# HG changeset patch
# User luca_milaz
# Date 1722692791 0
# Node ID f20e6f46ac24dcfdefe48ce9b92a3f31c4d42454
# Parent  1e5cb43eb7392d18aa35b598be44af137da95d7b
Uploaded

diff -r 1e5cb43eb739 -r f20e6f46ac24 marea_2/flux_to_map.xml
--- a/marea_2/flux_to_map.xml	Sat Aug 03 13:46:01 2024 +0000
+++ b/marea_2/flux_to_map.xml	Sat Aug 03 13:46:31 2024 +0000
@@ -1,4 +1,4 @@
-<tool id="FluxToMap" name="Metabolic Flux Enrichment Analysis" version="1.0.3">
+<tool id="FluxToMap" name="Metabolic Flux Enrichment Analysis" version="2.0.0">
 	<macros>
 		<import>marea_macros.xml</import>
 	</macros>
@@ -24,21 +24,8 @@
 	
         #if $cond.type_selector == 'datasets':
 
-			--using_RAS $cond.using_ras.check
 			--using_RPS $cond.using_rps.check
 
-			#if $cond.using_ras.check == 'true':
-				--input_datas
-				#for $data in $cond.using_ras.input_datasets:
-					${data.input}
-				#end for
-
-				--names
-				#for $data in $cond.using_ras.input_datasets:
-					${data.input_name}
-				#end for
-			#end if
-
 			#if $cond.using_rps.check == 'true':
 				--input_datas_rps
 				#for $data in $cond.using_rps.input_datasets_rps:
@@ -53,14 +40,8 @@
         
         #elif $cond.type_selector == 'dataset_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_all.check == 'true':
 				--input_data_rps ${cond.using_rps_all.input_data_rps}
 				--input_class_rps ${cond.using_rps_all.input_class_rps}
@@ -82,69 +63,36 @@
 			--fChange ${advanced.fChange}
 			--generate_svg ${advanced.generateSvg}
 			--generate_pdf ${advanced.generatePdf}
-			--net ${advanced.netRPS}
 		#else 
 			--pValue 0.05
 			--fChange 1.2
 			--generate_svg false
 			--generate_pdf true
-			--net false
 		#end if
         ]]>
 	</command>
 	
 	<inputs>
+
 		<conditional name="cond">
 			<param name="type_selector" argument="--option" type="select" label="Input format:">
-				<option value="datasets" selected="true">RAS of group 1 + RAS of group 2 + ... + RAS of group N</option>
-				<option value="dataset_class">RAS of all samples + sample group specification</option>
+				<option value="datasets" selected="true">Fluxes of group 1 + Fluxes of group 2 + ... + Fluxes of group N</option>
+				<option value="dataset_class">All fluxes + sample group specification</option>
 			</param>
 
 			<when value="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">
-							<param name="input" argument="--input_datas" type="data" format="tabular, csv, tsv" label="add dataset" />
-							<param name="input_name" argument="--names" type="text" label="Dataset's name:" value="Dataset" help="Default: Dataset" />
-						</repeat>
-					</when>
-				</conditional>
-
-				<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">
-							<param name="input_rps" argument="--input_datas_rps" type="data" format="tabular, csv, tsv" label="add dataset" />
-							<param name="input_name_rps" argument="--names_rps" type="text" label="Dataset's name:" value="Dataset" help="Default: Dataset" />
-						</repeat>
-					</when>
-				</conditional>
+				<repeat name="input_datasets_fluxes" title="Fluxes dataset" min="2">
+					<param name="input_rps" argument="--input_datas_rps" type="data" format="tabular, csv, tsv" label="add dataset" />
+					<param name="input_name_rps" argument="--names_rps" type="text" label="Dataset's name:" value="Dataset" help="Default: Dataset" />
+				</repeat>
 			</when>
 
 			<when value="dataset_class">
-				<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" />
-						<param name="input_class" argument="--input_class" type="data" format="tabular, csv, tsv" label="Sample group specification" />
-					</when>
-				</conditional>
-
-				<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" />
-						<param name="input_class_rps" argument="--input_class_rps" type="data" format="tabular, csv, tsv" label="Sample group specification" />
-					</when>
-			</conditional>
+				<param name="input_data_rps" argument="--input_data_rps" type="data" format="tabular, csv, tsv" label="All fluxes" />
+				<param name="input_class_rps" argument="--input_class_rps" type="data" format="tabular, csv, tsv" label="Sample group specification" />
 			</when>
 		</conditional>
-		
+
 		<conditional name="comparis">
 			<param name="comparison" argument="--comparison" type="select" label="Groups comparison:">
 				<option value="manyvsmany" selected="true">One vs One</option>
@@ -167,7 +115,7 @@
 				<param name="custom_map" argument="--custom_map" type="data" format="xml, svg" label="custom-map.svg"/>
 			</when>
 		</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.">
 				<option value="true" selected="true">No</option>
@@ -179,8 +127,6 @@
 				<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?" />
-			
-				<param name="netRPS" argument="--net" type="boolean" checked="false" label="Should RPS enrichment use net values?" help="If checked and RPS datasets are present the arrow tips of a reversible arrow will be colored with the net contribution of both directions' RPS values" />
 			</when>
 		</conditional>
 	</inputs>