--- a/tomo_reconstruct.xml	Thu Aug 18 15:40:59 2022 +0000
+++ b/tomo_reconstruct.xml	Fri Aug 19 20:16:56 2022 +0000
@@ -9,7 +9,9 @@
         $__tool_directory__/tomo_reconstruct.py
         -i '$red_stacks'
         -c '$config'
-        --center_offsets $center_offsets.lower_center_offset $center_offsets.upper_center_offset
+        #if str($center_offsets.type_selector) == "offsets_manual"
+            --center_offsets $center_offsets.lower_center_offset $center_offsets.upper_center_offset
+        #end if
         --output_data 'output_data.npz'
         --output_config 'output_config.yaml'
         -l '$log'
@@ -17,10 +19,17 @@
     <inputs>
         <expand macro="common_inputs"/>
         <param name="red_stacks" type='data' format='npz' optional='false' label="Reduced stacks"/>
-        <section name="center_offsets" title="Reconstruction center axis offsets">
-            <param name="lower_center_offset" type="float" value = "0" optional="false" label="Lower center offset"/>
-            <param name="upper_center_offset" type="float" value = "0" optional="false" label="Upper center offset"/>
-        </section>
+        <conditional name="center_offsets">
+            <param name="type_selector" type="select" label="Read reconstruction center axis offsets from file or enter enter manually">
+                <option value="offsets_from_file" selected="true">Read center axis offsets from file</option>
+                <option value="offsets_manual">Manually enter center axis offsets</option>
+            </param>
+            <when value="offsets_from_file"/>
+            <when value="offsets_manual">
+                <param name="lower_center_offset" type="float" value = "0" optional="false" label="Lower center offset"/>
+                <param name="upper_center_offset" type="float" value = "0" optional="false" label="Upper center offset"/>
+            </when>
+        </conditional>
     </inputs>
     <outputs>
         <expand macro="common_outputs"/>
@@ -28,7 +37,7 @@
         <collection name="center_slice_pngs" type="list" label="Recontructed slices midway in each dimension">
             <discover_datasets pattern="__name_and_ext__" directory="center_slice_pngs"/>
         </collection>
-        <data name="output_config" format="yaml" label="Output config reconstruction" from_work_dir="output_config.yaml"/>
+        <data name="output_config" format="tomo.config.yaml" label="Output config reconstruction" from_work_dir="output_config.yaml"/>
     </outputs>
     <help><![CDATA[
         Reconstruct tomography images.