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planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit 3989415663771a85b3a0be6c02308994ac4adc85
author ecology
date Wed, 23 Oct 2024 22:35:12 +0000
parents 0117fab93b87
children e1f41a25ff24
comparison
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0:0117fab93b87 1:84557c0b3eef
1 <tool id="aquainfra_ogc_api_processes" name="AquaINFRA OGC API Processes" version="0.1.0" profile="22.05"> 1 <tool id="aquainfra_ogc_api_processes" name="AquaINFRA OGC API Processes" version="0.2.0" profile="22.05">
2 <description/> 2 <description/>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <creator> 6 <creator>
7 <organization name="EOSC AquaINFRA" url="https://aquainfra.eu/"/> 7 <organization name="EOSC AquaINFRA" url="https://aquainfra.eu/"/>
8 </creator> 8 </creator>
9 <expand macro="requirements"/> 9 <expand macro="requirements"/>
10 <command detect_errors="exit_code"><![CDATA[ 10 <command detect_errors="exit_code"><![CDATA[
11 Rscript '$__tool_directory__/aquainfra_ogc_api_processes.R' 11 Rscript '$__tool_directory__/aquainfra_ogc_api_processes.R'
12 --outputData '$output_data' 12 --outputData '$output_data'
13 ]]></command> 13 ]]></command>
23 <option value="ts-selection-interpolation">ts-selection-interpolation: Select and Interpolate Time Series</option> 23 <option value="ts-selection-interpolation">ts-selection-interpolation: Select and Interpolate Time Series</option>
24 <option value="trend-analysis-mk">trend-analysis-mk: Man-Kendall Trend Analysis on Time Series</option> 24 <option value="trend-analysis-mk">trend-analysis-mk: Man-Kendall Trend Analysis on Time Series</option>
25 <option value="barplot-trend-results">barplot-trend-results: Visualisation of statistical analysis results</option> 25 <option value="barplot-trend-results">barplot-trend-results: Visualisation of statistical analysis results</option>
26 <option value="map-trends-static">map-trends-static: Spatial visualisation of regions and data points</option> 26 <option value="map-trends-static">map-trends-static: Spatial visualisation of regions and data points</option>
27 <option value="map-shapefile-points">map-shapefile-points: Spatial visualisation of regions and data points</option> 27 <option value="map-shapefile-points">map-shapefile-points: Spatial visualisation of regions and data points</option>
28 <option value="owt-classification">OWT-classification: Optical Water Type classification for ocean, coastal and inland waters</option>
28 </param> 29 </param>
29 <when value="points-att-polygon"> 30 <when value="points-att-polygon">
30 <param name="regions" label="Study region or study subregions" optional="false" help="URL (stored in a .txt file) to the study region, or several regions, to classify your input data into groups of interest. Currently it has to be provided as a shapefile. It can be in any coordinate system and will be transformed to WGS84 during this process." type="data" format="txt"/> 31 <param name="regions" label="Study region or study subregions" optional="false" help="URL (stored in a .txt file) to the study region, or several regions, to classify your input data into groups of interest. Currently it has to be provided as a shapefile. It can be in any coordinate system and will be transformed to WGS84 during this process." type="data" format="txt"/>
31 <param name="input_data" label="Table to be merged with study region" optional="false" help="URL (stored in a .txt file) to the input table containing the in-situ data points with coordinates. Can be provided as Excel file or CSV file (comma-separated text file). The coordinates have to be in WGS84 coordinate system." type="data" format="txt"/> 32 <param name="input_data" label="Table to be merged with study region" optional="false" help="URL (stored in a .txt file) to the input table containing the in-situ data points with coordinates. Can be provided as Excel file or CSV file (comma-separated text file). The coordinates have to be in WGS84 coordinate system." type="data" format="txt"/>
32 <param name="colname_long" label="Column name for longitude" optional="false" help="Name of the column that contains longitude values (in WGS84)." type="text"/> 33 <param name="colname_long" label="Column name for longitude" help="Name of the column that contains longitude values (in WGS84)." type="text"/>
33 <param name="colname_lat" label="Column name for latitude" optional="false" help="Name of the column that contains latitude values (in WGS84)." type="text"/> 34 <param name="colname_lat" label="Column name for latitude" help="Name of the column that contains latitude values (in WGS84)." type="text"/>
34 </when> 35 </when>
35 <when value="peri-conv"> 36 <when value="peri-conv">
36 <param name="input_data" label="Table to be grouped by date, with date colum" help="URL (stored in a .txt file) to the table with a column containing a date. It can have other columns which will not be changed during this process." type="data" format="txt"/> 37 <param name="input_data" label="Table to be grouped by date, with date colum" help="URL (stored in a .txt file) to the table with a column containing a date. It can have other columns which will not be changed during this process." type="data" format="txt"/>
37 <param name="colname_date" label="Date column name" optional="false" help="Column name of the date column in the format defined above. Example: 'visit date'." type="text"/> 38 <param name="colname_date" label="Date column name" optional="false" help="Column name of the date column in the format defined above. Example: 'visit date'." type="text"/>
38 <param name="date_format" label="Date format" optional="true" help="The date format used to parse the date, i.e. to extract day, month and year from the date column, e.g. or 'y-m-d' for dates like '1998-08-22' (this is the default) or 'y/m/d' for dates like '1998/08/22'." type="select"> 39 <param name="date_format" label="Date format" optional="true" help="The date format used to parse the date, i.e. to extract day, month and year from the date column, e.g. or 'y-m-d' for dates like '1998-08-22' (this is the default) or 'y/m/d' for dates like '1998/08/22'." type="select">
39 <option value="y-m-d">y-m-d</option> 40 <option value="y-m-d">y-m-d</option>
40 <option value="y/m/d">y/m/d</option> 41 <option value="y/m/d">y/m/d</option>
41 </param> 42 </param>
42 <param name="group_to_periods" label="Periods to group the data into" optional="true" help="Define the periods that you want the data to be grouped into. Please follow the example: 'Dec-01:Mar-01,Mar-02:May-30,Jun-01:Aug-30,Sep-01:Nov-30' (first three letters of each month, then a minus/hyphen, then the day (two digits), then comma, then the next period)." type="text"> 43 <param name="group_to_periods" label="Periods to group the data into" optional="true" help="Define the periods that you want the data to be grouped into. Please follow the example: 'Dec-01:Mar-01,Mar-02:May-30,Jun-01:Aug-30,Sep-01:Nov-30' (first three letters of each month, then a minus/hyphen, then the day (two digits), then comma, then the next period)." type="text">
43 <validator type="regex">^(Jan|Feb|Mar|Apr|May|Jun|Jul|Aug|Sep|Oct|Nov|Dec)-[0-3][0-9]:(Jan|Feb|Mar|Apr|May|Jun|Jul|Aug|Sep|Oct|Nov|Dec)-[0-3][0-9](,(Jan|Feb|Mar|Apr|May|Jun|Jul|Aug|Sep|Oct|Nov|Dec)-[0-3][0-9]:(Jan|Feb|Mar|Apr|May|Jun|Jul|Aug|Sep|Oct|Nov|Dec)-[0-3][0-9])*$</validator> 44 <validator type="regex">^(Jan|Feb|Mar|Apr|May|Jun|Jul|Aug|Sep|Oct|Nov|Dec)-[0-3][0-9]:(Jan|Feb|Mar|Apr|May|Jun|Jul|Aug|Sep|Oct|Nov|Dec)-[0-3][0-9](,(Jan|Feb|Mar|Apr|May|Jun|Jul|Aug|Sep|Oct|Nov|Dec)-[0-3][0-9]:(Jan|Feb|Mar|Apr|May|Jun|Jul|Aug|Sep|Oct|Nov|Dec)-[0-3][0-9])*$</validator>
44 </param> 45 </param>
45 <param name="group_labels" label="Period labels" optional="true" help="Define names for the periods defined above, separated by a comma. Example: 'winter,spring,summer,autumn'." type="text"/> 46 <param name="group_labels" label="Period labels" optional="true" help="Define names for the periods defined above, separated by a comma. Example: 'winter,spring,summer,autumn'." type="text"/>
46 <param name="year_starts_at_dec1" label="Include December into next year" help="Tell whether the years in your grouping starts at first of December ('true') or not ('false'). This has to be reflected in the period definitions, these should not contradict each other." type="boolean" truevalue="true" falsevalue="false" checked="true"/> 47 <param name="year_starts_at_dec1" label="Include December into next year" help="Tell whether the years in your grouping starts at first of December ('true') or not ('false'). This has to be reflected in the period definitions, these should not contradict each other." type="boolean" truevalue="true" falsevalue="false" checked="true"/>
63 <param name="colnames_relevant" label="Column names identifying group(s)" optional="false" help="Column name(s) identifying relevant groups in the dataset. These columns will be used to define unique groups for which separate trend analyses are performed." type="text"/> 64 <param name="colnames_relevant" label="Column names identifying group(s)" optional="false" help="Column name(s) identifying relevant groups in the dataset. These columns will be used to define unique groups for which separate trend analyses are performed." type="text"/>
64 <param name="colname_time" label="Column name for time" optional="false" help="The name of the column containing the time variable (e.g., year, month) to be used in the trend analysis. Example = 'year'." type="text"/> 65 <param name="colname_time" label="Column name for time" optional="false" help="The name of the column containing the time variable (e.g., year, month) to be used in the trend analysis. Example = 'year'." type="text"/>
65 <param name="colname_value" label="Column name for values" optional="false" help="The name of the column containing the values to be analyzed in the Man-Kendall trend test." type="text"/> 66 <param name="colname_value" label="Column name for values" optional="false" help="The name of the column containing the values to be analyzed in the Man-Kendall trend test." type="text"/>
66 </when> 67 </when>
67 <when value="barplot-trend-results"> 68 <when value="barplot-trend-results">
68 <param name="input_data" label="Input table" optional="false" help="URL (stored in a .txt file) to the input table containing statistical analysis results. The table must include columns for test values, p-values, and group identifiers." type="data" format="txt"/> 69 <param name="input_data" label="Input table" optional="false" help="URL (stored in a .txt file) to the input table containing statistical analysis results. The table must include columns for test values, p-values, and group identifiers." type="data" format="txt"/>
69 <param name="colname_id" label="Column name for identifier" optional="false" help="The name of the column containing group or sample identifiers, e.g., polygon id. Example = 'polygon_id'" type="text"/> 70 <param name="colname_id" label="Column name for identifier" optional="false" help="The name of the column containing group or sample identifiers, e.g., polygon id. Example = 'polygon_id'" type="text"/>
70 <param name="colname_test_value" label="Column name for test value" optional="false" help="The name of the column containing the test values (e.g., statistical coefficients) to be plotted on the Y-axis, e.g., Tau for Mann-Kendall test." type="text"/> 71 <param name="colname_test_value" label="Column name for test value" optional="false" help="The name of the column containing the test values (e.g., statistical coefficients) to be plotted on the Y-axis, e.g., Tau for Mann-Kendall test." type="text"/>
71 <param name="colname_p_value" label="Column name for p value" optional="false" help="The name of the column containing p values, used to determine bar transparency. Example = 'p_value'" type="text"/> 72 <param name="colname_p_value" label="Column name for p value" optional="false" help="The name of the column containing p values, used to determine bar transparency. Example = 'p_value'" type="text"/>
72 <param name="p_value_threshold" label="p value threshold for significance" optional="false" help="The threshold for distinguishing significant from insignificant values. It adjusts the transparency of bars in the plot. Example = 0.05" value="0.05" min="0.01" max="0.1" type="float"/> 73 <param name="p_value_threshold" label="p value threshold for significance" optional="false" help="The threshold for distinguishing significant from insignificant values. It adjusts the transparency of bars in the plot. Example = 0.05" value="0.05" min="0.01" max="0.1" type="float"/>
73 <param name="colname_group" label="Column name for subgroups" optional="false" help="The name of the column that defines the subgroups or categories to be displayed on the X-axis, e.g., seasons for every polygon_id." type="text"/> 74 <param name="colname_group" label="Column name for subgroups" optional="false" help="The name of the column that defines the subgroups or categories to be displayed on the X-axis, e.g., seasons for every polygon_id." type="text"/>
74 </when> 75 </when>
75 <when value="map-trends-static"> 76 <when value="map-trends-static">
76 <param name="regions" label="Study region or study subregions" optional="false" help="URL (stored in a .txt file) to the study region, or several regions, used to classify the input data into groups of interest. Currently it has to be provided as a shapefile. It can be in any coordinate system and will be transformed to WGS84 during this process." type="data" format="txt"/> 77 <param name="regions" label="Study region or study subregions" optional="false" help="URL (stored in a .txt file) to the study region, or several regions, used to classify the input data into groups of interest. Currently it has to be provided as a shapefile. It can be in any coordinate system and will be transformed to WGS84 during this process." type="data" format="txt"/>
77 <param name="input_data" label="Input table" optional="false" help="URL to the input table containing statistical analysis results. The table must include columns for test values, p-values, and identifiers linking to study region." type="data" format="txt"/> 78 <param name="input_data" label="Input table" optional="false" help="URL to the input table containing statistical analysis results. The table must include columns for test values, p-values, and identifiers linking to study region." type="data" format="txt"/>
78 <param name="colname_id_trend" label="Column name of study region identifier" optional="false" help="The name of the column containing identifiers for study regions, which must correspond to the identifiers in the shapefile (shp). Example = 'id'." type="text"/> 79 <param name="colname_id_trend" label="Column name of study region identifier" optional="false" help="The name of the column containing identifiers for study regions, which must correspond to the identifiers in the shapefile (shp). Example = 'id'." type="text"/>
79 <param name="colname_region_id" label="Column name of study region identifier" optional="false" help="The name of the column in the input data that contains identifiers for study regions, corresponding to the identifiers in the shapefile. Example = 'id'." type="text"/> 80 <param name="colname_region_id" label="Column name of study region identifier" optional="false" help="The name of the column in the input data that contains identifiers for study regions, corresponding to the identifiers in the shapefile. Example = 'id'." type="text"/>
80 <param name="colname_group" label="Column name for subgroups" optional="false" help="The name of the column that defines the subgroups or categories to be displayed on the X-axis, e.g., seasons for every polygon_id." type="text"/> 81 <param name="colname_group" label="Column name for subgroups" optional="false" help="The name of the column that defines the subgroups or categories to be displayed on the X-axis, e.g., seasons for every polygon_id." type="text"/>
81 <param name="p_value_threshold" label="p value threshold for significance" optional="false" help="The threshold for distinguishing significant from insignificant values. It adjusts the transparency of bars in the plot. Example = 0.05." value="0.05" min="0.01" max="0.1" type="float"/> 82 <param name="p_value_threshold" label="p value threshold for significance" optional="false" help="The threshold for distinguishing significant from insignificant values. It adjusts the transparency of bars in the plot. Example = 0.05." value="0.05" min="0.01" max="0.1" type="float"/>
82 <param name="colname_p_value" label="Column name for p value" optional="false" help="The name of the column containing p values, used to determine bar transparency. Example = 'p_value'" type="text"/> 83 <param name="colname_p_value" label="Column name for p value" optional="false" help="The name of the column containing p values, used to determine bar transparency. Example = 'p_value'" type="text"/>
83 </when> 84 </when>
84 <when value="map-shapefile-points"> 85 <when value="map-shapefile-points">
85 <param name="regions" label="Study region or study subregions" optional="false" help="URL (stored in a .txt file) to the study region, or several regions, to classify the input data into groups of interest. Currently it has to be provided as a shapefile. It can be in any coordinate system and will be transformed to WGS84 during this process." type="data" format="txt"/> 86 <param name="regions" label="Study region or study subregions" optional="false" help="URL (stored in a .txt file) to the study region, or several regions, to classify the input data into groups of interest. Currently it has to be provided as a shapefile. It can be in any coordinate system and will be transformed to WGS84 during this process." type="data" format="txt"/>
86 <param name="input_data" label="Data table to be plotted on top of study regions" optional="false" help="URL (stored in a .txt file) to the input table containing the in-situ data points with coordinates." type="data" format="txt"/> 87 <param name="input_data" label="Data table to be plotted on top of study regions" optional="false" help="URL (stored in a .txt file) to the input table containing the in-situ data points with coordinates." type="data" format="txt"/>
87 <param name="colname_long" label="Column name for longitude" optional="false" help="The name of the column containing longitude values for the data points." type="text"/> 88 <param name="colname_long" label="Column name for longitude" optional="false" help="The name of the column containing longitude values for the data points." type="text"/>
88 <param name="colname_lat" label="Column name for latiitude" optional="false" help="The name of the column containing latitude values for the data points." type="text"/> 89 <param name="colname_lat" label="Column name for latitude" optional="false" help="The name of the column containing latitude values for the data points." type="text"/>
89 <param name="colname_value_name" label="Column name of data point identifier" optional="false" help="The name of the column containing identifier (e.g., site name) or values (e.g., depth) to color the points according to their corresponding values." type="text"/> 90 <param name="colname_value_name" label="Column name of data point identifier" optional="false" help="The name of the column containing identifier (e.g., site name) or values (e.g., depth) to color the points according to their corresponding values." type="text"/>
90 <param name="colname_region_id" label="Column name of region identifier" optional="false" help="The name of the column containing identifiers (e.g., basin name) to distinguish the polygons on the map if multiple regions are present." type="text"/> 91 <param name="colname_region_id" label="Column name of region identifier" optional="false" help="The name of the column containing identifiers (e.g., basin name) to distinguish the polygons on the map if multiple regions are present." type="text"/>
91 </when> 92 </when>
93 <when value="owt-classification">
94 <param name="input_data_url" label="Input data" optional="false" help="URL (stored in a .txt file) to your input file. Find example data on https://github.com/bishun945/pyOWT/tree/main/projects/AquaINFRA." type="data" format="txt"/>
95 <param name="input_option" label="Type of input" optional="false" help="csv: for text data input (first line wavelength, following lines remote-sensing reflectance). sat: for satellite product input containing reflectance (e.g., Sentinel-3 OLCI Level-2)." type="select">
96 <option value="csv">csv</option>
97 <option value="sat">sat</option>
98 </param>
99 <param name="sensor" label="Sensor name" optional="false" help="Spectral band configuration of satellite mission (includes adaptation to sensor spectral response functions)." type="select">
100 <option value="HYPER">HYPER</option>
101 <option value="AERONET_OC_1">AERONET_OC_1</option>
102 <option value="AERONET_OC_2">AERONET_OC_2</option>
103 <option value="CMEMS_BAL_HROC">CMEMS_BAL_HROC</option>
104 <option value="CMEMS_BAL_NRT">CMEMS_BAL_NRT</option>
105 <option value="CMEMS_MED_MYINT">CMEMS_MED_MYINT</option>
106 <option value="CZCS">CZCS</option>
107 <option value="GOCI">GOCI</option>
108 <option value="HawkEye">HawkEye</option>
109 <option value="MERIS">MERIS</option>
110 <option value="ODIS_Aqua">ODIS_Aqua</option>
111 <option value="MODIS_Terra">MODIS_Terra</option>
112 <option value="MSI_S2A">MSI_S2A</option>
113 <option value="MSI_S2B">MSI_S2B</option>
114 <option value="OCTS">OCTS</option>
115 <option value="OLCI_S3A">OLCI_S3A</option>
116 <option value="OLCI_S3B">OLCI_S3B</option>
117 <option value="OLI">OLI</option>
118 <option value="SeaWiFS">SeaWiFS</option>
119 <option value="VIIRS_JPSS1">VIIRS_JPSS1</option>
120 <option value="VIIRS_JPSS2">VIIRS_JPSS2</option>
121 <option value="VIIRS_SNPP">VIIRS_SNPP</option>
122 </param>
123 <param name="output_option" label="Output option" help="1: for standard output with five variables. 2: for extensive output including memberships of all water types" optional="false" type="select">
124 <option value="1">1</option>
125 <option value="2">2</option>
126 </param>
127 </when>
92 </conditional> 128 </conditional>
93 </inputs> 129 </inputs>
94 <outputs> 130 <outputs>
95 <data name="output_data" format="txt" label="$select_process"/> 131 <data name="output_data" format="txt" label="$select_process"/>
96 </outputs> 132 </outputs>
97 <expand macro="tests"/> 133 <expand macro="tests"/>
98 <expand macro="help" /> 134 <expand macro="help" />
99 <expand macro="citations"/> 135 <expand macro="citations"/>
100 </tool> 136 </tool>