changeset 1:e44c5246247a draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/TableMerge/README.md	Thu Nov 14 12:33:41 2019 -0500
@@ -0,0 +1,52 @@
+Table Merge
+=======
+
+Metadata
+-----------
+
+ * **@name**: Table Merge
+ * **@version**: 1.0.1
+ * **@authors**: Melanie Petera (PFEM - INRA - MetaboHUB)
+ * **@init date**: 2015, June
+ * **@main usage**: This tool merges a data matrix file with a selected metadata file to obtain a single file.
+
+ 
+Context
+-----------
+
+This tool is provided as one of the [Workflow4Metabolomics](http://workflow4metabolomics.org) Galaxy instance statistical tools. 
+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.
+
+ 
+Configuration
+-----------
+
+### Requirement:
+ * R software: version > 3.0.0 recommended
+ * Specific R libraries: 'batch'
+
+
+Technical description
+-----------
+
+Main files:
+
+- tablemerge_script.R: R function (core script)
+- tablemerge_wrap.R: R script to link the main R function to inputs
+- tablemerge.xml: XML wrapper (interface for Galaxy)
+- RcheckLibrary.R and miniTools.R: additional R functions used by the core script (input checks and data handling)
+
+
+Services provided
+-----------
+
+ * Help and support: [e-mail]
+
+
+License
+-----------
+
+ * Cea Cnrs Inria Logiciel Libre License, version 2.1 (CECILL-2.1)

--- a/TableMerge/README.txt	Thu Feb 23 04:37:49 2017 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,39 +0,0 @@
-## ****** Table Merge environment: ****** ##
-# version 2016-07-20 M Petera
-
-## --- PERL compilator / libraries: --- ##
-NA
---
-
-## --- R bin and Packages: --- ##
-$ R --version
-R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
-Platform: x86_64-redhat-linux-gnu (64-bit)
-
-The dependent libs are :
-library(batch)
--- 
-
-## --- Binary dependencies --- ##
-NA
---
-
-## --- Config: --- ##
-NA
---
-
-## --- XML HELP PART --- ##
-NA
---
-
-## --- DATASETS --- ##
-No data set ! waiting for galaxy pages
---
-
-## --- ??? COMMENTS ??? --- ##
-!WARNING! : Its existence made obsolete the old "Filters" tool
---
-
-## --- Changelog/News --- ##
-NA
---
\ No newline at end of file

--- a/TableMerge/tablemerge.xml	Thu Feb 23 04:37:49 2017 -0500
+++ b/TableMerge/tablemerge.xml	Thu Nov 14 12:33:41 2019 -0500
@@ -108,10 +108,6 @@
 
 ---------------------------------------------------
 
----------------
-Working example
----------------
-
 
 .. class:: warningmark
 

--- a/TableMerge/tablemerge_wrap.R	Thu Feb 23 04:37:49 2017 -0500
+++ b/TableMerge/tablemerge_wrap.R	Thu Nov 14 12:33:41 2019 -0500
@@ -7,7 +7,8 @@
 # User: Galaxy                                                                                 #
 # Original data: used with tablemerge_script.R                                                 #
 # Starting date: 11-05-2015                                                                    #
-# V-1: Firt version of wrapper                                                                 #
+# V-1: First version of wrapper                                                                #
+# V-2: Addition of prints about input parameters and job info                                  #
 #                                                                                              #
 #                                                                                              #
 # Input files: dataMatrix ; Metadata file                                                      #
@@ -31,8 +32,22 @@
 if(length(args) < 4){ stop("NOT enough argument !!!") }
 
 
+cat('\nJob starting time:\n',format(Sys.time(), "%a %d %b %Y %X"),
+'\n\n--------------------------------------------------------------------', 
+'\nParameters used in "Table Merge":\n\n')
+print(args)
+cat('--------------------------------------------------------------------\n\n')
+
+
 tab.merge(args$dataMatrix_in, args$Metadata_in, args$metatype, args$combined_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)