# HG changeset patch
# User rv43
# Date 1679413542 0
# Node ID 7a7233e212be14394aaa63567499a174f2bf3c69
# Parent  b2d1826279f83f84b70b6ab947878e968c4aadb9
planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty

diff -r b2d1826279f8 -r 7a7233e212be tomo_find_center.xml
--- a/tomo_find_center.xml	Tue Mar 21 15:38:25 2023 +0000
+++ b/tomo_find_center.xml	Tue Mar 21 15:45:42 2023 +0000
@@ -3,10 +3,10 @@
     <macros>
         <import>tomo_macros.xml</import>
     </macros>
-    <expand macro="requirements" />
+    <expand macro="requirements"/>
     <command detect_errors="exit_code">
         <![CDATA[
-            mkdir find_center_pngs;
+            mkdir tomo_find_centers_plots;
             $__tool_directory__/tomo_find_center.py
             --input_file "$input_file"
             --output_file "output.yaml"
@@ -24,8 +24,8 @@
     </inputs>
     <outputs>
         <expand macro="common_outputs"/>
-        <collection name="find_center_pngs" type="list" label="Recontructed slice images">
-            <discover_datasets pattern="__name_and_ext__" directory="find_center_pngs"/>
+        <collection name="tomo_find_centers_plots" type="list" label="Find center images">
+            <discover_datasets pattern="__name_and_ext__" directory="tomo_find_centers_plots"/>
         </collection>
         <data name="output_file" format="yaml" label="Center axis info" from_work_dir="output.yaml"/>
     </outputs>
diff -r b2d1826279f8 -r 7a7233e212be tomo_reconstruct.py
--- a/tomo_reconstruct.py	Tue Mar 21 15:38:25 2023 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,113 +0,0 @@
-#!/usr/bin/env python3
-
-import logging
-
-import argparse
-import pathlib
-import sys
-#import tracemalloc
-
-from workflow.run_tomo import Tomo
-
-#from memory_profiler import profile
-#@profile
-def __main__():
-    # Parse command line arguments
-    parser = argparse.ArgumentParser(
-            description='Perform a tomography reconstruction')
-    parser.add_argument('-i', '--input_file',
-            required=True,
-            type=pathlib.Path,
-            help='''Full or relative path to the input file (in Nexus format).''')
-    parser.add_argument('-c', '--center_file',
-            required=True,
-            type=pathlib.Path,
-            help='''Full or relative path to the center info file (in yaml format).''')
-    parser.add_argument('-o', '--output_file',
-            required=False,
-            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('-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('--x_bounds',
-            required=False,
-            nargs=2,
-            type=int,
-            help='''Boundaries of reconstructed images in x-direction.''')
-    parser.add_argument('--y_bounds',
-            required=False,
-            nargs=2,
-            type=int,
-            help='''Boundaries of reconstructed images in y-direction.''')
-    args = parser.parse_args()
-
-    # Set log configuration
-    # When logging to file, the stdout log level defaults to WARNING
-    logging_format = '%(asctime)s : %(levelname)s - %(module)s : %(funcName)s - %(message)s'
-    level = logging.getLevelName(args.log_level)
-    if args.log is sys.stdout:
-        logging.basicConfig(format=logging_format, level=level, force=True,
-                handlers=[logging.StreamHandler()])
-    else:
-        if isinstance(args.log, str):
-            logging.basicConfig(filename=f'{args.log}', filemode='w',
-                    format=logging_format, level=level, force=True)
-        elif isinstance(args.log, io.TextIOWrapper):
-            logging.basicConfig(filemode='w', format=logging_format, level=level,
-                    stream=args.log, force=True)
-        else:
-            raise(ValueError(f'Invalid argument --log: {args.log}'))
-        stream_handler = logging.StreamHandler()
-        logging.getLogger().addHandler(stream_handler)
-        stream_handler.setLevel(logging.WARNING)
-        stream_handler.setFormatter(logging.Formatter(logging_format))
-
-    # Starting memory monitoring
-#    tracemalloc.start()
-
-    # Log command line arguments
-    logging.info(f'input_file = {args.input_file}')
-    logging.info(f'center_file = {args.center_file}')
-    logging.info(f'output_file = {args.output_file}')
-    logging.info(f'galaxy_flag = {args.galaxy_flag}')
-    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'x_bounds = {args.x_bounds}')
-    logging.info(f'y_bounds = {args.y_bounds}')
-
-    # Instantiate Tomo object
-    tomo = Tomo(galaxy_flag=args.galaxy_flag)
-
-    # Read input file
-    data = tomo.read(args.input_file)
-
-    # Read center data
-    center_data = tomo.read(args.center_file)
-
-    # Find the calibrated center axis info
-    data = tomo.reconstruct_data(data, center_data, x_bounds=args.x_bounds, y_bounds=args.y_bounds)
-
-    # Write output file
-    data = tomo.write(data, args.output_file)
-
-    # Displaying memory usage
-#    logging.info(f'Memory usage: {tracemalloc.get_traced_memory()}')
- 
-    # stopping memory monitoring
-#    tracemalloc.stop()
-
-    logging.info('Completed tomography reconstruction')
-
-
-if __name__ == "__main__":
-    __main__()
diff -r b2d1826279f8 -r 7a7233e212be tomo_reconstruct.xml
--- a/tomo_reconstruct.xml	Tue Mar 21 15:38:25 2023 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,48 +0,0 @@
-<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>
diff -r b2d1826279f8 -r 7a7233e212be tomo_reduce.xml
--- a/tomo_reduce.xml	Tue Mar 21 15:38:25 2023 +0000
+++ b/tomo_reduce.xml	Tue Mar 21 15:45:42 2023 +0000
@@ -3,7 +3,7 @@
     <macros>
         <import>tomo_macros.xml</import>
     </macros>
-    <expand macro="requirements" />
+    <expand macro="requirements"/>
     <command detect_errors="exit_code">
         <![CDATA[
             mkdir tomo_reduce_plots;
diff -r b2d1826279f8 -r 7a7233e212be workflow/.run_tomo.py.swp
Binary file workflow/.run_tomo.py.swp has changed