annotate tile.py @ 7:eb6c08714244 draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5

#!/usr/bin/env python

import argparse
import json

from cp_common_functions import (get_json_value,
                                 get_pipeline_lines,
                                 get_total_number_of_modules,
                                 INDENTATION, update_module_count,
                                 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)