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EODIE tool metadata

Miscellaneous

Name: EODIE

Description: converts simple features data between file formats

Id: eodie

Guid: toolshed.g2.bx.psu.edu/repos/climate/eodie/eodie/1.0.2

Version: 1.0.2

Version command string: None

Display in tool panel: True

Version lineage of this tool (guids ordered most recent to oldest)

toolshed.g2.bx.psu.edu/repos/climate/eodie/eodie/1.0.2 (this tool)

eodie

Requirements (dependencies defined in the <requirements> tag set)

Requirements:

name

version

type

eodie

1.0.2

package

python

3.9

package

shapely

1.8

package

rasterio

1.2

package

rasterstats

0.16

package

fiona

1.8

package

numpy

1.21

package

gdal

3.4.0

package

pyyaml

6.0

package

unzip

6.0

package

tar

1.34

package

Additional information about this tool

Command:

mkdir -p work/data_collection work/results results_csv results_tiffs &&
        cp '$config_tif' config_tif.yml && 
        cp '$config_s2'  config_s2.yml  && 
        cp '$config_ls8' config_ls8.yml && 
        cp '$user_config' user_config.yml && 
        cp '${input.extra_files_path}'/*  work/ &&
        cd work &&
        ln -s '${input_type.input_file}'  '${input_type.input_file.element_identifier}' &&
        #if $input_type.input_file.is_of_type("zip")
            unzip '$input_type.input_file' -d data_collection/    &&
        #elif $input_type.input_file.is_of_type("tar")
            tar -xf '$input_type.input_file' -C data_collection   &&
        #end if
        #if str($input_type.platform) == 's2'
            mkdir -p sentinel2_tiles_world &&
            (cp '$input_type.s2_shp.extra_files_path'/shapefile.shp sentinel2_tiles_world/sentinel2_tiles_world.shp || true )  &&
            (cp '$input_type.s2_shp.extra_files_path'/shapefile.shx sentinel2_tiles_world/sentinel2_tiles_world.shx || true )  &&
            (cp '$input_type.s2_shp.extra_files_path'/shapefile.dbf sentinel2_tiles_world/sentinel2_tiles_world.dbf || true )  &&
            (cp '$input_type.s2_shp.extra_files_path'/shapefile.prj sentinel2_tiles_world/sentinel2_tiles_world.prj || true )  &&
        #elif str($input_type.platform) == 'ls8'
            mkdir -p WRS2_descending &&
            (cp '$input_type.ls8_shp.extra_files_path'/shapefile.shp WRS2_descending/WRS2_descending.shp || true )  &&
            (cp '$input_type.ls8_shp.extra_files_path'/shapefile.shx WRS2_descending/WRS2_descending.shx || true )  &&
            (cp '$input_type.ls8_shp.extra_files_path'/shapefile.dbf WRS2_descending/WRS2_descending.dbf || true )  &&
            (cp '$input_type.ls8_shp.extra_files_path'/shapefile.prj WRS2_descending/WRS2_descending.prj || true )  &&
        #end if

        eodie_process.py
        --platform $input_type.platform
        #if str($input_type.platform) == 'tif'
            --file ${input_type.input_file.element_identifier}
        #else
            --dir data_collection
            --out ./results
        #end if
        --shp shapefile
        #for $i, $s in enumerate( $adv_options.statistics )
            #if str($i) == '0'
                --statistics_out
            --statistics 
            #end if
            #if $s.stats_input.stats and str($s.stats_input.stats) != '':
                #if str($s.stats_input.stats) == 'percentile':
                    '$s.stats_input.stats'_'$s.stats_input.p_value'
                #else
                    '$s.stats_input.stats'
                #end if
            #end if
        #end for
        #if $adv_options.indices and str($adv_options.indices) != '':
            --index 
            #for $idx in str($adv_options.indices).split(','):
                '$idx'
            #end for
        #end if
        #if $adv_options.start_date and str($adv_options.start_date) != '':
            --start int($adv_options.start_date)
        #end if
        #if $adv_options.end_date and str($adv_options.end_date) != '':
            --start int($adv_options.end_date)
        #end if
        $adv_options.exclude_border 
        $adv_options.exclude_splitshp 
        --id '$identifier'  &&

        mv results/*.log '$logfile'  &&
        bash '$__tool_directory__/postprocess_csv.sh' 'results' '../results_csv' &&
        ( mv results/*.tif ../results_tiffs/ || echo "No tiff files generated" ) &&
        echo "EODIE data extractor is done"

Interpreter: None

Forces a history refresh: False

Functional tests

name

inputs

outputs

required files

Test-1

name: value

smaller_area_20100401.tif
test_polygons/test_polygons.html
value

Test-2

name: value

LS8.tar
WRS2_descending/WRS2_descending.html
test_parcels_32635/test_parcels_32635.html
value

Test-3

name: value

S2.tar
sentinel2_tiles_world/sentinel2_tiles_world.html
test_parcels_32635/test_parcels_32635.html
value