--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scater-filter.xml	Thu Jul 18 11:13:41 2019 -0400
@@ -0,0 +1,68 @@
+<tool id="scater_filter" name="Scater: filter SCE" version="@TOOL_VERSION@">
+    <description>with user-defined parameters or PCA</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements">
+        <requirement type="package" version="2.0.9">r-mvoutlier</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.percent_counts_MT):
+        --percent-counts-MT ${filter_type.percent_counts_MT}
+    #end if
+#else:
+    Rscript '$__tool_directory__/scater-pca-filter.R'
+    -i '$input_loom'
+#end if
+-o '$output_loom'
+    ]]></command>
+    <inputs>
+        <param name="input_loom" type="data" format="loom" label="Input SingleCellLoomExperiment dataset" />
+        <conditional name="filter_type">
+            <param name="filter_type_selector" type="select" label="Type of filter">
+                <option value="manual">manual</option>
+                <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="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" />
+        </conditional>
+    </inputs>
+    <outputs>
+        <data name="output_loom" format="loom" label="${tool.name} on ${on_string}" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_loom" value="scater_qcready.loom" ftype="loom" />
+            <param name="filter_type_selector" value="manual" />
+            <param name="detection_limit" value="4" />
+            <param name="library_size" value="100000" />
+            <param name="percent_counts_MT" value="33.0" />
+            <output name="output_loom" file="scater_manual_filtered.loom" compare="sim_size" />
+        </test>
+        <test>
+            <param name="input_loom" value="scater_qcready.loom" ftype="loom" />
+            <param name="filter_type_selector" value="pca" />
+            <output name="output_loom" file="scater_pca_filtered.loom" compare="sim_size" />
+        </test>
+    </tests>
+    <help><![CDATA[
+Filter a SingleCellLoomExperiment object with Scater using one of the following methods:
+
+- user-defined parameters
+- PCA to automatically removes outliers.
+    ]]></help>
+    <expand macro="citations" />
+</tool>