--- a/scater-filter.xml	Tue Sep 03 14:27:39 2019 -0400
+++ b/scater-filter.xml	Thu Sep 09 12:24:17 2021 +0000
@@ -1,27 +1,31 @@
-<tool id="scater_filter" name="Scater: filter SCE" version="@TOOL_VERSION@">
+<tool id="scater_filter" name="Scater: filter SCE" version="@TOOL_VERSION@" profile="@PROFILE@">
     <description>with user-defined parameters or PCA</description>
+    <expand macro="bio_tools"/>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements">
-        <requirement type="package" version="2.0.9">r-mvoutlier</requirement>
+        <requirement type="package" version="0.93_8">r-robustbase</requirement>
     </expand>
     <command detect_errors="exit_code"><![CDATA[
 #if $filter_type.filter_type_selector == 'manual':
     Rscript '$__tool_directory__/scater-manual-filter.R'
     -i '$input_loom'
-    #if str($filter_type.detection_limit):
-        --detection-limit ${filter_type.detection_limit}
-    #end if
     #if str($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 ${filter_type.percent_counts_MT}
     #end if
+    #if str($filter_type.expressed_features):
+        --expressed-features ${filter_type.expressed_features}
+    #end if
+    #if str($filter_type.detection_limit):
+        --detection-limit ${filter_type.detection_limit}
+    #end if
+    #if str($filter_type.min_cells_expressed):
+        --min-cells-expressed ${filter_type.min_cells_expressed}
+    #end if
 #else:
     Rscript '$__tool_directory__/scater-pca-filter.R'
     -i '$input_loom'
@@ -36,10 +40,11 @@
                 <option value="pca">PCA</option>
             </param>
             <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" />
+                <param name="percent_counts_MT" argument="--percent-counts-MT" type="float" min="0" max="100" optional="true" label="Maximum % of mitochondrial genes expressed per cell" help="Cells that exceed this value will be filtered out" />
+                <param name="expressed_features" type="integer" value="100" optional="true" label="Remove cells that have less than the given number of expressed features" />
+                <param name="detection_limit" argument="--detection-limit" type="float" optional="true" label="Number of reads mapped to a feature above which it to be deemed as expressed" help="Raising this number will raise the stringency and may lower the number of expressed genes" />
+                <param name="min_cells_expressed" argument="---min-cells-expressed" type="integer" optional="true" label="Remove features that occur in less than the given number of cells" help="Features that exceed this value will be filtered out" />
             </when>
             <when value="pca" />
         </conditional>
@@ -53,8 +58,8 @@
             <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" />
+            <param name="min_cells_expressed" value="3" />
             <output name="output_loom" file="scater_manual_filtered.loom" compare="sim_size" />
         </test>
         <test>