# HG changeset patch
# User bimib
# Date 1584361513 14400
# Node ID 858500ec97670186c1445f6a3a320e37bcd058f1
# Parent  a61733753aec682a9e58efe55c195acdd5ad3c77
Uploaded

diff -r a61733753aec -r 858500ec9767 Marea/marea.xml
--- a/Marea/marea.xml	Mon Mar 16 08:21:29 2020 -0400
+++ b/Marea/marea.xml	Mon Mar 16 08:25:13 2020 -0400
@@ -1,4 +1,4 @@
-<tool id="MaREA" name="Metabolic Reaction Enrichment Analysis" version="1.0.8">
+<tool id="MaREA" name="Metabolic Reaction Enrichment Analysis" version="1.1.5">
 	<macros>
 		<import>marea_macros.xml</import>
 	</macros>
@@ -28,12 +28,15 @@
                 ${data.input_name}
             #end for
             --comparison ${cond.comparis.comparison}
-            #if $cond.advanced.cond_map == 'true':
-            	--custom_rules true
-            	--custom_rule ${cond.advanced.cond_map.custom_rule}
-            	--custom_map ${cond.advanced.cond_map.custom_map}
+			#if $cond.comparis.comparison == 'onevsmany'
+            	--control '${cond.comparis.controlgroup}'
             #end if
+            
             #if $cond.advanced.choice == 'true':
+				#if $cond.advanced.cond_map.cond_map_choice == 'true':
+					--custom_rules true
+					--custom_map ${cond.advanced.cond_map.custom_map}
+				#end if
       	       --pValue ${cond.advanced.pValue}
       	       --fChange ${cond.advanced.fChange}
 	           --generate_svg ${cond.advanced.generateSvg}
@@ -50,14 +53,13 @@
             --input_class ${input_class}
             --comparison ${cond.comparis.comparison}
             #if $cond.comparis.comparison == 'onevsmany'
-            	--control ${cond.comparis.controlgroup}
-            #end if
-            #if $cond.advanced.cond_map == 'true':
-            	--custom_rules true
-            	--custom_rule ${cond.advanced.cond_map.custom_rule}
-            	--custom_map ${cond.advanced.cond_map.custom_map}
+            	--control '${cond.comparis.controlgroup}'
             #end if
             #if $cond.advanced.choice == 'true':
+				#if $cond.advanced.cond_map.cond_map_choice == 'true':
+					--custom_rules true
+					--custom_map ${cond.advanced.cond_map.custom_map}
+				#end if
       	        --pValue ${cond.advanced.pValue}
       	        --fChange ${cond.advanced.fChange}
 	            --generate_svg ${cond.advanced.generateSvg}
@@ -100,12 +102,11 @@
 					<when value="false"></when>
 					<when value="true">
 						<conditional name="cond_map">
-						<param name="choice" type="boolean" checked="false" label="Use custom map and rules?" help="Use this option only if you have generated RAS using a custom set of rules">
+						<param name="cond_map_choice" type="boolean" checked="false" label="Use custom map?" help="Use this option only if you have generated RAS using a custom set of rules">
 							<option value="false" selected="true">No</option>
 							<option value="true">Yes</option>
 						</param>
-						<when value="true">	
-							<param name="Custom_rule" argument="--custom_rule" type="data" format="tabular, csv, tsv, xml" label="Custom rules" />					
+						<when value="true">				
 							<param name="Custom_map" argument="--custom_map" type="data" format="xml, svg" label="custom-map.svg"/>
 						</when>
 					</conditional>
@@ -137,13 +138,12 @@
 				<when value="false"></when>
 				<when value="true">
 					<conditional name="cond_map">
-						<param name="choice" type="boolean" checked="false" label="Use custom map?" help="Use this option only if you have generated RAS using a custom set of rules">
+						<param name="cond_map_choice" type="boolean" checked="false" label="Use custom map?" help="Use this option only if you have generated RAS using a custom set of rules">
 							<option value="false" selected="true">No</option>
 							<option value="true">Yes</option>
 						</param>
-						<when value="true">							
-							<param name="Custom_rule" argument="--custom_rule" type="data" format="tabular, csv, tsv, xml" label="Custom rules" />					
-							<param name="Custom_map" argument="--custom_map" type="data" format="xml, svg" label="custom-map.svg"/>
+						<when value="true">								
+							<param name="custom_map" argument="--custom_map" type="data" format="xml, svg" label="custom-map.svg"/>
 						</when>
 					</conditional>
 					<param name="pValue" argument="--pValue" type="float" size="20" value="0.01" max="1" min="0" label="P-value threshold:" help="min value 0" />