# HG changeset patch
# User rv43
# Date 1679338488 0
# Node ID 543dba81eb1595c5ccf9f041c45ea9f133632183
# Parent  9aa288729b9a409b70b6dda589e4582bace29209
planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty

diff -r 9aa288729b9a -r 543dba81eb15 tomo_reduce.py
--- a/tomo_reduce.py	Mon Mar 20 18:44:23 2023 +0000
+++ b/tomo_reduce.py	Mon Mar 20 18:54:48 2023 +0000
@@ -73,13 +73,14 @@
     logging.debug(f'log = {args.log}')
     logging.debug(f'is log stdout? {args.log is sys.stdout}')
     logging.debug(f'log_level = {args.log_level}')
-    return
 
     # Instantiate Tomo object
     tomo = Tomo(galaxy_flag=args.galaxy_flag)
 
     # Read input file
     data = tomo.read(args.input_file)
+    print('data:\n{data.tree}')
+    return
 
     # Generate reduced tomography images
     data = tomo.gen_reduced_data(data, img_x_bounds=args.img_x_bounds)
diff -r 9aa288729b9a -r 543dba81eb15 tomo_reduce.xml
--- a/tomo_reduce.xml	Mon Mar 20 18:44:23 2023 +0000
+++ b/tomo_reduce.xml	Mon Mar 20 18:54:48 2023 +0000
@@ -1,4 +1,4 @@
-<tool id="tomo_reduce" name="Tomo Reduce" version="0.1.1" python_template_version="3.9">
+<tool id="tomo_reduce" name="Tomo Reduce" version="0.1.2" python_template_version="3.9">
     <description>Reduce tomography images</description>
     <macros>
         <import>tomo_macros.xml</import>
diff -r 9aa288729b9a -r 543dba81eb15 workflow/run_tomo.py
--- a/workflow/run_tomo.py	Mon Mar 20 18:44:23 2023 +0000
+++ b/workflow/run_tomo.py	Mon Mar 20 18:54:48 2023 +0000
@@ -873,7 +873,10 @@
 
         # Select image bounds
         title = f'tomography image at theta={round(theta, 2)+0}'
-        if (img_x_bounds is not None and not is_index_range(img_x_bounds, ge=0,
+        if img_x_bounds is not None:
+            if is_int_pair(img_x_bounds)i and img_x_bounds[0] == -1 and img_x_bounds[1] == -1
+                img_x_bounds = None
+            elif not is_index_range(img_x_bounds, ge=0,
                 le=first_image.shape[0])):
             raise ValueError(f'Invalid parameter img_x_bounds ({img_x_bounds})')
         if nxentry.instrument.source.attrs['station'] in ('id1a3', 'id3a'):