diff Marea/marea.xml @ 31:944e15aa970a draft

Uploaded

--- a/Marea/marea.xml	Tue Oct 15 12:21:16 2019 -0400
+++ b/Marea/marea.xml	Tue Oct 15 12:22:43 2019 -0400
@@ -1,4 +1,4 @@
-<tool id="MaREA" name="Metabolic Reaction Enrichment Analysis" version="1.0.2">
+<tool id="MaREA" name="Metabolic Reaction Enrichment Analysis" version="1.0.3">
     <description></description>
     <macros>
         <import>marea_macros.xml</import>
@@ -22,21 +22,7 @@
                 --custom_map $cond_rule.cond_map.Custom_map
             #end if
         #end if
-	#if $advanced.choice == 'true':
-      	    --none ${advanced.None}
-      	    --pValue ${advanced.pValue}
-      	    --fChange ${advanced.fChange}
-	    --generate_svg ${advanced.generateSvg}
-	    --generate_pdf ${advanced.generatePdf}
-	    --generate_ras ${advanced.generateRas}
-	#else 
-	    --none true
-	    --pValue 0.05
-	    --fChange 1.5
-	    --generate_svg false
-	    --generate_pdf true
-	    --generate_ras false
-	#end if
+	
       	--tool_dir $__tool_directory__
       	--option $cond.type_selector
         --out_log $log		
@@ -50,13 +36,44 @@
             #for $data in $cond.input_Datasets:
                 ${data.input_name}
             #end for
+            #if $cond.advanced.choice == 'true':
+      	    --none ${cond.advanced.None}
+      	    --pValue ${cond.advanced.pValue}
+      	    --fChange ${cond.advanced.fChange}
+	    	--generate_svg ${cond.advanced.generateSvg}
+	    	--generate_pdf ${cond.advanced.generatePdf}
+	    --generate_ras ${cond.advanced.generateRas}
+	#else 
+	    --none true
+	    --pValue 0.05
+	    --fChange 1.5
+	    --generate_svg false
+	    --generate_pdf true
+	    --generate_ras false
+	#end if
         #elif $cond.type_selector == 'dataset_class':
             --input_data ${input_data}
             --input_class ${input_class}
+            #if $cond.advanced.choice == 'true':
+      	    --none ${cond.advanced.None}
+      	    --pValue ${cond.advanced.pValue}
+      	    --fChange ${cond.advanced.fChange}
+	    --generate_svg ${cond.advanced.generateSvg}
+	    --generate_pdf ${cond.advanced.generatePdf}
+	    --generate_ras ${cond.advanced.generateRas}
+	#else 
+	    --none true
+	    --pValue 0.05
+	    --fChange 1.5
+	    --generate_svg false
+	    --generate_pdf true
+	    --generate_ras false
+	#end if
         #end if
         #if $cond.type_selector == 'datasets_rasonly':
             --input_datas ${input_Datasets}
             --single_ras_file $ras_single
+            --none ${cond.advanced.None}
         #end if
         ]]>
     </command>
@@ -94,48 +111,66 @@
                     <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">
+					<param name="choice" type="boolean" checked="false" label="Use advanced options?" help="Use this options to choose custom rules for evaluation: 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>
+					<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="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" />		
+					</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)?" /> 
             </when>
             <when value="dataset_class">
                 <param name="input_data" argument="--input_data" type="data" format="tabular, csv, tsv" label="RNAseq of all samples" />
                 <param name="input_class" argument="--input_class" type="data" format="tabular, csv, tsv" label="Sample group specification" />
+                <conditional name="advanced">
+					<param name="choice" type="boolean" checked="false" label="Use advanced options?" help="Use this options to choose custom rules for evaluation: 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>
+					<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="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" />		
+					</when>
+    	</conditional>
             </when>
         </conditional>
        
-       
-       <!--TODO: NASCONDERE ADVANCED SE RAS ONLY-->
+      
        
-	<conditional name="advanced">
-		<param name="choice" type="boolean" checked="false" label="Use advanced options?" help="Use this options to choose custom rules for evaluation: 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>
-		<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="pValue" argument="--pValue" type="float" size="20" value="0.05" max="1" min="0" label="P-value threshold:" help="min value 0" />
-		    <param name="fChange" argument="--fChange" type="float" size="20" value="1.5" 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" />		
-		</when>
-    	</conditional>
+	
     </inputs>
 
     <outputs>
-        <data format="txt" name="log" label="${tool.name} - Log" />
-        <data format="tabular" name="ras_single" label="${tool.name} - RAS">
+        <data format="txt" name="log" label="MaREA - Log" />
+        <data format="tabular" name="ras_single" label="MaREA - RAS - ${cond.input_name}">
         	<filter>cond['type_selector'] == "datasets_rasonly"</filter>
         </data>
-        <collection name="results" type="list" label="${tool.name} - Results">
+        <collection name="results" type="list" label="MaREA - Results">
         <filter>cond['type_selector'] == "datasets" or cond['type_selector'] == "dataset_class"</filter>
             <discover_datasets pattern="__name_and_ext__" directory="result"/>
         </collection>
-	<collection name="ras" type="list" label="${tool.name} - RAS list" format_source="tabular">
-	    <filter>advanced['choice'] and advanced['generateRas']</filter>
+	<collection name="ras" type="list" label="MaREA - RAS list" format_source="tabular">
+	    <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>