Add metashrimps tool suite

tools/metashrimps/.shed.yml

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+name: MetaShRIMPS 
+owner: ecology 
+description: Tools to operate machine actionnable actions on EML metadata
+homepage_url: https://github.com/tanguygen/metacure
+long_description: |
+    Tools to operate machine actionnable jobs to EML metadata from MetaShRIMPS, a project from the PNDB (French hub for biodiversity data)
+remote_repository_url: https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline
+type: unrestricted
+categories:
+- Ecology
+auto_tool_repositories:
+  name_template: "{{ tool_id }}"
+  description_template: "MetaShRIMPS: {{ tool_name }}"
+suite:
+  name: "suite_metashrimps"
+  description: Tools to operate machine actionnable jobs on EML metadata
+  long_description: |
+    Tools to operate machine actionnable jobs to EML metadata from MetaShRIMPS, a project from the PNDB (French hub for biodiversity data).

tools/metashrimps/DataPaper.R

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+##07/06/2023
+##Genthon Tanguy
+### Data Paper draft production
+
+#load arguments
+args = commandArgs(trailingOnly=TRUE)
+if (length(args)==0)
+{
+  stop("This tool needs at least one argument")
+}else{
+  path_temp <- args[1]
+  data <- args[2]
+  edit <- args[3]
+}
+
+library(dplyr)
+#####################################################################################################
+#Functions for creation of Data Papers
+
+#' map_geographical_coverage
+#'Make a map from EML
+#' @param eml Metadata using EML standard in XML format
+#'
+#' @return A map
+#' @export
+map_geographical_coverage <- function(eml,editable=edit){
+  name <- xml2::xml_find_all(eml, "//geographicCoverage/geographicDescription")
+  name <- unlist(xml2::as_list(name))
+
+  west <- xml2::xml_find_all(eml, "//geographicCoverage/boundingCoordinates/westBoundingCoordinate")
+  west <- as.numeric(unlist(xml2::as_list(west)))
+
+  east <- xml2::xml_find_all(eml, "//geographicCoverage/boundingCoordinates/eastBoundingCoordinate")
+  east <- as.numeric(unlist(xml2::as_list(east)))
+
+  north <- xml2::xml_find_all(eml, "//geographicCoverage/boundingCoordinates/northBoundingCoordinate")
+  north <- as.numeric(unlist(xml2::as_list(north)))
+
+  south <- xml2::xml_find_all(eml, "//geographicCoverage/boundingCoordinates/southBoundingCoordinate")
+  south <- as.numeric(unlist(xml2::as_list(south)))
+
+  geo_info <- data.frame(name = name,
+                         west = west, east = east,
+                         south = south, north = north)
+
+  map <- leaflet::leaflet(geo_info) %>%
+    leaflet::addProviderTiles("CartoDB.Positron") %>%
+    leaflet::addRectangles(
+      lng1 = west, lat1 = south,
+      lng2 = east, lat2 = north,
+      popup = name,
+      fillColor = "transparent"
+    )
+  if (editable=="true") {
+    mapview::mapshot(map,file="map.png")
+  }
+  mapview::mapshot(map, url = "map.html")
+}
+
+
+##' Render EML metadata into a webpage
+##'
+##' Pass in an xml file of EML metadata and generate a nice webpage describing
+##' the dataset.
+##'
+##' @title Render EML
+##' @param eml A valid Ecological Metadata Language file to be rendered to html.
+##' @param open Whether to open the file in a browser. Defaults to TRUE.
+##' @param publish_mode TRUE. If TRUE the website is pretty without warnings for weird stuff.
+##' @param output_dir directory where will be stored the result file
+##' @param encoding "" encoding of the EML file if necessary
+##' @return HTML file containing dataset information
+render_eml <- function(eml, open = FALSE,
+                       publish_mode = TRUE, output_dir = "/docs",
+                       encoding = "",editable) {
+  eml <- xml2::read_xml(eml, encoding = encoding)
+  if (editable=="true"){
+    style2 <- xml2::read_xml(paste0(path_temp,"/bootstrap2.xsl"))
+    html <- xslt::xml_xslt(eml, style2)
+    # make map
+    xml2::write_html(html, "DataPaper2.html")
+    rmarkdown::pandoc_convert("DataPaper2.html", output="DataPaper.docx", options =c("--standalone"))
+    file.copy("DataPaper.docx",".")
+  }
+  style <- xml2::read_xml(paste0(path_temp,"/bootstrap.xsl"))
+  html <- xslt::xml_xslt(eml, style)
+  # make map
+  map_geographical_coverage(eml)
+  xml2::write_html(html, "DataPaper.html")
+}
+
+#######################################################################################################
+#exportation of Data Paper
+
+render_eml(data,editable=edit)
+
+

tools/metashrimps/DataPaper.xml

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+<tool id="metashrimp_datapaper" name="Production of a draft of Data Paper" version="0.1.0+galaxy0" profile="22.05">
+    <description>Create a draft of Data Paper from metadata</description>
+    <requirements>
+	   <requirement type="package">r-base</requirement>
+	   <requirement type="package">r-dplyr</requirement>
+	   <requirement type="package">r-xml2</requirement>
+       	   <requirement type="package">r-xslt</requirement>
+	   <requirement type="package">r-mapview</requirement>
+	   <requirement type="package">r-leaflet</requirement>
+	   <requirement type="package">gmp</requirement>
+	   <requirement type="package" version="2.1.1">phantomjs</requirement>
+	   <requirement type="package" version="2.19.2">pandoc</requirement>
+	   <requirement type="package" version="2.23">r-rmarkdown</requirement>
+	   <requirement type="package" version="0.2_18">r-codetools</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+    Rscript
+        '$__tool_directory__/DataPaper.R'
+        '$__tool_directory__/template_emldown'
+        '$data'
+        '$editable'
+    ]]></command>
+    <inputs>
+        <param name="data" type="data" format="xml" label="Upload metadata" help="Insert only metadata using EML standard"/>
+        <param name="editable" type="boolean" checked="false" label="Would you like to include a docx editable file instead of an HTML?" help= "HTML files are better for visualisation but are more difficult to edit than a docx."/>
+    </inputs>
+    <outputs>
+        <collection name="draft_html" type="list" label="Data Paper Draft">
+            <data name="DataPaper" from_work_dir="DataPaper.html" format="html" label="Data Paper"/>
+            <data name="map" from_work_dir="map.html" format="html" label="Leaflet Map"/>
+        </collection>
+        <collection name="draft_docx" type="list" label="Editable Data Paper Draft">
+            <data name="DataPaper" from_work_dir="DataPaper.docx" format="docx" label="Data Paper docx"/>
+            <data name="map" from_work_dir="map.png" format="png" label="Leaflet Map Image"/>
+            <filter>editable</filter>
+        </collection>
+    </outputs>
+    <tests>
+         <test expect_num_outputs="6"> 
+            <param name="data" value="Assessing_the_importance_of_field_margins_for_bat_species.xml"/>
+            <param name="editable" value="true"/>
+            <output_collection name="draft_html" type="list">
+                <element name="DataPaper" file="DataPaper.html" ftype="html" />
+            </output_collection>
+            <output_collection name="draft_docx" type="list">
+                <element name="DataPaper" file="DataPaper.docx" ftype="docx" />
+                <element name="map" file="map.png" ftype="png" />
+            </output_collection>
+        </test>
+    </tests>
+<help><![CDATA[
+
+.. class:: warningmark
+
+'''TIP''' This tool requires metadata with **XML** format and using **EML** standard
+
+**What it does?**
+--------------------
+
+This tool aims to produce, from a metadata using EML standard, a draft of Data Paper.
+A Data Paper is an scientific publication describing the collect of data and thus highlighting the work of all data producers.
+This Draft of Data Paper may be used to present your metadata in a more esthetetic and comprehensible way to others or can be modified and completed to help
+the data producers redacting their publication.
+
+**How to use it?**
+--------------------
+
+To use this tool, you have to upload a metadata written in XML and using EML standard.
+You can then select whether you want an editable version of your Data Paper.
+By clicking the **Execute** button, the work will launch and you will be able to get your results in the historic on your right.
+
+
+]]></help>
+<citations>
+           <citation type="bibtex">@misc{githubsurvey2023,
+           author       = {ropensci-archive },
+           title        = {{EMLdown}},
+           publisher    = {Github},
+           url          = {https://github.com/ropensci-archive/emldown}
+           }
+          }</citation>
+    </citations>
+</tool>