--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tomo_setup.xml	Thu Mar 24 17:02:54 2022 +0000
@@ -0,0 +1,70 @@
+<tool id="tomo_setup" name="Tomo Setup" version="0.1.0" python_template_version="3.9">
+    <description>Preprocess tomography images</description>
+    <requirements>
+        <requirement type="package" version="1.11.0">tomopy</requirement>
+        <requirement type="package" version="0.2.12">pyinputplus</requirement>
+        <requirement type="package" version="3.6.0">h5py</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        cp '$inputfiles' inputfiles.txt &&
+        $__tool_directory__/tomo_setup.py
+        -i inputfiles.txt
+        -c '$config'
+        --theta_range '$thetas.theta_start $thetas.theta_end $thetas.num_thetas'
+        --dark '$dark'
+        --bright '$bright'
+        --tomo '$tomo'
+        --detectorbounds '$detectorbounds'
+        --output_data '$output_data'
+        --output_config '$output_config'
+        -l '$log'
+#for $s in $tomo_sets# ${s.offset} ${s.num} #end for
+    ]]></command>
+    <configfiles>
+         <configfile name="inputfiles"><![CDATA[#slurp
+#for $s in $tomo_sets
+#for $input in $s.inputs
+#echo str($input) + '\t' + $input.element_identifier #
+#end for
+#end for
+]]></configfile>
+    </configfiles>
+    <inputs>
+        <param name="config" type='data' format='yaml' optional='false' label="Input config"/>
+        <section name="thetas" title="Tomography angles">
+            <param name="theta_start" type="float" min="0.0" max="360.0" value="0.0" label="Lower bound"/>
+            <param name="theta_end" type="float" min="0.0" max="360.0" value="0.0" label="Upper bound"/>
+            <param name="num_thetas" type="integer" min="0" label="Number of angles"/>
+        </section>
+        <repeat name='tomo_sets' title="Tomography image sets">
+            <param name="inputs" type="data_collection" label="Image file collection"/>
+            <param name="offset" type="integer" min="0" label="Image index offset"/>
+            <param name="num" type="integer" min="1" label="Number of images"/>
+        </repeat>
+    </inputs>
+    <outputs>
+        <data name="inputfiles" format="txt" label="Input files" from_work_dir="inputfiles.txt" hidden="true"/>
+        <data name="dark" format="png" label="Dark field"/>
+        <data name="bright" format="png" label="Bright field"/>
+        <data name="tomo" format="png" label="First tomography image"/>
+        <data name="detectorbounds" format="png" label="Detector bounds"/>
+        <data name="output_data" format="npz" label="Preprocessed tomography data"/>
+        <data name="output_config" format="txt" label="Output config"/>
+        <data name="log" format="txt" label="Log"/>
+    </outputs>
+    <help><![CDATA[
+        Preprocess tomography images.
+    ]]></help>
+    <citations>
+        <citation type="bibtex">
+@misc{githubsum_files,
+  author = {Verberg, Rolf},
+  year = {2022},
+  title = {Tomo Setup},
+  publisher = {GitHub},
+  journal = {GitHub repository},
+  url = {somewhere},
+}</citation>
+    </citations>
+
+</tool>