Mercurial > repos > ecology > obis_data
annotate robis.xml @ 0:1fcd81d65467 draft default tip
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit b377ff767e3051f301c2f02cfe3e1a17b285ede4
author | ecology |
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date | Thu, 18 Jan 2024 09:33:52 +0000 |
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rev | line source |
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0
1fcd81d65467
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit b377ff767e3051f301c2f02cfe3e1a17b285ede4
ecology
parents:
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changeset
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1 <tool id="obis_data" name="OBIS occurences" version="@VERSION@" profile="20.01"> |
1fcd81d65467
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit b377ff767e3051f301c2f02cfe3e1a17b285ede4
ecology
parents:
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2 <description>retrieve data</description> |
1fcd81d65467
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit b377ff767e3051f301c2f02cfe3e1a17b285ede4
ecology
parents:
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3 <macros> |
1fcd81d65467
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit b377ff767e3051f301c2f02cfe3e1a17b285ede4
ecology
parents:
diff
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4 <import>macro.xml</import> |
1fcd81d65467
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit b377ff767e3051f301c2f02cfe3e1a17b285ede4
ecology
parents:
diff
changeset
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5 </macros> |
1fcd81d65467
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit b377ff767e3051f301c2f02cfe3e1a17b285ede4
ecology
parents:
diff
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6 <expand macro="topic"/> |
1fcd81d65467
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit b377ff767e3051f301c2f02cfe3e1a17b285ede4
ecology
parents:
diff
changeset
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7 <expand macro="requirements"> |
1fcd81d65467
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit b377ff767e3051f301c2f02cfe3e1a17b285ede4
ecology
parents:
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8 <requirement type="package" version="2.11.3">r-robis</requirement> |
1fcd81d65467
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit b377ff767e3051f301c2f02cfe3e1a17b285ede4
ecology
parents:
diff
changeset
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9 </expand> |
1fcd81d65467
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit b377ff767e3051f301c2f02cfe3e1a17b285ede4
ecology
parents:
diff
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10 <required_files> |
1fcd81d65467
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit b377ff767e3051f301c2f02cfe3e1a17b285ede4
ecology
parents:
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11 <include type="literal" path="robis.r"/> |
1fcd81d65467
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit b377ff767e3051f301c2f02cfe3e1a17b285ede4
ecology
parents:
diff
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12 </required_files> |
1fcd81d65467
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit b377ff767e3051f301c2f02cfe3e1a17b285ede4
ecology
parents:
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13 <command detect_errors="exit_code"><![CDATA[ |
1fcd81d65467
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit b377ff767e3051f301c2f02cfe3e1a17b285ede4
ecology
parents:
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14 Rscript |
1fcd81d65467
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit b377ff767e3051f301c2f02cfe3e1a17b285ede4
ecology
parents:
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15 '$__tool_directory__/robis.r' |
1fcd81d65467
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit b377ff767e3051f301c2f02cfe3e1a17b285ede4
ecology
parents:
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16 '$species' |
1fcd81d65467
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit b377ff767e3051f301c2f02cfe3e1a17b285ede4
ecology
parents:
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17 '$taxon' |
1fcd81d65467
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit b377ff767e3051f301c2f02cfe3e1a17b285ede4
ecology
parents:
diff
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18 '$lat_min' |
1fcd81d65467
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit b377ff767e3051f301c2f02cfe3e1a17b285ede4
ecology
parents:
diff
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19 '$lat_max' |
1fcd81d65467
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit b377ff767e3051f301c2f02cfe3e1a17b285ede4
ecology
parents:
diff
changeset
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20 '$long_min' |
1fcd81d65467
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit b377ff767e3051f301c2f02cfe3e1a17b285ede4
ecology
parents:
diff
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21 '$long_max' |
1fcd81d65467
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit b377ff767e3051f301c2f02cfe3e1a17b285ede4
ecology
parents:
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22 '$output' |
1fcd81d65467
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit b377ff767e3051f301c2f02cfe3e1a17b285ede4
ecology
parents:
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23 ]]> |
1fcd81d65467
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit b377ff767e3051f301c2f02cfe3e1a17b285ede4
ecology
parents:
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24 </command> |
1fcd81d65467
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit b377ff767e3051f301c2f02cfe3e1a17b285ede4
ecology
parents:
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25 <inputs> |
1fcd81d65467
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit b377ff767e3051f301c2f02cfe3e1a17b285ede4
ecology
parents:
diff
changeset
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26 <param name="species" type="text" label="Scientific name of the species" help="Genus species format, eg : Scomber scombrus"> |
1fcd81d65467
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit b377ff767e3051f301c2f02cfe3e1a17b285ede4
ecology
parents:
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27 <validator type="regex">^[A-Za-z ]*$</validator> |
1fcd81d65467
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit b377ff767e3051f301c2f02cfe3e1a17b285ede4
ecology
parents:
diff
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28 </param> |
1fcd81d65467
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit b377ff767e3051f301c2f02cfe3e1a17b285ede4
ecology
parents:
diff
changeset
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29 <param name="taxon" type="text" label="Taxon ID"> |
1fcd81d65467
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit b377ff767e3051f301c2f02cfe3e1a17b285ede4
ecology
parents:
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30 <validator type="regex">^[0-9]*$</validator> |
1fcd81d65467
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit b377ff767e3051f301c2f02cfe3e1a17b285ede4
ecology
parents:
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31 </param> |
1fcd81d65467
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit b377ff767e3051f301c2f02cfe3e1a17b285ede4
ecology
parents:
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changeset
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32 <param name="lat_min" type="float" min="-90" max="90" value="0" label="Input latitude min (+north/-south):" optional="true"/> |
1fcd81d65467
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit b377ff767e3051f301c2f02cfe3e1a17b285ede4
ecology
parents:
diff
changeset
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33 <param name="lat_max" type="float" min="-90" max="90" value="0" label="Input latitude max (+north/-south):" optional="true"/> |
1fcd81d65467
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit b377ff767e3051f301c2f02cfe3e1a17b285ede4
ecology
parents:
diff
changeset
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34 <param name="long_min" type="float" min="-90" max="90" value="0" label="Input longitude min (+east/-west):" optional="true"/> |
1fcd81d65467
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit b377ff767e3051f301c2f02cfe3e1a17b285ede4
ecology
parents:
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35 <param name="long_max" type="float" min="-90" max="90" value="0" label="Input longitude max (+east/-west):" optional="true"/> |
1fcd81d65467
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit b377ff767e3051f301c2f02cfe3e1a17b285ede4
ecology
parents:
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36 </inputs> |
1fcd81d65467
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit b377ff767e3051f301c2f02cfe3e1a17b285ede4
ecology
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37 <outputs> |
1fcd81d65467
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit b377ff767e3051f301c2f02cfe3e1a17b285ede4
ecology
parents:
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38 <data name="output" format="tabular" from_work_dir="output.tab" label="Species occurences"/> |
1fcd81d65467
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit b377ff767e3051f301c2f02cfe3e1a17b285ede4
ecology
parents:
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39 </outputs> |
1fcd81d65467
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit b377ff767e3051f301c2f02cfe3e1a17b285ede4
ecology
parents:
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40 <tests> |
1fcd81d65467
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit b377ff767e3051f301c2f02cfe3e1a17b285ede4
ecology
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41 <test expect_num_outputs="1"> |
1fcd81d65467
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit b377ff767e3051f301c2f02cfe3e1a17b285ede4
ecology
parents:
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42 <param name="species" value="Scomber scombrus"/> |
1fcd81d65467
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit b377ff767e3051f301c2f02cfe3e1a17b285ede4
ecology
parents:
diff
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43 <output name="output"> |
1fcd81d65467
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit b377ff767e3051f301c2f02cfe3e1a17b285ede4
ecology
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44 <assert_contents> |
1fcd81d65467
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit b377ff767e3051f301c2f02cfe3e1a17b285ede4
ecology
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45 <has_text text="Scombridae"/> |
1fcd81d65467
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit b377ff767e3051f301c2f02cfe3e1a17b285ede4
ecology
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46 <has_n_columns n="163"/> |
1fcd81d65467
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit b377ff767e3051f301c2f02cfe3e1a17b285ede4
ecology
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47 </assert_contents> |
1fcd81d65467
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit b377ff767e3051f301c2f02cfe3e1a17b285ede4
ecology
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48 </output> |
1fcd81d65467
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit b377ff767e3051f301c2f02cfe3e1a17b285ede4
ecology
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49 </test> |
1fcd81d65467
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit b377ff767e3051f301c2f02cfe3e1a17b285ede4
ecology
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50 <test expect_num_outputs="1"> |
1fcd81d65467
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit b377ff767e3051f301c2f02cfe3e1a17b285ede4
ecology
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51 <param name="lat_min" value="6"/> |
1fcd81d65467
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit b377ff767e3051f301c2f02cfe3e1a17b285ede4
ecology
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diff
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52 <param name="lat_max" value="12"/> |
1fcd81d65467
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit b377ff767e3051f301c2f02cfe3e1a17b285ede4
ecology
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53 <param name="long_min" value="40"/> |
1fcd81d65467
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit b377ff767e3051f301c2f02cfe3e1a17b285ede4
ecology
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54 <param name="long_max" value="43"/> |
1fcd81d65467
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit b377ff767e3051f301c2f02cfe3e1a17b285ede4
ecology
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55 <output name="output"> |
1fcd81d65467
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit b377ff767e3051f301c2f02cfe3e1a17b285ede4
ecology
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56 <assert_contents> |
1fcd81d65467
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit b377ff767e3051f301c2f02cfe3e1a17b285ede4
ecology
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57 <has_text text="basisOfRecord"/> |
1fcd81d65467
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit b377ff767e3051f301c2f02cfe3e1a17b285ede4
ecology
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58 <has_n_columns n="144"/> |
1fcd81d65467
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit b377ff767e3051f301c2f02cfe3e1a17b285ede4
ecology
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59 </assert_contents> |
1fcd81d65467
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit b377ff767e3051f301c2f02cfe3e1a17b285ede4
ecology
parents:
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60 </output> |
1fcd81d65467
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit b377ff767e3051f301c2f02cfe3e1a17b285ede4
ecology
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61 </test> |
1fcd81d65467
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit b377ff767e3051f301c2f02cfe3e1a17b285ede4
ecology
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62 </tests> |
1fcd81d65467
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit b377ff767e3051f301c2f02cfe3e1a17b285ede4
ecology
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63 <help><![CDATA[ |
1fcd81d65467
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit b377ff767e3051f301c2f02cfe3e1a17b285ede4
ecology
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64 =========================== |
1fcd81d65467
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit b377ff767e3051f301c2f02cfe3e1a17b285ede4
ecology
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65 Get species occurences data |
1fcd81d65467
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit b377ff767e3051f301c2f02cfe3e1a17b285ede4
ecology
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66 =========================== |
1fcd81d65467
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit b377ff767e3051f301c2f02cfe3e1a17b285ede4
ecology
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67 **What it does** |
1fcd81d65467
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit b377ff767e3051f301c2f02cfe3e1a17b285ede4
ecology
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68 |
1fcd81d65467
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit b377ff767e3051f301c2f02cfe3e1a17b285ede4
ecology
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69 Search and retrieve species occurences across OBIS database. |
1fcd81d65467
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit b377ff767e3051f301c2f02cfe3e1a17b285ede4
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70 |
1fcd81d65467
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit b377ff767e3051f301c2f02cfe3e1a17b285ede4
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71 | |
1fcd81d65467
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit b377ff767e3051f301c2f02cfe3e1a17b285ede4
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72 |
1fcd81d65467
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit b377ff767e3051f301c2f02cfe3e1a17b285ede4
ecology
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73 **How to use it** |
1fcd81d65467
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit b377ff767e3051f301c2f02cfe3e1a17b285ede4
ecology
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74 |
1fcd81d65467
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit b377ff767e3051f301c2f02cfe3e1a17b285ede4
ecology
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75 Enter a species scientific name, be careful that the tool is case sensitive. Eg : Scomber scombrus. |
1fcd81d65467
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit b377ff767e3051f301c2f02cfe3e1a17b285ede4
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76 |
1fcd81d65467
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit b377ff767e3051f301c2f02cfe3e1a17b285ede4
ecology
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77 Or enter the latitude longitude of the area you want to retrieve data from. |
1fcd81d65467
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit b377ff767e3051f301c2f02cfe3e1a17b285ede4
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78 |
1fcd81d65467
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit b377ff767e3051f301c2f02cfe3e1a17b285ede4
ecology
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79 |
1fcd81d65467
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit b377ff767e3051f301c2f02cfe3e1a17b285ede4
ecology
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80 | |
1fcd81d65467
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit b377ff767e3051f301c2f02cfe3e1a17b285ede4
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81 |
1fcd81d65467
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit b377ff767e3051f301c2f02cfe3e1a17b285ede4
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82 **Output** |
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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit b377ff767e3051f301c2f02cfe3e1a17b285ede4
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83 |
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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit b377ff767e3051f301c2f02cfe3e1a17b285ede4
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84 The tool returns a table with the species observations available in OBIS database. |
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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit b377ff767e3051f301c2f02cfe3e1a17b285ede4
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85 |
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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit b377ff767e3051f301c2f02cfe3e1a17b285ede4
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86 Output file will have at least the following attributes : BasisOfRecords, longitude, latitude, species, individualcount. |
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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit b377ff767e3051f301c2f02cfe3e1a17b285ede4
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87 |
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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit b377ff767e3051f301c2f02cfe3e1a17b285ede4
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88 | |
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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit b377ff767e3051f301c2f02cfe3e1a17b285ede4
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89 |
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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit b377ff767e3051f301c2f02cfe3e1a17b285ede4
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90 **How it works** |
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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit b377ff767e3051f301c2f02cfe3e1a17b285ede4
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91 |
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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit b377ff767e3051f301c2f02cfe3e1a17b285ede4
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92 This tool use the robis R package. |
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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit b377ff767e3051f301c2f02cfe3e1a17b285ede4
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93 |
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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit b377ff767e3051f301c2f02cfe3e1a17b285ede4
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94 |
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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit b377ff767e3051f301c2f02cfe3e1a17b285ede4
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95 Includes functionality for retrieving species occurrence data, and combining those data. |
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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit b377ff767e3051f301c2f02cfe3e1a17b285ede4
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96 ]]></help> |
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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit b377ff767e3051f301c2f02cfe3e1a17b285ede4
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97 <expand macro="obis_doiref"/> |
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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit b377ff767e3051f301c2f02cfe3e1a17b285ede4
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98 </tool> |