| Previous changeset 2:22c54afd1cf3 (2019-06-13) |
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Commit message:
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/gdal commit b8d429fc9c59d401a4a55fcd806050939ed41b8b |
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modified:
gdal_macros.xml ogr2ogr.xml |
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added:
test-data/ogr2ogr_fromgbif.tabular test-data/ogr2ogr_gbif_to_json.json |
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| diff -r 22c54afd1cf3 -r e12db3b4d3a6 gdal_macros.xml --- a/gdal_macros.xml Thu Jun 13 11:29:34 2019 -0400 +++ b/gdal_macros.xml Thu Jun 20 06:53:44 2019 -0400 |
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| @@ -128,11 +128,11 @@ </param> </xml> -<!-- need to upgrade gdal version to use <xml name="gdal_param_oo"> - <param name="oo" type="text" label="-oo NAME=VALUE" value="" /> + <repeat name="series_oo" title="Add an input dataset open option"> + <param name="oo" type="text" label="Input dataset open option" help="-oo NAME=VALUE. eg : X_POSSIBLE_NAMES=longitude. Format specific, can be used multiple times." value="" /> + </repeat> </xml> ---> <xml name="gdal_input_raster_multiple"> <param type="data" name="input" format="gtiff,tiff,netcdf,VRT,txt,xml" help="Formats currently supported are : GTiff, netCDF and VRT" label="Gdal supported input file" multiple="true"/> |
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| diff -r 22c54afd1cf3 -r e12db3b4d3a6 ogr2ogr.xml --- a/ogr2ogr.xml Thu Jun 13 11:29:34 2019 -0400 +++ b/ogr2ogr.xml Thu Jun 20 06:53:44 2019 -0400 |
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| @@ -5,6 +5,9 @@ </macros> <expand macro="gdal_requirements" /> <command detect_errors="exit_code"><![CDATA[ + #if $input.is_of_type("tabular") + cp '$input' '$input''.tsv' && + #end if ogr2ogr -f '$f' #if $f=='ESRI Shapefile' @@ -14,9 +17,18 @@ #end if #if $input.is_of_type("shp") ${os.path.join( $input.extra_files_path, 'shapefile.shp' )} - #else + #else if $input.is_of_type("tabular") + '$input''.tsv' + #else '$input' #end if + #if $settings.advanced=='advanced' + #for $i in $settings.series_oo + #if str('${i.oo}').strip()!='' + -oo ${i.oo} + #end if + #end for + #end if #if $f=='ESRI Shapefile' && mkdir ${shapefile.extra_files_path} && @@ -24,7 +36,7 @@ #end if ]]></command> <inputs> - <param type="data" name="input" format="shp,xml,json,txt" label="Gdal supported input file" help="http://www.gdal.org/ogr_formats.html"/> + <param type="data" name="input" format="shp,xml,json,tabular,txt" label="Gdal supported input file" help="http://www.gdal.org/ogr_formats.html"/> <param type="select" name="f" label="Conversion format" value="" help="Select the format to convert your input file. Currently supported : Shapefile, GeoJSON, GML, KML and WFS."> <option value="ESRI Shapefile">ESRI Shapefile</option> <option value="GeoJSON">GEOJSON</option> @@ -32,6 +44,12 @@ <option value="KML">KML</option> <option value="WFS">WFS</option> </param> + <conditional name="settings"> + <expand macro="gdal_advanced_params_select"/> + <when value="advanced"> + <expand macro="gdal_param_oo"/> + </when> + </conditional> </inputs> <outputs> <data name="output" from_work_dir="output" format="xml" label="${on_string}.${f}"> @@ -57,6 +75,7 @@ <composite_data value="shp_compositefiles/shapefile.sbx"/> </param> <param name="f" value="KML"/> + <param name="advanced" value="simple"/> <output file="ogr2ogr_KML.kml" name="output"/> </test> <test> @@ -68,6 +87,7 @@ <composite_data value="shp_compositefiles/shapefile.sbx"/> </param> <param name="f" value="GML"/> + <param name="advanced" value="simple"/> <output file="ogr2ogr_GML.gml" name="output"/> </test> <test> @@ -79,16 +99,19 @@ <composite_data value="shp_compositefiles/shapefile.sbx"/> </param> <param name="f" value="GeoJSON"/> + <param name="advanced" value="simple"/> <output file="ogr2ogr_geojson.json" name="output"/> </test> <test> <param name="input" value="ogr2ogr_KML.kml" ftype="xml"/> <param name="f" value="GeoJSON"/> + <param name="advanced" value="simple"/> <output file="ogr2ogr_test2_geojson.json" name="output"/> </test> <test> <param name="input" value="ogr2ogr_KML.kml" ftype="xml"/> <param name="f" value="ESRI Shapefile"/> + <param name="advanced" value="simple"/> <output file="shp_compositefiles/ogr2ogr_shapefile2.html" name="shapefile"> <extra_files type="file" name="shapefile.dbf" value="shp_compositefiles/ogr2ogr_shapefile2.dbf" compare="sim_size" delta="50"/> <extra_files type="file" name="shapefile.prj" value="shp_compositefiles/ogr2ogr_shapefile2.prj"/> @@ -99,9 +122,18 @@ <test> <param name="input" value="ogr2ogr_KML.kml" ftype="xml"/> <param name="f" value="GML"/> + <param name="advanced" value="simple"/> <output file="ogr2ogr_GML2.gml" name="output"/> </test> - </tests> + <test> + <param name="input" value="ogr2ogr_fromgbif.tabular" ftype="tabular"/> + <param name="f" value="GeoJSON"/> + <param name="advanced" value="advanced"/> + <param name="oo" value="X_POSSIBLE_NAMES=longitude"/> + <param name="oo" value="Y_POSSIBLE_NAMES=latitude"/> + <output file="ogr2ogr_gbif_to_json.json" name="output" lines_diff="2"/> + </test> +</tests> <help><![CDATA[ ======== Ogrinfo |
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| diff -r 22c54afd1cf3 -r e12db3b4d3a6 test-data/ogr2ogr_fromgbif.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ogr2ogr_fromgbif.tabular Thu Jun 20 06:53:44 2019 -0400 |
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| @@ -0,0 +1,6 @@ +"date" "providedScientificName" "year" "countryCode" "providedCounty" "ambiguous" "verbatimLocality" "latlon" "computedCountyFips" "occurrenceID" "longitude" "basisOfRecord" "providedCommonName" "collectionID" "ownerInstitutionCollectionCode" "name" "institutionID" "computedStateFips" "license" "TSNs" "providerID" "stateProvince" "latitude" "recordedBy" "geo" "provider" "calculatedCounty" "catalogNumber" "ITISscientificName" "pointPath" "kingdom" "calculatedState" "hierarchy_homonym_string" "centroid" "ITIScommonName" "resourceID" "ITIStsn" "prov" +"1957-01-01" "Canis lupus Linnaeus, 1758" "1957" "US" "Washington" "FALSE" "BANK OF ILLINOIS RIVER, WEDINGTON" "-94.2184168,35.9712088" "05143" "919969407" "-94.21841" "specimen" "DOG" "http://fulbright.uark.edu/deans-office/facilities/university-collections-facility/museum-collections.php" "UAFMC Mammals" "Canis lupus" "http://fulbright.uark.edu/collections/index.php" "05" "CC0_1_0" "180596" "359" "Arkansas" "35.97121" "COLE M" "-94.2184168 35.9712088" "University of Arkansas Collections Facility, UAFMC" "Washington" "0074-0001-0007" "Canis lupus" "/-94.2184168,35.9712088/specimen/centroid" "Animalia" "Arkansas" "-202423-914154-914156-158852-331030-914179-914181-179913-179916-179925-180539-552303-180594-180595-180596-" "county" "Gray Wolf;Wolf;Lobo gris;loup" "359,202522" "180596" "bison" +"1972-01-09" "Canis lupus Linnaeus, 1758" "1972" "US" "Marion" "FALSE" "UNKNOWN" "-92.678588,36.2666562" "05089" "919969412" "-92.67859" "specimen" "DOG" "http://fulbright.uark.edu/deans-office/facilities/university-collections-facility/museum-collections.php" "UAFMC Mammals" "Canis lupus" "http://fulbright.uark.edu/collections/index.php" "05" "CC0_1_0" "180596" "359" "Arkansas" "36.26666" "ROBINSON CHARLES" "-92.678588 36.2666562" "University of Arkansas Collections Facility, UAFMC" "Marion" "0072-0409-0001" "Canis lupus" "/-92.678588,36.2666562/specimen/centroid" "Animalia" "Arkansas" "-202423-914154-914156-158852-331030-914179-914181-179913-179916-179925-180539-552303-180594-180595-180596-" "county" "Gray Wolf;Wolf;Lobo gris;loup" "359,202522" "180596" "bison" +"1970-01-01" "Canis lupus Linnaeus, 1758" "1970" "US" "Stone" "FALSE" "IN QUARRY WEST OF HWY 9, SOUTH OF MTN VIEW, NEAR BEAR CREEK" "-92.1404942,35.8569888" "05137" "919969420" "-92.14050" "specimen" "DOG" "http://fulbright.uark.edu/deans-office/facilities/university-collections-facility/museum-collections.php" "UAFMC Mammals" "Canis lupus" "http://fulbright.uark.edu/collections/index.php" "05" "CC0_1_0" "180596" "359" "Arkansas" "35.85699" "TAYLOR J" "-92.1404942 35.8569888" "University of Arkansas Collections Facility, UAFMC" "Stone" "0074-0001-0041" "Canis lupus" "/-92.1404942,35.8569888/specimen/centroid" "Animalia" "Arkansas" "-202423-914154-914156-158852-331030-914179-914181-179913-179916-179925-180539-552303-180594-180595-180596-" "county" "Gray Wolf;Wolf;Lobo gris;loup" "359,202522" "180596" "bison" +NA "Canis lupus Linnaeus, 1758" NA "US" "Sebastian" "FALSE" "FT SMITH" "-94.274989,35.1969808" "05131" "919969655" "-94.27499" "specimen" "DOG" "http://fulbright.uark.edu/deans-office/facilities/university-collections-facility/museum-collections.php" "UAFMC Mammals" "Canis lupus" "http://fulbright.uark.edu/collections/index.php" "05" "CC0_1_0" "180596" "359" "Arkansas" "35.19698" "GIPSON B H" "-94.274989 35.1969808" "University of Arkansas Collections Facility, UAFMC" "Sebastian" "0085-0046-0282" "Canis lupus" "/-94.274989,35.1969808/specimen/centroid" "Animalia" "Arkansas" "-202423-914154-914156-158852-331030-914179-914181-179913-179916-179925-180539-552303-180594-180595-180596-" "county" "Gray Wolf;Wolf;Lobo gris;loup" "359,202522" "180596" "bison" +"1970-01-01" "Canis lupus Linnaeus, 1758" "1970" "US" "Sebastian" "FALSE" "FT SMITH" "-94.274989,35.1969808" "05131" "919969656" "-94.27499" "specimen" "DOG" "http://fulbright.uark.edu/deans-office/facilities/university-collections-facility/museum-collections.php" "UAFMC Mammals" "Canis lupus" "http://fulbright.uark.edu/collections/index.php" "05" "CC0_1_0" "180596" "359" "Arkansas" "35.19698" "GIPSON B H" "-94.274989 35.1969808" "University of Arkansas Collections Facility, UAFMC" "Sebastian" "0085-0046-0283" "Canis lupus" "/-94.274989,35.1969808/specimen/centroid" "Animalia" "Arkansas" "-202423-914154-914156-158852-331030-914179-914181-179913-179916-179925-180539-552303-180594-180595-180596-" "county" "Gray Wolf;Wolf;Lobo gris;loup" "359,202522" "180596" "bison" |
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| diff -r 22c54afd1cf3 -r e12db3b4d3a6 test-data/ogr2ogr_gbif_to_json.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ogr2ogr_gbif_to_json.json Thu Jun 20 06:53:44 2019 -0400 |
| [ |
| @@ -0,0 +1,11 @@ +{ +"type": "FeatureCollection", +"name": "dataset_4.dat", +"features": [ +{ "type": "Feature", "properties": { "date": "1957-01-01", "providedScientificName": "Canis lupus Linnaeus, 1758", "year": "1957", "countryCode": "US", "providedCounty": "Washington", "ambiguous": "FALSE", "verbatimLocality": "BANK OF ILLINOIS RIVER, WEDINGTON", "latlon": "-94.2184168,35.9712088", "computedCountyFips": "05143", "occurrenceID": "919969407", "longitude": -94.21841, "basisOfRecord": "specimen", "providedCommonName": "DOG", "collectionID": "http:\/\/fulbright.uark.edu\/deans-office\/facilities\/university-collections-facility\/museum-collections.php", "ownerInstitutionCollectionCode": "UAFMC Mammals", "name": "Canis lupus", "institutionID": "http:\/\/fulbright.uark.edu\/collections\/index.php", "computedStateFips": "05", "license": "CC0_1_0", "TSNs": "180596", "providerID": "359", "stateProvince": "Arkansas", "latitude": 35.97121, "recordedBy": "COLE M", "geo": "-94.2184168 35.9712088", "provider": "University of Arkansas Collections Facility, UAFMC", "calculatedCounty": "Washington", "catalogNumber": "0074-0001-0007", "ITISscientificName": "Canis lupus", "pointPath": "\/-94.2184168,35.9712088\/specimen\/centroid", "kingdom": "Animalia", "calculatedState": "Arkansas", "hierarchy_homonym_string": "-202423-914154-914156-158852-331030-914179-914181-179913-179916-179925-180539-552303-180594-180595-180596-", "centroid": "county", "ITIScommonName": "Gray Wolf;Wolf;Lobo gris;loup", "resourceID": "359,202522", "ITIStsn": "180596", "prov": "bison" }, "geometry": { "type": "Point", "coordinates": [ -94.21841, 35.97121 ] } }, +{ "type": "Feature", "properties": { "date": "1972-01-09", "providedScientificName": "Canis lupus Linnaeus, 1758", "year": "1972", "countryCode": "US", "providedCounty": "Marion", "ambiguous": "FALSE", "verbatimLocality": "UNKNOWN", "latlon": "-92.678588,36.2666562", "computedCountyFips": "05089", "occurrenceID": "919969412", "longitude": -92.67859, "basisOfRecord": "specimen", "providedCommonName": "DOG", "collectionID": "http:\/\/fulbright.uark.edu\/deans-office\/facilities\/university-collections-facility\/museum-collections.php", "ownerInstitutionCollectionCode": "UAFMC Mammals", "name": "Canis lupus", "institutionID": "http:\/\/fulbright.uark.edu\/collections\/index.php", "computedStateFips": "05", "license": "CC0_1_0", "TSNs": "180596", "providerID": "359", "stateProvince": "Arkansas", "latitude": 36.26666, "recordedBy": "ROBINSON CHARLES", "geo": "-92.678588 36.2666562", "provider": "University of Arkansas Collections Facility, UAFMC", "calculatedCounty": "Marion", "catalogNumber": "0072-0409-0001", "ITISscientificName": "Canis lupus", "pointPath": "\/-92.678588,36.2666562\/specimen\/centroid", "kingdom": "Animalia", "calculatedState": "Arkansas", "hierarchy_homonym_string": "-202423-914154-914156-158852-331030-914179-914181-179913-179916-179925-180539-552303-180594-180595-180596-", "centroid": "county", "ITIScommonName": "Gray Wolf;Wolf;Lobo gris;loup", "resourceID": "359,202522", "ITIStsn": "180596", "prov": "bison" }, "geometry": { "type": "Point", "coordinates": [ -92.67859, 36.26666 ] } }, +{ "type": "Feature", "properties": { "date": "1970-01-01", "providedScientificName": "Canis lupus Linnaeus, 1758", "year": "1970", "countryCode": "US", "providedCounty": "Stone", "ambiguous": "FALSE", "verbatimLocality": "IN QUARRY WEST OF HWY 9, SOUTH OF MTN VIEW, NEAR BEAR CREEK", "latlon": "-92.1404942,35.8569888", "computedCountyFips": "05137", "occurrenceID": "919969420", "longitude": -92.1405, "basisOfRecord": "specimen", "providedCommonName": "DOG", "collectionID": "http:\/\/fulbright.uark.edu\/deans-office\/facilities\/university-collections-facility\/museum-collections.php", "ownerInstitutionCollectionCode": "UAFMC Mammals", "name": "Canis lupus", "institutionID": "http:\/\/fulbright.uark.edu\/collections\/index.php", "computedStateFips": "05", "license": "CC0_1_0", "TSNs": "180596", "providerID": "359", "stateProvince": "Arkansas", "latitude": 35.85699, "recordedBy": "TAYLOR J", "geo": "-92.1404942 35.8569888", "provider": "University of Arkansas Collections Facility, UAFMC", "calculatedCounty": "Stone", "catalogNumber": "0074-0001-0041", "ITISscientificName": "Canis lupus", "pointPath": "\/-92.1404942,35.8569888\/specimen\/centroid", "kingdom": "Animalia", "calculatedState": "Arkansas", "hierarchy_homonym_string": "-202423-914154-914156-158852-331030-914179-914181-179913-179916-179925-180539-552303-180594-180595-180596-", "centroid": "county", "ITIScommonName": "Gray Wolf;Wolf;Lobo gris;loup", "resourceID": "359,202522", "ITIStsn": "180596", "prov": "bison" }, "geometry": { "type": "Point", "coordinates": [ -92.1405, 35.85699 ] } }, +{ "type": "Feature", "properties": { "date": "NA", "providedScientificName": "Canis lupus Linnaeus, 1758", "year": "NA", "countryCode": "US", "providedCounty": "Sebastian", "ambiguous": "FALSE", "verbatimLocality": "FT SMITH", "latlon": "-94.274989,35.1969808", "computedCountyFips": "05131", "occurrenceID": "919969655", "longitude": -94.27499, "basisOfRecord": "specimen", "providedCommonName": "DOG", "collectionID": "http:\/\/fulbright.uark.edu\/deans-office\/facilities\/university-collections-facility\/museum-collections.php", "ownerInstitutionCollectionCode": "UAFMC Mammals", "name": "Canis lupus", "institutionID": "http:\/\/fulbright.uark.edu\/collections\/index.php", "computedStateFips": "05", "license": "CC0_1_0", "TSNs": "180596", "providerID": "359", "stateProvince": "Arkansas", "latitude": 35.19698, "recordedBy": "GIPSON B H", "geo": "-94.274989 35.1969808", "provider": "University of Arkansas Collections Facility, UAFMC", "calculatedCounty": "Sebastian", "catalogNumber": "0085-0046-0282", "ITISscientificName": "Canis lupus", "pointPath": "\/-94.274989,35.1969808\/specimen\/centroid", "kingdom": "Animalia", "calculatedState": "Arkansas", "hierarchy_homonym_string": "-202423-914154-914156-158852-331030-914179-914181-179913-179916-179925-180539-552303-180594-180595-180596-", "centroid": "county", "ITIScommonName": "Gray Wolf;Wolf;Lobo gris;loup", "resourceID": "359,202522", "ITIStsn": "180596", "prov": "bison" }, "geometry": { "type": "Point", "coordinates": [ -94.27499, 35.19698 ] } }, +{ "type": "Feature", "properties": { "date": "1970-01-01", "providedScientificName": "Canis lupus Linnaeus, 1758", "year": "1970", "countryCode": "US", "providedCounty": "Sebastian", "ambiguous": "FALSE", "verbatimLocality": "FT SMITH", "latlon": "-94.274989,35.1969808", "computedCountyFips": "05131", "occurrenceID": "919969656", "longitude": -94.27499, "basisOfRecord": "specimen", "providedCommonName": "DOG", "collectionID": "http:\/\/fulbright.uark.edu\/deans-office\/facilities\/university-collections-facility\/museum-collections.php", "ownerInstitutionCollectionCode": "UAFMC Mammals", "name": "Canis lupus", "institutionID": "http:\/\/fulbright.uark.edu\/collections\/index.php", "computedStateFips": "05", "license": "CC0_1_0", "TSNs": "180596", "providerID": "359", "stateProvince": "Arkansas", "latitude": 35.19698, "recordedBy": "GIPSON B H", "geo": "-94.274989 35.1969808", "provider": "University of Arkansas Collections Facility, UAFMC", "calculatedCounty": "Sebastian", "catalogNumber": "0085-0046-0283", "ITISscientificName": "Canis lupus", "pointPath": "\/-94.274989,35.1969808\/specimen\/centroid", "kingdom": "Animalia", "calculatedState": "Arkansas", "hierarchy_homonym_string": "-202423-914154-914156-158852-331030-914179-914181-179913-179916-179925-180539-552303-180594-180595-180596-", "centroid": "county", "ITIScommonName": "Gray Wolf;Wolf;Lobo gris;loup", "resourceID": "359,202522", "ITIStsn": "180596", "prov": "bison" }, "geometry": { "type": "Point", "coordinates": [ -94.27499, 35.19698 ] } } +] +} |