# HG changeset patch
# User rv43
# Date 1679408723 0
# Node ID da3116b620b35f9af64e1d1337fb0e43ac4c6780
# Parent  e4963769076b9364cfa818edae3a7754ef50f876
planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty

diff -r e4963769076b -r da3116b620b3 tomo_reduce.xml
--- a/tomo_reduce.xml	Tue Mar 21 14:07:35 2023 +0000
+++ b/tomo_reduce.xml	Tue Mar 21 14:25:23 2023 +0000
@@ -9,7 +9,7 @@
             mkdir tomo_reduce_plots;
             $__tool_directory__/tomo_reduce.py
             --input_file '$input_file'
-            --output_file 'output.nxs'
+            --output_file 'output.nex'
             --galaxy_flag
             --img_x_bounds $img_x_bounds.low $img_x_bounds.upp
             -l '$log'
@@ -30,7 +30,7 @@
         <collection name="tomo_reduce_plots" type="list" label="Data reduction images">
             <discover_datasets pattern="__name_and_ext__" directory="tomo_reduce_plots"/>
         </collection>
-        <data name="output_file" format="nxs" label="Reduced tomography data" from_work_dir="output.nxs"/>
+        <data name="output_file" format="nex" label="Reduced tomography data" from_work_dir="output.nex"/>
     </outputs>
     <help>
         <![CDATA[
diff -r e4963769076b -r da3116b620b3 workflow/run_tomo.py
--- a/workflow/run_tomo.py	Tue Mar 21 14:07:35 2023 +0000
+++ b/workflow/run_tomo.py	Tue Mar 21 14:25:23 2023 +0000
@@ -374,7 +374,7 @@
         if self.test_mode:
             lower_row = self.test_config['lower_row']
         elif self.galaxy_flag:
-            if center_rows is None:
+            if center_rows is None or center_rows[0] = -1:
                 lower_row = 0
             else:
                 lower_row = min(center_rows)
@@ -400,7 +400,7 @@
         if self.test_mode:
             upper_row = self.test_config['upper_row']
         elif self.galaxy_flag:
-            if center_rows is None:
+            if center_rows is None or center_rows[1] = -1:
                 upper_row = tomo_fields_shape[2]-1
             else:
                 upper_row = max(center_rows)