# HG changeset patch
# User melpetera
# Date 1576751397 18000
# Node ID bb19b1d15732574adee0d8d6292f104400806e1a
# Parent  b7a6a88f518ab26efe2d12a4c1e7534c1a729f1f
Uploaded

diff -r b7a6a88f518a -r bb19b1d15732 IDchoice/.gitmodules
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/IDchoice/.gitmodules	Thu Dec 19 05:29:57 2019 -0500
@@ -0,0 +1,3 @@
+[submodule "easyrlibrary-lib"]
+	path = easyrlibrary-lib
+	url = https://github.com/workflow4metabolomics/easyrlibrary-lib.git
diff -r b7a6a88f518a -r bb19b1d15732 IDchoice/IDchoice.xml
--- a/IDchoice/IDchoice.xml	Thu Oct 11 05:47:29 2018 -0400
+++ b/IDchoice/IDchoice.xml	Thu Dec 19 05:29:57 2019 -0500
@@ -1,4 +1,4 @@
-<tool id="idchoice" name="ID choice" version="18.01">
+<tool id="idchoice" name="ID choice" version="19.12">
   <description>Choosing a particular column in your metadata to be considered as Identifiers</description>
   <requirements>
 	    <requirement type="package" version="1.1_4">r-batch</requirement>
@@ -106,9 +106,9 @@
 	| It should include a column containing your wanted IDs. 
 	| 
 
-----------
-Parameter
-----------
+-----------
+Parameters
+-----------
 
 Which ID do you want to change?
 	| This must be consistant with the metadata file you chose as input
@@ -124,9 +124,9 @@
 	|
 
 
-------------
-Output file
-------------
+-------------
+Output files
+-------------
 
 ID_metadata
 	| tabular output
diff -r b7a6a88f518a -r bb19b1d15732 IDchoice/IDchoice_script.R
--- a/IDchoice/IDchoice_script.R	Thu Oct 11 05:47:29 2018 -0400
+++ b/IDchoice/IDchoice_script.R	Thu Dec 19 05:29:57 2019 -0500
@@ -4,6 +4,7 @@
 # User: Galaxy                                                                                 #
 # Starting date: 01-06-2017                                                                    #
 # V-0.1: First version of code                                                                 #
+# V-1.0: Code adjusted to user feedback                                                        #
 #                                                                                              #
 #                                                                                              #
 # Input files: dataMatrix ; Metadata file                                                      #
@@ -46,6 +47,10 @@
 table.check <- match2(DM,meta,metype)
 check.err(table.check)
 
+# Keep metadata original order tracked ----------------------------------------
+
+meta <- data.frame(meta,ori=1:nrow(meta))
+
 
 # Checking unicity of new IDs ----------------------------------------
 
@@ -67,11 +72,11 @@
 	
   }else{
     #Making unique names
-	meta <- cbind(meta,newID=make.unique(meta[,numcol],sep="_"),ori=c(1:nrow(meta)))
+	meta <- cbind(meta,newID=make.unique(meta[,numcol],sep="_"))
   }
 }else{
   #No unicity problem
-  meta <- cbind(meta,newID=meta[,numcol],ori=c(1:nrow(meta)))
+  meta <- cbind(meta,newID=meta[,numcol])
 }
 
 
@@ -92,12 +97,12 @@
 
 # Changing IDs -------------------------------------------------------
 
-DM <- comb.data[,-c(1:(ncol(meta)-2),ncol(meta))]
+DM <- comb.data[,-c(1:(ncol(meta)-1))]
 if(makeun=="no"){
   comb.data <- comb.data[,c(numcol,which(colnames(meta)!=coloname))]
   meta <- comb.data[,c(1:(ncol(meta)-2))]
 }else{
-  meta <- comb.data[,c(ncol(meta)-1,1:(ncol(meta)-2))]
+  meta <- comb.data[,c(ncol(meta),1:(ncol(meta)-2))]
 }
 
 #Transposing back the dataMatrix if necessary
diff -r b7a6a88f518a -r bb19b1d15732 IDchoice/IDchoice_wrap.R
--- a/IDchoice/IDchoice_wrap.R	Thu Oct 11 05:47:29 2018 -0400
+++ b/IDchoice/IDchoice_wrap.R	Thu Dec 19 05:29:57 2019 -0500
@@ -7,7 +7,8 @@
 # User: Galaxy                                                                                 #
 # Original data: used with IDchoice_script.R                                                   #
 # Starting date: 01-06-2017                                                                    #
-# V-1: Firt version of wrapper                                                                 #
+# V-1: First version of wrapper                                                                #
+# V-2: Additional information in stdout                                                        #
 #                                                                                              #
 #                                                                                              #
 # Input files: dataMatrix ; Metadata file                                                      #
@@ -31,8 +32,22 @@
 if(length(args) < 7){ stop("NOT enough argument !!!") }
 
 
+cat('\nJob starting time:\n',format(Sys.time(), "%a %d %b %Y %X"),
+'\n\n--------------------------------------------------------------------', 
+'\nParameters used in "ID choice":\n\n')
+print(args)
+cat('--------------------------------------------------------------------\n\n')
+
+
 id.choice(args$dataMatrix_in, args$Metadata_in, args$metatype, args$col_name, args$makeunique, args$DM_out, args$meta_out)
 
 
+cat('\n--------------------------------------------------------------------',
+'\nInformation about R (version, Operating System, attached or loaded packages):\n\n')
+sessionInfo()
+cat('--------------------------------------------------------------------\n',
+'\nJob ending time:\n',format(Sys.time(), "%a %d %b %Y %X"))
+
+
 #delete the parameters to avoid the passage to the next tool in .RData image
 rm(args)
diff -r b7a6a88f518a -r bb19b1d15732 IDchoice/README.md
--- a/IDchoice/README.md	Thu Oct 11 05:47:29 2018 -0400
+++ b/IDchoice/README.md	Thu Dec 19 05:29:57 2019 -0500
@@ -5,7 +5,7 @@
 -----------
 
  * **@name**: ID choice
- * **@version**: 17.11
+ * **@version**: 19.12
  * **@authors**: Melanie Petera - PFEM ; INRA ; MetaboHUB 
  * **@init date**: 2017/06/07
  * **@main usage**: This tool is designed to make you choose a particular column in your metadata file to be considered as identifiers for your W4M-3-tables-format data. 
@@ -14,7 +14,7 @@
 Context
 -----------
 
-This tool is one of the [Workflow4Metabolomics](http://workflow4metabolomics.org) Galaxy instance utilities. W4M is a French infrastructure providing software tools to process, analyse and annotate metabolomics data. 
+This tool is provided as one of the [Workflow4Metabolomics](http://workflow4metabolomics.org) Galaxy instance utilities. W4M is a French infrastructure providing software tools to process, analyse and annotate metabolomics data. 
 
 User interface is based on the Galaxy platform (homepage: https://galaxyproject.org/). It is an open, web-based platform for data intensive biomedical research. Whether on the free public server or your own instance, you can perform, reproduce, and share complete analyses.
 
@@ -28,7 +28,6 @@
  * Submodule: [easyRlibrary](https://github.com/workflow4metabolomics/easyrlibrary-lib) (Required for internal input quality checks)
 
 ### Deploy:
- * [get project data](https://github.com/workflow4metabolomics/idchoice)
  * How to get the submodule files:
 When pulling this module's Git repository, you may only obtain an empty folder for the needed submodule.
 You can initialise it then with the following command:
@@ -37,13 +36,6 @@
 ```
 
 
-Travis test
------------
-
-[![Build Status](https://travis-ci.org/workflow4metabolomics/idchoice.svg?branch=master)](https://travis-ci.org/workflow4metabolomics/idchoice)
-Test and Deploy with Confidence. Easily sync your GitHub projects with Travis CI and you'll be testing your code in minutes!
-
-
 Technical description
 -----------
 
@@ -58,3 +50,9 @@
 -----------
 
  * Help and support: support@workflow4metabolomics.org
+
+
+License
+-----------
+
+ * Cea Cnrs Inria Logiciel Libre License, version 2.1 (CECILL-2.1)