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first version of hirondelle crim ogc api processes (#114)
* first version of hirondelle crim ogc api processes * remove credentials from input parameters, pass them as file, needs to be changed to user preferences later * add file to test * correct r file name * add expect_failure * rm No description provided texts
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| categories: | ||
| - Ecology | ||
| owner: ecology | ||
| remote_repository_url: https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper | ||
| homepage_url: https://github.com/AquaINFRA/galaxy | ||
| long_description: | | ||
| This tool is a wrapper for OGC API Processes coming from https://osf.io/gfbws/. | ||
| type: unrestricted | ||
| auto_tool_repositories: | ||
| name_template: "{{ tool_id }}" | ||
| description_template: "Wrapper for OGC API Processes: {{ tool_name }}." |
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tools/hirondelle_crim_ogc_api_processes/crim_project_ogc_api_processes.xml
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| <tool id="hirondelle_crim" name="Hirondelle CRIM OGC API Processes" version="0.1.0" profile="22.05"> | ||
| <description>executes remote processes.</description> | ||
| <macros> | ||
| <import>macros.xml</import> | ||
| </macros> | ||
| <expand macro="requirements"/> | ||
| <command detect_errors="exit_code"><![CDATA[ | ||
| Rscript '$__tool_directory__/ogc_api_processes_wrapper.R' | ||
| --outputData '$output_data' | ||
| ]]></command> | ||
| <configfiles> | ||
| <inputs name="inputs" filename="inputs.json" data_style="paths"/> | ||
| </configfiles> | ||
| <inputs> | ||
| <conditional name="conditional_process"> | ||
| <param name="select_process" type="select" label="Select process"> | ||
| <option value="algae-usecase-workflow-copernicus">algae-usecase-workflow-copernicus: Algae bloom for water quality assessment on Sentinel-2 imagery offered by Copernicus platform.</option> | ||
| <option value="algae-usecase-workflow-copernicus-process">algae-usecase-workflow-copernicus-process: Processing on Sentinel-2 bands to evaluate algae bloom.</option> | ||
| <option value="algae-usecase-workflow-earth-search">algae-usecase-workflow-earth-search: Algae bloom for water quality assessment on Sentinel-2 L2A imagery offered by Earth-Search platform.</option> | ||
| <option value="algae-usecase-workflow-earth-search-process">algae-usecase-workflow-earth-search-process: Processing on Sentinel-2 L2A bands to evaluate algae bloom.</option> | ||
| <option value="calculate-band">calculate-band: Performs a calculation with bands.</option> | ||
| <option value="download-band-sentinel2-product-safe">download-band-sentinel2-product-safe: Downloads Copernicus products.</option> | ||
| <option value="download-band-sentinel2-stac-item">download-band-sentinel2-stac-item: Downloads Sentinel-2 GeoTiff from STAC Item.</option> | ||
| <option value="EchoProcess">EchoProcess</option> | ||
| <option value="file_index_selector">file_index_selector: File Index Selector</option> | ||
| <option value="file2string_array">file2string_array: File to String-Array</option> | ||
| <option value="jsonarray2netcdf">jsonarray2netcdf: JSON array to NetCDF</option> | ||
| <option value="metalink2netcdf">metalink2netcdf: Metalink to NetCDF</option> | ||
| <option value="ogc-tb16-land-cover-mapping">ogc-tb16-land-cover-mapping: OGC Testbed-16 Pixel-Wise Classifier for Land Cover Mapping</option> | ||
| <option value="plot-image">plot-image: Plots an image with colors.</option> | ||
| <option value="reproject-image">reproject-image: Performs image reprojection.</option> | ||
| <option value="select-products-sentinel2">select-products-sentinel2: Searches the specified catalog for Sentinel-2 products matching filtering criteria.</option> | ||
| </param> | ||
| <when value="algae-usecase-workflow-copernicus"> | ||
| <param name="user_credentials" label="user_credentials" optional="false" type="data" format="json"/> | ||
| <param name="cookie" label="cookie" optional="false" value="" type="text"/> | ||
| <param name="date" label="date" optional="false" value="" type="text"/> | ||
| <param name="delta_Array_integer" label="delta" optional="false" value="" help="Please provide comma-seperated values of type integer here." type="text"/> | ||
| <param name="aoi" label="aoi" optional="false" value="" type="data" format="txt"/> | ||
| <param name="collection" label="collection" optional="false" value="" type="text"/> | ||
| <param name="cloud_cover_Array_float" label="cloud_cover" optional="false" value="" help="Please provide comma-seperated values of type float here." type="text"/> | ||
| </when> | ||
| <when value="algae-usecase-workflow-copernicus-process"> | ||
| <param name="user_credentials" label="user_credentials" optional="false" type="data" format="json"/> | ||
| <param name="cookie" label="cookie" optional="false" value="" type="text"/> | ||
| <param name="product_url" label="product_url" optional="false" value="" type="text"/> | ||
| </when> | ||
| <when value="algae-usecase-workflow-earth-search"> | ||
| <param name="cookie" label="cookie" optional="false" value="" type="text"/> | ||
| <param name="date_Array_text" label="date" optional="false" value="" help="Please provide comma-seperated values of type text here." type="text"/> | ||
| <param name="delta_Array_integer" label="delta" optional="false" value="" help="Please provide comma-seperated values of type integer here." type="text"/> | ||
| <param name="toi_Array_text" label="toi" optional="false" value="" help="Please provide comma-seperated values of type text here." type="text"/> | ||
| <param name="aoi" label="aoi" optional="false" value="" help="Polygon defining the area of interest." type="data" format="txt"/> | ||
| <param name="collection" label="collection" optional="false" value="" type="text"/> | ||
| <param name="cloud_cover_Array_float" label="cloud_cover" optional="false" value="" help="Please provide comma-seperated values of type float here." type="text"/> | ||
| </when> | ||
| <when value="algae-usecase-workflow-earth-search-process"> | ||
| <param name="cookie" label="cookie" optional="false" value="" type="text"/> | ||
| <param name="product_url" label="product_url" optional="false" value="" help="The STAC Item should contain Assets with Sentinel-2 product bands." type="text"/> | ||
| </when> | ||
| <when value="calculate-band"> | ||
| <param name="cookie" label="cookie" optional="false" value="" type="text"/> | ||
| <param name="name" label="name" optional="false" value="" help="Name to apply for the output GeoTiff file." type="text"/> | ||
| <param name="calc" label="calc" optional="false" value="" help="Calculation to perform with band references." type="text"/> | ||
| <param name="band_a" label="band_a" optional="false" value="" type="text"/> | ||
| <param name="band_b" label="band_b" optional="false" value="" type="text"/> | ||
| <param name="band_c" label="band_c" optional="false" value="" type="text"/> | ||
| <param name="band_d" label="band_d" optional="false" value="" type="text"/> | ||
| <param name="band_e" label="band_e" optional="false" value="" type="text"/> | ||
| <param name="band_f" label="band_f" optional="false" value="" type="text"/> | ||
| <param name="band_g" label="band_g" optional="false" value="" type="text"/> | ||
| <param name="band_h" label="band_h" optional="false" value="" type="text"/> | ||
| <param name="band_i" label="band_i" optional="false" value="" type="text"/> | ||
| <param name="band_j" label="band_j" optional="false" value="" type="text"/> | ||
| <param name="band_k" label="band_k" optional="false" value="" type="text"/> | ||
| <param name="band_l" label="band_l" optional="false" value="" type="text"/> | ||
| <param name="band_m" label="band_m" optional="false" value="" type="text"/> | ||
| <param name="band_n" label="band_n" optional="false" value="" type="text"/> | ||
| <param name="band_o" label="band_o" optional="false" value="" type="text"/> | ||
| <param name="band_p" label="band_p" optional="false" value="" type="text"/> | ||
| <param name="band_q" label="band_q" optional="false" value="" type="text"/> | ||
| <param name="band_r" label="band_r" optional="false" value="" type="text"/> | ||
| <param name="band_s" label="band_s" optional="false" value="" type="text"/> | ||
| <param name="band_t" label="band_t" optional="false" value="" type="text"/> | ||
| <param name="band_u" label="band_u" optional="false" value="" type="text"/> | ||
| <param name="band_v" label="band_v" optional="false" value="" type="text"/> | ||
| <param name="band_w" label="band_w" optional="false" value="" type="text"/> | ||
| <param name="band_x" label="band_x" optional="false" value="" type="text"/> | ||
| <param name="band_y" label="band_y" optional="false" value="" type="text"/> | ||
| <param name="band_z" label="band_z" optional="false" value="" type="text"/> | ||
| </when> | ||
| <when value="download-band-sentinel2-product-safe"> | ||
| <param name="user_credentials" label="user_credentials" optional="false" type="data" format="json"/> | ||
| <param name="cookie" label="cookie" optional="false" value="" type="text"/> | ||
| <param name="product_url" label="product_url" optional="false" value="" type="text"/> | ||
| <param name="resolution_Array_text" label="resolution" optional="false" value="" help="Please provide comma-seperated values of type text here." type="text"/> | ||
| <param name="band" label="band" optional="false" value="" type="select"> | ||
| <option value="B01">B01</option> | ||
| <option value="B02">B02</option> | ||
| <option value="B03">B03</option> | ||
| <option value="B04">B04</option> | ||
| <option value="B05">B05</option> | ||
| <option value="B06">B06</option> | ||
| <option value="B07">B07</option> | ||
| <option value="B08">B08</option> | ||
| <option value="B8A">B8A</option> | ||
| <option value="B09">B09</option> | ||
| <option value="B11">B11</option> | ||
| <option value="B12">B12</option> | ||
| <option value="AOT">AOT</option> | ||
| <option value="SCL">SCL</option> | ||
| <option value="TCI">TCI</option> | ||
| <option value="WVP">WVP</option> | ||
| </param> | ||
| <param name="debug_Array_boolean" label="debug" value="" help="Please provide comma-seperated values of type boolean here." type="text"/> | ||
| </when> | ||
| <when value="download-band-sentinel2-stac-item"> | ||
| <param name="cookie" label="cookie" optional="false" value="" type="text"/> | ||
| <param name="product_url" label="product_url" optional="false" value="" type="text"/> | ||
| <param name="band" label="band" optional="false" value="" type="select"> | ||
| <option value="B01">B01</option> | ||
| <option value="B02">B02</option> | ||
| <option value="B03">B03</option> | ||
| <option value="B04">B04</option> | ||
| <option value="B05">B05</option> | ||
| <option value="B06">B06</option> | ||
| <option value="B07">B07</option> | ||
| <option value="B08">B08</option> | ||
| <option value="B8A">B8A</option> | ||
| <option value="B09">B09</option> | ||
| <option value="B11">B11</option> | ||
| <option value="B12">B12</option> | ||
| <option value="AOT">AOT</option> | ||
| <option value="SCL">SCL</option> | ||
| <option value="TCI">TCI</option> | ||
| <option value="WVP">WVP</option> | ||
| </param> | ||
| </when> | ||
| <when value="EchoProcess"> | ||
| <param name="cookie" label="cookie" optional="false" value="" type="text"/> | ||
| <param name="stringInput" label="stringInput" optional="false" value="" type="select"> | ||
| <option value="Value1">Value1</option> | ||
| <option value="Value2">Value2</option> | ||
| <option value="Value3">Value3</option> | ||
| </param> | ||
| <param name="measureInput" label="measureInput" optional="false" help="This is an example of a NUMERIC literal with an associated unit of measure." type="text"/> | ||
| <param name="dateInput" label="dateInput" optional="false" value="" help="This is an example of a DATE literal input." type="text"/> | ||
| <param name="doubleInput" label="doubleInput" optional="false" value="" help="This is an example of a DOUBLE literal input that is bounded between a value greater than 0 and 10. The default value is 5." type="float"/> | ||
| <param name="arrayInput_Array_integer" label="arrayInput" optional="false" value="" help="Please provide comma-seperated values of type integer here." type="text"/> | ||
| <param name="complexObjectInput" label="complexObjectInput" optional="false" help="This is an example of a complex object input." type="text"/> | ||
| <param name="geometryInput" label="geometryInput" optional="false" value="" help="This is an example of a geometry input. In this case the geometry can be expressed as a GML of GeoJSON geometry." type="text"/> | ||
| <param name="boundingBoxInput" label="boundingBoxInput" optional="false" help="This is an example of an image input. In this case, the input is an array of up to 150 images that might, for example, be a set of tiles. The oneOf[] conditional is used to indicate the acceptable image content types; GeoTIFF and JPEG 2000 in this case. Each input image in the input array can be included inline in the execute request as a base64-encoded string or referenced using the link.yaml schema. The use of a base64-encoded string is implied by the specification and does not need to be specified in the definition of the input." type="data" format="txt"/> | ||
| <param name="imagesInput" label="imagesInput" optional="false" help="This is an example of an image input. In this case, the input is an array of up to 150 images that might, for example, be a set of tiles. The oneOf[] conditional is used to indicate the acceptable image content types; GeoTIFF and JPEG 2000 in this case. Each input image in the input array can be included inline in the execute request as a base64-encoded string or referenced using the link.yaml schema. The use of a base64-encoded string is implied by the specification and does not need to be specified in the definition of the input." type="data" format="txt"/> | ||
| <param name="featureCollectionInput" label="featureCollectionInput" optional="false" help="This is an example of an input that is a feature collection that can be encoded in one of three ways. As a GeoJSON feature collection, as a GML feature collection retrieved from a WFS or as a KML document." type="text"/> | ||
| </when> | ||
| <when value="file_index_selector"> | ||
| <param name="cookie" label="cookie" optional="false" value="" type="text"/> | ||
| <param name="files" label="files" optional="false" type="data" format="txt"/> | ||
| <param name="index" label="index" optional="false" value="" type="integer"/> | ||
| </when> | ||
| <when value="file2string_array"> | ||
| <param name="cookie" label="cookie" optional="false" value="" type="text"/> | ||
| <param name="input" label="input" optional="false" value="" type="data" format="txt"/> | ||
| </when> | ||
| <when value="jsonarray2netcdf"> | ||
| <param name="cookie" label="cookie" optional="false" value="" type="text"/> | ||
| <param name="input" label="input" optional="false" value="" help="JSON file formed of an array of file URIs, each representing NetCDF contents." type="text"/> | ||
| </when> | ||
| <when value="metalink2netcdf"> | ||
| <param name="cookie" label="cookie" optional="false" value="" type="text"/> | ||
| <param name="input" label="input" optional="false" type="text"/> | ||
| <param name="index" label="index" optional="false" value="" help="Index of the MetaLink file to extract. This index is 1-based." type="integer"/> | ||
| </when> | ||
| <when value="ogc-tb16-land-cover-mapping"> | ||
| <param name="cookie" label="cookie" optional="false" value="" type="text"/> | ||
| <param name="raster_file" label="raster_file" optional="false" help="Input raster onto which to run object classification. Either a Sentinel-2 SAFE ZIP or a RBG-NIR GeoTiff." type="data" format="txt"/> | ||
| <param name="raster_bands_Array_integer" label="raster_bands" optional="false" value="" help="Please provide comma-seperated values of type integer here." type="text"/> | ||
| <param name="raster_mean_Array_float" label="raster_mean" optional="false" value="" help="Please provide comma-seperated values of type float here." type="text"/> | ||
| <param name="raster_std_Array_float" label="raster_std" optional="false" value="" help="Please provide comma-seperated values of type float here." type="text"/> | ||
| <param name="patch_size_Array_integer" label="patch_size" optional="false" value="" help="Please provide comma-seperated values of type integer here." type="text"/> | ||
| <param name="batch_size_Array_integer" label="batch_size" optional="false" value="" help="Please provide comma-seperated values of type integer here." type="text"/> | ||
| <param name="device_Array_text" label="device" optional="false" value="" help="Please provide comma-seperated values of type text here." type="text"/> | ||
| </when> | ||
| <when value="plot-image"> | ||
| <param name="cookie" label="cookie" optional="false" value="" type="text"/> | ||
| <param name="input_image" label="input_image" optional="false" value="" help="Image to map with the colors bins." type="data" format="txt"/> | ||
| <param name="color_scale" label="color_scale" optional="false" value="" help="JSON-like array with each item being an array of 2 elements, the first for the bin scale value and the second for the RGB color. Each RGB value can be either a [0-1] floating point or a [0-255] integer. Example: '[ [0, [0,0,0]], [20, [0,0,255]], [50, [255,100,0]] ]'" type="text"/> | ||
| <param name="output_name_Array_text" label="output_name" optional="false" value="" help="Please provide comma-seperated values of type text here." type="text"/> | ||
| <param name="plot_name_Array_text" label="plot_name" optional="false" value="" help="Please provide comma-seperated values of type text here." type="text"/> | ||
| <param name="plot_title_Array_text" label="plot_title" optional="false" value="" help="Please provide comma-seperated values of type text here." type="text"/> | ||
| </when> | ||
| <when value="reproject-image"> | ||
| <param name="cookie" label="cookie" optional="false" value="" type="text"/> | ||
| <param name="input_image" label="input_image" optional="false" type="data" format="txt"/> | ||
| <param name="output_dimensions_Array_integer" label="output_dimensions" optional="false" value="" help="Please provide comma-seperated values of type integer here." type="text"/> | ||
| <param name="output_resolution_Array_integer" label="output_resolution" optional="false" value="" help="Please provide comma-seperated values of type integer here." type="text"/> | ||
| <param name="output_name" label="output_name" optional="false" value="" help="Name to apply for the output GeoTiff file." type="text"/> | ||
| </when> | ||
| <when value="select-products-sentinel2"> | ||
| <param name="cookie" label="cookie" optional="false" value="" type="text"/> | ||
| <param name="date_Array_text" label="date" optional="false" value="" help="Please provide comma-seperated values of type text here." type="text"/> | ||
| <param name="delta_Array_integer" label="delta" optional="false" value="" help="Please provide comma-seperated values of type integer here." type="text"/> | ||
| <param name="toi_Array_text" label="toi" optional="false" value="" help="Please provide comma-seperated values of type text here." type="text"/> | ||
| <param name="aoi" label="aoi" optional="false" value="" help="Polygon defining the area of interest." type="data" format="txt"/> | ||
| <param name="collection" label="collection" optional="false" value="" type="text"/> | ||
| <param name="product_level_Array_text" label="product_level" optional="false" value="" help="Please provide comma-seperated values of type text here." type="text"/> | ||
| <param name="catalog" label="catalog" optional="false" value="" type="select"> | ||
| <option value="copernicus">copernicus</option> | ||
| <option value="earth-search">earth-search</option> | ||
| </param> | ||
| <param name="cloud_cover_Array_float" label="cloud_cover" optional="false" value="" help="Please provide comma-seperated values of type float here." type="text"/> | ||
| </when> | ||
| </conditional> | ||
| </inputs> | ||
| <outputs> | ||
| <data name="output_data" format="txt" label="$select_process"/> | ||
| </outputs> | ||
| <expand macro="tests"/> | ||
| <help>Use the dropdown menu at the top to select the process and then complete the corresponding from, which is different for every process.</help> | ||
| <expand macro="citations"/> | ||
| </tool> |
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