--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/coreograph.xml	Wed May 19 21:34:38 2021 +0000
@@ -0,0 +1,56 @@
+<tool id="unet_coreograph" name="UNetCoreograph" version="@VERSION@.3" profile="17.09">
+    <description>Coreograph uses UNet, a deep learning model, to identify complete/incomplete tissue cores on a tissue microarray. It has been trained on 9 TMA slides of different sizes and tissue types.</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+ 
+    <expand macro="requirements"/>
+    @VERSION_CMD@
+
+    <command detect_errors="exit_code"><![CDATA[
+        #set $type_corrected = str($source_image)[:-3]+'ome.tif'
+        ln -s $source_image `basename $type_corrected`;
+
+        @CMD_BEGIN@
+        --imagePath `basename $type_corrected`
+        --downsampleFactor $downsamplefactor
+        --channel $channel
+        --buffer $buffer
+        --sensitivity $sensitivity
+
+        ##if $usegrid
+        ##--useGrid
+        ##end if
+
+        #if $cluster
+        --cluster
+        #end if
+
+        --outputPath .;
+        
+    ]]></command>
+
+
+    <inputs>
+        <param name="source_image" type="data" format="tiff" label="Registered TIFF"/>
+        <param name="downsamplefactor" type="integer" value="5" label="Down Sample Factor"/>
+        <param name="channel" type="integer" value="0" label="Channel"/>
+        <param name="buffer" type="float" value="2.0" label="Buffer"/>
+        <param name="sensitivity" type="float" value="0.3" label="Sensitivity"/>
+        <!--<param name="usegrid" type="boolean" label="Use Grid"/>-->
+        <param name="cluster" type="boolean" checked="false" label="Cluster"/>
+    </inputs>
+
+    <outputs>
+        <collection name="tma_sections" type="list" label="${tool.name} on ${on_string}: Images">
+            <discover_datasets pattern="(?P&lt;designation&gt;[0-9]+)\.tif" format="tiff" visible="false"/>
+        </collection>
+        <collection name="masks" type="list" label="${tool.name} on ${on_string}: Masks">
+            <discover_datasets pattern="(?P&lt;designation&gt;[0-9]+)_mask\.tif" directory="masks" format="tiff" visible="false"/>
+        </collection>
+        <data name="TMA_MAP" format="tiff" label="${tool.name} on ${on_string}: TMA Map" from_work_dir="TMA_MAP.tif"/>
+    </outputs>
+    <help><![CDATA[
+    ]]></help>
+    <expand macro="citations" />
+</tool>