galaxyecology · Alanamosse · Mar 14, 2019 · Mar 15, 2019 · Mar 15, 2019 · Mar 15, 2019
diff --git a/tools/Rdata-reader/.shed.yml b/tools/Rdata-reader/.shed.yml
@@ -0,0 +1,33 @@
+categories:
+    - Ecology
+description: Rtools that allow to load and export data from a binary Rdata file.
+long_description: |
+   The two R scripts are rdata_reader and rdata_parser. The first loads an Rdata file and gives a quick insight of its content. Then the parser tools try to extract and write chosen attributes in the most appropriate way. A specified option will bind the available data into a single table file when possible. 
+
+homepage_url: https://github.com/galaxyecology/tools-ecology/tools/Rdata
+name: rdata-reader
+owner: ecology 
+remote_repository_url: https://github.com/galaxyecology/tools-ecology/tools/Rdata
+type: unrestricted
+
+repositories:
+  rdata_reader:
+    description: The rdata reader tool loads a rdata binary file, returns its attributes and a general summary.
+    owner: ecology
+    include:
+      - rdata_reader.xml
+      - rdata_reader.R
+      - rdata_macros.xml
+      - test-data/rdata_test.Rdata
+      - test-data/attributes.tabular
+      - test-data/summary.tabular
+
+  rdata_parser:
+    description: The rdata parser tool extracts and writes selected attributes from a binary Rdata file.
+    owner: ecology
+    include:
+      - rdata_parser.xml
+      - rdata_parser.R
+      - rdata_macros.xml
+      - test-data/rdata_test.Rdata
+      - test-data/attributes.tabular
diff --git a/tools/Rdata-reader/rdata_macros.xml b/tools/Rdata-reader/rdata_macros.xml
@@ -0,0 +1,11 @@
+<macros>
+    <token name="@VERSION@">0.1.0</token>  
+    <xml name="rdata_requirements">
+        <requirements>
+            <requirement type="package" version="1.20.2">r-getopt</requirement>
+        </requirements>
+    </xml>
+    <xml name="rdata_input1">
+        <param format="rdata" name="input1" type="data" label="Rdata binary file to explore"/>
+    </xml>i
+</macros>
diff --git a/tools/Rdata-reader/rdata_parser.R b/tools/Rdata-reader/rdata_parser.R
@@ -0,0 +1,86 @@
+#!/usr/bin/env Rscript
+#Use a Rdata file and attributes to extract
+#Get every argument and write a file with its values(s)
+
+cat("Load rdata file\n")
+
+#get the rdata file
+args = commandArgs(trailingOnly=TRUE)
+rdata<-load(args[1])
+rdata<-get(rdata)
+#sum<-summary(rdata) 
+
+#get the selected attributes to explore
+attributes_selected <- commandArgs(trailingOnly=TRUE)[2]
+attributes<-strsplit(attributes_selected, ",") #List of elements
+
+#write.table(sum,file = "summary.tabular",sep='\t',row.names=FALSE)
+len<-length(attributes[[1]])
+bind<-tail(args,n=1)
+
+#file type definition
+file_ext<-function(ext,attribute){
+	file<-paste("attribute_",attribute,ext,sep="") #Filename definition
+        file<-paste("outputs/",file,sep="")
+	return(file)
+}
+
+cat("Write element(s) : ")
+for (i in 1:len){
+	attribute<-attributes[[1]][i] #Get the attribute i 
+	if(! any(names(rdata)==attribute)){
+		error<-paste(attribute, " doesn't exist in the RData. Check the inputs files")
+		write(error, stderr())
+	}
+
+	attribute_val<-eval(parse(text=paste("rdata$",attribute,sep=""))) #Extract the value(s)
+
+	if(is.null(attribute_val)){ #Galaxy can't produce output if NULL
+		file<-file_ext(".txt",attribute)
+                cat(paste(attribute,", ",sep=""))
+		write("Return NULL value",file=file)
+		next #Exit loop
+	}
+
+	if (typeof(attribute_val)=="list"){ #Need to be corrected, fail in galaxy but not in R
+		if(length(attribute_val)=="0"){
+			file<-file_ext(".txt",attribute)
+			sink(file=file)
+			print("Empty list :") #If the list is empty without element, file is empty and an error occur in galaxy
+			print(attribute_val)
+			sink()
+			next
+		}else{
+			attribute_val<-as.data.frame(do.call(rbind, attribute_val))
+			file<-file_ext(".tabular",attribute)
+                        cat(paste(attribute,", ",sep=""))
+			write.table(attribute_val,file=file,row.names=FALSE)
+			next
+		}
+	}else if (typeof(attribute_val)=="language"){ #OK
+		attribute_val<-toString(attribute_val,width = NULL)
+		file<-file_ext(".txt",attribute)
+                cat(paste(attribute,", ",sep=""))
+		write(attribute_val,file=file)
+		next
+	}
+        file<-file_ext(".tabular",attribute)
+        dataframe<-as.data.frame(attribute_val)
+        names(dataframe)<-attribute
+        if(bind=="nobind"){
+            cat(paste(attribute,", ",sep=""))
+            write.table(dataframe,file=file,row.names=FALSE,sep="    ")
+        }else{
+            cat(paste(attribute,", ",sep=""))
+            if(!exists("alldataframe")){
+                alldataframe<-dataframe
+            }else{
+    	        alldataframe<-cbind(alldataframe, dataframe)
+            }
+        }
+}
+
+if(exists("alldataframe")&&bind=="bind"){
+    write.table(alldataframe,file="outputs/all_attributes.tabular",row.names=FALSE,sep="	")
+}
+q('no')
diff --git a/tools/Rdata-reader/rdata_parser.xml b/tools/Rdata-reader/rdata_parser.xml
@@ -0,0 +1,75 @@
+<tool id="rdata_parser" name="Rdata binary file parser" version="@VERSION@">
+    <macros>
+        <import>rdata_macros.xml</import>
+    </macros>
+    <expand macro="rdata_requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+        mkdir outputs &&
+	Rscript '$__tool_directory__/rdata_parser.R' '$input1' $selected_attributes '$other' '$bind_dataframe'
+]]>
+    </command>
+    <inputs>
+        <expand macro="rdata_input1"/>
+        <param name="rdata_attributes" type="data" label="File with .Rdata content details" format="tabular" help="Tabular file with Rdata attributes list. It can come from the Rdata reader tool : 'List of attributes from RDATAFILE'"/>
+        <param name="selected_attributes" label="Select which attribute(s) you want to extract" type="select" optional="false" multiple="true">
+            <options from_dataset="rdata_attributes">
+                <column name="value" index="0"/>
+            </options>
+        </param>
+        <param name="bind_dataframe" label="Bind attributes in a single tabular when its possible" type="boolean" truevalue="bind" falsevalue="nobind" checked="true"/>
+    </inputs>
+    <outputs>
+        <data name="other">
+            <discover_datasets pattern="__designation_and_ext__" visible="true" directory="outputs" />
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input1" value="rdata_test.Rdata"/>
+            <param name="rdata_attributes" value="attributes.tabular"/>
+            <param name="selected_attributes" value="ID,Age,Name"/>
+            <param name="bind_dataframe" value="TRUE"/>
+            <output name="other">
+                <discovered_dataset designation="all_attributes">
+                    <assert_contents>
+                        <has_line line="&quot;ID&quot;&#009;&quot;Age&quot;&#009;&quot;Name&quot;"/>
+                    </assert_contents>
+                </discovered_dataset>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+==========================
+Rdata parser
+==========================
+**What it does**        
+
+
+The Rdata parser tool allows to extract informations from a file in .RData format. 
+
+|
+
+**How to use it**
+
+First use the Rdata reader tool to get the list of attributes available in the binary file.
+
+Use the reader tool output to select the attribute(s) you want to extract.
+
+If the selected variables can be displayed alongside in a tabular files the option \"Bind\" will attempt to do so.
+
+|
+
+**Outputs**
+
+The tool will produce one file per attribute selected unless the \"Bind\" option is set to \"Yes\".
+
+If the data can be displayed as a table the file will be a .tabular.
+
+|
+
+**More informations**
+
+More informations concerning R Data format and save / load functions can be found here:  http://www.sthda.com/english/wiki/saving-data-into-r-data-format-rds-and-rdata.
+    ]]></help>
+</tool>
diff --git a/tools/Rdata-reader/rdata_reader.R b/tools/Rdata-reader/rdata_reader.R
@@ -0,0 +1,12 @@
+#!/usr/bin/env Rscript
+#Return list of attributes from a Rdata file
+
+args = commandArgs(trailingOnly=TRUE)
+rda<-load(args[1]) #Load the rdata
+rdata<-get(rda)
+names<-names(rdata) #Get the attributes
+write(names, file = "rdata_list_attr")
+
+sum<-summary(rdata) 
+write.table(sum,file = "summary.tabular",sep='\t',row.names=FALSE)
+#print(str(rdata)) #Other xay to give informations
diff --git a/tools/Rdata-reader/rdata_reader.xml b/tools/Rdata-reader/rdata_reader.xml
@@ -0,0 +1,53 @@
+<tool id="rdata_reader" name="Rdata binary file reader" version="@VERSION@">
+    <macros>
+        <import>rdata_macros.xml</import>
+    </macros>
+    <expand macro="rdata_requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+        Rscript '$__tool_directory__/rdata_reader.R' '$input1' '$rdata_list_attr' ]]>
+    </command>
+    <inputs>
+        <expand macro="rdata_input1"/>
+    </inputs>
+    <outputs>
+        <data format="tabular" name="rdata_list_attr" from_work_dir="rdata_list_attr" label="List of attributes from ${input1.name}"/>
+        <data name="summary" from_work_dir="summary.tabular" format="tabular" label="Summary of ${input1.name} attributes"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input1" value="rdata_test.Rdata"/>
+            <output name="rdata_list_attr" file="attributes.tabular"/>
+            <output name="summary" file="summary.tabular"/>
+        </test>
+    </tests>
+    <help>
+==========================
+Rdata binary file reader
+==========================
+**What it does**
+
+The Rdata reader tool gives informations on the content of a binary Rdata file.
+
+|
+
+**How to use it**
+
+Select a file in Rdata format and execute the tool.
+
+Use this tool before considering to use "Rdata binary file parser".
+
+|
+
+**Outputs**
+
+A list of the available dimensions in the Rdata (tabular output file).
+
+Summary file of the inner attributes and their values.
+
+|
+
+**More informations**
+
+More informations concerning R Data format and save / load functions can be found here: http://www.sthda.com/english/wiki/saving-data-into-r-data-format-rds-and-rdata.
+    </help>
+</tool>
diff --git a/tools/Rdata-reader/test-data/attributes.tabular b/tools/Rdata-reader/test-data/attributes.tabular
@@ -0,0 +1,3 @@
+ID
+Age
+Name
diff --git a/tools/Rdata-reader/test-data/rdata_test.Rdata b/tools/Rdata-reader/test-data/rdata_test.Rdata
diff --git a/tools/Rdata-reader/test-data/summary.tabular b/tools/Rdata-reader/test-data/summary.tabular
@@ -0,0 +1,7 @@
+"      ID"	"     Age"	"  Name"
+"Min.   :1  "	"Min.   :12.0  "	"Dora:1  "
+"1st Qu.:2  "	"1st Qu.:12.0  "	"John:1  "
+"Median :3  "	"Median :15.0  "	"name:3  "
+"Mean   :3  "	"Mean   :16.2  "	NA
+"3rd Qu.:4  "	"3rd Qu.:21.0  "	NA
+"Max.   :5  "	"Max.   :21.0  "	NA
-Original file line number
+Diff line change
@@ -0,0 +1,3 @@
+    ID
+    Age
+    Name