Mercurial > repos > ecology > srs_process_data
annotate comparison_div.xml @ 0:cf69ad260611 draft default tip
planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
author | ecology |
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date | Mon, 09 Jan 2023 13:36:02 +0000 |
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rev | line source |
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0
cf69ad260611
planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
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changeset
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1 <tool id="srs_process_data" name="Compare diversity indicators" version="@VERSION@" profile="20.01"> |
cf69ad260611
planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
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2 <description>with remote sensing data</description> |
cf69ad260611
planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
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changeset
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3 <macros> |
cf69ad260611
planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff
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4 <import>macro.xml</import> |
cf69ad260611
planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff
changeset
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5 </macros> |
cf69ad260611
planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff
changeset
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6 <expand macro="SRS_requirements"/> |
cf69ad260611
planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
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7 <command detect_errors="exit_code"><![CDATA[ |
cf69ad260611
planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
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changeset
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8 #import re |
cf69ad260611
planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff
changeset
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9 #if $method.type == 'envi_bil': |
cf69ad260611
planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff
changeset
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10 #set input_raster = $method.input_raster |
cf69ad260611
planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff
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11 #set input_raster_identifier = re.sub('[^\s\w\-]', '_', str($input_raster.element_identifier)) |
cf69ad260611
planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff
changeset
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12 #set input_header = $method.input_header |
cf69ad260611
planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff
changeset
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13 #set input_header_identifier = re.sub('[^\s\w\-]+[^.hdr]', '_', str($input_header.element_identifier)) |
cf69ad260611
planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
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14 cp '${input_raster}' '${input_raster_identifier}' && |
cf69ad260611
planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff
changeset
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15 cp '${input_header}' '${input_header_identifier}' && |
cf69ad260611
planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff
changeset
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16 #end if |
cf69ad260611
planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff
changeset
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17 Rscript |
cf69ad260611
planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff
changeset
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18 '$__tool_directory__/comparison_div.r' |
cf69ad260611
planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff
changeset
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19 #if $method.type == 'envi_bil': |
cf69ad260611
planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff
changeset
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20 '$input_raster_identifier' |
cf69ad260611
planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff
changeset
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21 '$input_header_identifier' |
cf69ad260611
planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff
changeset
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22 '' |
cf69ad260611
planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff
changeset
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23 #else: |
cf69ad260611
planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff
changeset
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24 '' |
cf69ad260611
planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff
changeset
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25 '' |
cf69ad260611
planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff
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26 '$method.input' |
cf69ad260611
planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff
changeset
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27 #end if |
cf69ad260611
planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff
changeset
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28 '$input_plot' |
cf69ad260611
planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff
changeset
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29 '$choice' |
cf69ad260611
planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff
changeset
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30 '$__tool_directory__/functions.r' |
cf69ad260611
planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff
changeset
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31 '$typepca' |
cf69ad260611
planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff
changeset
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32 '$output_div' |
cf69ad260611
planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff
changeset
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33 '$output_beta' |
cf69ad260611
planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff
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34 '$plots' |
cf69ad260611
planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff
changeset
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35 ]]> |
cf69ad260611
planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff
changeset
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36 </command> |
cf69ad260611
planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff
changeset
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37 <inputs> |
cf69ad260611
planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff
changeset
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38 <conditional name="method"> |
cf69ad260611
planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff
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39 <param name="type" type="select" label="In which format are your data ?"> |
cf69ad260611
planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff
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40 <option value="zipper">The data you are using are in a zip folder Reflectance</option> |
cf69ad260611
planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff
changeset
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41 <option value="envi_bil">Your already have the files in ENVI BIL format</option> |
cf69ad260611
planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff
changeset
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42 </param> |
cf69ad260611
planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff
changeset
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43 <when value="zipper"> |
cf69ad260611
planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff
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44 <param name="input" type="data" format="zip" multiple="true" label="Input data"/> |
cf69ad260611
planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff
changeset
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45 </when> |
cf69ad260611
planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff
changeset
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46 <when value="envi_bil"> |
cf69ad260611
planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff
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47 <param name="input_raster" type="data" format="bil" label="Input raster" help="It can be the raw data in bil or the PCA raster layer in bil"/> |
cf69ad260611
planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff
changeset
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48 <param name="input_header" type="data" format="hdr" label="Input header"/> |
cf69ad260611
planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff
changeset
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49 </when> |
cf69ad260611
planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff
changeset
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50 </conditional> |
cf69ad260611
planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff
changeset
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51 <param name="input_plot" type="data" format="data" label="Plots folder zip"/> |
cf69ad260611
planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff
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52 <param name="choice" type="select" label="Do you want to compute beta diversity (needs mutliple locations) ?" display="radio"> |
cf69ad260611
planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
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53 <option value="Y">Yes</option> |
cf69ad260611
planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff
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54 <option value="N">No</option> |
cf69ad260611
planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
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55 </param> |
cf69ad260611
planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff
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56 <param name="typepca" type="select" label="Do you want to do a PCA or a SPCA ?" display="radio" help="If you choose PCA there is no rescaling of the data as oppposed as if you choose SPCA"> |
cf69ad260611
planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff
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57 <option value="SPCA">SPCA</option> |
cf69ad260611
planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
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58 <option value="PCA">PCA</option> |
cf69ad260611
planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff
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59 </param> |
cf69ad260611
planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff
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60 </inputs> |
cf69ad260611
planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff
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61 <outputs> |
cf69ad260611
planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
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62 <data name="output_div" from_work_dir="Diversity.tabular" format="tabular" label="Global diversity"> |
cf69ad260611
planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff
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63 </data> |
cf69ad260611
planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff
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64 <data name="output_beta" from_work_dir="BrayCurtis.tabular" format="tabular" label="Bray Curtis"> |
cf69ad260611
planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
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65 <filter>choice == 'Y'</filter> |
cf69ad260611
planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff
changeset
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66 </data> |
cf69ad260611
planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
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67 <collection type="list" name="plots" label="Comparison plot"> |
cf69ad260611
planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
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68 <discover_datasets pattern="(?P<designation>.+)\.png" visible="false" format="png"/> |
cf69ad260611
planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff
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69 <filter>choice =='Y'</filter> |
cf69ad260611
planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff
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70 </collection> |
cf69ad260611
planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff
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71 </outputs> |
cf69ad260611
planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff
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72 <tests> |
cf69ad260611
planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
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73 <test> |
cf69ad260611
planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
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74 <param name="type" value="envi_bil"/> |
cf69ad260611
planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
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75 <param name="input_raster" value="S2A_Subset"/> |
cf69ad260611
planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
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76 <param name="input_header" value="S2A_Subset.hdr"/> |
cf69ad260611
planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
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77 <param name="input_plot" value="S2A_T33NUD_Plots.zip"/> |
cf69ad260611
planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff
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78 <param name="choice" value="Y"/> |
cf69ad260611
planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff
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79 <output name="output_div"> |
cf69ad260611
planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
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80 <assert_contents> |
cf69ad260611
planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
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81 <has_n_lines n="25"/> |
cf69ad260611
planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff
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82 </assert_contents> |
cf69ad260611
planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff
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83 </output> |
cf69ad260611
planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff
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84 <output name="output_beta"> |
cf69ad260611
planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff
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85 <assert_contents> |
cf69ad260611
planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
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86 <has_n_lines n="25"/> |
cf69ad260611
planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff
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87 </assert_contents> |
cf69ad260611
planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
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88 </output> |
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89 <output_collection name="plots" type="list" count="1"/> |
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90 </test> |
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91 </tests> |
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92 <help><![CDATA[ |
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93 ======================================================================== |
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94 Process satellite remote sensing data to produce biodiversity indicators |
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95 ======================================================================== |
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96 |
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97 |
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98 **What it does** |
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99 |
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100 Féret and Asner (2014) developed a method for **tropical forest** diversity mapping based on very high spatial resolution airborne imaging spectroscopy. |
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101 |
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102 The goal of this tool using the package biodivMapR is to compute diversity indices over each spatial polygon of a shapefile of plots, if available, in order to compare field inventories with diversity indices estimated from remotely-sensed images. |
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103 |
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104 **Input description** |
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105 |
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106 It expects an image file as input, with a specific data format. ENVI HDR image with BIL interleave required. |
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107 The image is an ENVI raster including : |
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108 |
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109 - A binary file (which has no extension here). |
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110 |
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111 - A header file (with .hdr extension). |
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112 |
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113 The header file is a text file including all necessary metadata which can be read with a text editor. It includes image dimensions, projection, and the name and central wavelength for each spectral band. |
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114 |
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115 In order to get such input we advise to use the tool preprocessing sentinel 2 data. |
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116 |
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117 +--------------+----------+--------------+ |
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118 | BIL | ENVI HDR | Shapefiles | |
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119 +==============+==========+==============+ |
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120 | raster stack | Metadata | plots.zip | |
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121 +--------------+----------+--------------+ |
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122 | ... | ... | ... | |
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123 +--------------+----------+--------------+ |
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124 |
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125 **Output** |
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126 |
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127 - Two tabulars : |
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128 - One matrix for Bray-Curtis indicator |
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129 - One table for the following indicators; Species richness, shannon, fisher, simpson, richness, eveness, divergence |
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130 |
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131 - One comparison png plot in the Pcoa space that summarizes α- and β-diversity in scatterplots and illustrates that the combination of the three components computed with PCoA allows proper differentiation among vegetation types: |
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132 - PCoA#1 allows differentiating medium and high diversity forests from low diversity forest and low vegetation, but does not discriminate medium and high diversity forests. |
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133 - PCoA#2 allows differentiating low diversity forest from medium/high diversity forests and low vegetation |
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134 - PCoA#3 allows differentiating medium diversity forests from high diversity forests and low vegetation. |
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135 |
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136 ]]> </help> |
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137 <expand macro="SRS_BDMRref"/> |
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138 </tool> |