# HG changeset patch
# User bimib
# Date 1716502191 0
# Node ID 8fd1883e8168623bb42c323f542e095186dd8d5e
# Parent  8974d26d499d10ad9558036496e9ff207413074c
Uploaded

diff -r 8974d26d499d -r 8fd1883e8168 marea_2_0/marea.xml
--- a/marea_2_0/marea.xml	Thu May 23 21:21:12 2024 +0000
+++ b/marea_2_0/marea.xml	Thu May 23 22:09:51 2024 +0000
@@ -19,44 +19,51 @@
 
       	--tool_dir $__tool_directory__
       	--option $cond.type_selector
-		--using_RAS $cond.using_RAS.check
-		--using_RPS $cond.using_RPS.check
+
         --out_log $log
 	
         #if $cond.type_selector == 'datasets':
-			#if $cond.using_RAS.check == 'true':
+
+			--using_RAS $cond.using_ras.check
+			--using_RPS $cond.using_rps.check
+
+			#if $cond.using_ras.check == 'true':
 				--input_datas
-				#for $data in $cond.input_Datasets:
+				#for $data in $cond.using_ras.input_Datasets:
 					${data.input}
 				#end for
 
 				--names
-				#for $data in $cond.input_Datasets:
+				#for $data in $cond.using_ras.input_Datasets:
 					${data.input_name}
 				#end for
 			#end if
 
-			#if $cond.using_RPS.check == 'true':
+			#if $cond.using_rps.check == 'true':
 				--input_datas_rps
-				#for $data in $cond.input_Datasets_RPS:
+				#for $data in $cond.using_rps.input_Datasets_RPS:
 					${data.input_rps}
 				#end for
 
 				--names_rps
-				#for $data in $cond.input_Datasets_RPS:
+				#for $data in $cond.using_rps.input_Datasets_RPS:
 					${data.input_name_rps}
 				#end for
 			#end if
         
         #elif $cond.type_selector == 'dataset_class':
-			#if $cond.using_RAS.check == 'true':
-				--input_data ${cond.input_data}
-				--input_class ${cond.input_class}
+
+			--using_RAS $cond.using_ras_all.check
+			--using_RPS $cond.using_rps_all.check
+
+			#if $cond.using_ras_all.check == 'true':
+				--input_data ${cond.using_ras_all.input_data}
+				--input_class ${cond.using_ras_all.input_class}
 			#end if
 
-			#if $cond.using_RPS.check == 'true':
-				--input_data_rps ${cond.input_data_rps}
-				--input_class_rps ${cond.input_class_rps}
+			#if $cond.using_rps_all.check == 'true':
+				--input_data_rps ${cond.using_rps_all.input_data_rps}
+				--input_class_rps ${cond.using_rps_all.input_class_rps}
 			#end if
         #end if
 
@@ -94,8 +101,8 @@
 			</param>
 
 			<when value="datasets">
-				<conditional name = "using_RAS">
-					<param name = "check" argument = "--using_RAS" type = "boolean" checked = "true" label = "Using RAS datasets." />
+				<conditional name = "using_ras">
+					<param name = "check" argument = "--using_ras" type = "boolean" checked = "true" label = "Using RAS datasets." />
 
 					<when value = "true">
 						<repeat name="input_Datasets" title="RAS dataset" min="2">
@@ -105,8 +112,8 @@
 					</when>
 				</conditional>
 
-				<conditional name = "using_RPS">
-					<param name = "check" argument = "--using_RPS" type = "boolean" checked = "false" label = "Using RPS datasets." />
+				<conditional name = "using_rps">
+					<param name = "check" argument = "--using_rps" type = "boolean" checked = "false" label = "Using RPS datasets." />
 
 					<when value = "true">
 						<repeat name="input_Datasets_RPS" title="RPS dataset" min="2">
@@ -118,8 +125,8 @@
 			</when>
 
 			<when value="dataset_class">
-				<conditional name = "using_RAS">
-					<param name = "check" argument = "--using_RAS" type = "boolean" checked = "true" label = "Using RAS datasets." />
+				<conditional name = "using_ras_all">
+					<param name = "check" argument = "--using_ras_all" type = "boolean" checked = "true" label = "Using RAS datasets." />
 
 					<when value = "true">
 						<param name="input_data" argument="--input_data" type="data" format="tabular, csv, tsv" label="RAS of all samples" />
@@ -127,8 +134,8 @@
 					</when>
 				</conditional>
 
-				<conditional name = "using_RPS">
-					<param name = "check" argument = "--using_RPS" type = "boolean" checked = "false" label = "Using RPS datasets." />
+				<conditional name = "using_rps_all">
+					<param name = "check" argument = "--using_rps_all" type = "boolean" checked = "false" label = "Using RPS datasets." />
 
 					<when value = "true">
 						<param name="input_data_rps" argument="--input_data_rps" type="data" format="tabular, csv, tsv" label="RPS of all samples" />