# HG changeset patch
# User bimib
# Date 1571224357 14400
# Node ID b795e3e163e0041ebbe949f7934197dd60e61e55
# Parent  944e15aa970a3dcbaac66b466b86c27b13854e60
bug fix

diff -r 944e15aa970a -r b795e3e163e0 Marea/marea.xml
--- a/Marea/marea.xml	Tue Oct 15 12:22:43 2019 -0400
+++ b/Marea/marea.xml	Wed Oct 16 07:12:37 2019 -0400
@@ -1,4 +1,4 @@
-<tool id="MaREA" name="Metabolic Reaction Enrichment Analysis" version="1.0.3">
+<tool id="MaREA" name="Metabolic Reaction Enrichment Analysis" version="1.0.4">
     <description></description>
     <macros>
         <import>marea_macros.xml</import>
@@ -22,11 +22,11 @@
                 --custom_map $cond_rule.cond_map.Custom_map
             #end if
         #end if
-	
+
       	--tool_dir $__tool_directory__
       	--option $cond.type_selector
-        --out_log $log		
-	
+        --out_log $log
+
         #if $cond.type_selector == 'datasets':
             --input_datas
             #for $data in $cond.input_Datasets:
@@ -43,7 +43,7 @@
 	    	--generate_svg ${cond.advanced.generateSvg}
 	    	--generate_pdf ${cond.advanced.generatePdf}
 	    --generate_ras ${cond.advanced.generateRas}
-	#else 
+	#else
 	    --none true
 	    --pValue 0.05
 	    --fChange 1.5
@@ -61,7 +61,7 @@
 	    --generate_svg ${cond.advanced.generateSvg}
 	    --generate_pdf ${cond.advanced.generatePdf}
 	    --generate_ras ${cond.advanced.generateRas}
-	#else 
+	#else
 	    --none true
 	    --pValue 0.05
 	    --fChange 1.5
@@ -73,7 +73,7 @@
         #if $cond.type_selector == 'datasets_rasonly':
             --input_datas ${input_Datasets}
             --single_ras_file $ras_single
-            --none ${cond.advanced.None}
+            --none ${None}
         #end if
         ]]>
     </command>
@@ -108,7 +108,7 @@
             </param>
             <when value="datasets">
                 <repeat name="input_Datasets" title="RNAseq" min="2">
-                    <param name="input" argument="--input_datas" type="data" format="tabular, csv, tsv" label="add dataset" />	
+                    <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>
                 <conditional name="advanced">
@@ -119,19 +119,19 @@
 					<when value="false">
 					</when>
 					<when value="true">
-		    			<param name="None" argument="--none" type="boolean" truevalue="true" falsevalue="false" checked="true" label="(A and NaN) solved as (A)?" /> 
+		    			<param name="None" argument="--none" type="boolean" truevalue="true" falsevalue="false" checked="true" label="(A and NaN) solved as (A)?" />
 		    			<param name="pValue" argument="--pValue" type="float" size="20" value="0.01" max="1" min="0" label="P-value threshold:" help="min value 0" />
 		    			<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="generateRas" argument="--generateRas" type="boolean" checked="false" label="Generate Reaction Activity Score for each table" help="Generate Reaction Activity Score for each table" />		
+		    			<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="generateRas" argument="--generateRas" type="boolean" checked="false" label="Generate Reaction Activity Score for each table" help="Generate Reaction Activity Score for each table" />
 					</when>
     	</conditional>
             </when>
             <when value="datasets_rasonly">
                 <param name="input_Datasets" 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" />
-                <param name="None" argument="--none" type="boolean" truevalue="true" falsevalue="false" checked="true" label="(A and NaN) solved as (A)?" /> 
+                <param name="None" argument="--none" type="boolean" truevalue="true" falsevalue="false" checked="true" label="(A and NaN) solved as (A)?" />
             </when>
             <when value="dataset_class">
                 <param name="input_data" argument="--input_data" type="data" format="tabular, csv, tsv" label="RNAseq of all samples" />
@@ -144,20 +144,20 @@
 					<when value="false">
 					</when>
 					<when value="true">
-		    			<param name="None" argument="--none" type="boolean" truevalue="true" falsevalue="false" checked="true" label="(A and NaN) solved as (A)?" /> 
+		    			<param name="None" argument="--none" type="boolean" truevalue="true" falsevalue="false" checked="true" label="(A and NaN) solved as (A)?" />
 		    			<param name="pValue" argument="--pValue" type="float" size="20" value="0.01" max="1" min="0" label="P-value threshold:" help="min value 0" />
 		    			<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="generateRas" argument="--generateRas" type="boolean" checked="false" label="Generate Reaction Activity Score for each table" help="Generate Reaction Activity Score for each table" />		
+		    			<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="generateRas" argument="--generateRas" type="boolean" checked="false" label="Generate Reaction Activity Score for each table" help="Generate Reaction Activity Score for each table" />
 					</when>
     	</conditional>
             </when>
         </conditional>
-       
-      
-       
-	
+
+
+
+
     </inputs>
 
     <outputs>
@@ -173,7 +173,7 @@
 	    <filter>cond['type_selector'] != "datasets_rasonly" and cond['advanced']['choice'] and cond['advanced']['generateRas']</filter>
     	    <discover_datasets pattern="__name_and_ext__" directory="ras" format="tabular"/>
 	</collection>
-	
+
     </outputs>
     <tests>
         <test>
@@ -189,7 +189,7 @@
 
 This tool analyzes RNA-seq dataset(s) as described in Graudenzi et al."`MaREA`_: Metabolic feature extraction, enrichment and visualization of RNAseq data" bioRxiv (2018): 248724.
 
-Accepted files are: 
+Accepted files are:
     - option 1) two or more RNA-seq datasets, each referring to samples in a given condition/class. The user can specify a label for each class (as e.g. "*classA*" and "*classB*");
     - option 2) one RNA dataset and one class-file specifying the class/condition each sample belongs to.
 
@@ -225,7 +225,7 @@
 
 **"RNAseq of group 1 + RNAseq of group 2 + ... + RNAseq of group N"** option:
 
-RNA-seq Dataset 1:						
+RNA-seq Dataset 1:
 
 @DATASET_EXEMPLE1@
 
@@ -241,14 +241,14 @@
 
 Class-file:
 
-+------------+------------+   
-| Patient_ID |    class   |   
-+============+============+   
-| TCGAAA3529 |     MSI    |   
-+------------+------------+    
-| TCGAA62671 |     MSS    |    
-+------------+------------+    
-| TCGAA62672 |     MSI    |   
++------------+------------+
+| Patient_ID |    class   |
++============+============+
+| TCGAAA3529 |     MSI    |
++------------+------------+
+| TCGAA62671 |     MSS    |
++------------+------------+
+| TCGAA62672 |     MSI    |
 +------------+------------+
 
 |
@@ -271,4 +271,3 @@
     </help>
     <expand macro="citations" />
 </tool>
-