--- a/scater-filter.xml	Thu Jul 18 11:13:41 2019 -0400
+++ b/scater-filter.xml	Tue Sep 03 14:27:39 2019 -0400
@@ -16,6 +16,9 @@
     #if str($filter_type.library_size):
         --library-size ${filter_type.library_size}
     #end if
+    #if str($filter_type.expressed_genes):
+        --expressed-genes ${filter_type.expressed_genes}
+    #end if
     #if str($filter_type.percent_counts_MT):
         --percent-counts-MT ${filter_type.percent_counts_MT}
     #end if
@@ -35,6 +38,7 @@
             <when value="manual">
                 <param name="detection_limit" argument="--detection-limit" type="float" optional="true" label="Number of reads mapped to a gene for it to be counted as expressed" help="Raising this number will raise the stringency and may lower the number of expressed genes" />
                 <param name="library_size" argument="--library-size" type="integer" optional="true" label="Minimum library size (mapped reads) to filter cells on" help="Raising this number will raise the stringency and may lower the number of included cells" />
+                <param name="expressed_genes" argument="--expressed-genes" type="integer" optional="true" label="Minimum number of expressed genes to filter cells on" />
                 <param name="percent_counts_MT" argument="--percent-counts-MT" type="float" optional="true" label="Maximum % of mitochondrial genes expressed per cell" help="Cells that exceed this value will be filtered out" />
             </when>
             <when value="pca" />
@@ -49,6 +53,7 @@
             <param name="filter_type_selector" value="manual" />
             <param name="detection_limit" value="4" />
             <param name="library_size" value="100000" />
+            <param name="expressed_genes" value="400" />
             <param name="percent_counts_MT" value="33.0" />
             <output name="output_loom" file="scater_manual_filtered.loom" compare="sim_size" />
         </test>