Adding crs_converter to Galaxy ecology

tools/crs_converter/.shed.yml

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+name: crs_converter
+owner: ecology 
+description: Geospatial transformation of a shapefile Coordinate Reference Systems
+homepage_url: https://github.com/Rassine/Rassine-tools-Gecology/tree/master/tools/crs_converter
+long_description: |
+  This tool was created to be part of a phylodiversity workflow. It creates a PROJ4 string from the option selected by the users and use the string to convert the coordinate reference system of a given geospatial file into another one. This tool also offers to produce output in different formats for wider options of manipulation and visualisation.
+remote_repository_url: https://github.com/galaxyecology/tools-ecology/tree/master/tools/crs_converter
+type: unrestricted
+categories:
+- Ecology
+auto_tool_repositories:
+  name_template: "{{ tool_id }}"
+  description_template: "Convert Coordinate Reference Systems of shapefiles"

tools/crs_converter/CRS_macros.xml

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+<macros>
+    <xml name='ellps_options'>
+        <param name ='ellps' type='select' checked='true'
+               label='Ellipsoid and Datum' help='The name of built-in ellipsoid definition. Defines shape and center of earth simplified model used for projection.
+               See https://proj.org/en/9.4/usage/ellipsoids.html#ellipsoids for more informations.'>
+            <option value='GRS80'>GRS80</option>
+            <option value='airy'>airy</option>
+            <option value='bessel'>bessel</option>
+            <option value='clrk66'>clrk66</option>
+            <option value='WGS60'>WGS60</option>
+            <option value='WGS66'>WGS66</option>
+            <option value='WGS72'>WGS72</option>
+            <option value='WGS84' selected='true'>WGS84</option>
+            <option value='sphere'>sphere</option>
+        </param>
+    </xml>
+
+
+    <xml name='latitude_options'>
+        <param name ='lat_0' type='integer' value='0'
+               label='Latitude' help='Latitude of natural origin, 
+               latitude of false origin or latitude of projection centre 
+               (naming and meaning depend on the projection method).'/>
+    </xml>
+
+
+    <xml name='latitude_1_options'>
+        <param name ='lat_1' type='integer' value='1' 
+               label='Latitude 1' help='First standard parallel.'/>
+    </xml>
+
+
+    <xml name='latitude_2_options'>
+        <param name ='lat_2' type='integer' value='1' 
+               label='Latitude 2' help='Second standard parallel.'/>
+    </xml>
+
+
+    <xml name='latitude_ts_options'>
+        <param name ='lat_ts' type='integer' value='0' 
+               label='Latitude of true scale' help='Defines the latitude where scale is not distorted. 
+               Takes precedence over scale factor K if both options are used together.'/>
+    </xml>
+
+
+    <xml name='longitude_options'>
+        <param name ='lon_0' type='integer' value='0' 
+               label='Longitude' help='Central meridian/longitude of natural origin, 
+               longitude of origin or longitude of false origin 
+               (naming and meaning depend on the projection method).'/>
+    </xml>
+
+
+    <xml name='X_options'>
+        <param name ='x_0' type='integer' value='0' 
+               label='X' help='False easting, easting at false origin or easting at projection centre.
+               (naming and meaning depend on the projection method). Always in meters. Use Ex: Shifting projection on an East-Weast axis'/>
+    </xml>
+
+
+    <xml name='Y_options'>
+        <param name ='y_0' type='integer' value='0' 
+               label='Y' help='False northing, northing at false origin or northing at projection centre. 
+               (naming and meaning depend on the projection method). Always in meters. Use Ex: Shifting projection on a North-South axis'/>
+    </xml>
+
+
+    <xml name='K_options'>
+        <param name='k_0' type='integer' value='1' min='1'
+               label='Scale factor K' help='Scale factor. Determines scale factor used in the projection.'/>
+    </xml>
+
+
+    <xml name='zone_options'>
+        <param name ='zone' type='integer' value='1' min='1' max='60'
+               label='Select which UTM zone to use' help='Can be a value between 1-60.'/>
+    </xml>
+
+
+    <xml name='south_options'>
+        <param name ='south' type='boolean' checked='false'
+               label='South hemisphere' help='Add this flag when using the UTM on the southern hemisphere.'/>
+    </xml>
+
+
+    <xml name='approx_options'>
+        <param name ='approx' type='boolean' checked='false'
+               label='Approximation algorithm' help='Use faster, less accurate algorithm for the Transverse Mercator.'/>
+    </xml>
+
+
+    <xml name='algo_options'>
+        <param name ='algo' type='select' optional='false'
+               label='Selects the algorithm to use.' help='Default value is poder_engsager. 
+               When using auto, an heuristics based on the input coordinate is used to 
+               determine if the faster Evenden-Snyder method can be used for faster 
+               computation without causing an error greater than 0.1 mm 
+               (for an ellipsoid of the size of Earth)'>
+            <option value='auto'>Auto</option>
+            <option value='evenden_snyder'>Evenden Snyder</option>
+            <option value='poder_engsager' selected='true'>Poder Engsager</option>
+        </param>
+    </xml>
+
+
+    <xml name='asc_lon_options'>
+        <param name ='asc_lon' type='integer' value='0' 
+               label='Ascending Longitude' help='Longitude of the ascending node for the orbit (decimal degrees).'/>
+    </xml>
+
+
+    <xml name='inc_angle_options'>
+        <param name ='inc_angle' type='integer' value='90' 
+               label='Inclination angle' help='Inclination (vertical tilt) of the orbit 
+               with respect to the reference plane, measured at the ascending node (decimal degrees).'/>
+    </xml>
+
+
+    <xml name='ps_rev_options'>
+        <param name ='ps_rev' type='integer' value='1' 
+               label='Revolution time' help='Time required for a single orbit (days).'/>
+    </xml>
+
+
+    <xml name='units_options'>
+        <param name ='units' type='select' checked='true'
+               label='Units' help='Default is meter.'>
+            <option value='m' selected='true'>m</option>
+            <option value='mm'>mm</option>
+            <option value='cm'>cm</option>
+            <option value='dm'>dm</option>
+            <option value='km'>km</option>
+            <option value='kmi'>International Nautical Mile (kmi)</option>
+            <option value='us-in'>US in</option>
+            <option value='us-ft'>US ft</option>
+            <option value='us-yd'>US yd</option>
+            <option value='us-mi'>US mi</option>  
+        </param>
+    </xml>
+</macros>

tools/crs_converter/CRSconverter.R

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+#!/bin/Rscript
+
+library(sf)
+library(tidyr)
+
+args = commandArgs(trailingOnly=TRUE)
+output_list <- strsplit(as.character(args[2]), ',')[[1]]
+
+
+
+save_as_pdf_fun <- function(){
+
+    pdf(file = 'PDF_output.pdf')
+    plot(st_geometry(Transformed_spacial_coordinates))
+    dev.off()
+}
+
+
+save_as_shp_fun <- function(){
+
+    write_sf(Transformed_spacial_coordinates, 'shapefile.shp')
+}
+
+
+save_as_image_fun <- function(format){
+
+    img_fun = as.list(paste(format, '_output.', format, sep = '', collapse = NULL))
+    do.call(format, img_fun)
+    plot(st_geometry(Transformed_spacial_coordinates))
+    dev.off()
+}
+
+
+
+if (length(args)<2){stop('Insufficient number of argument, please review command Line')
+}else{
+    Spacial_coordinates_files <- read_sf(as.character(args[1]), layer = 'shapefile')
+    projection <- as.character(args[4])
+
+    for (n_arg in 5:length(args)) {
+        projection <- paste(projection, as.character(args[n_arg]),sep = '', collapse = NULL)
+    }
+
+    projection <- paste(projection, ' +no_defs',sep = '', collapse = NULL)
+    Transformed_spacial_coordinates <- st_transform(Spacial_coordinates_files, crs = projection)
+    for (a in output_list) {
+        if (as.character(a) == 'pdf') {
+        save_as_pdf_fun()
+        next
+
+        } else if (as.character(a) == 'shp') {
+        save_as_shp_fun()
+        next
+
+        } else { save_as_image_fun(as.character(a)) }
+    }}