Mercurial > repos > iuc > geopandas_table2geojson
annotate table2geojson.xml @ 2:402faa5eab62 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/geopandas commit 28236fa503017adc781fc8e7bee547eeb44182f2
| author | iuc |
|---|---|
| date | Tue, 18 Nov 2025 22:46:21 +0000 |
| parents | fb5081261c10 |
| children |
| rev | line source |
|---|---|
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2
402faa5eab62
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/geopandas commit 28236fa503017adc781fc8e7bee547eeb44182f2
iuc
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1 <tool id="geopandas_table2geojson" name="Table to GeoJSON" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT"> |
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7bc130112fa3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/geopandas commit 76226199cd9ac3de12c81cc36b38c86bf4d676f5
iuc
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2 <description></description> |
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7bc130112fa3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/geopandas commit 76226199cd9ac3de12c81cc36b38c86bf4d676f5
iuc
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3 <macros> |
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1
fb5081261c10
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/geopandas commit d884ec05f204bf49251c3c1238fe192394fe5d90
iuc
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4 <token name="@TOOL_VERSION@">1.1.1</token> |
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402faa5eab62
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/geopandas commit 28236fa503017adc781fc8e7bee547eeb44182f2
iuc
parents:
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5 <token name="@VERSION_SUFFIX@">1</token> |
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402faa5eab62
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/geopandas commit 28236fa503017adc781fc8e7bee547eeb44182f2
iuc
parents:
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6 <token name="@PROFILE@">24.2</token> |
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7bc130112fa3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/geopandas commit 76226199cd9ac3de12c81cc36b38c86bf4d676f5
iuc
parents:
diff
changeset
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7 </macros> |
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7bc130112fa3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/geopandas commit 76226199cd9ac3de12c81cc36b38c86bf4d676f5
iuc
parents:
diff
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8 <requirements> |
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7bc130112fa3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/geopandas commit 76226199cd9ac3de12c81cc36b38c86bf4d676f5
iuc
parents:
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9 <requirement type="package" version="@TOOL_VERSION@">geopandas</requirement> |
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7bc130112fa3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/geopandas commit 76226199cd9ac3de12c81cc36b38c86bf4d676f5
iuc
parents:
diff
changeset
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10 </requirements> |
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7bc130112fa3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/geopandas commit 76226199cd9ac3de12c81cc36b38c86bf4d676f5
iuc
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11 <command detect_errors="exit_code"><![CDATA[ |
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7bc130112fa3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/geopandas commit 76226199cd9ac3de12c81cc36b38c86bf4d676f5
iuc
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12 python '$csv2geojson' |
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7bc130112fa3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/geopandas commit 76226199cd9ac3de12c81cc36b38c86bf4d676f5
iuc
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13 ]]></command> |
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7bc130112fa3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/geopandas commit 76226199cd9ac3de12c81cc36b38c86bf4d676f5
iuc
parents:
diff
changeset
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14 <configfiles> |
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7bc130112fa3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/geopandas commit 76226199cd9ac3de12c81cc36b38c86bf4d676f5
iuc
parents:
diff
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15 <configfile name="csv2geojson"> |
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7bc130112fa3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/geopandas commit 76226199cd9ac3de12c81cc36b38c86bf4d676f5
iuc
parents:
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16 import json |
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7bc130112fa3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/geopandas commit 76226199cd9ac3de12c81cc36b38c86bf4d676f5
iuc
parents:
diff
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17 import pandas as pd |
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7bc130112fa3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/geopandas commit 76226199cd9ac3de12c81cc36b38c86bf4d676f5
iuc
parents:
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18 import geopandas as gpd |
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402faa5eab62
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/geopandas commit 28236fa503017adc781fc8e7bee547eeb44182f2
iuc
parents:
1
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19 |
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402faa5eab62
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/geopandas commit 28236fa503017adc781fc8e7bee547eeb44182f2
iuc
parents:
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20 df = pd.read_csv('$infile', encoding="utf-8", sep=None, engine='python', header=None if '$has_header' == "false" else 0) |
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7bc130112fa3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/geopandas commit 76226199cd9ac3de12c81cc36b38c86bf4d676f5
iuc
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21 |
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2
402faa5eab62
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/geopandas commit 28236fa503017adc781fc8e7bee547eeb44182f2
iuc
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22 inc = [int(x)-1 for x in str('$include_columns').split(",") if x.strip().isdigit()] if '$include_columns' and str('$include_columns').lower() != "none" else [] |
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402faa5eab62
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/geopandas commit 28236fa503017adc781fc8e7bee547eeb44182f2
iuc
parents:
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23 exc = [int(x)-1 for x in str('$exclude_columns').split(",") if x.strip().isdigit()] if '$exclude_columns' and str('$exclude_columns').lower() != "none" else [] |
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402faa5eab62
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/geopandas commit 28236fa503017adc781fc8e7bee547eeb44182f2
iuc
parents:
1
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24 |
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7bc130112fa3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/geopandas commit 76226199cd9ac3de12c81cc36b38c86bf4d676f5
iuc
parents:
diff
changeset
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25 property_df = df |
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7bc130112fa3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/geopandas commit 76226199cd9ac3de12c81cc36b38c86bf4d676f5
iuc
parents:
diff
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26 |
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2
402faa5eab62
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/geopandas commit 28236fa503017adc781fc8e7bee547eeb44182f2
iuc
parents:
1
diff
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27 if inc: |
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402faa5eab62
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/geopandas commit 28236fa503017adc781fc8e7bee547eeb44182f2
iuc
parents:
1
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28 property_df = df.iloc[:, inc] |
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402faa5eab62
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/geopandas commit 28236fa503017adc781fc8e7bee547eeb44182f2
iuc
parents:
1
diff
changeset
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29 if exc: |
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402faa5eab62
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/geopandas commit 28236fa503017adc781fc8e7bee547eeb44182f2
iuc
parents:
1
diff
changeset
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30 property_df = property_df.drop(columns=df.columns[exc]) |
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7bc130112fa3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/geopandas commit 76226199cd9ac3de12c81cc36b38c86bf4d676f5
iuc
parents:
diff
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31 |
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7bc130112fa3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/geopandas commit 76226199cd9ac3de12c81cc36b38c86bf4d676f5
iuc
parents:
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32 gdf = gpd.GeoDataFrame( |
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7bc130112fa3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/geopandas commit 76226199cd9ac3de12c81cc36b38c86bf4d676f5
iuc
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33 property_df, |
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2
402faa5eab62
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/geopandas commit 28236fa503017adc781fc8e7bee547eeb44182f2
iuc
parents:
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34 geometry=gpd.points_from_xy( |
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402faa5eab62
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/geopandas commit 28236fa503017adc781fc8e7bee547eeb44182f2
iuc
parents:
1
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35 df.iloc[:, int($lat_column)-1], |
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402faa5eab62
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/geopandas commit 28236fa503017adc781fc8e7bee547eeb44182f2
iuc
parents:
1
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36 df.iloc[:, int($long_column)-1]), |
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402faa5eab62
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/geopandas commit 28236fa503017adc781fc8e7bee547eeb44182f2
iuc
parents:
1
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37 crs="$crs" |
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402faa5eab62
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/geopandas commit 28236fa503017adc781fc8e7bee547eeb44182f2
iuc
parents:
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38 ) |
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7bc130112fa3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/geopandas commit 76226199cd9ac3de12c81cc36b38c86bf4d676f5
iuc
parents:
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39 |
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7bc130112fa3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/geopandas commit 76226199cd9ac3de12c81cc36b38c86bf4d676f5
iuc
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40 # drop_id: bool, default: False |
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7bc130112fa3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/geopandas commit 76226199cd9ac3de12c81cc36b38c86bf4d676f5
iuc
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41 data = json.loads(gdf.to_json()) |
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7bc130112fa3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/geopandas commit 76226199cd9ac3de12c81cc36b38c86bf4d676f5
iuc
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42 with open('outfile.geojson', "w", encoding="utf8") as f: |
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7bc130112fa3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/geopandas commit 76226199cd9ac3de12c81cc36b38c86bf4d676f5
iuc
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43 ## Minify output json |
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7bc130112fa3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/geopandas commit 76226199cd9ac3de12c81cc36b38c86bf4d676f5
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44 f.write(json.dumps(data, indent=4)) |
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7bc130112fa3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/geopandas commit 76226199cd9ac3de12c81cc36b38c86bf4d676f5
iuc
parents:
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45 </configfile> |
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7bc130112fa3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/geopandas commit 76226199cd9ac3de12c81cc36b38c86bf4d676f5
iuc
parents:
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46 </configfiles> |
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7bc130112fa3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/geopandas commit 76226199cd9ac3de12c81cc36b38c86bf4d676f5
iuc
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47 <inputs> |
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7bc130112fa3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/geopandas commit 76226199cd9ac3de12c81cc36b38c86bf4d676f5
iuc
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48 <param name="infile" type="data" format="csv,tabular,tsv" label="The file you want to convert"/> |
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402faa5eab62
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/geopandas commit 28236fa503017adc781fc8e7bee547eeb44182f2
iuc
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49 <param name="has_header" type="boolean" truevalue="true" falsevalue="false" label="First row contains column names (header)?" help="Does your input file consists of a header"/> |
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402faa5eab62
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/geopandas commit 28236fa503017adc781fc8e7bee547eeb44182f2
iuc
parents:
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50 <param name="lat_column" type="integer" value="1" label="Latitude column"/> |
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402faa5eab62
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/geopandas commit 28236fa503017adc781fc8e7bee547eeb44182f2
iuc
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51 <param name="long_column" type="integer" value="2" label="Longitude column"/> |
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7bc130112fa3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/geopandas commit 76226199cd9ac3de12c81cc36b38c86bf4d676f5
iuc
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52 <param name="include_columns" type="data_column" data_ref="infile" use_header_names="true" multiple="true" optional="true" |
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7bc130112fa3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/geopandas commit 76226199cd9ac3de12c81cc36b38c86bf4d676f5
iuc
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53 label="Include the following columns" help="Either include or exclude columns, by default, all columns will be taken over into the properties field"/> |
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7bc130112fa3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/geopandas commit 76226199cd9ac3de12c81cc36b38c86bf4d676f5
iuc
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54 <param name="exclude_columns" type="data_column" data_ref="infile" use_header_names="true" multiple="true" optional="true" |
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7bc130112fa3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/geopandas commit 76226199cd9ac3de12c81cc36b38c86bf4d676f5
iuc
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55 label="Exclude the following columns" help="Either include or exclude columns, by default, all columns will be taken over into the properties field"/> |
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7bc130112fa3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/geopandas commit 76226199cd9ac3de12c81cc36b38c86bf4d676f5
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56 <param name="crs" type="select" label="Coordinate Reference System" help="Choose the Coordinate Reference Systems (CRS) your data is using"> |
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7bc130112fa3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/geopandas commit 76226199cd9ac3de12c81cc36b38c86bf4d676f5
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57 <option value="EPSG:3857">Web Mercator projection</option> |
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7bc130112fa3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/geopandas commit 76226199cd9ac3de12c81cc36b38c86bf4d676f5
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58 <option value="EPSG:4326" selected="true">WGS84 projection (used by Google Earth)</option> |
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7bc130112fa3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/geopandas commit 76226199cd9ac3de12c81cc36b38c86bf4d676f5
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59 </param> |
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7bc130112fa3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/geopandas commit 76226199cd9ac3de12c81cc36b38c86bf4d676f5
iuc
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60 |
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7bc130112fa3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/geopandas commit 76226199cd9ac3de12c81cc36b38c86bf4d676f5
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61 </inputs> |
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7bc130112fa3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/geopandas commit 76226199cd9ac3de12c81cc36b38c86bf4d676f5
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62 <outputs> |
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7bc130112fa3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/geopandas commit 76226199cd9ac3de12c81cc36b38c86bf4d676f5
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63 <data name="outfile" format="geojson" from_work_dir="outfile.geojson" label="${tool.name} on ${on_string}" /> |
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7bc130112fa3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/geopandas commit 76226199cd9ac3de12c81cc36b38c86bf4d676f5
iuc
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64 </outputs> |
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7bc130112fa3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/geopandas commit 76226199cd9ac3de12c81cc36b38c86bf4d676f5
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65 <tests> |
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7bc130112fa3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/geopandas commit 76226199cd9ac3de12c81cc36b38c86bf4d676f5
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66 <test expect_num_outputs="1"> |
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7bc130112fa3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/geopandas commit 76226199cd9ac3de12c81cc36b38c86bf4d676f5
iuc
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67 <param name="infile" value="geolocation.csv"/> |
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2
402faa5eab62
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/geopandas commit 28236fa503017adc781fc8e7bee547eeb44182f2
iuc
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68 <param name="has_header" value="true"/> |
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7bc130112fa3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/geopandas commit 76226199cd9ac3de12c81cc36b38c86bf4d676f5
iuc
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69 <param name="lat_column" value="1"/> |
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7bc130112fa3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/geopandas commit 76226199cd9ac3de12c81cc36b38c86bf4d676f5
iuc
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70 <param name="long_column" value="2"/> |
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7bc130112fa3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/geopandas commit 76226199cd9ac3de12c81cc36b38c86bf4d676f5
iuc
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71 <param name="crs" value="EPSG:3857"/> |
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7bc130112fa3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/geopandas commit 76226199cd9ac3de12c81cc36b38c86bf4d676f5
iuc
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72 <output name="outfile" file="geolocation_1.geojson"> |
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7bc130112fa3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/geopandas commit 76226199cd9ac3de12c81cc36b38c86bf4d676f5
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73 <assert_contents> |
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7bc130112fa3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/geopandas commit 76226199cd9ac3de12c81cc36b38c86bf4d676f5
iuc
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74 <has_json_property_with_text property="type" text="FeatureCollection"/> |
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7bc130112fa3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/geopandas commit 76226199cd9ac3de12c81cc36b38c86bf4d676f5
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75 <!-- all 5 columns are includes as properties, nothing excluded, nothing explicitly included --> |
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7bc130112fa3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/geopandas commit 76226199cd9ac3de12c81cc36b38c86bf4d676f5
iuc
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76 <has_text text='value": 10'/> |
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7bc130112fa3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/geopandas commit 76226199cd9ac3de12c81cc36b38c86bf4d676f5
iuc
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77 <has_text text='temperature": 23'/> |
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78 <has_text text='longitude'/> |
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79 <has_text text='latitude'/> |
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80 <has_text text='timestamp": "2023-01-01T12:05:00Z"'/> |
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81 <has_n_lines n="371"/> |
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82 </assert_contents> |
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83 </output> |
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84 </test> |
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85 <test expect_num_outputs="1"> |
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86 <param name="infile" value="geolocation_without_header.csv"/> |
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87 <param name="has_header" value="false"/> |
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88 <param name="lat_column" value="1"/> |
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89 <param name="long_column" value="2"/> |
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90 <param name="crs" value="EPSG:3857"/> |
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91 <output name="outfile"> |
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92 <assert_contents> |
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93 <has_json_property_with_text property="type" text="FeatureCollection"/> |
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94 <has_n_lines n="371"/> |
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95 </assert_contents> |
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96 </output> |
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97 </test> |
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98 <test expect_num_outputs="1"> |
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99 <param name="infile" value="geolocation.csv"/> |
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100 <param name="has_header" value="true"/> |
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101 <param name="lat_column" value="1"/> |
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102 <param name="long_column" value="2"/> |
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103 <param name="include_columns" value="3,4"/> |
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104 <param name="crs" value="EPSG:3857"/> |
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105 <output name="outfile" ftype="geojson" file="geolocation_2.geojson"> |
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106 <assert_contents> |
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107 <!-- 2 columns are explicitly included as properties --> |
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108 <has_text text='timestamp": "2023-01-01T12:05:00Z"'/> |
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109 <has_text text='value": 10'/> |
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110 <has_text text="FeatureCollection"/> |
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111 <has_n_lines n="311"/> |
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112 </assert_contents> |
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113 </output> |
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114 </test> |
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115 <test expect_num_outputs="1"> |
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116 <param name="infile" value="geolocation.csv"/> |
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117 <param name="has_header" value="true"/> |
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118 <param name="lat_column" value="1"/> |
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119 <param name="long_column" value="2"/> |
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120 <param name="exclude_columns" value="5"/> |
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121 <param name="crs" value="EPSG:3857"/> |
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122 <output name="outfile" ftype="geojson" file="geolocation_3.geojson"> |
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123 <assert_contents> |
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124 <has_json_property_with_text property="type" text="FeatureCollection"/> |
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125 <!-- 4 columns are includes as properties ... one is excluded --> |
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126 <has_text text='value": 10'/> |
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127 <has_text text='longitude'/> |
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128 <has_text text='latitude'/> |
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129 <has_text text='timestamp": "2023-01-01T12:05:00Z"'/> |
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130 <has_n_lines n="351"/> |
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131 </assert_contents> |
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132 </output> |
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133 </test> |
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134 |
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135 </tests> |
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136 <help format="markdown"><. |
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145 |
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146 ## What is GeoJSON? |
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147 |
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148 GeoJSON is a widely-used format for encoding geographic data structures using JSON (JavaScript Object Notation). |
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149 A GeoJSON file contains an array of geographic features, where each feature includes: |
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150 * A geometry field describing the spatial shape (e.g., point, line, polygon), |
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151 * A properties field containing non-spatial attributes. |
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152 |
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153 GeoJSON uses the WGS84 coordinate system by default (EPSG:4326), with coordinates expressed in decimal degrees. |
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154 To explore and edit GeoJSON interactively, visit [geojson.io](https://geojson.io), select a location or shape, and inspect the resulting GeoJSON output. |
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155 |
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156 📌 Pro Tip, Galaxy can visualise GeoJSON files. |
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157 |
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158 ]]></help> |
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159 <citations> |
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160 <citation type="doi">10.5281/zenodo.3946761</citation> |
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161 </citations> |
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162 </tool> |