--- a/ashlar.xml	Tue Sep 20 17:33:50 2022 +0000
+++ b/ashlar.xml	Fri Feb 09 22:48:46 2024 +0000
@@ -51,6 +51,10 @@
 
         -c $adv.align_channel
 
+        #if $adv.stitch_alpha
+        --stitch-alpha $adv.stitch_alpha
+        #end if
+
         #if $adv.filter_sigma
         --filter-sigma $adv.filter_sigma
         #end if
@@ -73,20 +77,10 @@
             #end for
         #end if
 
-        $adv.pyramid
         $adv.flip_mosaic_x
         $adv.flip_mosaic_y
 
-        -f registered.ome.tif;
-
-        #if $upgrade.decide == "do_upgrade"
-            python3 '${__tool_directory__}/pyramid_upgrade.py'
-            registered.ome.tif
-
-            #if $upgrade.markers_file
-                -n `echo \$(cat $upgrade.markers_file | tail -n +2 | awk -F, '{print \$3}')`;
-            #end if
-        #end if
+        -o registered.ome.tif;
     ]]></command>
 
     <inputs>
@@ -96,24 +90,13 @@
         <param name="flip_x" type="boolean" truevalue="--flip-x" falsevalue="" label="Flip X-axis"/>
         <param name="flip_y" type="boolean" truevalue="--flip-y" falsevalue="" label="Flip Y-axis"/>
         <param name="max_shift" type="integer" value="30" label="Maximum allowed per-tile corrective shift" help="In micros"/>
-        <conditional name="upgrade">
-            <param name="decide" type="select" label="Upgrade to BF6-Compliant OME-TIFF Pyramid">
-                <option value="do_upgrade">Upgrade Pyramid</option>
-                <option value="dont_upgrade">Leave Legacy Pyramid</option>
-            </param>
-            <when value="do_upgrade">
-                <param name="markers_file" type="data" format="csv,tabular" optional="true" label="Markers File (optional)"/>
-            </when>
-            <when value="dont_upgrade">
-            </when>
-        </conditional>
         <section name="adv" title="Advanced Options" expanded="false">
             <param name="align_channel" type="integer" value="0" label="Align Channel Number"/>
+            <param name="stitch_alpha" type="float" optional="true" label="Alpha"/>
             <param name="filter_sigma" type="float" optional="true" label="Sigma"/>
             <param name="tile_size" type="integer"  optional="true" label="Cyto Mask Channel"/>
             <param name="flip_mosaic_x" type="boolean" truevalue="--flip-mosaic-x" falsevalue="" label="Flip output image horizontally"/>
             <param name="flip_mosaic_y" type="boolean" truevalue="--flip-mosaic-y" falsevalue="" label="Flip output image vertically"/>
-            <param name="pyramid" type="boolean" checked="true" truevalue="--pyramid" falsevalue="" label="Write output as a single pyramidal TIFF"/>
         </section>
     </inputs>
 
@@ -130,7 +113,7 @@
             </param>
             <output name="output" ftype="ome.tiff">
                 <assert_contents>
-                    <has_size value="4000000" delta="1000000" />
+                    <has_size value="500000" delta="400000" />
                 </assert_contents>
             </output>
         </test>