diff tile.py @ 4:3a05117669cf draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tile.py	Sat Feb 06 10:02:20 2021 +0000
@@ -0,0 +1,100 @@
+#!/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"
+                 ])
+
+    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)