changeset 3:2433c6fa4de2 draft

planemo upload commit b931b0c4ca182ea28a9ed1365bece9b2326fd64c
author lecorguille
date Mon, 28 Mar 2016 15:51:28 -0400
parents b6298c38e53f
children e1a77f4a20dc
files Makefile README.md abims_anova.r abims_anova.xml galaxy/stat_anova/.travis/setup_custom_dependencies.bash galaxy/stat_anova/Makefile galaxy/stat_anova/abims_anova.r galaxy/stat_anova/abims_anova.xml galaxy/stat_anova/static/images/anova_filtered.png galaxy/stat_anova/static/images/anova_pvalue.png galaxy/stat_anova/static/images/anova_workflow.png galaxy/stat_anova/test-data/dataMatrix.tsv galaxy/stat_anova/test-data/dataMatrix.tsv_anova_filtered.tabular galaxy/stat_anova/test-data/dataMatrix.tsv_anova_pvalue.tabular galaxy/stat_anova/test-data/sampleMetadata.tsv galaxy/stat_anova/tool_dependencies.xml static/images/anova_filtered.png static/images/anova_pvalue.png static/images/anova_workflow.png test-data/dataMatrix.tsv test-data/dataMatrix.tsv_anova_filtered.tabular test-data/dataMatrix.tsv_anova_pvalue.tabular test-data/sampleMetadata.tsv tool_dependencies.xml
diffstat 24 files changed, 476 insertions(+), 503 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Makefile	Mon Mar 28 15:51:28 2016 -0400
@@ -0,0 +1,23 @@
+# USAGE: make [install|clean]
+
+# -------- VARIABLE --------
+
+OBJ=anova.tgz
+DEP=abims_anova.r abims_anova.xml static test-data
+
+
+# ------------------------
+
+all: $(OBJ)
+
+$(OBJ): $(DEP)
+	tar --exclude=".svn" -zchf $@ $^
+
+# ------------------------
+
+install: $(OBJ)
+	mv *.tgz ~
+
+clean:
+	rm *.tgz
+
--- a/README.md	Mon Mar 28 15:49:04 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,26 +0,0 @@
-Anova for Galaxy
-=================
-
-
-Our project
------------
-The [Workflow4Metabolomics](http://workflow4metabolomics.org), W4M in short, is a French infrastructure offering software tool processing, analyzing and annotating metabolomics data. It is based on the Galaxy platform.
-
-
-Anova
-------
-Analysis of variance (ANOVA) is a collection of statistical models used to analyze the differences among group means and their associated procedures (such as "variation" among and between groups), developed by statistician and evolutionary biologist Ronald Fisher.
-
-Source: [https://en.wikipedia.org/wiki/Analysis_of_variance](https://en.wikipedia.org/wiki/Analysis_of_variance)
-
-
-Galaxy
-------
-Galaxy 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. 
-
-Homepage: [https://galaxyproject.org/](https://galaxyproject.org/)
-
-
-Historic contributors
----------------------
- - Gildas Le Corguillé @lecorguille - [ABiMS](http://abims.sb-roscoff.fr/) / [IFB](http://www.france-bioinformatique.fr/) - [UPMC](www.upmc.fr)/[CNRS](www.cnrs.fr) - [Station Biologique de Roscoff](http://www.sb-roscoff.fr/) - France
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/abims_anova.r	Mon Mar 28 15:51:28 2016 -0400
@@ -0,0 +1,132 @@
+#!/usr/local/public/bin/Rscript
+# version="1.1"
+
+# date: 06-06-2012
+# update: 18-02-2014
+# **Authors** Gildas Le Corguille  ABiMS - UPMC/CNRS - Station Biologique de Roscoff - gildas.lecorguille|at|sb-roscoff.fr 
+
+# abims_anova.r version 20140218
+
+library(batch)
+
+
+# function avova
+anova = function (file, sampleinfo, mode="column", condition=1, interaction=F, method="BH", threshold=0.01, selection_method="intersection", sep=";", dec=".", outputdatapvalue="anova.data.output", outputdatafiltered="anova.datafiltered.output") {
+	
+ 
+	if (sep=="tabulation") sep="\t"
+    	if (sep=="semicolon") sep=";"
+    	if (sep=="comma") sep=","
+
+	anova_formula_operator = "+"
+	if (interaction) anova_formula_operator = "*"
+  
+  	# -- import --
+	data=read.table(file, header = TRUE, row.names=1, sep = sep, quote="\"", dec = dec, fill = TRUE, comment.char="",na.strings = "NA")
+	
+  	if (mode == "row") data=t(data)
+	
+	sampleinfoTab=read.table(sampleinfo, header = TRUE, row.names=1, sep = sep, quote="\"")
+	rownames(sampleinfoTab) = make.names(rownames(sampleinfoTab))
+
+	
+	# -- group --
+	match_data_sampleinfoTab = match(rownames(data),rownames(sampleinfoTab))
+	if (sum(is.na(match_data_sampleinfoTab)) > 0) {
+	  write("ERROR: There is a problem during to match sample names from the data matrix and from the sample info (presence of NA).", stderr())
+	  write("You may need to use change the mode (column/row)", stderr())
+	  write("10 first sample names in the data matrix:", stderr())
+	  write(head(colnames(data)), stderr())
+	  write("10 first sample names in the sample info:", stderr())
+	  write(head(rownames(sampleinfoTab)), stderr())
+	  quit("no",status=10)
+	}
+  
+	
+	# -- anova --
+  
+  	# formula
+	grps=list()
+	anova_formula_s = "data ~ "
+	cat("\ncontrasts:\n")
+	for (i in 1:length(condition)) {
+	  grps[[i]] = factor(sampleinfoTab[,condition[i]][match_data_sampleinfoTab])
+	  anova_formula_s = paste(anova_formula_s, "grps[[",i,"]]",anova_formula_operator, sep="")
+	  cat(condition[i],"\t",levels(grps[[i]]),"\n")
+	# write("Current groups: ", stderr())
+	# write(grp[[i]], stderr())
+	}
+	anova_formula_s = substr(anova_formula_s, 1, nchar(anova_formula_s)-1)
+	anova_formula = as.formula(anova_formula_s)
+
+
+	
+	# anova
+	manovaObjectList = manova(anova_formula)
+	manovaList = summary.aov(manovaObjectList)
+	
+  	# condition renaming
+	manovaRownames = gsub(" ","",rownames(manovaList[[1]]))
+	manovaNbrPvalue = length(manovaRownames)-1
+	manovaRownames = manovaRownames[-(manovaNbrPvalue+1)]
+	
+	for (i in 1:length(condition)) {
+	  manovaRownames = sub(paste("grps\\[\\[",i,"\\]\\]",sep=""),condition[i],manovaRownames)
+  	  anova_formula_s = sub(paste("grps\\[\\[",i,"\\]\\]",sep=""),condition[i],anova_formula_s)
+	}
+
+  	# log
+  	cat("\nanova_formula",anova_formula_s,"\n")
+	
+	# p-value
+	aovPValue = sapply(manovaList,function(x){x[-(manovaNbrPvalue+1),5]})
+	if(length(condition) == 1) aovPValue = t(aovPValue)
+	rownames(aovPValue) = paste("pvalue_",manovaRownames,sep="")
+  
+	# p-value adjusted
+	if(length(condition) == 1) {
+		aovAdjPValue = t(p.adjust(aovPValue,method=method))
+	} else {
+		aovAdjPValue = apply(aovPValue,2,p.adjust, method=method)
+	}
+	rownames(aovAdjPValue) = paste("pvalueadjusted.",method,".",manovaRownames,sep="")
+	
+	# selection
+	colSumThreshold = colSums(aovAdjPValue <= threshold)
+	if (selection_method == "intersection") {
+		datafiltered = data[,colSumThreshold == nrow(aovAdjPValue )]
+	} else {
+		datafiltered = data[,colSumThreshold != 0]
+	}
+	
+	#data=rbind(data, aovPValue, aovAdjPValue)
+	data=rbind(data, aovAdjPValue)
+
+	
+	if (mode == "row") {
+	  data=t(data)
+	  datafiltered=t(datafiltered)
+	}
+	
+	# -- output / return --
+	write.table(data, outputdatapvalue, sep=sep, quote=F, col.names = NA)
+	write.table(datafiltered, outputdatafiltered, sep=sep, quote=F, col.names = NA)
+	
+	# log 
+	cat("\nthreshold:",threshold,"\n")
+	cat("result:",nrow(datafiltered),"/",nrow(data),"\n")
+  
+	quit("no",status=0)
+}
+
+# log
+cat("ANOVA\n\n")
+cat("Arguments\n")
+args <- commandArgs(trailingOnly = TRUE)
+print(args)
+
+listArguments = parseCommandArgs(evaluate=FALSE)
+do.call(anova, listArguments)
+
+
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/abims_anova.xml	Mon Mar 28 15:51:28 2016 -0400
@@ -0,0 +1,258 @@
+<tool id="abims_anova" name="Anova" version="1.1.3">
+    
+    <description>N-way anova. With ou Without interactions</description>
+    
+    <requirements>
+        <requirement type="package" version="3.1.2">R</requirement>
+	<requirement type="binary">Rscript</requirement>
+	<requirement type="package" version="1.1-4">batch</requirement>
+    </requirements>
+
+    <stdio>
+        <exit_code range="1:" level="fatal" />
+    </stdio>
+
+    <command interpreter="Rscript">
+abims_anova.r file "$input" sampleinfo "$sampleinfo" mode "$mode" 
+condition "c('$condition_1'
+#for $i, $s in enumerate( $conditions )
+,'${s.condition}'
+#end for
+)"
+interaction $interaction method $method threshold $threshold selection_method $selection_method sep "$sep" dec "$dec" outputdatapvalue $dataMatrixPValue outputdatafiltered $dataMatrixFiltered
+    </command> 
+
+    <inputs>
+        <param name="input" type="data" label="Data Matrix file" format="tabular" help="Matrix of numeric data with headers." />
+        <param name="sampleinfo" type="data" label="Sample Metadata file" format="tabular" help="Tabular file with the data metadata : one sample per line and at least two columns : ids and one condition" />
+        
+        <param name="mode" type="select" help="Perform the anova tests on column/row" format="text" optional="true">
+            <label>Mode</label>
+            <option value="row">row</option>
+            <option value="column">column</option>
+        </param>
+    
+        <param name="condition_1" type="text" label="Condition" value="" help="The column name of the condition. ex: hour or treatment" optional="false" />
+        <repeat name="conditions" title="Conditions for N-ways anova">
+            <param name="condition" type="text" label="Condition" value="" help="The column name of the condition. ex: hour or treatment" />
+        </repeat>
+
+        <param name="interaction" type="boolean" label="Enable interaction response p-values" truevalue="T" falsevalue="F" help="Used if more than 1 conditon. The anova will produse p-value according to the interaction between your condition (ex: condition1:conditions2, condition1:conditions3, condition2:conditions3 and condition1:condition2:conditions3)" />
+            
+        <param name="method" type="select" help="Method used to apply a correction on the pvalue because of the number of test" format="text" optional="true">
+            <label>PValue adjusted method</label>
+            <option value="BH">BH</option>
+            <option value="holm">holm</option>
+            <option value="bonferroni">bonferroni</option>
+            <option value="hochberg">hochberg</option>
+            <option value="hommel">hommel</option>
+            <option value="BY">BY</option>
+            <option value="fdr">fdr</option>
+            <option value="none">none</option>		
+        </param>        
+        
+        <param name="threshold" type="float" label="Threshold" value="0.01" help="max adjusted p.value accepted" />
+
+        <param name="selection_method" type="select" format="text" help="Intersection: all condition p-value must be under the threshold. Union: at least condition p-value must be under the threshold. ">
+            <label>Selection method</label>
+            <option value="intersection" selected="true">intersection / strong</option>
+            <option value="union">union / weak</option>
+        </param>
+
+        <param name="sep" type="select" format="text">
+            <label>Separator of columns</label>
+            <option value="tabulation">tabulation</option>
+            <option value="semicolon">;</option>
+            <option value="comma">,</option>
+        </param>
+        
+        <param name="dec" type="text" label="Decimal separator" value="." help="" />
+
+    </inputs>
+
+    <outputs>
+        <data name="dataMatrixPValue" format_source="input" label="${input.name}_anova_pvalue.${input.ext}"/>
+        <data name="dataMatrixFiltered" format_source="input" label="${input.name}_anova_filtered.${input.ext}"/>
+    </outputs>
+    
+    <tests>
+        <test>
+            <param name="input" value="dataMatrix.tsv"/>
+            <param name="sampleinfo" value="sampleMetadata.tsv"/>
+            <param name="mode" value="row"/>
+            <param name="condition_1" value="age"/>
+            <param name="conditions_0|condition" value="gender"/>
+            <param name="interaction" value="F"/>
+            <param name="method" value="BH"/>
+            <param name="threshold" value="0.05"/>
+            <param name="selection_method" value="union"/>
+            <param name="sep" value="tabulation"/>
+            <param name="dev" value="."/>
+            <output name="dataMatrixPValue" file="dataMatrix.tsv_anova_pvalue.tabular" />
+            <output name="dataMatrixFiltered" file="dataMatrix.tsv_anova_filtered.tabular" />
+        </test>
+    </tests>
+
+    <help>
+
+.. class:: infomark
+
+**Authors** Gildas Le Corguille  ABiMS - UPMC/CNRS - Station Biologique de Roscoff - gildas.lecorguille|at|sb-roscoff.fr 
+
+---------------------------------------------------
+
+=====
+Anova
+=====
+
+-----------
+Description
+-----------
+
+Analysis of variance (ANOVA) is used to analyze the differences between group means and their associated procedures,
+in which the observed variance in a particular variable is partitioned into components attributable to different sources of variation.
+
+
+
+-----------
+Input files
+-----------
+
++---------------------------+------------+
+| Parameter : num + label   |   Format   |
++===========================+============+
+| 1 : Data Matrix file      | Tabular    |
++---------------------------+------------+
+| 2 : Sample Metadata file  | Tabular    |
++---------------------------+------------+
+
+
+
+------------
+Output files
+------------
+
+
+
+***.anova_pvalue.tabular**
+
+    | A tabular file which represents for each metabolite (row), the value of the intensity in each sample (column) + two columns (aovPValue and aovAdjPValue).
+
+***.anova_filtered.tabular**
+
+    | The tabular file xset.anova_pvalue.tabular containing only the metabolites that have been filtered by aovAdjPValue.
+    
+    
+------
+
+.. class:: infomark 
+
+The outputs ***.anova_filtered.tabular** or ***.anova_pvalue.tabular** are tabular files. You can continue your analysis using it in the following tools:
+    | PCA
+    | Hierarchical Clustering
+
+    
+    
+---------------------------------------------------
+
+---------------
+Working example
+---------------
+
+
+Input files
+-----------
+
+**>A part of an example of Data Matrix file input**
+    
+
++--------+------------------+----------------+
+| Name   | Bur-eH_FSP_12    | Bur-eH_FSP_24  |	                                       
++========+==================+================+
+|M202T601| 91206595.7559783 |106808979.08546 |
++--------+------------------+----------------+
+|M234T851| 27249137.275504  |28824971.3177926|  
++--------+------------------+----------------+       
+
+**>A part of an example of Sample Metadata file input**
+    
+    
++---------------------------+------------+------------+------------+
+| Sample name               |   class    |   time     |   batch    |
++===========================+============+============+============+
+| Bur-eH_FSP_12             | Bur-eH     |    12      |     1      |
++---------------------------+------------+------------+------------+
+| Bur-eH_FSP_24             | Bur-eH     |    24      |     1      |
++---------------------------+------------+------------+------------+
+| Bur-NI_FSP_12             | Bur-NI     |    12      |     2      |
++---------------------------+------------+------------+------------+
+| Bur-NI_FSP_24             | Bur-NI     |    24      |     2      |
++---------------------------+------------+------------+------------+
+
+Parameters
+----------
+
+    | Mode -> **row**
+    | column name of condition -> **class**
+    | Separator of columns: -> **tabulation**
+    | Decimal separator -> **.**
+    | PValue adjusted method -> **BH**
+    | Threshold -> **0.001**
+    
+
+
+Output files
+------------
+
+**Part of an example of xset.anova_filtered.tabular:**
+
+.. image:: anova_pvalue.png
+
+**Part of an example of xset.anova_pvalue.tabular:**
+
+.. image:: anova_filtered.png
+
+
+---------------------------------------------------
+
+    
+---------------------------
+Position in workflow4metabo
+---------------------------
+
+
+**Upstream tools**
+
++---------------------------+----------------------------------------+--------+------------------------+
+| Name                      | Output file                            | Format | parameter              |   
++===========================+========================================+========+========================+
+|xcms.diffreport            |xset.diffreport.data_matrix.tsv         | Tabular| Data table file        |   
++---------------------------+----------------------------------------+--------+------------------------+
+|CAMERA.annotateDiffreport  |xset.annotatediffreport.data_matrix.tsv | Tabular| Data table file        |   
++---------------------------+----------------------------------------+--------+------------------------+
+|xcms.xcmsSet               |sample_info.tab                         | Tabular| sample info table file |
++---------------------------+----------------------------------------+--------+------------------------+
+
+
+**Downstream tools**
+
++---------------------------+---------------------------------------------------------+--------+
+| Name                      | Output file                                             | Format | 
++===========================+=========================================================+========+
+|PCA                        |xset.anova_pvalue.tabular OR xset.anova_filtered.tabular | Tabular|
++---------------------------+---------------------------------------------------------+--------+
+|Hierarchical Clustering    |xset.anova_pvalue.tabular OR xset.anova_filtered.tabular | Tabular|
++---------------------------+---------------------------------------------------------+--------+
+
+
+**General schema of the metabolomic workflow**
+
+.. image:: anova_workflow.png
+
+    </help>
+
+    <citations>
+        <citation>Ronald A. Fisher in the 1930s</citation>
+    </citations>
+
+</tool>
--- a/galaxy/stat_anova/.travis/setup_custom_dependencies.bash	Mon Mar 28 15:49:04 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-#!/bin/bash
--- a/galaxy/stat_anova/Makefile	Mon Mar 28 15:49:04 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,23 +0,0 @@
-# USAGE: make [install|clean]
-
-# -------- VARIABLE --------
-
-OBJ=anova.tgz
-DEP=abims_anova.r abims_anova.xml static test-data
-
-
-# ------------------------
-
-all: $(OBJ)
-
-$(OBJ): $(DEP)
-	tar --exclude=".svn" -zchf $@ $^
-
-# ------------------------
-
-install: $(OBJ)
-	mv *.tgz ~
-
-clean:
-	rm *.tgz
-
--- a/galaxy/stat_anova/abims_anova.r	Mon Mar 28 15:49:04 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,132 +0,0 @@
-#!/usr/local/public/bin/Rscript
-# version="1.1"
-
-# date: 06-06-2012
-# update: 18-02-2014
-# **Authors** Gildas Le Corguille  ABiMS - UPMC/CNRS - Station Biologique de Roscoff - gildas.lecorguille|at|sb-roscoff.fr 
-
-# abims_anova.r version 20140218
-
-library(batch)
-
-
-# function avova
-anova = function (file, sampleinfo, mode="column", condition=1, interaction=F, method="BH", threshold=0.01, selection_method="intersection", sep=";", dec=".", outputdatapvalue="anova.data.output", outputdatafiltered="anova.datafiltered.output") {
-	
- 
-	if (sep=="tabulation") sep="\t"
-    	if (sep=="semicolon") sep=";"
-    	if (sep=="comma") sep=","
-
-	anova_formula_operator = "+"
-	if (interaction) anova_formula_operator = "*"
-  
-  	# -- import --
-	data=read.table(file, header = TRUE, row.names=1, sep = sep, quote="\"", dec = dec, fill = TRUE, comment.char="",na.strings = "NA")
-	
-  	if (mode == "row") data=t(data)
-	
-	sampleinfoTab=read.table(sampleinfo, header = TRUE, row.names=1, sep = sep, quote="\"")
-	rownames(sampleinfoTab) = make.names(rownames(sampleinfoTab))
-
-	
-	# -- group --
-	match_data_sampleinfoTab = match(rownames(data),rownames(sampleinfoTab))
-	if (sum(is.na(match_data_sampleinfoTab)) > 0) {
-	  write("ERROR: There is a problem during to match sample names from the data matrix and from the sample info (presence of NA).", stderr())
-	  write("You may need to use change the mode (column/row)", stderr())
-	  write("10 first sample names in the data matrix:", stderr())
-	  write(head(colnames(data)), stderr())
-	  write("10 first sample names in the sample info:", stderr())
-	  write(head(rownames(sampleinfoTab)), stderr())
-	  quit("no",status=10)
-	}
-  
-	
-	# -- anova --
-  
-  	# formula
-	grps=list()
-	anova_formula_s = "data ~ "
-	cat("\ncontrasts:\n")
-	for (i in 1:length(condition)) {
-	  grps[[i]] = factor(sampleinfoTab[,condition[i]][match_data_sampleinfoTab])
-	  anova_formula_s = paste(anova_formula_s, "grps[[",i,"]]",anova_formula_operator, sep="")
-	  cat(condition[i],"\t",levels(grps[[i]]),"\n")
-	# write("Current groups: ", stderr())
-	# write(grp[[i]], stderr())
-	}
-	anova_formula_s = substr(anova_formula_s, 1, nchar(anova_formula_s)-1)
-	anova_formula = as.formula(anova_formula_s)
-
-
-	
-	# anova
-	manovaObjectList = manova(anova_formula)
-	manovaList = summary.aov(manovaObjectList)
-	
-  	# condition renaming
-	manovaRownames = gsub(" ","",rownames(manovaList[[1]]))
-	manovaNbrPvalue = length(manovaRownames)-1
-	manovaRownames = manovaRownames[-(manovaNbrPvalue+1)]
-	
-	for (i in 1:length(condition)) {
-	  manovaRownames = sub(paste("grps\\[\\[",i,"\\]\\]",sep=""),condition[i],manovaRownames)
-  	  anova_formula_s = sub(paste("grps\\[\\[",i,"\\]\\]",sep=""),condition[i],anova_formula_s)
-	}
-
-  	# log
-  	cat("\nanova_formula",anova_formula_s,"\n")
-	
-	# p-value
-	aovPValue = sapply(manovaList,function(x){x[-(manovaNbrPvalue+1),5]})
-	if(length(condition) == 1) aovPValue = t(aovPValue)
-	rownames(aovPValue) = paste("pvalue_",manovaRownames,sep="")
-  
-	# p-value adjusted
-	if(length(condition) == 1) {
-		aovAdjPValue = t(p.adjust(aovPValue,method=method))
-	} else {
-		aovAdjPValue = apply(aovPValue,2,p.adjust, method=method)
-	}
-	rownames(aovAdjPValue) = paste("pvalueadjusted.",method,".",manovaRownames,sep="")
-	
-	# selection
-	colSumThreshold = colSums(aovAdjPValue <= threshold)
-	if (selection_method == "intersection") {
-		datafiltered = data[,colSumThreshold == nrow(aovAdjPValue )]
-	} else {
-		datafiltered = data[,colSumThreshold != 0]
-	}
-	
-	#data=rbind(data, aovPValue, aovAdjPValue)
-	data=rbind(data, aovAdjPValue)
-
-	
-	if (mode == "row") {
-	  data=t(data)
-	  datafiltered=t(datafiltered)
-	}
-	
-	# -- output / return --
-	write.table(data, outputdatapvalue, sep=sep, quote=F, col.names = NA)
-	write.table(datafiltered, outputdatafiltered, sep=sep, quote=F, col.names = NA)
-	
-	# log 
-	cat("\nthreshold:",threshold,"\n")
-	cat("result:",nrow(datafiltered),"/",nrow(data),"\n")
-  
-	quit("no",status=0)
-}
-
-# log
-cat("ANOVA\n\n")
-cat("Arguments\n")
-args <- commandArgs(trailingOnly = TRUE)
-print(args)
-
-listArguments = parseCommandArgs(evaluate=FALSE)
-do.call(anova, listArguments)
-
-
-
--- a/galaxy/stat_anova/abims_anova.xml	Mon Mar 28 15:49:04 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,258 +0,0 @@
-<tool id="abims_anova" name="Anova" version="1.1.3">
-    
-    <description>N-way anova. With ou Without interactions</description>
-    
-    <requirements>
-        <requirement type="package" version="3.1.2">R</requirement>
-	<requirement type="binary">Rscript</requirement>
-	<requirement type="package" version="1.1-4">batch</requirement>
-    </requirements>
-
-    <stdio>
-        <exit_code range="1:" level="fatal" />
-    </stdio>
-
-    <command interpreter="Rscript">
-abims_anova.r file "$input" sampleinfo "$sampleinfo" mode "$mode" 
-condition "c('$condition_1'
-#for $i, $s in enumerate( $conditions )
-,'${s.condition}'
-#end for
-)"
-interaction $interaction method $method threshold $threshold selection_method $selection_method sep "$sep" dec "$dec" outputdatapvalue $dataMatrixPValue outputdatafiltered $dataMatrixFiltered
-    </command> 
-
-    <inputs>
-        <param name="input" type="data" label="Data Matrix file" format="tabular" help="Matrix of numeric data with headers." />
-        <param name="sampleinfo" type="data" label="Sample Metadata file" format="tabular" help="Tabular file with the data metadata : one sample per line and at least two columns : ids and one condition" />
-        
-        <param name="mode" type="select" help="Perform the anova tests on column/row" format="text" optional="true">
-            <label>Mode</label>
-            <option value="row">row</option>
-            <option value="column">column</option>
-        </param>
-    
-        <param name="condition_1" type="text" label="Condition" value="" help="The column name of the condition. ex: hour or treatment" optional="false" />
-        <repeat name="conditions" title="Conditions for N-ways anova">
-            <param name="condition" type="text" label="Condition" value="" help="The column name of the condition. ex: hour or treatment" />
-        </repeat>
-
-        <param name="interaction" type="boolean" label="Enable interaction response p-values" truevalue="T" falsevalue="F" help="Used if more than 1 conditon. The anova will produse p-value according to the interaction between your condition (ex: condition1:conditions2, condition1:conditions3, condition2:conditions3 and condition1:condition2:conditions3)" />
-            
-        <param name="method" type="select" help="Method used to apply a correction on the pvalue because of the number of test" format="text" optional="true">
-            <label>PValue adjusted method</label>
-            <option value="BH">BH</option>
-            <option value="holm">holm</option>
-            <option value="bonferroni">bonferroni</option>
-            <option value="hochberg">hochberg</option>
-            <option value="hommel">hommel</option>
-            <option value="BY">BY</option>
-            <option value="fdr">fdr</option>
-            <option value="none">none</option>		
-        </param>        
-        
-        <param name="threshold" type="float" label="Threshold" value="0.01" help="max adjusted p.value accepted" />
-
-        <param name="selection_method" type="select" format="text" help="Intersection: all condition p-value must be under the threshold. Union: at least condition p-value must be under the threshold. ">
-            <label>Selection method</label>
-            <option value="intersection" selected="true">intersection / strong</option>
-            <option value="union">union / weak</option>
-        </param>
-
-        <param name="sep" type="select" format="text">
-            <label>Separator of columns</label>
-            <option value="tabulation">tabulation</option>
-            <option value="semicolon">;</option>
-            <option value="comma">,</option>
-        </param>
-        
-        <param name="dec" type="text" label="Decimal separator" value="." help="" />
-
-    </inputs>
-
-    <outputs>
-        <data name="dataMatrixPValue" format_source="input" label="${input.name}_anova_pvalue.${input.ext}"/>
-        <data name="dataMatrixFiltered" format_source="input" label="${input.name}_anova_filtered.${input.ext}"/>
-    </outputs>
-    
-    <tests>
-        <test>
-            <param name="input" value="dataMatrix.tsv"/>
-            <param name="sampleinfo" value="sampleMetadata.tsv"/>
-            <param name="mode" value="row"/>
-            <param name="condition_1" value="age"/>
-            <param name="conditions_0|condition" value="gender"/>
-            <param name="interaction" value="F"/>
-            <param name="method" value="BH"/>
-            <param name="threshold" value="0.05"/>
-            <param name="selection_method" value="union"/>
-            <param name="sep" value="tabulation"/>
-            <param name="dev" value="."/>
-            <output name="dataMatrixPValue" file="dataMatrix.tsv_anova_pvalue.tabular" />
-            <output name="dataMatrixFiltered" file="dataMatrix.tsv_anova_filtered.tabular" />
-        </test>
-    </tests>
-
-    <help>
-
-.. class:: infomark
-
-**Authors** Gildas Le Corguille  ABiMS - UPMC/CNRS - Station Biologique de Roscoff - gildas.lecorguille|at|sb-roscoff.fr 
-
----------------------------------------------------
-
-=====
-Anova
-=====
-
------------
-Description
------------
-
-Analysis of variance (ANOVA) is used to analyze the differences between group means and their associated procedures,
-in which the observed variance in a particular variable is partitioned into components attributable to different sources of variation.
-
-
-
------------
-Input files
------------
-
-+---------------------------+------------+
-| Parameter : num + label   |   Format   |
-+===========================+============+
-| 1 : Data Matrix file      | Tabular    |
-+---------------------------+------------+
-| 2 : Sample Metadata file  | Tabular    |
-+---------------------------+------------+
-
-
-
-------------
-Output files
-------------
-
-
-
-***.anova_pvalue.tabular**
-
-    | A tabular file which represents for each metabolite (row), the value of the intensity in each sample (column) + two columns (aovPValue and aovAdjPValue).
-
-***.anova_filtered.tabular**
-
-    | The tabular file xset.anova_pvalue.tabular containing only the metabolites that have been filtered by aovAdjPValue.
-    
-    
-------
-
-.. class:: infomark 
-
-The outputs ***.anova_filtered.tabular** or ***.anova_pvalue.tabular** are tabular files. You can continue your analysis using it in the following tools:
-    | PCA
-    | Hierarchical Clustering
-
-    
-    
----------------------------------------------------
-
----------------
-Working example
----------------
-
-
-Input files
------------
-
-**>A part of an example of Data Matrix file input**
-    
-
-+--------+------------------+----------------+
-| Name   | Bur-eH_FSP_12    | Bur-eH_FSP_24  |	                                       
-+========+==================+================+
-|M202T601| 91206595.7559783 |106808979.08546 |
-+--------+------------------+----------------+
-|M234T851| 27249137.275504  |28824971.3177926|  
-+--------+------------------+----------------+       
-
-**>A part of an example of Sample Metadata file input**
-    
-    
-+---------------------------+------------+------------+------------+
-| Sample name               |   class    |   time     |   batch    |
-+===========================+============+============+============+
-| Bur-eH_FSP_12             | Bur-eH     |    12      |     1      |
-+---------------------------+------------+------------+------------+
-| Bur-eH_FSP_24             | Bur-eH     |    24      |     1      |
-+---------------------------+------------+------------+------------+
-| Bur-NI_FSP_12             | Bur-NI     |    12      |     2      |
-+---------------------------+------------+------------+------------+
-| Bur-NI_FSP_24             | Bur-NI     |    24      |     2      |
-+---------------------------+------------+------------+------------+
-
-Parameters
-----------
-
-    | Mode -> **row**
-    | column name of condition -> **class**
-    | Separator of columns: -> **tabulation**
-    | Decimal separator -> **.**
-    | PValue adjusted method -> **BH**
-    | Threshold -> **0.001**
-    
-
-
-Output files
-------------
-
-**Part of an example of xset.anova_filtered.tabular:**
-
-.. image:: anova_pvalue.png
-
-**Part of an example of xset.anova_pvalue.tabular:**
-
-.. image:: anova_filtered.png
-
-
----------------------------------------------------
-
-    
----------------------------
-Position in workflow4metabo
----------------------------
-
-
-**Upstream tools**
-
-+---------------------------+----------------------------------------+--------+------------------------+
-| Name                      | Output file                            | Format | parameter              |   
-+===========================+========================================+========+========================+
-|xcms.diffreport            |xset.diffreport.data_matrix.tsv         | Tabular| Data table file        |   
-+---------------------------+----------------------------------------+--------+------------------------+
-|CAMERA.annotateDiffreport  |xset.annotatediffreport.data_matrix.tsv | Tabular| Data table file        |   
-+---------------------------+----------------------------------------+--------+------------------------+
-|xcms.xcmsSet               |sample_info.tab                         | Tabular| sample info table file |
-+---------------------------+----------------------------------------+--------+------------------------+
-
-
-**Downstream tools**
-
-+---------------------------+---------------------------------------------------------+--------+
-| Name                      | Output file                                             | Format | 
-+===========================+=========================================================+========+
-|PCA                        |xset.anova_pvalue.tabular OR xset.anova_filtered.tabular | Tabular|
-+---------------------------+---------------------------------------------------------+--------+
-|Hierarchical Clustering    |xset.anova_pvalue.tabular OR xset.anova_filtered.tabular | Tabular|
-+---------------------------+---------------------------------------------------------+--------+
-
-
-**General schema of the metabolomic workflow**
-
-.. image:: anova_workflow.png
-
-    </help>
-
-    <citations>
-        <citation>Ronald A. Fisher in the 1930s</citation>
-    </citations>
-
-</tool>
Binary file galaxy/stat_anova/static/images/anova_filtered.png has changed
Binary file galaxy/stat_anova/static/images/anova_pvalue.png has changed
Binary file galaxy/stat_anova/static/images/anova_workflow.png has changed
--- a/galaxy/stat_anova/test-data/dataMatrix.tsv	Mon Mar 28 15:49:04 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,16 +0,0 @@
-dataMatrix	HU_017	HU_028	HU_034	HU_051	HU_060	HU_078	HU_091	HU_093	HU_099	HU_110	HU_130	HU_134	HU_138	HU_149	HU_152	HU_175	HU_178	HU_185	HU_204	HU_208
-HMDB03193	76043	412165	44943	27242	436566	173175	242549	57066	559869	3732	339188	471368	262271	127285	451270	212500	79673	NA	891129	43907
-HMDB01101	30689	6877586	52217	3158	10789748	229568	4763576	3878773	976436	831937	608298	1605075	72021	442510	1107705	1464339	31250	2724553	72900	32742
-HMDB10348	47259	544877	60885	34582	529874	168264	176500	76457	610110	16262	279156	524468	451573	591487	433529	161069	214392	13781	1580343	39315
-HMDB59717	357351	1030464	301983	67604	306862	1028110	1530493	270027	1378535	289677	808334	1132813	871209	895435	715190	1563158	784738	146195	994336	239030
-HMDB00822	483755	579287	1132413	157113	1577570	1469735	1085454	477909	814755	245417	610681	763706	2406336	827531	992508	569605	355321	150259	1334200	271010
-HMDB13189	2644620	727587	1661412	619181	136278	2755434	593863	837865	3526136	2003278	1608814	3446611	1941527	113937	3132404	2893445	2092753	1034666	1517319	841661
-HMDB00299	250551	1046138	456162	159386	1013302	808657	614370	250403	768004	242085	504108	1014041	1362408	1057660	1110050	566050	411886	142233	1992420	284775
-HMDB00191	560002	771533	575790	392284	888498	785428	645785	591569	960658	910201	639437	1092885	1409045	2292023	1246459	1945577	710519	773384	1061418	622898
-HMDB00518	34236	58249	85944	NA	342102	129886	175800	13154	230242	NA	440223	315368	10657	419508	48673	28361	514579	23108	867108	73831
-HMDB00715	1252089	2547452	905408	371059	4983588	5140022	2658555	814523	2558923	859466	4184204	3865723	3236644	2615560	3820724	3577833	2295288	625924	7517724	1341900
-HMDB01032	2569205	26023086	1604999	430453	8103558	26222916	257139	675754	59906109	263055	31151730	18648127	14989438	1554658	20249262	5588731	871010	15920	9120781	44276
-HMDB00208	747080	13420742	595872	1172376	7172632	3143654	4059767	1433702	5593888	5402629	2477288	3346077	4230072	7621236	8960828	10335722	7037373	1574738	3359238	2540044
-HMDB04824	374028	1144386	539206	178517	1046190	959381	605191	310260	1253319	477259	477995	825691	1157093	1089284	1411802	1020206	782673	346761	1824553	387811
-HMDB00512	53304	319783	280560	85009	1333877	556003	590779	209285	342532	198512	569970	525240	246282	1140422	542345	1171008	827723	222953	438839	85554
-HMDB00251	368600	616555	94936	622468	180988	293988	352855	767894	268331	167246	310918	1248919	577184	10985	335711	403815	80614	63393	454489	616061
--- a/galaxy/stat_anova/test-data/dataMatrix.tsv_anova_filtered.tabular	Mon Mar 28 15:49:04 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,3 +0,0 @@
-	HU_017	HU_028	HU_034	HU_051	HU_060	HU_078	HU_091	HU_093	HU_099	HU_110	HU_130	HU_134	HU_138	HU_149	HU_152	HU_175	HU_178	HU_185	HU_204	HU_208
-HMDB00208	747080	13420742	595872	1172376	7172632	3143654	4059767	1433702	5593888	5402629	2477288	3346077	4230072	7621236	8960828	10335722	7037373	1574738	3359238	2540044
-HMDB00512	53304	319783	280560	85009	1333877	556003	590779	209285	342532	198512	569970	525240	246282	1140422	542345	1171008	827723	222953	438839	85554
--- a/galaxy/stat_anova/test-data/dataMatrix.tsv_anova_pvalue.tabular	Mon Mar 28 15:49:04 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,16 +0,0 @@
-	HU_017	HU_028	HU_034	HU_051	HU_060	HU_078	HU_091	HU_093	HU_099	HU_110	HU_130	HU_134	HU_138	HU_149	HU_152	HU_175	HU_178	HU_185	HU_204	HU_208	pvalueadjusted.BH.age	pvalueadjusted.BH.gender
-HMDB03193	76043	412165	44943	27242	436566	173175	242549	57066	559869	3732	339188	471368	262271	127285	451270	212500	79673	NA	891129	43907	0.740856975457218	0.740856975457218
-HMDB01101	30689	6877586	52217	3158	10789748	229568	4763576	3878773	976436	831937	608298	1605075	72021	442510	1107705	1464339	31250	2724553	72900	32742	0.347623051099051	0.234554902330543
-HMDB10348	47259	544877	60885	34582	529874	168264	176500	76457	610110	16262	279156	524468	451573	591487	433529	161069	214392	13781	1580343	39315	0.720303175717481	0.720303175717481
-HMDB59717	357351	1030464	301983	67604	306862	1028110	1530493	270027	1378535	289677	808334	1132813	871209	895435	715190	1563158	784738	146195	994336	239030	0.252979062487671	0.517822514350462
-HMDB00822	483755	579287	1132413	157113	1577570	1469735	1085454	477909	814755	245417	610681	763706	2406336	827531	992508	569605	355321	150259	1334200	271010	0.808532959173048	0.808532959173048
-HMDB13189	2644620	727587	1661412	619181	136278	2755434	593863	837865	3526136	2003278	1608814	3446611	1941527	113937	3132404	2893445	2092753	1034666	1517319	841661	0.329174238111018	0.329174238111018
-HMDB00299	250551	1046138	456162	159386	1013302	808657	614370	250403	768004	242085	504108	1014041	1362408	1057660	1110050	566050	411886	142233	1992420	284775	0.995859884733937	0.995859884733937
-HMDB00191	560002	771533	575790	392284	888498	785428	645785	591569	960658	910201	639437	1092885	1409045	2292023	1246459	1945577	710519	773384	1061418	622898	0.15341384456659	0.15341384456659
-HMDB00518	34236	58249	85944	NA	342102	129886	175800	13154	230242	NA	440223	315368	10657	419508	48673	28361	514579	23108	867108	73831	0.439012867631325	0.596200901535843
-HMDB00715	1252089	2547452	905408	371059	4983588	5140022	2658555	814523	2558923	859466	4184204	3865723	3236644	2615560	3820724	3577833	2295288	625924	7517724	1341900	0.814406453193777	0.814406453193777
-HMDB01032	2569205	26023086	1604999	430453	8103558	26222916	257139	675754	59906109	263055	31151730	18648127	14989438	1554658	20249262	5588731	871010	15920	9120781	44276	0.288354536353544	0.288354536353544
-HMDB00208	747080	13420742	595872	1172376	7172632	3143654	4059767	1433702	5593888	5402629	2477288	3346077	4230072	7621236	8960828	10335722	7037373	1574738	3359238	2540044	0.659785284053633	0.00376251274734483
-HMDB04824	374028	1144386	539206	178517	1046190	959381	605191	310260	1253319	477259	477995	825691	1157093	1089284	1411802	1020206	782673	346761	1824553	387811	0.646714644805001	0.646714644805001
-HMDB00512	53304	319783	280560	85009	1333877	556003	590779	209285	342532	198512	569970	525240	246282	1140422	542345	1171008	827723	222953	438839	85554	0.13976111393526	0.0491480895853803
-HMDB00251	368600	616555	94936	622468	180988	293988	352855	767894	268331	167246	310918	1248919	577184	10985	335711	403815	80614	63393	454489	616061	0.565910223149305	0.565910223149305
--- a/galaxy/stat_anova/test-data/sampleMetadata.tsv	Mon Mar 28 15:49:04 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,21 +0,0 @@
-sampleMetadata	injectionOrder	mode	age	bmi	gender
-HU_017	2	pos	40-50	23.03	M
-HU_028	7	pos	40-50	23.92	F
-HU_034	9	pos	50-60	23.37	M
-HU_051	20	pos	20-30	23.23	F
-HU_060	24	pos	50-60	28.72	F
-HU_078	34	pos	40-50	25.18	M
-HU_091	42	pos	60-70	26.12	M
-HU_093	43	pos	50-60	21.71	M
-HU_099	46	pos	20-30	21.3	M
-HU_110	53	pos	50-60	20.9	F
-HU_130	63	pos	30-40	26.06	M
-HU_134	67	pos	40-50	22.89	M
-HU_138	68	pos	40-50	21.88	M
-HU_149	72	pos	30-40	19.49	F
-HU_152	75	pos	20-30	17.58	F
-HU_175	87	pos	30-40	21.26	F
-HU_178	88	pos	60-70	32.87	F
-HU_185	95	pos	40-50	21.09	F
-HU_204	104	pos	30-40	29.06	M
-HU_208	106	pos	20-30	18.61	F
--- a/galaxy/stat_anova/tool_dependencies.xml	Mon Mar 28 15:49:04 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,7 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="R" version="3.1.2">
-        <repository changeset_revision="c987143177d4" name="package_r_3_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
-	<repository changeset_revision="82494b082f2f" name="package_r_batch_1_1_4" owner="lecorguille" toolshed="https://toolshed.g2.bx.psu.edu" />
-    </package>
-</tool_dependency>
Binary file static/images/anova_filtered.png has changed
Binary file static/images/anova_pvalue.png has changed
Binary file static/images/anova_workflow.png has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/dataMatrix.tsv	Mon Mar 28 15:51:28 2016 -0400
@@ -0,0 +1,16 @@
+dataMatrix	HU_017	HU_028	HU_034	HU_051	HU_060	HU_078	HU_091	HU_093	HU_099	HU_110	HU_130	HU_134	HU_138	HU_149	HU_152	HU_175	HU_178	HU_185	HU_204	HU_208
+HMDB03193	76043	412165	44943	27242	436566	173175	242549	57066	559869	3732	339188	471368	262271	127285	451270	212500	79673	NA	891129	43907
+HMDB01101	30689	6877586	52217	3158	10789748	229568	4763576	3878773	976436	831937	608298	1605075	72021	442510	1107705	1464339	31250	2724553	72900	32742
+HMDB10348	47259	544877	60885	34582	529874	168264	176500	76457	610110	16262	279156	524468	451573	591487	433529	161069	214392	13781	1580343	39315
+HMDB59717	357351	1030464	301983	67604	306862	1028110	1530493	270027	1378535	289677	808334	1132813	871209	895435	715190	1563158	784738	146195	994336	239030
+HMDB00822	483755	579287	1132413	157113	1577570	1469735	1085454	477909	814755	245417	610681	763706	2406336	827531	992508	569605	355321	150259	1334200	271010
+HMDB13189	2644620	727587	1661412	619181	136278	2755434	593863	837865	3526136	2003278	1608814	3446611	1941527	113937	3132404	2893445	2092753	1034666	1517319	841661
+HMDB00299	250551	1046138	456162	159386	1013302	808657	614370	250403	768004	242085	504108	1014041	1362408	1057660	1110050	566050	411886	142233	1992420	284775
+HMDB00191	560002	771533	575790	392284	888498	785428	645785	591569	960658	910201	639437	1092885	1409045	2292023	1246459	1945577	710519	773384	1061418	622898
+HMDB00518	34236	58249	85944	NA	342102	129886	175800	13154	230242	NA	440223	315368	10657	419508	48673	28361	514579	23108	867108	73831
+HMDB00715	1252089	2547452	905408	371059	4983588	5140022	2658555	814523	2558923	859466	4184204	3865723	3236644	2615560	3820724	3577833	2295288	625924	7517724	1341900
+HMDB01032	2569205	26023086	1604999	430453	8103558	26222916	257139	675754	59906109	263055	31151730	18648127	14989438	1554658	20249262	5588731	871010	15920	9120781	44276
+HMDB00208	747080	13420742	595872	1172376	7172632	3143654	4059767	1433702	5593888	5402629	2477288	3346077	4230072	7621236	8960828	10335722	7037373	1574738	3359238	2540044
+HMDB04824	374028	1144386	539206	178517	1046190	959381	605191	310260	1253319	477259	477995	825691	1157093	1089284	1411802	1020206	782673	346761	1824553	387811
+HMDB00512	53304	319783	280560	85009	1333877	556003	590779	209285	342532	198512	569970	525240	246282	1140422	542345	1171008	827723	222953	438839	85554
+HMDB00251	368600	616555	94936	622468	180988	293988	352855	767894	268331	167246	310918	1248919	577184	10985	335711	403815	80614	63393	454489	616061
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/dataMatrix.tsv_anova_filtered.tabular	Mon Mar 28 15:51:28 2016 -0400
@@ -0,0 +1,3 @@
+	HU_017	HU_028	HU_034	HU_051	HU_060	HU_078	HU_091	HU_093	HU_099	HU_110	HU_130	HU_134	HU_138	HU_149	HU_152	HU_175	HU_178	HU_185	HU_204	HU_208
+HMDB00208	747080	13420742	595872	1172376	7172632	3143654	4059767	1433702	5593888	5402629	2477288	3346077	4230072	7621236	8960828	10335722	7037373	1574738	3359238	2540044
+HMDB00512	53304	319783	280560	85009	1333877	556003	590779	209285	342532	198512	569970	525240	246282	1140422	542345	1171008	827723	222953	438839	85554
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/dataMatrix.tsv_anova_pvalue.tabular	Mon Mar 28 15:51:28 2016 -0400
@@ -0,0 +1,16 @@
+	HU_017	HU_028	HU_034	HU_051	HU_060	HU_078	HU_091	HU_093	HU_099	HU_110	HU_130	HU_134	HU_138	HU_149	HU_152	HU_175	HU_178	HU_185	HU_204	HU_208	pvalueadjusted.BH.age	pvalueadjusted.BH.gender
+HMDB03193	76043	412165	44943	27242	436566	173175	242549	57066	559869	3732	339188	471368	262271	127285	451270	212500	79673	NA	891129	43907	0.740856975457218	0.740856975457218
+HMDB01101	30689	6877586	52217	3158	10789748	229568	4763576	3878773	976436	831937	608298	1605075	72021	442510	1107705	1464339	31250	2724553	72900	32742	0.347623051099051	0.234554902330543
+HMDB10348	47259	544877	60885	34582	529874	168264	176500	76457	610110	16262	279156	524468	451573	591487	433529	161069	214392	13781	1580343	39315	0.720303175717481	0.720303175717481
+HMDB59717	357351	1030464	301983	67604	306862	1028110	1530493	270027	1378535	289677	808334	1132813	871209	895435	715190	1563158	784738	146195	994336	239030	0.252979062487671	0.517822514350462
+HMDB00822	483755	579287	1132413	157113	1577570	1469735	1085454	477909	814755	245417	610681	763706	2406336	827531	992508	569605	355321	150259	1334200	271010	0.808532959173048	0.808532959173048
+HMDB13189	2644620	727587	1661412	619181	136278	2755434	593863	837865	3526136	2003278	1608814	3446611	1941527	113937	3132404	2893445	2092753	1034666	1517319	841661	0.329174238111018	0.329174238111018
+HMDB00299	250551	1046138	456162	159386	1013302	808657	614370	250403	768004	242085	504108	1014041	1362408	1057660	1110050	566050	411886	142233	1992420	284775	0.995859884733937	0.995859884733937
+HMDB00191	560002	771533	575790	392284	888498	785428	645785	591569	960658	910201	639437	1092885	1409045	2292023	1246459	1945577	710519	773384	1061418	622898	0.15341384456659	0.15341384456659
+HMDB00518	34236	58249	85944	NA	342102	129886	175800	13154	230242	NA	440223	315368	10657	419508	48673	28361	514579	23108	867108	73831	0.439012867631325	0.596200901535843
+HMDB00715	1252089	2547452	905408	371059	4983588	5140022	2658555	814523	2558923	859466	4184204	3865723	3236644	2615560	3820724	3577833	2295288	625924	7517724	1341900	0.814406453193777	0.814406453193777
+HMDB01032	2569205	26023086	1604999	430453	8103558	26222916	257139	675754	59906109	263055	31151730	18648127	14989438	1554658	20249262	5588731	871010	15920	9120781	44276	0.288354536353544	0.288354536353544
+HMDB00208	747080	13420742	595872	1172376	7172632	3143654	4059767	1433702	5593888	5402629	2477288	3346077	4230072	7621236	8960828	10335722	7037373	1574738	3359238	2540044	0.659785284053633	0.00376251274734483
+HMDB04824	374028	1144386	539206	178517	1046190	959381	605191	310260	1253319	477259	477995	825691	1157093	1089284	1411802	1020206	782673	346761	1824553	387811	0.646714644805001	0.646714644805001
+HMDB00512	53304	319783	280560	85009	1333877	556003	590779	209285	342532	198512	569970	525240	246282	1140422	542345	1171008	827723	222953	438839	85554	0.13976111393526	0.0491480895853803
+HMDB00251	368600	616555	94936	622468	180988	293988	352855	767894	268331	167246	310918	1248919	577184	10985	335711	403815	80614	63393	454489	616061	0.565910223149305	0.565910223149305
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sampleMetadata.tsv	Mon Mar 28 15:51:28 2016 -0400
@@ -0,0 +1,21 @@
+sampleMetadata	injectionOrder	mode	age	bmi	gender
+HU_017	2	pos	40-50	23.03	M
+HU_028	7	pos	40-50	23.92	F
+HU_034	9	pos	50-60	23.37	M
+HU_051	20	pos	20-30	23.23	F
+HU_060	24	pos	50-60	28.72	F
+HU_078	34	pos	40-50	25.18	M
+HU_091	42	pos	60-70	26.12	M
+HU_093	43	pos	50-60	21.71	M
+HU_099	46	pos	20-30	21.3	M
+HU_110	53	pos	50-60	20.9	F
+HU_130	63	pos	30-40	26.06	M
+HU_134	67	pos	40-50	22.89	M
+HU_138	68	pos	40-50	21.88	M
+HU_149	72	pos	30-40	19.49	F
+HU_152	75	pos	20-30	17.58	F
+HU_175	87	pos	30-40	21.26	F
+HU_178	88	pos	60-70	32.87	F
+HU_185	95	pos	40-50	21.09	F
+HU_204	104	pos	30-40	29.06	M
+HU_208	106	pos	20-30	18.61	F
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Mon Mar 28 15:51:28 2016 -0400
@@ -0,0 +1,7 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="R" version="3.1.2">
+        <repository changeset_revision="c987143177d4" name="package_r_3_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+	<repository changeset_revision="82494b082f2f" name="package_r_batch_1_1_4" owner="lecorguille" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+</tool_dependency>