# HG changeset patch
# User iuc
# Date 1745335092 0
# Node ID 7bc130112fa3d4d0f3669e94beb0b352c6e5e278

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/geopandas commit 76226199cd9ac3de12c81cc36b38c86bf4d676f5

diff -r 000000000000 -r 7bc130112fa3 table2geojson.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/table2geojson.xml	Tue Apr 22 15:18:12 2025 +0000
@@ -0,0 +1,142 @@
+<tool id="geopandas_table2geojson" name="Table to GeoJSON" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="24.2" license="MIT">
+    <description></description>
+    <macros>
+        <token name="@TOOL_VERSION@">1.0.1</token>
+        <token name="@VERSION_SUFFIX@">0</token>
+    </macros>
+
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">geopandas</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        python '$csv2geojson'
+    ]]></command>
+    <configfiles>
+        <configfile name="csv2geojson">
+import json
+import pandas as pd
+import geopandas as gpd
+df = pd.read_csv('$infile', encoding="utf-8")
+
+#set exc = [int($col) - 1 for $col in $exclude_columns]
+#set inc = [int($col) - 1 for $col in $include_columns]
+property_df = df
+
+if "$include_columns" != "None":
+    property_df = df.iloc[:, $inc]
+
+if "$exclude_columns" != "None":
+    property_df = df.drop(columns=df.columns[$exc])
+       
+gdf = gpd.GeoDataFrame(
+    property_df,
+    geometry=gpd.points_from_xy(df.iloc[:,$lat_column-1], df.iloc[:,$long_column-1]),
+    crs="$crs",
+    )
+        
+# drop_id: bool, default: False
+data = json.loads(gdf.to_json())
+with open('outfile.geojson', "w", encoding="utf8") as f:
+    ## Minify output json
+    f.write(json.dumps(data, indent=4))
+        </configfile>
+    </configfiles>
+    <inputs>
+        <param name="infile" type="data" format="csv,tabular,tsv" label="The file you want to convert"/>
+        <param name="lat_column" type="data_column" data_ref="infile" use_header_names="true" label="Latitude column"/>
+        <param name="long_column" type="data_column" data_ref="infile" use_header_names="true" label="Longitude column"/>
+        <param name="include_columns" type="data_column" data_ref="infile" use_header_names="true" multiple="true" optional="true"
+            label="Include the following columns" help="Either include or exclude columns, by default, all columns will be taken over into the properties field"/>
+        <param name="exclude_columns" type="data_column" data_ref="infile" use_header_names="true" multiple="true" optional="true"
+            label="Exclude the following columns" help="Either include or exclude columns, by default, all columns will be taken over into the properties field"/>
+        <param name="crs" type="select" label="Coordinate Reference System" help="Choose the Coordinate Reference Systems (CRS) your data is using">
+            <option value="EPSG:3857">Web Mercator projection</option>
+            <option value="EPSG:4326" selected="true">WGS84 projection (used by Google Earth)</option>
+        </param>
+
+    </inputs>
+    <outputs>
+        <data name="outfile" format="geojson" from_work_dir="outfile.geojson" label="${tool.name} on ${on_string}" />
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="infile" value="geolocation.csv"/>
+            <param name="lat_column" value="1"/>
+            <param name="long_column" value="2"/>
+            <param name="crs" value="EPSG:3857"/>
+            <output name="outfile" file="geolocation_1.geojson">
+                <assert_contents>
+                    <has_json_property_with_text property="type" text="FeatureCollection"/>
+                    <!-- all 5 columns are includes as properties, nothing excluded, nothing explicitly included -->
+                    <has_text text='value": 10'/>
+                    <has_text text='temperature": 23'/>
+                    <has_text text='longitude'/>
+                    <has_text text='latitude'/>
+                    <has_text text='timestamp": "2023-01-01T12:05:00Z"'/>
+                    <has_n_lines n="371"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="infile" value="geolocation.csv"/>
+            <param name="lat_column" value="1"/>
+            <param name="long_column" value="2"/>
+            <param name="include_columns" value="3,4"/>
+            <param name="crs" value="EPSG:3857"/>
+            <output name="outfile" ftype="geojson" file="geolocation_2.geojson">
+                <assert_contents>
+                    <!-- 2 columns are explicitly included as properties -->
+                    <has_text text='timestamp": "2023-01-01T12:05:00Z"'/>
+                    <has_text text='value": 10'/>
+                    <has_text text="FeatureCollection"/>
+                    <has_n_lines n="311"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="infile" value="geolocation.csv"/>
+            <param name="lat_column" value="1"/>
+            <param name="long_column" value="2"/>
+            <param name="exclude_columns" value="5"/>
+            <param name="crs" value="EPSG:3857"/>
+            <output name="outfile" ftype="geojson" file="geolocation_3.geojson">
+                <assert_contents>
+                    <has_json_property_with_text property="type" text="FeatureCollection"/>
+                    <!-- 4 columns are includes as properties ... one is excluded -->
+                    <has_text text='value": 10'/>
+                    <has_text text='longitude'/>
+                    <has_text text='latitude'/>
+                    <has_text text='timestamp": "2023-01-01T12:05:00Z"'/>
+                    <has_n_lines n="351"/>
+                </assert_contents>
+            </output>
+        </test>
+
+    </tests>
+    <help format="markdown"><![CDATA[
+
+# 💡 Convert CSV or Tabular Data to GeoJSON Format
+
+## Understanding Coordinate Reference Systems (CRS)
+
+A Coordinate Reference System (CRS) defines how the coordinate values in your data relate to real-world locations on Earth. Without a CRS,
+the coordinates in a GeoSeries or GeoDataFrame are simply numbers in an undefined space.
+To find reference codes for widely used CRS projections, visit [spatialreference.org](https://spatialreference.org).
+
+## What is GeoJSON?
+
+GeoJSON is a widely-used format for encoding geographic data structures using JSON (JavaScript Object Notation).
+A GeoJSON file contains an array of geographic features, where each feature includes:
+* A geometry field describing the spatial shape (e.g., point, line, polygon),
+* A properties field containing non-spatial attributes.
+
+GeoJSON uses the WGS84 coordinate system by default (EPSG:4326), with coordinates expressed in decimal degrees.
+To explore and edit GeoJSON interactively, visit [geojson.io](https://geojson.io), select a location or shape, and inspect the resulting GeoJSON output.
+
+📌 Pro Tip, Galaxy can visualise GeoJSON files.
+
+    ]]></help>
+    <citations>
+        <citation type="doi">10.5281/zenodo.3946761</citation>
+    </citations>
+</tool>
diff -r 000000000000 -r 7bc130112fa3 test-data/geolocation.csv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/geolocation.csv	Tue Apr 22 15:18:12 2025 +0000
@@ -0,0 +1,21 @@
+latitude,longitude,timestamp,value,temperature
+37.7749,-122.4194,2023-01-01T12:00:00Z,10,23
+37.7751,-122.4190,2023-01-01T12:05:00Z,15,23
+37.7753,-122.4185,2023-01-01T12:10:00Z,20,23
+37.7755,-122.4180,2023-01-01T12:15:00Z,25,24
+37.7757,-122.4175,2023-01-01T12:20:00Z,30,25
+37.7759,-122.4170,2023-01-01T12:25:00Z,35,23
+37.7761,-122.4165,2023-01-01T12:30:00Z,40,23
+37.7763,-122.4160,2023-01-01T12:35:00Z,45,23
+37.7765,-122.4155,2023-01-01T12:40:00Z,50,23
+37.7767,-122.4150,2023-01-01T12:45:00Z,55,23
+37.7769,-122.4145,2023-01-01T12:50:00Z,60,23
+37.7771,-122.4140,2023-01-01T12:55:00Z,65,23
+37.7773,-122.4135,2023-01-01T13:00:00Z,70,23
+37.7775,-122.4130,2023-01-01T13:05:00Z,75,23
+37.7777,-122.4125,2023-01-01T13:10:00Z,80,23
+37.7779,-122.4120,2023-01-01T13:15:00Z,85,23
+37.7781,-122.4115,2023-01-01T13:20:00Z,90,23
+37.7783,-122.4110,2023-01-01T13:25:00Z,95,23
+37.7785,-122.4105,2023-01-01T13:30:00Z,100,23
+37.7787,-122.4100,2023-01-01T13:35:00Z,105,23
\ No newline at end of file
diff -r 000000000000 -r 7bc130112fa3 test-data/geolocation_1.geojson
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/geolocation_1.geojson	Tue Apr 22 15:18:12 2025 +0000
@@ -0,0 +1,371 @@
+{
+    "type": "FeatureCollection",
+    "features": [
+        {
+            "id": "0",
+            "type": "Feature",
+            "properties": {
+                "latitude": 37.7749,
+                "longitude": -122.4194,
+                "timestamp": "2023-01-01T12:00:00Z",
+                "value": 10,
+                "temperature": 23
+            },
+            "geometry": {
+                "type": "Point",
+                "coordinates": [
+                    37.7749,
+                    -122.4194
+                ]
+            }
+        },
+        {
+            "id": "1",
+            "type": "Feature",
+            "properties": {
+                "latitude": 37.7751,
+                "longitude": -122.419,
+                "timestamp": "2023-01-01T12:05:00Z",
+                "value": 15,
+                "temperature": 23
+            },
+            "geometry": {
+                "type": "Point",
+                "coordinates": [
+                    37.7751,
+                    -122.419
+                ]
+            }
+        },
+        {
+            "id": "2",
+            "type": "Feature",
+            "properties": {
+                "latitude": 37.7753,
+                "longitude": -122.4185,
+                "timestamp": "2023-01-01T12:10:00Z",
+                "value": 20,
+                "temperature": 23
+            },
+            "geometry": {
+                "type": "Point",
+                "coordinates": [
+                    37.7753,
+                    -122.4185
+                ]
+            }
+        },
+        {
+            "id": "3",
+            "type": "Feature",
+            "properties": {
+                "latitude": 37.7755,
+                "longitude": -122.418,
+                "timestamp": "2023-01-01T12:15:00Z",
+                "value": 25,
+                "temperature": 24
+            },
+            "geometry": {
+                "type": "Point",
+                "coordinates": [
+                    37.7755,
+                    -122.418
+                ]
+            }
+        },
+        {
+            "id": "4",
+            "type": "Feature",
+            "properties": {
+                "latitude": 37.7757,
+                "longitude": -122.4175,
+                "timestamp": "2023-01-01T12:20:00Z",
+                "value": 30,
+                "temperature": 25
+            },
+            "geometry": {
+                "type": "Point",
+                "coordinates": [
+                    37.7757,
+                    -122.4175
+                ]
+            }
+        },
+        {
+            "id": "5",
+            "type": "Feature",
+            "properties": {
+                "latitude": 37.7759,
+                "longitude": -122.417,
+                "timestamp": "2023-01-01T12:25:00Z",
+                "value": 35,
+                "temperature": 23
+            },
+            "geometry": {
+                "type": "Point",
+                "coordinates": [
+                    37.7759,
+                    -122.417
+                ]
+            }
+        },
+        {
+            "id": "6",
+            "type": "Feature",
+            "properties": {
+                "latitude": 37.7761,
+                "longitude": -122.4165,
+                "timestamp": "2023-01-01T12:30:00Z",
+                "value": 40,
+                "temperature": 23
+            },
+            "geometry": {
+                "type": "Point",
+                "coordinates": [
+                    37.7761,
+                    -122.4165
+                ]
+            }
+        },
+        {
+            "id": "7",
+            "type": "Feature",
+            "properties": {
+                "latitude": 37.7763,
+                "longitude": -122.416,
+                "timestamp": "2023-01-01T12:35:00Z",
+                "value": 45,
+                "temperature": 23
+            },
+            "geometry": {
+                "type": "Point",
+                "coordinates": [
+                    37.7763,
+                    -122.416
+                ]
+            }
+        },
+        {
+            "id": "8",
+            "type": "Feature",
+            "properties": {
+                "latitude": 37.7765,
+                "longitude": -122.4155,
+                "timestamp": "2023-01-01T12:40:00Z",
+                "value": 50,
+                "temperature": 23
+            },
+            "geometry": {
+                "type": "Point",
+                "coordinates": [
+                    37.7765,
+                    -122.4155
+                ]
+            }
+        },
+        {
+            "id": "9",
+            "type": "Feature",
+            "properties": {
+                "latitude": 37.7767,
+                "longitude": -122.415,
+                "timestamp": "2023-01-01T12:45:00Z",
+                "value": 55,
+                "temperature": 23
+            },
+            "geometry": {
+                "type": "Point",
+                "coordinates": [
+                    37.7767,
+                    -122.415
+                ]
+            }
+        },
+        {
+            "id": "10",
+            "type": "Feature",
+            "properties": {
+                "latitude": 37.7769,
+                "longitude": -122.4145,
+                "timestamp": "2023-01-01T12:50:00Z",
+                "value": 60,
+                "temperature": 23
+            },
+            "geometry": {
+                "type": "Point",
+                "coordinates": [
+                    37.7769,
+                    -122.4145
+                ]
+            }
+        },
+        {
+            "id": "11",
+            "type": "Feature",
+            "properties": {
+                "latitude": 37.7771,
+                "longitude": -122.414,
+                "timestamp": "2023-01-01T12:55:00Z",
+                "value": 65,
+                "temperature": 23
+            },
+            "geometry": {
+                "type": "Point",
+                "coordinates": [
+                    37.7771,
+                    -122.414
+                ]
+            }
+        },
+        {
+            "id": "12",
+            "type": "Feature",
+            "properties": {
+                "latitude": 37.7773,
+                "longitude": -122.4135,
+                "timestamp": "2023-01-01T13:00:00Z",
+                "value": 70,
+                "temperature": 23
+            },
+            "geometry": {
+                "type": "Point",
+                "coordinates": [
+                    37.7773,
+                    -122.4135
+                ]
+            }
+        },
+        {
+            "id": "13",
+            "type": "Feature",
+            "properties": {
+                "latitude": 37.7775,
+                "longitude": -122.413,
+                "timestamp": "2023-01-01T13:05:00Z",
+                "value": 75,
+                "temperature": 23
+            },
+            "geometry": {
+                "type": "Point",
+                "coordinates": [
+                    37.7775,
+                    -122.413
+                ]
+            }
+        },
+        {
+            "id": "14",
+            "type": "Feature",
+            "properties": {
+                "latitude": 37.7777,
+                "longitude": -122.4125,
+                "timestamp": "2023-01-01T13:10:00Z",
+                "value": 80,
+                "temperature": 23
+            },
+            "geometry": {
+                "type": "Point",
+                "coordinates": [
+                    37.7777,
+                    -122.4125
+                ]
+            }
+        },
+        {
+            "id": "15",
+            "type": "Feature",
+            "properties": {
+                "latitude": 37.7779,
+                "longitude": -122.412,
+                "timestamp": "2023-01-01T13:15:00Z",
+                "value": 85,
+                "temperature": 23
+            },
+            "geometry": {
+                "type": "Point",
+                "coordinates": [
+                    37.7779,
+                    -122.412
+                ]
+            }
+        },
+        {
+            "id": "16",
+            "type": "Feature",
+            "properties": {
+                "latitude": 37.7781,
+                "longitude": -122.4115,
+                "timestamp": "2023-01-01T13:20:00Z",
+                "value": 90,
+                "temperature": 23
+            },
+            "geometry": {
+                "type": "Point",
+                "coordinates": [
+                    37.7781,
+                    -122.4115
+                ]
+            }
+        },
+        {
+            "id": "17",
+            "type": "Feature",
+            "properties": {
+                "latitude": 37.7783,
+                "longitude": -122.411,
+                "timestamp": "2023-01-01T13:25:00Z",
+                "value": 95,
+                "temperature": 23
+            },
+            "geometry": {
+                "type": "Point",
+                "coordinates": [
+                    37.7783,
+                    -122.411
+                ]
+            }
+        },
+        {
+            "id": "18",
+            "type": "Feature",
+            "properties": {
+                "latitude": 37.7785,
+                "longitude": -122.4105,
+                "timestamp": "2023-01-01T13:30:00Z",
+                "value": 100,
+                "temperature": 23
+            },
+            "geometry": {
+                "type": "Point",
+                "coordinates": [
+                    37.7785,
+                    -122.4105
+                ]
+            }
+        },
+        {
+            "id": "19",
+            "type": "Feature",
+            "properties": {
+                "latitude": 37.7787,
+                "longitude": -122.41,
+                "timestamp": "2023-01-01T13:35:00Z",
+                "value": 105,
+                "temperature": 23
+            },
+            "geometry": {
+                "type": "Point",
+                "coordinates": [
+                    37.7787,
+                    -122.41
+                ]
+            }
+        }
+    ],
+    "crs": {
+        "type": "name",
+        "properties": {
+            "name": "urn:ogc:def:crs:EPSG::3857"
+        }
+    }
+}
\ No newline at end of file
diff -r 000000000000 -r 7bc130112fa3 test-data/geolocation_2.geojson
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/geolocation_2.geojson	Tue Apr 22 15:18:12 2025 +0000
@@ -0,0 +1,311 @@
+{
+    "type": "FeatureCollection",
+    "features": [
+        {
+            "id": "0",
+            "type": "Feature",
+            "properties": {
+                "timestamp": "2023-01-01T12:00:00Z",
+                "value": 10
+            },
+            "geometry": {
+                "type": "Point",
+                "coordinates": [
+                    37.7749,
+                    -122.4194
+                ]
+            }
+        },
+        {
+            "id": "1",
+            "type": "Feature",
+            "properties": {
+                "timestamp": "2023-01-01T12:05:00Z",
+                "value": 15
+            },
+            "geometry": {
+                "type": "Point",
+                "coordinates": [
+                    37.7751,
+                    -122.419
+                ]
+            }
+        },
+        {
+            "id": "2",
+            "type": "Feature",
+            "properties": {
+                "timestamp": "2023-01-01T12:10:00Z",
+                "value": 20
+            },
+            "geometry": {
+                "type": "Point",
+                "coordinates": [
+                    37.7753,
+                    -122.4185
+                ]
+            }
+        },
+        {
+            "id": "3",
+            "type": "Feature",
+            "properties": {
+                "timestamp": "2023-01-01T12:15:00Z",
+                "value": 25
+            },
+            "geometry": {
+                "type": "Point",
+                "coordinates": [
+                    37.7755,
+                    -122.418
+                ]
+            }
+        },
+        {
+            "id": "4",
+            "type": "Feature",
+            "properties": {
+                "timestamp": "2023-01-01T12:20:00Z",
+                "value": 30
+            },
+            "geometry": {
+                "type": "Point",
+                "coordinates": [
+                    37.7757,
+                    -122.4175
+                ]
+            }
+        },
+        {
+            "id": "5",
+            "type": "Feature",
+            "properties": {
+                "timestamp": "2023-01-01T12:25:00Z",
+                "value": 35
+            },
+            "geometry": {
+                "type": "Point",
+                "coordinates": [
+                    37.7759,
+                    -122.417
+                ]
+            }
+        },
+        {
+            "id": "6",
+            "type": "Feature",
+            "properties": {
+                "timestamp": "2023-01-01T12:30:00Z",
+                "value": 40
+            },
+            "geometry": {
+                "type": "Point",
+                "coordinates": [
+                    37.7761,
+                    -122.4165
+                ]
+            }
+        },
+        {
+            "id": "7",
+            "type": "Feature",
+            "properties": {
+                "timestamp": "2023-01-01T12:35:00Z",
+                "value": 45
+            },
+            "geometry": {
+                "type": "Point",
+                "coordinates": [
+                    37.7763,
+                    -122.416
+                ]
+            }
+        },
+        {
+            "id": "8",
+            "type": "Feature",
+            "properties": {
+                "timestamp": "2023-01-01T12:40:00Z",
+                "value": 50
+            },
+            "geometry": {
+                "type": "Point",
+                "coordinates": [
+                    37.7765,
+                    -122.4155
+                ]
+            }
+        },
+        {
+            "id": "9",
+            "type": "Feature",
+            "properties": {
+                "timestamp": "2023-01-01T12:45:00Z",
+                "value": 55
+            },
+            "geometry": {
+                "type": "Point",
+                "coordinates": [
+                    37.7767,
+                    -122.415
+                ]
+            }
+        },
+        {
+            "id": "10",
+            "type": "Feature",
+            "properties": {
+                "timestamp": "2023-01-01T12:50:00Z",
+                "value": 60
+            },
+            "geometry": {
+                "type": "Point",
+                "coordinates": [
+                    37.7769,
+                    -122.4145
+                ]
+            }
+        },
+        {
+            "id": "11",
+            "type": "Feature",
+            "properties": {
+                "timestamp": "2023-01-01T12:55:00Z",
+                "value": 65
+            },
+            "geometry": {
+                "type": "Point",
+                "coordinates": [
+                    37.7771,
+                    -122.414
+                ]
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\ No newline at end of file
diff -r 000000000000 -r 7bc130112fa3 test-data/geolocation_3.geojson
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/geolocation_3.geojson	Tue Apr 22 15:18:12 2025 +0000
@@ -0,0 +1,351 @@
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\ No newline at end of file