diff Marea/marea.xml @ 28:e6831924df01 draft

small fixes (elbow plot and output managment)

--- a/Marea/marea.xml	Mon Oct 07 13:48:01 2019 -0400
+++ b/Marea/marea.xml	Mon Oct 14 05:01:08 2019 -0400
@@ -54,6 +54,10 @@
             --input_data ${input_data}
             --input_class ${input_class}
         #end if
+        #if $cond.type_selector == 'datasets_rasonly':
+            --input_datas ${input_Datasets}
+            --single_ras_file $ras_single
+        #end if
         ]]>
     </command>
 
@@ -83,6 +87,7 @@
             <param name="type_selector" argument="--option" type="select" label="Input format:">
                 <option value="datasets" selected="true">RNAseq of group 1 + RNAseq of group 2 + ... + RNAseq of group N</option>
                 <option value="dataset_class">RNAseq of all samples + sample group specification</option>
+                <option value="datasets_rasonly" selected="true">RNAseq dataset</option>
             </param>
             <when value="datasets">
                 <repeat name="input_Datasets" title="RNAseq" min="2">
@@ -90,12 +95,18 @@
                     <param name="input_name" argument="--names" type="text" label="Dataset's name:" value="Dataset" help="Default: Dataset" />
                 </repeat>
             </when>
+            <when value="datasets_rasonly">
+                <param name="input_Datasets" argument="--input_datas" type="data" format="tabular, csv, tsv" label="add dataset" />
+            </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" />
             </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>
@@ -116,13 +127,18 @@
 
     <outputs>
         <data format="txt" name="log" label="${tool.name} - Log" />
+        <data format="tabular" name="ras_single" label="${tool.name} - RAS">
+        	<filter>cond['type_selector'] == "datasets_rasonly"</filter>
+        </data>
         <collection name="results" type="list" label="${tool.name} - Results">
+        <filter>cond['type_selector'] == "datasets" or cond['type_selector'] == "dataset_class"</filter>
             <discover_datasets pattern="__name_and_ext__" directory="result"/>
         </collection>
-	<collection name="ras" type="list" label="${tool.name} - RAS" format_source="tabular">
+	<collection name="ras" type="list" label="${tool.name} - RAS list" format_source="tabular">
 	    <filter>advanced['choice'] and advanced['generateRas']</filter>
     	    <discover_datasets pattern="__name_and_ext__" directory="ras" format="tabular"/>
 	</collection>
+	
     </outputs>
     <tests>
         <test>