--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Sat May 13 12:31:10 2023 +0000
@@ -0,0 +1,56 @@
+
+<macros>
+    <!-- The documentation says a v1.0 is in the works
+         but the repository has seen no changes for 3-4 years -->
+    <token name="@VERSION@">0.17.17</token>
+    <token name="@SAMTOOLS_OPTS@"><![CDATA[
+    --samtools-threads \${GALAXY_SLOTS:-1}
+    --samtools-memory \${GALAXY_MEMORY_MB:-100}
+    ]]></token>
+    <token name="@LOOMOUT@"><![CDATA[
+    -o "."
+    -e "output"
+    ]]></token>
+    
+    <xml name="bcffile" >
+        <param argument="-b" type="data" format="tabular,txt" optional="true"
+               label="Barcodes file to filter BAM"
+               help="If -bcfile is not specified the file will be searched in the default position outputted by 'dropest_bc_correct'. Otherwise an error will be thrown" />
+    </xml>
+    <xml name="loomdtype" token_16_selected="true" token_32_selected="false" >
+        <param argument="-t" type="select" optional="true"
+               label="Datatype of Loom layers"
+               help="The dtype of the loom file layers - if more than 6000 molecules/reads per gene per cell are expected set uint32
+                     to avoid truncation" >
+            <option value="uint16" selected="@16_SELECTED@">uint16</option>
+            <option value="uint32" selected="@32_SELECTED@">uint32</option>
+        </param>
+    </xml>
+    <xml name="repmask" >
+        <param argument="-m" type="data" format="gtf" optional="true"
+               label="Intervals to mask" />
+    </xml>
+    <xml name="notuniquemappings" >
+        <param argument="-M" type="boolean" truevalue="-M" falsevalue="" checked="false"
+               label="Consider not unique mappings?" help="(not recommended)" />
+    </xml>
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.1038/s41586-018-0414-6</citation>
+        </citations>
+    </xml>
+    <xml name="edam">
+        <edam_topics>
+            <edam_topic>topic_3512</edam_topic>
+            <edam_topic>topic_3320</edam_topic>
+        </edam_topics>
+        <edam_operations>
+            <edam_operation>operation_3800</edam_operation>
+        </edam_operations>
+    </xml>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@VERSION@" >velocyto.py</requirement>
+        </requirements>
+    </xml>
+</macros>
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