--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/signac_createAssayObject.xml	Tue Aug 02 19:11:27 2022 +0000
@@ -0,0 +1,36 @@
+<tool id="signac_createAssayObject" name="Create Assay Object" version="0.1.0" python_template_version="3.5">
+<description> Create Assay Object and Normalize Data</description>
+<macros>
+    <import>signac_macros.xml</import>
+</macros>
+<expand macro="requirements"/>
+<stdio>
+    <exit_code range="1:" />
+</stdio>
+<command><![CDATA[
+    Rscript '${__tool_directory__}'/signac-createAssayObject.R --signac-object $signac_object --counts $counts --name $name --min-cells $min_cells --min-features $min_features --method $method --scale-factor $scale_factor --margin $margin --output-object-file $rds_signac_seurat_file 
+]]></command>
+<inputs>
+    <param type="data" name="signac_object" label="Signac object." format="rdata" multiple="false" optional="false"/>
+    <param type="data" name="counts" label="Counts Matrix (Output of Gene Activity)" format="rdata" multiple="false" optional="true"/>
+    <param type="text" name="name" label="Assay Name." multiple="false" optional="true" value="RNA"/>    
+    <param type="integer" name="min_cells" label="Min Cells." multiple="false" optional="false" value="0"/>
+    <param type="integer" name="min_features" label="Min Features." multiple="false" optional="false" value="0"/>
+    <param type="select" name="method" label="Method for normalization." value="LogNormalize">
+        <option value="LogNormalize">LogNormalize</option>
+        <option value="CLR">CLR</option>
+        <option value="RC">RC</option>
+    </param>
+    <param type="float" name="scale_factor" value='10000' label="Sets the scale factor for cell-level normalization."/>
+    <param type="select" name="margin" label="If performing CLR normalization, normalize across features (1) or cells (2)." value="1">
+        <option value="1">1</option>
+        <option value="2">2</option>
+    </param>
+</inputs>
+<outputs>
+    <data name="rds_signac_seurat_file" format="rdata" label="Signac Object RDS (Create Assay Object - Normalized)"/>
+</outputs>
+<help><![CDATA[
+This tool creates a new assay and runs the NormalizeData function.
+    ]]></help>
+</tool>