--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tomo_reconstruct.xml	Tue Mar 21 15:38:25 2023 +0000
@@ -0,0 +1,48 @@
+<tool id="tomo_reconstruct" name="Tomo Reconstruction" version="0.3.0" 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;
+            $__tool_directory__/tomo_reconstruct.py
+            --input_file '$input_file'
+            --center_file '$center_file'
+            --output_file 'output.nex'
+            --galaxy_flag
+            #if str($center_offsets.type_selector) == "offsets_manual"
+                --center_offsets $center_offsets.low $center_offsets.upp
+            #end if
+            -l '$log'
+        ]]>
+    </command>
+    <inputs>
+        <expand macro="common_inputs"/>
+        <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="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="low" type="float" value = "0" optional="false" label="Lower center offset"/>
+                <param name="upp" type="float" value = "0" optional="false" label="Upper center offset"/>
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <expand macro="common_outputs"/>
+        <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_file" format="nex" label="Reconstructed tomography data" from_work_dir="output.nex"/>
+    </outputs>
+    <help><![CDATA[
+        Reconstruct tomography images.
+    ]]></help>
+    <expand macro="citations"/>
+</tool>