Mercurial > repos > pieterlukasse > prims_metabolomics

changeset 8:ddef5534c294

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
new tool diffreport
author pieter.lukasse@wur.nl
date Thu, 06 Nov 2014 13:06:25 +0100
parents 504be42b4927
children 31ec089d20a4
files metams_lcms_annotate.xml static/images/diffreport.png static/images/test/out2/fig_eic/001.png static/images/test/out2/fig_eic/002.png static/images/test/out2/fig_eic/003.png static/images/test/out2/fig_eic/004.png static/images/test/out2/fig_eic/005.png static/images/test/out2/fig_eic/006.png static/images/test/out2/fig_eic/007.png static/images/test/out2/fig_eic/008.png static/images/test/out2/fig_eic/009.png static/images/test/out2/fig_eic/010.png xcms_differential_analysis.r xcms_differential_analysis.xml
diffstat 14 files changed, 59 insertions(+), 9 deletions(-) [+]
line wrap: on
line diff
--- a/metams_lcms_annotate.xml	Thu Nov 06 11:32:16 2014 +0100
+++ b/metams_lcms_annotate.xml	Thu Nov 06 13:06:25 2014 +0100
@@ -1,4 +1,4 @@
-<tool id="metams_lcms_annotate" name="METAMS-LC/MS Annotate"  version="0.0.1">
+<tool id="metams_lcms_annotate" name="METAMS-LC/MS Annotate"  version="0.0.3">
 	<description> Runs metaMS process for LC/MS feature grouping and annotation</description>
 	<requirements>
 		<requirement type="package" version="3.1.1">R_bioc_metams</requirement>
Binary file static/images/diffreport.png has changed
Binary file static/images/test/out2/fig_eic/001.png has changed
Binary file static/images/test/out2/fig_eic/002.png has changed
Binary file static/images/test/out2/fig_eic/003.png has changed
Binary file static/images/test/out2/fig_eic/004.png has changed
Binary file static/images/test/out2/fig_eic/005.png has changed
Binary file static/images/test/out2/fig_eic/006.png has changed
Binary file static/images/test/out2/fig_eic/007.png has changed
Binary file static/images/test/out2/fig_eic/008.png has changed
Binary file static/images/test/out2/fig_eic/009.png has changed
Binary file static/images/test/out2/fig_eic/010.png has changed
--- a/xcms_differential_analysis.r	Thu Nov 06 11:32:16 2014 +0100
+++ b/xcms_differential_analysis.r	Thu Nov 06 13:06:25 2014 +0100
@@ -38,22 +38,17 @@
 			xcmsSet <- readRDS(args.xsetData)
 			
 			# info: levels(xcmsSet@phenoData$class) also gives access to the class names
-			
-			reporttab <- diffreport(xcmsSet, args.class1, args.class2, args.htmlReportFile.files_path, args.topcount, metlin = 0.15, h=480, w=640)
+			dir.create(file.path(args.htmlReportFile.files_path), showWarnings = FALSE)
+			reporttab <- diffreport(xcmsSet, args.class1, args.class2, paste(args.htmlReportFile.files_path,"/fig", sep=""), args.topcount, metlin = 0.15, h=480, w=640)
 			
 			# write out tsv table:
 			write.table(reporttab, args.outTable, sep="\t", row.names=FALSE)
 			
 			message("\nGenerating report.........")
-			# report
-			dir.create(file.path(args.htmlReportFile.files_path), showWarnings = FALSE)
-			# setwd(file.path(args.htmlReportFile.files_path))
-			file.rename("fig_eic", paste(args.htmlReportFile.files_path, "/fig_eic"))
-			
 			
 			cat("<html><body><h1>Differential analysis report</h1>", file= args.htmlReportFile)
 			#HTML(reporttab[1:args.topcount,], file= args.htmlReportFile)
-			figuresPath <- paste(args.htmlReportFile.files_path, "_eic", sep="")
+			figuresPath <- paste(args.htmlReportFile.files_path, "/fig_eic", sep="")
 			message(figuresPath)
 			listOfFiles <- list.files(path = figuresPath)
 			for (i in 1:length(listOfFiles))  
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/xcms_differential_analysis.xml	Thu Nov 06 13:06:25 2014 +0100
@@ -0,0 +1,55 @@
+<tool id="xcms_differential_analysis" name="XCMS Differential Analsysis"  version="0.0.1">
+	<description> Runs xcms diffreport function for differential Analsysis</description>
+	<requirements>
+		<requirement type="package" version="3.1.1">R_bioc_metams</requirement>
+	</requirements>	
+	<command interpreter="Rscript">
+		xcms_differential_analysis.r 
+	    $xsetData
+		$class1
+		$class2
+		$topcount
+		$outTable 
+		$outLogFile
+		$htmlReportFile
+		$htmlReportFile.files_path
+	</command>
+<inputs>
+	
+	<param name="xsetData" type="data" format="rdata" label="xset xcms data file" help="E.g. output data file resulting from METAMS run"/>
+	
+	
+	<param name="class1" type="text" size="30" label="Class1 name" value="" help="Name of first class for the comparison"/>
+	<param name="class2" type="text" size="30" label="Class2 name" value="" help="Name of second class for the comparison"/>
+	
+	<param name="topcount" type="integer" size="10" value="10" label="Number of items to return" help="Top X differential items. E.g. if 10, it will return top 10 differential items." />
+	
+</inputs>
+<outputs>
+	<data name="outTable" format="tabular" label="${tool.name} on ${on_string} - Top differential items (TSV)"/>
+	<data name="outLogFile" format="txt" label="${tool.name} on ${on_string} - differential log (LOG)"/>
+	<data name="htmlReportFile" format="html" label="${tool.name} on ${on_string} - differential report (HTML)"/>
+</outputs>
+<tests>
+	<test>
+	</test>
+</tests>
+<help>
+
+.. class:: infomark
+  
+Runs xcms diffreport for showing the most significant differences between two sets/classes of samples. This tool also creates extracted ion chromatograms (EICs) for 
+the most significant differences. The figure below shows an example of such an EIC.
+
+.. image:: $PATH_TO_IMAGES/diffreport.png 
+
+
+
+
+  </help>
+  <citations>
+        <citation type="doi">10.1021/ac051437y</citation> <!-- example 
+        see also https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Ccitations.3E_tag_set
+        -->
+   </citations>
+</tool>
\ No newline at end of file