Mercurial > repos > ecology > aquainfra_ogc_api_processes

changeset 10:090444e57d60 draft default tip

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planemo upload for repository https://github.com/AquaINFRA/tools-ecology/tree/master commit f3dbb3ebcf25cc60d5ae6c1f37486949d5261ccd
author ecology
date Thu, 02 Oct 2025 15:56:54 +0000
parents 7b003d6604f8
children
files aquainfra_ogc_api_processes.xml
diffstat 1 files changed, 50 insertions(+), 1 deletions(-) [+]
line wrap: on
line diff
--- a/aquainfra_ogc_api_processes.xml	Mon Aug 18 10:12:19 2025 +0000
+++ b/aquainfra_ogc_api_processes.xml	Thu Oct 02 15:56:54 2025 +0000
@@ -1,4 +1,4 @@
-<tool id="aquainfra_ogc_api_processes" name="AquaINFRA OGC API Processes" version="0.7.0" profile="22.05">
+<tool id="aquainfra_ogc_api_processes" name="AquaINFRA OGC API Processes" version="0.8.0" profile="22.05">
     <description/>
     <macros>
         <import>macros.xml</import>
@@ -35,6 +35,11 @@
                 <option value="check-names">check-names: Check species names in biodiversity data from separate sources</option>
                 <option value="pred-extract">pred-extract: pred extract for extraction of environmnetal data</option>
                 <option value="multidetect-and-clean">multidetect-and-clean: Run multidetect and clean the data</option>
+                <option value="heat1">heat1: Reproducing HEAT HOLAS results: Generate the Assessment Units</option>
+                <option value="heat2">heat2: Reproducing HEAT HOLAS results: Combine the samples</option>
+                <option value="heat3">heat3: Reproducing HEAT HOLAS results: Compute Annual Indicators</option>
+                <option value="heat4">heat4: Reproducing HEAT HOLAS results: Compute Assessment Indicators</option>
+                <option value="heat5">heat5: Reproducing HEAT HOLAS results: Compute Assessment</option>
             </param>
             <when value="points-att-polygon">
                 <param name="input_data" label="Table to be merged with study region" optional="false" help="URL 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. (URL must be stored in a .txt file)" type="data" format="txt"/>
@@ -273,6 +278,50 @@
                 <param name="classifymode" label="Cuts data into classess" optional="true" help="Categorize data base on the correlation coefficient manner based on Akoglu 2018. Example: med" type="integer"/>
                 <param name="eif_bool" label="Emprical Influence Function" optional="true" help="Computes the Emprical Influence Function for classified outliers." type="boolean" truevalue="True" falsevalue="False"/>
             </when>
+            <when value="heat1">
+                <param name="assessment_period" label="Assessment Period" optional="false" help="The HOLAS assessment period which is used for the HEAT analysis. It can be HOLAS-2 (2011-2016) or HOLAS-3 (2016-2021) or custom for whole monitoring period (1877-9999). Note that assessment period defines the indicators used and integrations rules, where as the sample data needs to be defined separately. Allowed values: HOLAS-2, HOLAS-3, Other." type="select">
+                    <option value="HOLAS-2">HOLAS-2</option>
+                    <option value="HOLAS-3">HOLAS-3</option>
+                    <option value="Other">Other</option>
+                </param>
+            </when>
+            <when value="heat2">
+                <param name="assessment_period" label="Assessment Period" optional="false" help="The HOLAS assessment period which is used for the HEAT analysis. It can be HOLAS-2 (2011-2016) or HOLAS-3 (2016-2021) or custom for whole monitoring period (1877-9999). Note that assessment period defines the indicators used and integrations rules, where as the sample data needs to be defined separately. Allowed values: HOLAS-2, HOLAS-3, Other." type="select">
+                    <option value="holas-2">holas-2</option>
+                    <option value="holas-3">holas-3</option>
+                    <option value="Other">Other</option>
+                </param>
+                <param name="bottle_data" label="Input samples (bottle)" optional="true" help="In-situ bottle sample data (nutrients, chl-a)(StationSamplesBOT.csv). ICES Oceanographic data type 'BOT'. Write 'default' for default data. Leave out for none at all." type="text"/>
+                <param name="ctd_data" label="Input samples (CTD)" optional="true" help=" CTD depth profiles, relevant for oxygen debt indicator (StationSamplesCTD.csv). ICES Oceanographic data type 'CTD'. Write 'default' for default data. Leave out for none at all." type="text"/>
+                <param name="pump_data" label="Input samples (pump)" optional="true" help="Ferrybox data (chl-a) (StationSamplesPMP.csv). ICES Oceanographic data type 'PMP'. Write 'default' for default data. Leave out for none at all." type="text"/>
+                <param name="units_gridded" label="Gridded assessment units" optional="false" help="Grid used for confidence assessment (10k, 30k, 60k). These are generated by heat1. For default spatial units for each assessment period, write 'default'. (URL must be stored in a .txt file)" type="data" format="txt"/>
+            </when>
+            <when value="heat3">
+                <param name="assessment_period" label="Assessment Period" optional="false" help="The HOLAS assessment period which is used for the HEAT analysis. It can be HOLAS-2 (2011-2016) or HOLAS-3 (2016-2021) or custom for whole monitoring period (1877-9999). Note that assessment period defines the indicators used and integrations rules, where as the sample data needs to be defined separately. Allowed values: HOLAS-2, HOLAS-3, Other." type="select">
+                    <option value="HOLAS-2">HOLAS-2</option>
+                    <option value="HOLAS-3">HOLAS-3</option>
+                    <option value="Other">Other</option>
+                </param>
+                <param name="station_samples" label="Station samples (combined)" optional="false" help="Merged sample data of BOT, PMP and CTD data for indicator calculation (StationSamples.csv). (URL must be stored in a .txt file)" type="data" format="txt"/>
+                <param name="combined_Chlorophylla_IsWeighted" label="Chlorophyll A Weighted?" optional="false" checked="false" help="If true, script calculates combined chlorophyll a indicator results per assessment unit as a weighted average from BOT, PMP and EO. If false, then simple average." type="boolean" truevalue="True" falsevalue="False"/>
+                <param name="units_cleaned" label="Non-gridded assessment units" optional="false" help="Non-gridded Assessment units which were cleaned, slightly adapted (e.g. some stations added manually), and extended (e.g. with the units's area and a UnitID). (URL must be stored in a .txt file)" type="data" format="txt"/>
+            </when>
+            <when value="heat4">
+                <param name="assessment_period" label="Assessment Period" optional="false" help="The HOLAS assessment period which is used for the HEAT analysis. It can be HOLAS-2 (2011-2016) or HOLAS-3 (2016-2021) or custom for whole monitoring period (1877-9999). Note that assessment period defines the indicators used and integrations rules, where as the sample data needs to be defined separately. Allowed values: HOLAS-2, HOLAS-3, Other." type="select">
+                    <option value="HOLAS-2">HOLAS-2</option>
+                    <option value="HOLAS-3">HOLAS-3</option>
+                    <option value="Other">Other</option>
+                </param>
+                <param name="annual_indicators" label="Annual Indicators Table" optional="false" help="CSV file of calculated HEAT EQRS per indicator per year per assessment unit (AnnualIndicators.csv). (URL must be stored in a .txt file)" type="data" format="txt"/>
+            </when>
+            <when value="heat5">
+                <param name="assessment_period" label="Assessment Period" optional="false" help="The HOLAS assessment period which is used for the HEAT analysis. It can be HOLAS-2 (2011-2016) or HOLAS-3 (2016-2021) or custom for whole monitoring period (1877-9999). Note that assessment period defines the indicators used and integrations rules, where as the sample data needs to be defined separately. Allowed values: HOLAS-2, HOLAS-3, Other." type="select">
+                    <option value="HOLAS-2">HOLAS-2</option>
+                    <option value="HOLAS-3">HOLAS-3</option>
+                    <option value="Other">Other</option>
+                </param>
+                <param name="assessment_indicators" label="Assessment Indicators Table" optional="false" help="CSV file of calculated EQRS per assessment period per assessment unit (AssessmentIndicators.csv). (URL must be stored in a .txt file)" type="data" format="txt"/>
+            </when>
         </conditional>
     </inputs>
     <outputs>