diff vkmz.xml @ 5:04079c34452a draft

planemo upload for repository https://github.com/HegemanLab/VKMZ commit 3e37abe007f126480b9b748ad5322755445ac95b-dirty

--- a/vkmz.xml	Wed May 30 18:35:57 2018 -0400
+++ b/vkmz.xml	Thu May 31 12:06:20 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="VKMZ" name="VKMZ" version="1.1">
+<tool id="VKMZ" name="VKMZ" version="1.1.1">
 
   <description>metabolomics formula prediction and van Krevelen diagram generation</description>
   
@@ -34,6 +34,9 @@
     --output vkmz
     --error $prediction.error
     --database $prediction.database_type.database
+    #if $prediction.unique=="True":
+      --unique
+    #end if
     --size $diagram.size
     --size-algorithm $diagram.sizealgorithm
     --directory $__tool_directory__/
@@ -81,6 +84,7 @@
           <param name="database" label="Database" type="data" format="tabular" help="Select a custom tabular database" />
         </when>
       </conditional>
+      <param name="unique" label="Unique matches" type="boolean" truevalue="True" help="Only output features with a single prediction" />
     </section>
     <section name="diagram" title="Diagram Options" expanded="true">
       <param name="size" label="Minimum Maker Size" type="integer" value="5" min="0" help="Set the base size of diagram's markers" />
@@ -163,6 +167,8 @@
 
 *Database* can be set to heuristically generated databases for unlabeled and labeled chemcials [2] or to a custom database.
 
+*Unique matches* removes features from the output which have multiple predictions. Low mass molecules are less affected by this filter than high mass molecules.
+
 **Diagram Options**
 
 Predicted features are plotted as markers. The size of each marker is determined by the minimum marker size and a marker size algorithm. The marker size algorithms use minimum marker size as a variable.