diff mergeMutationDatasets.xml @ 41:9806198df91f

fix

--- a/mergeMutationDatasets.xml	Fri Jul 31 21:29:17 2015 -0700
+++ b/mergeMutationDatasets.xml	Thu Aug 06 00:27:05 2015 -0700
@@ -1,26 +1,27 @@
-<tool id="mergeMutationDatasets" description="Merge two Xena positional mutation datasets into a new dataset" name="Merge Positional Mutation Data" version="0.0.1">
-  <description>
-    Given two mutation datasets, merge them to create a larger dataset with the mutations from both datasets. Output this larger dataset, along with a 2-column matrix indicating the source of each mutation
-  </description>
+<tool id="mergeMutationDatasets" description="Merge two Xena positional mutation datasets into a new dataset" name="Merge Xena Mutation by Position Data" version="0.0.1">
   <command interpreter="python">
       mergeXenaMutation.py $outputC $outputSourceMatrix $errorLog  $inputA $inputB 
       #if $labelForDatasetA
           --aLabel "${labelForDatasetA}"
+      #else
+          --aLabel "${inputA.name}"
       #end if
       #if $labelForDatasetB
           --bLabel "${labelForDatasetB}"
+      #else
+          --bLabel "${inputB.name}"
       #end if
   </command>
   <inputs>
-    <param name="inputA" format="tabular" type="data" label="Mutation Dataset A"/>
-    <param type="text" name="labelForDatasetA"  label="Dataset A Label (optional)" optional="true"/>
-    <param name="inputB" format="tabular" type="data" label="Mutation Dataset B"/> 
-    <param type="text" name="labelForDatasetB"  label="Dataset B Label (optional)" optional="true"/>
+    <param name="inputA" format="tabular" type="data" label="Xena Mutation by Position Dataset A"/>
+    <param type="text" name="labelForDatasetA"  label="Dataset A Label (eg. A)" value="dataset A"/>
+    <param name="inputB" format="tabular" type="data" label="Xena Mutation by Position Dataset B"/> 
+    <param type="text" name="labelForDatasetB"  label="Dataset B Label (eg. B)" value="dataset B"/>
  </inputs>
   <outputs>
     <data name="errorLog" format="data" label="Execution Log"/>
-    <data name="outputSourceMatrix" format="tabular" label="Mutation Data Sources"/> 
-    <data name="outputC" format="tabular" label="Merged Mutation Data"/>
+    <data name="outputSourceMatrix" format="tabular" label="Data Source ${labelForDatasetB}+${labelForDatasetA}"/> 
+    <data name="outputC" format="tabular" label="Mutation by Position ${labelForDatasetB}+${labelForDatasetA}"/>
   </outputs>
   <help>
     ***Merge Xena Positional Mutation Datasets***