Mercurial > repos > rv43 > tomo

changeset 74:4f4ee8db5f67 draft

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planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
author rv43
date Tue, 21 Mar 2023 17:40:03 +0000
parents adb84c450789
children d5e1d4ea2b7e
files tomo_reduce.py tomo_reduce.xml tomopy_galaxy.yml
diffstat 3 files changed, 53 insertions(+), 46 deletions(-) [+]
line wrap: on
line diff
--- a/tomo_reduce.py	Mon Mar 20 17:30:24 2023 +0000
+++ b/tomo_reduce.py	Tue Mar 21 17:40:03 2023 +0000
@@ -15,30 +15,30 @@
     # Parse command line arguments
     parser = argparse.ArgumentParser(
             description='Reduce tomography data')
-#    parser.add_argument('-i', '--input_file',
-#            required=True,
-#            type=pathlib.Path,
-#            help='''Full or relative path to the input file (in yaml or nxs format).''')
-#    parser.add_argument('-o', '--output_file',
-#            required=True,
-#            type=pathlib.Path,
-#            help='''Full or relative path to the output file (in Nexus format).''')
-#    parser.add_argument('--galaxy_flag',
-#            action='store_true',
-#            help='''Use this flag to run the scripts as a galaxy tool.''')
-#    parser.add_argument('--img_x_bounds',
-#            required=False,
-#            nargs=2,
-#            type=int,
-#            help='Vertical data reduction image range')
+    parser.add_argument('-i', '--input_file',
+            required=True,
+            type=pathlib.Path,
+            help='''Full or relative path to the input file (in yaml or nxs format).''')
+    parser.add_argument('-o', '--output_file',
+            required=True,
+            type=pathlib.Path,
+            help='''Full or relative path to the output file (in Nexus format).''')
+    parser.add_argument('--galaxy_flag',
+            action='store_true',
+            help='''Use this flag to run the scripts as a galaxy tool.''')
+    parser.add_argument('--img_x_bounds',
+            required=False,
+            nargs=2,
+            type=int,
+            help='Vertical data reduction image range')
     parser.add_argument('-l', '--log',
 #            type=argparse.FileType('w'),
             default=sys.stdout,
             help='Logging stream or filename')
-#    parser.add_argument('--log_level',
-#            choices=logging._nameToLevel.keys(),
-#            default='INFO',
-#            help='''Specify a preferred logging level.''')
+    parser.add_argument('--log_level',
+            choices=logging._nameToLevel.keys(),
+            default='INFO',
+            help='''Specify a preferred logging level.''')
     args = parser.parse_args()
 
     # Set log configuration
@@ -66,28 +66,25 @@
 #    tracemalloc.start()
 
     # Log command line arguments
-#    logging.info(f'input_file = {args.input_file}')
-#    logging.info(f'output_file = {args.output_file}')
-#    logging.info(f'galaxy_flag = {args.galaxy_flag}')
-#    logging.info(f'img_x_bounds = {args.img_x_bounds}')
-#    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}')
-    logging.info(f'log = {args.log}')
-    logging.info(f'is log stdout? {args.log is sys.stdout}')
-    print('Done')
+    logging.info(f'input_file = {args.input_file}')
+    logging.info(f'output_file = {args.output_file}')
+    logging.info(f'galaxy_flag = {args.galaxy_flag}')
+    logging.info(f'img_x_bounds = {args.img_x_bounds}')
+    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}')
 
     # Instantiate Tomo object
-#    tomo = Tomo(galaxy_flag=args.galaxy_flag)
+    tomo = Tomo(galaxy_flag=args.galaxy_flag)
 
     # Read input file
-#    data = tomo.read(args.input_file)
+    data = tomo.read(args.input_file)
 
     # Generate reduced tomography images
-#    data = tomo.gen_reduced_data(data, img_x_bounds=args.img_x_bounds)
+    data = tomo.gen_reduced_data(data, img_x_bounds=args.img_x_bounds)
 
     # Write output file
-#    data = tomo.write(data, args.output_file)
+    data = tomo.write(data, args.output_file)
 
     # Displaying memory usage
 #    logging.info(f'Memory usage: {tracemalloc.get_traced_memory()}')
--- a/tomo_reduce.xml	Mon Mar 20 17:30:24 2023 +0000
+++ b/tomo_reduce.xml	Tue Mar 21 17:40:03 2023 +0000
@@ -1,24 +1,34 @@
-<tool id="tomo_reduce" name="Tomo Reduce" version="0.1.1" python_template_version="3.9">
+<tool id="tomo_reduce" name="Tomo Reduce" version="0.1.0" python_template_version="3.9">
     <description>Reduce tomography images</description>
+    <macros>
+        <import>tomo_macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
     <command detect_errors="exit_code">
         <![CDATA[
+            mkdir tomo_reduce_plots;
             $__tool_directory__/tomo_reduce.py
+            --input_file '$input_file'
+            --output_file 'output.nxs'
+            --galaxy_flag
+            --img_x_bounds $x_bounds.x_bound_low $x_bounds.x_bound_upp
             -l '$log'
         ]]>
     </command>
+    <inputs>
+        <param name="input_file" type="data" optional="false" label="Input file"/>
+    </inputs>
     <outputs>
-        <data name="log" format="txt" label="Log"/>
+        <expand macro="common_outputs"/>
+        <collection name="tomo_reduce_plots" type="list" label="Tomo 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"/>
     </outputs>
     <help>
         <![CDATA[
             Reduce tomography images.
         ]]>
     </help>
-    <citations>
-        <citation type="bibtex">
-@misc{tomo,
-  author = {Verberg, Rolf},
-  year = {2022}
-}</citation>
-    </citations>
+    <expand macro="citations"/>
 </tool>
--- a/tomopy_galaxy.yml	Mon Mar 20 17:30:24 2023 +0000
+++ b/tomopy_galaxy.yml	Tue Mar 21 17:40:03 2023 +0000
@@ -3,9 +3,9 @@
   - conda-forge
   - defaults
 dependencies:
-  - lmfit==1.0.3
-  - matplotlib==3.5.2
+  - lmfit==1.1.0
+  - matplotlib==3.7.1
   - nexusformat==1.0.0
-  - pip==22.3.1
+  - pip==23.0.1
   - python==3.9.13
   - tomopy==1.12.2