diff tile.py @ 2:443638c10c61 draft default tip

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

--- a/tile.py	Fri Feb 26 14:13:03 2021 +0000
+++ b/tile.py	Sun Nov 05 09:31:03 2023 +0000
@@ -3,85 +3,100 @@
 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
-
+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"])
+    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"
-                               ])
+    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')
+    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')
+    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')
+        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')
+        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')
+    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')
+    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"
-         ])
+        [
+            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']
+        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"
-                 ])
+                [
+                    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'
-    )
+    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)