--- a/scmap_index_cell.xml	Mon May 04 07:14:01 2020 -0400
+++ b/scmap_index_cell.xml	Wed Jul 15 09:24:15 2020 -0400
@@ -1,4 +1,4 @@
-<tool id="scmap_index_cell" name="Scmap index cells" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@">
+<tool id="scmap_index_cell" name="Scmap index cells" version="@TOOL_VERSION@+galaxy3" profile="@PROFILE@">
     <description>creates a cell index for a dataset to enable fast approximate nearest neighbour search</description>
     <macros>
         <import>scmap_macros.xml</import>
@@ -6,15 +6,22 @@
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
         scmap-preprocess-sce.R --input-object "${input_single_cell_experiment}" --output-sce-object sce_object_preprocessed.rds &&
-        scmap-index-cell.R --input-object-file sce_object_preprocessed.rds --number-chunks '$n_chunks' --number-clusters '$n_clusters' --output-object-file '$output_single_cell_experiment' --random-seed '$random_seed'
+        scmap-index-cell.R --input-object-file sce_object_preprocessed.rds --output-object-file '$output_single_cell_experiment' --random-seed '$random_seed'
         #if $train_id
         --train-id '${train_id}' 
         #end if
+        #if $n_chunks
+        --number-chunks '$n_chunks'
+        #end if
+        #if $n_clusters
+        --number-clusters '$n_clusters' 
+        #end if
+
     ]]></command>
     <inputs>
         <param type="data" name="input_single_cell_experiment" label="SingleCellExperiment object" format="rdata" help="File with serialized SingleCellExperiment object as produced by 'scmap select features'" />
-        <param name="n_chunks" type="integer" label="Number of chunks" value='' help="Number of chunks into which the expr matrix is split" />
-        <param name="n_clusters" type="integer" label="Number of clusters" value='' help="Number of clusters per group for k-means clustering" />
+        <param name="n_chunks" type="integer" label="Number of chunks" optional="true" help="Number of chunks into which the expr matrix is split" />
+        <param name="n_clusters" type="integer" label="Number of clusters" optional="true" help="Number of clusters per group for k-means clustering" />
         <param type="text" name="train_id" label="Dataset ID" help="ID of the training dataset" />
         <param name="random_seed" type="integer" label="Random seed" value='1' help="scmap-cell contains k-means step which makes it stochastic, i.e. running it multiple times will provide slightly different results. A fixed random seed ensures reproducibility." />
     </inputs>
@@ -23,8 +30,6 @@
     </outputs>
     <tests>
         <test>
-            <param name="n_chunks" value="50" />
-            <param name="n_clusters" value="9" />
             <param name="input_single_cell_experiment" value="select_features.rds" ftype="rdata"/>
             <output name="output_single_cell_experiment" file="index_cell.rds" compare="sim_size"/>
         </test>