# HG changeset patch
# User ecology
# Date 1704709945 0
# Node ID d07fcc660f3c21540c7cfb8d0427a89694119e4c

planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation commit 450e4496f243d6e94d5238358873bbc014fe2f08

diff -r 000000000000 -r d07fcc660f3c run_idw_interpolation.R
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/run_idw_interpolation.R	Mon Jan 08 10:32:25 2024 +0000
@@ -0,0 +1,100 @@
+library("getopt")
+library("sf")
+library("tmap")
+library("RColorBrewer")
+library("raster")
+library("gstat")
+
+args = commandArgs(trailingOnly=TRUE)
+option_specification = matrix(c(
+    'observationsCsv', 'i1', 1, 'character',
+    'latitudeColumn', 'i2', 1, 'double',
+    'longitudeColumn', 'i3', 1, 'double',
+    'observationsColumn', 'i4', 1, 'double',
+    'studyArea', 'i5', 1, 'character',
+    'idwPower', 'i6', 1, 'double',
+    'samplePoints', 'i7', 1, 'double',
+    'sampleType', 'i8', 1, 'character',
+    'legendLabel', 'i9', 1, 'character',
+    'legendPosition', 'i10', 1, 'character',
+    'numberClasses', 'i11', 1, 'double',
+    'dotSize', 'i12', 1, 'double',
+    'colorType', 'i13', 1, 'character',
+    'testCase', 'i14', 1, 'character',
+    'outputData', 'o', 2, 'character'
+), byrow=TRUE, ncol=4);
+options = getopt(option_specification);
+
+obsData <- read.csv(file=options$observationsCsv, sep = ',', header = TRUE)
+latitudeColumn <- options$latitudeColumn
+longitudeColumn <- options$longitudeColumn
+observationsColumn <- options$observationsColumn
+studyArea <- options$studyArea
+idwPower <- options$idwPower
+samplePoints <- options$samplePoints
+sampleType <- options$sampleType
+legendLabel <- options$legendLabel
+legendPosition <- options$legendPosition
+numberClasses <- options$numberClasses
+dotSize <- options$dotSize
+colorType <- options$colorType
+testCase <- options$testCase
+
+#cat("\n observationsCsv", options$observationsCsv)
+cat("\n latitudeColumn", latitudeColumn)
+cat("\n longitudeColumn", longitudeColumn)
+cat("\n observationsColumn", observationsColumn)
+#cat("\n studyArea", studyArea)
+cat("\n idwPower", idwPower)
+cat("\n samplePoints", samplePoints)
+cat("\n sampleType", sampleType)
+cat("\n legendLabel", legendLabel)
+cat("\n legendposition", legendPosition)
+cat("\n numberClasses", numberClasses)
+cat("\n dotSize", dotSize)
+cat("\n colorType", colorType)
+cat("\n testCase", testCase)
+#cat("\n outputData: ", options$outputData)
+
+coordinates(obsData) <- c(colnames(obsData)[longitudeColumn], colnames(obsData)[latitudeColumn])
+sf_obsData <- as_Spatial(st_as_sf(obsData))
+
+polygon <- as_Spatial(st_read(studyArea))
+sf_obsData@bbox<-polygon@bbox
+
+runInterpolation <- function(points, values, interpolation_power, sample_points, sample_type){
+  if (testCase == "true") {
+    cat("\n set seed!")
+    set.seed(123)
+  }
+  grd              <- as.data.frame(spsample(points, sample_type, n=sample_points))
+  names(grd)       <- c("X", "Y")
+  coordinates(grd) <- c("X", "Y")
+  gridded(grd)     <- TRUE
+  fullgrid(grd)    <- TRUE
+  
+  proj4string(points) <- proj4string(points)
+  proj4string(grd) <- proj4string(points)
+  return(gstat::idw(values ~ 1, points, newdata=grd, idp=interpolation_power))
+}
+
+plotInterpolationMap <- function(raster, points, legend_label){
+  plot <- tm_shape(raster) + 
+    tm_raster(n=numberClasses,palette = rev(brewer.pal(7, colorType)), auto.palette.mapping = FALSE,
+              title=legend_label) +
+    tm_shape(points) + tm_dots(size=dotSize) +
+    tm_legend(legend.outside=legendPosition)
+  return(plot)
+}
+
+sf_obsData.idw <- runInterpolation(sf_obsData, obsData$measurement, idwPower, samplePoints, sampleType)
+
+raster_object       <- raster(sf_obsData.idw)
+raster_object.mask  <- mask(raster_object, polygon)
+
+idw <- plotInterpolationMap(raster_object.mask, sf_obsData, legendLabel)
+idw
+
+png(options$outputData)
+idw
+dev.off()
\ No newline at end of file
diff -r 000000000000 -r d07fcc660f3c run_idw_interpolation.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/run_idw_interpolation.xml	Mon Jan 08 10:32:25 2024 +0000
@@ -0,0 +1,102 @@
+<tool id="interpolation_run_idw_interpolation" name="Run interpolation" version="1.0" profile="22.05">
+    <description>based on Inverse Distance Weighting (IDW)</description>
+    <requirements>
+        <requirement type="package" version="1.20.4">r-getopt</requirement>
+        <requirement type="package" version="3.3_4">r-tmap</requirement>
+        <requirement type="package" version="3.6_26">r-raster</requirement>
+        <requirement type="package" version="2.1_1">r-gstat</requirement>
+    </requirements>
+    <command detect_errors='exit_code'><![CDATA[
+    Rscript '$__tool_directory__/run_idw_interpolation.R'
+        --observationsCsv '$observations_csv'
+        --latitudeColumn '$latitude_column'
+        --longitudeColumn '$longitude_column'
+        --observationsColumn '$observations_column' 
+        --studyArea '$study_area'
+        --idwPower '$idw_power' 
+        --samplePoints '$sample_points' 
+        --sampleType '$sample_type'
+        --legendLabel '$legend_label'
+        --legendPosition '$legend_position'
+        --numberClasses '$number_classes'
+        --dotSize '$dot_size'
+        --colorType '$color_type'
+        --testCase '$test_case'  
+        --outputData '$output'
+    ]]></command>
+    <inputs>
+        <param type="data" format="csv" name="observations_csv" label="Select the .csv file including the observations"/>
+        <param type="data" format="geojson" name="study_area" label="Select the .geojson containing the study area"/>
+        <param name="latitude_column" type="data_column" data_ref="observations_csv" label="In which column are the latitude coordinates?"/>
+        <param name="longitude_column" type="data_column" data_ref="observations_csv" label="In which column are the longitude coordinates?"/>
+        <param name="observations_column" type="data_column" data_ref="observations_csv" label="In which column are the observation values?"/>
+        <param value="2" min="0.1" max="5" type="float" name="idw_power" label="Select the interpolation power of the IDW method"/>
+        <param value="50000" min="1000" max="100000" type="integer" name="sample_points" label="Select the number of sample points"/>
+        <param type="select" name="sample_type" label="Select a sample type">
+            <option value="regular">Regular</option>
+            <option value="random">Random</option>
+            <option value="stratified">Stratified</option>
+            <option value="nonaligned">Nonaligned</option>
+        </param>
+        <param type="text" name="legend_label" label="Enter a label for the legend"/>
+        <param type="select" name="legend_position" label="Should the legend be displayed inside or outside the frame?">
+            <option value="false">Inside</option>
+            <option value="true">Outside</option>
+        </param>
+        <param value="0.2" min="0.1" max="2" type="float" name="dot_size" label="Select the dot size of the points shown on the map"/>
+        <param value="10" min="1" max="100" type="integer" name="number_classes" label="Number of classes" help="Note: Not all values are possible. tmap tries to generate a number of classes which are as close to the indicated value as possible"/>
+        <param type="select" name="color_type" label="Select a color palette">
+            <option value="RdBu">RdBu</option>
+            <option value="Blues">Blues</option>
+            <option value="BuGn">BuGn</option>
+            <option value="BuPu">BuPu</option>
+            <option value="GnBu">GnBu</option>
+            <option value="Greens">Greens</option>
+            <option value="Greys">Greys</option>
+            <option value="Oranges">Oranges</option>
+            <option value="OrRd">OrRd</option>
+            <option value="PuBu">PuBu</option>
+            <option value="PuBuGn ">PuBuGn</option>
+            <option value="PuRd">PuRd</option>
+            <option value="Purples">Purples</option>
+            <option value="RdPu">RdPu</option>
+            <option value="Reds">Reds</option>
+            <option value="YlGn">YlGn</option>
+            <option value="YlGnBu">YlGnBu</option>
+            <option value="YlOrBr">YlOrBr</option>
+            <option value="YlOrRd">YlOrRd</option>
+        </param>
+        <param type="boolean" name="test_case" label="Should a seed be set?" truevalue="true" falsevalue="false" />
+    </inputs>
+    <outputs>
+        <data name="output" format="png" />
+    </outputs>
+    <tests>
+        <!-- Run test with: planemo test - -biocontainers plotInterpolationMap.xml - -test_output=plotInterpolationMap.html -->
+        <test>
+            <param name="observations_csv" value="run_idw_interpolation_test_input1.csv"/>
+            <param name="latitude_column" value="3"/>
+            <param name="longitude_column" value="4"/>
+            <param name="observations_column" value="5"/>
+            <param name="study_area" value="run_idw_interpolation_test_input2.geojson"/>
+            <param name="idw_power" value="2"/>
+            <param name="sample_points" value="50000"/>
+            <param name="sample_type" value="regular"/>
+            <param name="legend_label" value="Legend"/>
+            <param name="legend_position" value="false"/>
+            <param name="number_classes" value="10"/>
+            <param name="dot_size" value="1"/>
+            <param name="color_type" value="RdBu"/>
+            <param name="test_case" value="true"/>
+            <output name="output" file="run_idw_interpolation_test_output.png" compare="sim_size" delta_frac="0.1"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+        IDW stands for Inverse Distance Weighting. The .csv file contains the observations and the .geojson file the study area. The plot is stored as a .png file. 
+    ]]></help>
+    <citations>
+        <citation type="doi">10.32614/RJ-2018-009</citation>
+        <citation type="doi">10.18637/jss.v084.i06</citation>
+        <citation type="doi">10.32614/RJ-2016-014</citation>
+    </citations>
+</tool>
diff -r 000000000000 -r d07fcc660f3c test-data/run_idw_interpolation_test_input1.csv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/run_idw_interpolation_test_input1.csv	Mon Jan 08 10:32:25 2024 +0000
@@ -0,0 +1,11 @@
+sensor_id,attribute,latitude,longitude,measurement,accuracy,unit,date,quality_level,data_processing
+1,waterTemp,51.95690094,7.61361456,10.428,0.002,celsius,03.04.2023 10:00,checked,adjusted
+2,waterTemp,51.9558893,7.616701107,10.181,0.1,celsius,03.04.2023 10:00,checked,adjusted
+3,waterTemp,51.95355062,7.606799142,11.653,0.1,celsius,03.04.2023 10:00,checked,raw
+4,waterTemp,51.95258302,7.608679928,10.619,0.002,celsius,03.04.2023 10:00,unchecked,adjusted
+5,waterTemp,51.95078585,7.604339653,10.124,0.002,celsius,03.04.2023 10:00,checked,adjusted
+6,waterTemp,51.94994044,7.605288084,10.834,0.1,celsius,03.04.2023 10:00,checked,raw
+7,waterTemp,51.94679837,7.596725189,11.244,0.002,celsius,03.04.2023 10:00,checked,adjusted
+8,waterTemp,51.94552117,7.600045848,20.575,0.002,celsius,03.04.2023 10:00,unchecked,raw
+9,waterTemp,51.94244725,7.594818813,10.669,0.002,celsius,03.04.2023 10:00,checked,adjusted
+10,waterTemp,51.94294707,7.597031164,10.702,0.1,celsius,03.04.2023 10:00,checked,adjusted
diff -r 000000000000 -r d07fcc660f3c test-data/run_idw_interpolation_test_input2.geojson
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/run_idw_interpolation_test_input2.geojson	Mon Jan 08 10:32:25 2024 +0000
@@ -0,0 +1,1005 @@
+{
+  "type": "FeatureCollection",
+  "generator": "overpass-ide",
+  "copyright": "The data included in this document is from www.openstreetmap.org. The data is made available under ODbL.",
+  "timestamp": "2023-04-03T13:52:54Z",
+  "features": [
+    {
+      "type": "Feature",
+      "properties": {
+        "@id": "relation/13763746",
+        "basin": "retention",
+        "boat": "permissive",
+        "intermittent": "no",
+        "maxdepth": "2",
+        "name": "Aasee",
+        "name:de": "Aasee",
+        "name:ru": "Аазе",
+        "natural": "water",
+        "salt": "no",
+        "tidal": "no",
+        "type": "multipolygon",
+        "water": "lake",
+        "website": "https://www.aaseepark.de/",
+        "wikidata": "Q303434",
+        "wikipedia": "de:Aasee (Münster)"
+      },
+      "geometry": {
+        "type": "Polygon",
+        "coordinates": [
+          [
+            [
+              7.6157143,
+              51.9575375
+            ],
+            [
+              7.6156899,
+              51.9575098
+            ],
+            [
+              7.6156437,
+              51.9574789
+            ],
+            [
+              7.6155894,
+              51.9574596
+            ],
+            [
+              7.6155282,
+              51.9574454
+            ],
+            [
+              7.6154684,
+              51.957442
+            ],
+            [
+              7.61547,
+              51.9574267
+            ],
+            [
+              7.6153516,
+              51.9574452
+            ],
+            [
+              7.6150165,
+              51.9574975
+            ],
+            [
+              7.6144566,
+              51.9575722
+            ],
+            [
+              7.6140497,
+              51.9576357
+            ],
+            [
+              7.6140325,
+              51.9576375
+            ],
+            [
+              7.6137887,
+              51.9575415
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+            [
+              7.6137702,
+              51.957534
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+            [
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+            ],
+            [
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+              51.9494198
+            ],
+            [
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+              51.9491001
+            ],
+            [
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+            ],
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+}
\ No newline at end of file
diff -r 000000000000 -r d07fcc660f3c test-data/run_idw_interpolation_test_output.png
Binary file test-data/run_idw_interpolation_test_output.png has changed