# HG changeset patch
# User ethevenot
# Date 1519827347 18000
# Node ID cc0e9eff0de2a4014a6cdb81c801cf876628c800
# Parent  0ccfc3e15710ed8c87f9b64bd0af0a8dc1cb9e76
planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit 60ebb3e8919c09c18f89a5362750ae45ca84d0c2

diff -r 0ccfc3e15710 -r cc0e9eff0de2 build.xml
--- a/build.xml	Tue Jun 06 11:55:21 2017 -0400
+++ b/build.xml	Wed Feb 28 09:15:47 2018 -0500
@@ -36,7 +36,7 @@
 			<arg value="--conda_prefix"/>
 			<arg value="${conda.dir}"/>
 			<arg value="--galaxy_branch"/>
-			<arg value="release_16.01"/>
+			<arg value="release_17.05"/>
 			<arg value="--conda_dependency_resolution"/>
 			<arg value="${tool.xml}"/>
 		</exec>
diff -r 0ccfc3e15710 -r cc0e9eff0de2 runit/output/information.txt
--- a/runit/output/information.txt	Tue Jun 06 11:55:21 2017 -0400
+++ b/runit/output/information.txt	Wed Feb 28 09:15:47 2018 -0500
@@ -1,5 +1,5 @@
 
-Start of the 'Transformation' module: Thu 04 Aug 2016 08:58:11 PM
+Start of the 'Transformation' module: Thu 03 Aug 2017 16:41:30
 
 Missing values in the 'dataMatrix': 4 (4%)
 
@@ -7,4 +7,24 @@
 
 'Square root' transformation
 
-End of the 'Transformation' Galaxy module call: Thu 04 Aug 2016 08:58:11 PM
+End of the 'Transformation' Galaxy module call: Thu 03 Aug 2017 16:41:30
+
+
+
+============================================================================
+Additional information about the call:
+
+1) Parameters:
+               value                         
+dataMatrix_in  "runit/input/dataMatrix.tsv"  
+dataMatrix_out "runit/output/dataMatrix.tsv" 
+information    "runit/output/information.txt"
+method         "sqrt"                        
+
+2) Session Info:
+R version 3.4.1 (2017-06-30) 
+Main packages:
+batch 1.1.4 	
+Other loaded packages:
+compiler 3.4.1 	
+============================================================================
diff -r 0ccfc3e15710 -r cc0e9eff0de2 runit/transformation_runtests.R
diff -r 0ccfc3e15710 -r cc0e9eff0de2 transformation_config.xml
--- a/transformation_config.xml	Tue Jun 06 11:55:21 2017 -0400
+++ b/transformation_config.xml	Wed Feb 28 09:15:47 2018 -0500
@@ -2,7 +2,7 @@
   <description>Transforms the dataMatrix intensity values</description>
   
   <requirements>
-    <requirement type="package">r-batch</requirement>
+    <requirement type="package" version="1.1_4">r-batch</requirement>
   </requirements>
 
   <stdio>
@@ -78,7 +78,6 @@
 |
     
 .. image:: transformation_workflowPositionImage.png
-:width: 600
     
     
     
diff -r 0ccfc3e15710 -r cc0e9eff0de2 transformation_wrapper.R
--- a/transformation_wrapper.R	Tue Jun 06 11:55:21 2017 -0400
+++ b/transformation_wrapper.R	Wed Feb 28 09:15:47 2018 -0500
@@ -2,6 +2,22 @@
 
 library(batch) ## parseCommandArgs
 
+# Constants
+argv <- commandArgs(trailingOnly = FALSE)
+script.path <- sub("--file=","",argv[grep("--file=",argv)])
+prog.name <- basename(script.path)
+
+# Print help
+if (length(grep('-h', argv)) >0) {
+	cat("Usage:", prog.name,
+	    "dataMatrix_in myDataMatrixInput.tsv",
+	    "method log2|log10|sqrt",
+	    "dataMatrix_out myDataMatrixOutput.tsv",
+	    "information information.txt",
+		"\n")
+	quit(status = 0)
+}
+
 source_local <- function(fname){
     argv <- commandArgs(trailingOnly = FALSE)
     base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))