--- a/tomo_reconstruct.xml	Tue Mar 21 17:40:03 2023 +0000
+++ b/tomo_reconstruct.xml	Thu Mar 23 13:39:14 2023 +0000
@@ -1,43 +1,58 @@
-<tool id="tomo_reconstruct" name="Tomo Reconstruction" version="0.2.0" python_template_version="3.9">
+<tool id="tomo_reconstruct" name="Tomo Reconstruction" version="1.0.0" python_template_version="3.9">
     <description>Perform a tomography reconstruction</description>
     <macros>
         <import>tomo_macros.xml</import>
     </macros>
-    <expand macro="requirements" />
-    <command detect_errors="exit_code"><![CDATA[
-        mkdir center_slice_pngs;
-        $__tool_directory__/tomo_reconstruct.py
-        -i '$red_stacks'
-        -c '$config'
-        #if str($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'
-    ]]></command>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code">
+        <![CDATA[
+            mkdir tomo_reconstruct_plots;
+            $__tool_directory__/tomo_reconstruct.py
+            --input_file "$input_file"
+            --center_file "$center_file"
+            --output_file "output.nex"
+            --galaxy_flag
+            #if str($x_bounds.type_selector) == "enter_range"
+                --x_bounds $x_bounds.low $x_bounds.upp
+            #end if
+            #if str($y_bounds.type_selector) == "enter_range"
+                --y_bounds $y_bounds.low $y_bounds.upp
+            #end if
+            -l "$log"
+        ]]>
+    </command>
     <inputs>
-        <expand macro="common_inputs"/>
-        <param name="red_stacks" type='data' format='npz' optional='false' label="Reduced stacks"/>
-        <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 name="input_file" type="data" format="nex" optional="false" label="Reduced tomography data"/>
+        <param name="center_file" type="data" format="yaml" optional="false" label="Center axis input file"/>
+        <conditional name="x_bounds">
+            <param name="type_selector" type="select" label="Choose reconstructed image range in x-direction">
+                <option value="full_range" selected="true">Use the full image range</option>
+                <option value="enter_range">Manually enter the image range</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 value="full_range"/>
+            <when value="enter_range">
+                <param name="low" type="integer" value="-1" optional="false" label="Lower image range index in x-direction"/>
+                <param name="upp" type="integer" value="-1" optional="false" label="Upper image range index in x-direction"/>
+            </when>
+        </conditional>
+        <conditional name="y_bounds">
+            <param name="type_selector" type="select" label="Choose reconstructed image range in y-direction">
+                <option value="full_range" selected="true">Use the full image range</option>
+                <option value="enter_range">Manually enter the image range</option>
+            </param>
+            <when value="full_range"/>
+            <when value="enter_range">
+                <param name="low" type="integer" value="-1" optional="false" label="Lower image range index in y-direction"/>
+                <param name="upp" type="integer" value="-1" optional="false" label="Upper image range index in y-direction"/>
             </when>
         </conditional>
     </inputs>
     <outputs>
         <expand macro="common_outputs"/>
-        <data name="output_data" format="npz" label="Reconstructed tomography stacks" from_work_dir="output_data.npz"/>
-        <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 name="tomo_reconstruct_plots" type="list" label="Data recontruction images">
+            <discover_datasets pattern="__name_and_ext__" directory="tomo_reconstruct_plots"/>
         </collection>
-        <data name="output_config" format="tomo.config.yaml" label="Output config reconstruction" from_work_dir="output_config.yaml"/>
+        <data name="output_file" format="nex" label="Reconstructed tomography data" from_work_dir="output.nex"/>
     </outputs>
     <help><![CDATA[
         Reconstruct tomography images.