </valid>
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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42 </sanitizer>
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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43 </param>
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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44 <param name="input5" type="boolean" label="Display the geographical coordinates ?"/>
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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45 </inputs>
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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46 <outputs>
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47 <data name="output" from_work_dir="map.pdf" format="pdf" label="map.pdf"/>
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48 </outputs>
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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49 <tests>
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50 <test>
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51 <param name="input1" value="GRECO/GRECO_l93.html" ftype="shp">
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52 <composite_data value="GRECO/GRECO_l93.shp"/>
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53 <composite_data value="GRECO/GRECO_l93.shx"/>
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54 <composite_data value="GRECO/GRECO_l93.dbf"/>
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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55 <composite_data value="GRECO/GRECO_l93.prj"/>
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56 </param>
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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57 <param name='input2' value="evolution_rate.tsv"/>
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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58 <param name='input3' value="Taux d'évolution du volume des bois favorables à la biodiversité par GRECO"/>
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59 <param name='input4' value="Taux d'évolution (%) \nentre les périodes \n2008-2012 et 2013-2017"/>
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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60 <param name='input5' value="true"/>
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61 <output name='output' value="map.pdf"/>
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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62 </test>
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63 </tests>
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64 <help><![CDATA[
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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65 ==================
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66 **What it does ?**
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67 ==================
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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68
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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69 This tool allows to build a map from a shapefile and color the areas according to a percentage (case study dead wood evolution rate).
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70
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71 ]]></help>
ce9979488ebb planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow commit 3f11e193fd9ba5bf0c706cd5d65d6398166776cb
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72 </tool>