Mercurial > repos > bgruening > cp_export_to_spreadsheet
view tile.py @ 5:d0178bdcd00e draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 7d7a519c3a2cc612d38695b335d0f6c75a099de3"
author | bgruening |
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date | Fri, 26 Feb 2021 14:12:26 +0000 |
parents | f8fa0f6718a3 |
children | f24c370e5ea4 |
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#!/usr/bin/env python import argparse import json from cp_common_functions import get_json_value from cp_common_functions import get_pipeline_lines from cp_common_functions import get_total_number_of_modules from cp_common_functions import INDENTATION from cp_common_functions import update_module_count from cp_common_functions import write_pipeline MODULE_NAME = "Tile" OUTPUT_FILENAME = "output.cppipe" def build_header(module_name, module_number): result = "|".join([f"{module_name}:[module_num:{module_number}", "svn_version:\\'Unknown\\'", "variable_revision_number:1", "show_window:True", "notes:\\x5B\\'Tile the original color image, the outlined image and the image of tracked labels together.\\'\\x5D", "batch_state:array(\\x5B\\x5D, dtype=uint8)", "enabled:True", "wants_pause:False]\n"]) return result def build_main_block(input_params): result = INDENTATION.join([f"{INDENTATION}Select an input image:{get_json_value(input_params,'input_image')}\n", f"Name the output image:{get_json_value(input_params,'output_image_name')}\n", f"Tile assembly method:{get_json_value(input_params,'con_assembly_method.assembly_method')}\n" ]) calc_rows = get_json_value(input_params, 'con_assembly_method.con_calc_no_row.calc_no_row') no_of_rows = 8 calc_cols = get_json_value(input_params, 'con_assembly_method.con_calc_no_cols.calc_no_cols') no_of_cols = 12 if calc_rows == "No": no_of_rows = get_json_value(input_params, 'con_assembly_method.con_calc_no_row.no_of_row') if calc_cols == "No": no_of_cols = get_json_value(input_params, 'con_assembly_method.con_calc_no_cols.no_of_cols') corner_to_begin = get_json_value(input_params, 'con_assembly_method.corner_to_begin') direction_tiling = get_json_value(input_params, 'con_assembly_method.direction') meander = get_json_value(input_params, 'con_assembly_method.meander_mode') assembly_method = get_json_value(input_params, 'con_assembly_method.assembly_method') result += INDENTATION.join( [f"{INDENTATION}Final number of rows:{str(no_of_rows)}\n", f"Final number of columns:{str(no_of_cols)}\n", f"Image corner to begin tiling:{corner_to_begin}\n", f"Direction to begin tiling:{direction_tiling}\n", f"Use meander mode?:{meander}\n", f"Automatically calculate number of rows?:{calc_rows}\n", f"Automatically calculate number of columns?:{calc_cols}\n" ]) if assembly_method == "Within cycles": additionals = input_params['con_assembly_method']['rpt_additional_image'] for img in additionals: result += INDENTATION.join( [f"{INDENTATION}Select an additional image to tile:{get_json_value(img, 'additional_img')}\n" ]) result = result.rstrip("\n") return result if __name__ == "__main__": parser = argparse.ArgumentParser() parser.add_argument( '-p', '--pipeline', help='CellProfiler pipeline' ) parser.add_argument( '-i', '--inputs', help='JSON inputs from Galaxy' ) args = parser.parse_args() pipeline_lines = get_pipeline_lines(args.pipeline) inputs_galaxy = json.load(open(args.inputs, "r")) current_module_num = get_total_number_of_modules(pipeline_lines) current_module_num += 1 pipeline_lines = update_module_count(pipeline_lines, current_module_num) header_block = build_header(MODULE_NAME, current_module_num) main_block = build_main_block(inputs_galaxy) module_pipeline = f"\n{header_block}{main_block}\n" pipeline_lines.append(module_pipeline) write_pipeline(OUTPUT_FILENAME, pipeline_lines)