# HG changeset patch
# User francesco_lapi
# Date 1747393022 0
# Node ID bc8cbaacafd0a384a12b3eeb766357c517f9b6d6
# Parent  1402c2beb8f2a7ccf3cb60b7185b3ea6ce73524d
Uploaded

diff -r 1402c2beb8f2 -r bc8cbaacafd0 COBRAxy/marea.xml
--- a/COBRAxy/marea.xml	Fri May 16 10:56:44 2025 +0000
+++ b/COBRAxy/marea.xml	Fri May 16 10:57:02 2025 +0000
@@ -78,13 +78,17 @@
 		#end if
 		
 		#if $advanced.choice == 'true':
+			--test ${advanced.test}
 			--pValue ${advanced.pValue}
+			--adjusted ${advanced.adjusted}
 			--fChange ${advanced.fChange}
 			--generate_svg ${advanced.generateSvg}
 			--generate_pdf ${advanced.generatePdf}
 			--net ${advanced.netRPS}
 		#else 
+			--test 'ks'
 			--pValue 0.05
+			--adjusted false
 			--fChange 1.2
 			--generate_svg false
 			--generate_pdf true
@@ -169,7 +173,7 @@
 		</conditional>
 		
 		<conditional name="advanced">
-			<param name="choice" type="boolean" checked="false" label="Use advanced options?" help="Use this options to choose custom parameters for evaluation: pValue, Fold-Change threshold, how to solve (A and NaN) and specify output maps.">
+			<param name="choice" type="boolean" checked="false" label="Use advanced options?" help="Use this options to choose custom parameters for evaluation: statistical test, pValue, Fold-Change threshold, how to solve (A and NaN) and specify output maps.">
 				<option value="true" selected="true">No</option>
 				<option value="false">Yes</option>
 			</param>
@@ -183,6 +187,7 @@
 					<option value="mw">Mann-Whitney</option>
 				</param>
 				<param name="pValue" argument="--pValue" type="float" size="20" value="0.05" max="1" min="0" label="P-value threshold:" help="min value 0" />
+				<param name="adjusted" argument="--adjusted" type="boolean" checked="false" label="Use adjusted p-values" help="Should the program adjust the P-values based on the FDR (Benjamini-Hochberg) correction?" />
 				<param name="fChange" argument="--fChange" type="float" size="20" value="1.2" min="1" label="Fold-Change threshold:" help="min value 1" />
 				<param name="generateSvg" argument="--generateSvg" type="boolean" checked="false" label="Generate SVG map" help="should the program generate an editable svg map of the processes?" />
 				<param name="generatePdf" argument="--generatePdf" type="boolean" checked="true" label="Generate PDF map" help="should the program return a non editable (but displayble) pdf map of the processes?" />
@@ -303,7 +308,8 @@
 Advanced options
 ----------------
 
-P-Value threshold: the threshold used for significance Kolmogorov-Smirnov (KS) test, to verify whether the distributions of RASs over the samples in two sets are significantly different
+Statistical test: the statistical test to use for the analysis based on your data and the amount of replicates. The Kolmogorov-Smirnov test is the default option, but you can choose between T-test (paired), T-test (unpaired), Wilcoxon and Mann-Whitney tests.
+P-Value threshold: the threshold used for significance in the selected test, to verify whether the distributions of RASs over the samples in two sets are significantly different
 
 Fold-Change threshold: threshold of the fold-change between the average RAS of two groups. Among the reactions that pass the KS test, only fold-change values larger than the indicated threshold will be visualized on the output metabolic map;