--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/signac_add_gene_annotations.xml	Tue Aug 02 19:11:27 2022 +0000
@@ -0,0 +1,31 @@
+<tool id="signac_add_gene_annotations" name="Add gene annotations" version="0.1.0" python_template_version="3.5">
+<description> to your Signac object.</description>
+<macros>
+    <import>signac_macros.xml</import>
+</macros>
+<expand macro="requirements"/>
+<stdio>
+    <exit_code range="1:" />
+</stdio>
+<command><![CDATA[
+    Rscript '${__tool_directory__}'/signac-add_gene_annotations.R --signac-object $signac_object --ens-db-genome $ens_db_genome --annotations $annotations --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="select" name="ens_db_genome" label="EnsDB genome version" multiple="false" format="text" optional="false">
+        <option value="EnsDb.Hsapiens.v75">EnsDb.Hsapiens.v75</option>
+        <option value="EnsDb.Mmusculus.v79">EnsDb.Mmusculus.v79</option>
+    </param>
+    <param type="select" name="annotations" label="" multiple="false" format="text" optional="false">
+	<option value="GRCh38">GRCh38</option>
+        <option value="hg19">hg19</option>
+	<option value="mm10">mm10</option>
+    </param>
+</inputs>
+<outputs>
+    <data name="rds_signac_seurat_file" format="rdata" label="Signac Object RDS (genes annotated)"/>
+</outputs>
+<help><![CDATA[
+This tool runs the second step in the Signac pipeline, which will add gene annotations to the Signac object.
+    ]]></help>
+</tool>