diff overlay_outlines.py @ 6:27edbb90ab2b draft default tip

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

--- a/overlay_outlines.py	Fri Feb 26 14:09:57 2021 +0000
+++ b/overlay_outlines.py	Sun Nov 05 09:26:05 2023 +0000
@@ -3,12 +3,11 @@
 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 = "OverlayOutlines"
 OUTPUT_FILENAME = "output.cppipe"
@@ -16,65 +15,85 @@
 
 def build_ctg_header(module_name, module_number):
     """Creates the first line of a module given the name and module number"""
-    result = "|".join([f"{module_name}:[module_num:{module_number}",
-                       "svn_version:\\'Unknown\\'",
-                       "variable_revision_number:4",
-                       "show_window:True",
-                       "notes:\\x5B\\'Overlay the embryo outlines on the grayscale image.\\'\\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:4",
+            "show_window:True",
+            "notes:\\x5B\\'Overlay the embryo outlines on the grayscale image.\\'\\x5D",
+            "batch_state:array(\\x5B\\x5D, dtype=uint8)",
+            "enabled:True",
+            "wants_pause:False]\n",
+        ]
+    )
     return result
 
 
 def build_main_block(input_params):
     result = f"{INDENTATION}Display outlines on a blank image?:{get_json_value(input_params,'con_blank_img.blank_img')}\n"
 
-    on_blank = get_json_value(input_params, 'con_blank_img.blank_img')
+    on_blank = get_json_value(input_params, "con_blank_img.blank_img")
     # defaults
     img_to_display = "None"
-    display_mode = get_json_value(input_params, 'con_blank_img.con_display_mode.display_mode')
+    display_mode = get_json_value(
+        input_params, "con_blank_img.con_display_mode.display_mode"
+    )
     method_brightness = "Max of image"
-    howto = get_json_value(input_params, 'howto_outline')
+    howto = get_json_value(input_params, "howto_outline")
     outline_color = "#FF0000"
     obj_to_display = "None"
 
-    name_output_img = get_json_value(input_params, 'name_output_image')
+    name_output_img = get_json_value(input_params, "name_output_image")
 
     if on_blank == "No":
-        img_to_display = get_json_value(input_params, 'con_blank_img.image_to_outline')
+        img_to_display = get_json_value(input_params, "con_blank_img.image_to_outline")
 
     result += INDENTATION.join(
-        [f"{INDENTATION}Select image on which to display outlines:{img_to_display}\n",
-         f"Name the output image:{name_output_img}\n",
-         f"Outline display mode:{display_mode}\n"
-         ])
+        [
+            f"{INDENTATION}Select image on which to display outlines:{img_to_display}\n",
+            f"Name the output image:{name_output_img}\n",
+            f"Outline display mode:{display_mode}\n",
+        ]
+    )
 
     if on_blank == "No" and display_mode == "Grayscale":
-        method_brightness = get_json_value(input_params, 'con_blank_img.con_display_mode.method_brightness')
+        method_brightness = get_json_value(
+            input_params, "con_blank_img.con_display_mode.method_brightness"
+        )
 
     result += INDENTATION.join(
-        [f"{INDENTATION}Select method to determine brightness of outlines:{method_brightness}\n",
-         f"How to outline:{howto}\n"
-         ])
+        [
+            f"{INDENTATION}Select method to determine brightness of outlines:{method_brightness}\n",
+            f"How to outline:{howto}\n",
+        ]
+    )
 
     obj_outline_str = ""
 
     if display_mode == "Color":
-        for obj in input_params['con_blank_img']['con_display_mode']['rpt_obj_to_display']:
-            outline_color = get_json_value(obj, 'outline_color')
-            obj_to_display = get_json_value(obj, 'obj_to_display')
+        for obj in input_params["con_blank_img"]["con_display_mode"][
+            "rpt_obj_to_display"
+        ]:
+            outline_color = get_json_value(obj, "outline_color")
+            obj_to_display = get_json_value(obj, "obj_to_display")
             obj_outline_str += INDENTATION.join(
-                [f"{INDENTATION}Select outline color:{outline_color}\n",
-                 f"Select objects to display:{obj_to_display}\n"
-                 ])
+                [
+                    f"{INDENTATION}Select outline color:{outline_color}\n",
+                    f"Select objects to display:{obj_to_display}\n",
+                ]
+            )
     else:  # grayscale
-        for obj in input_params['con_blank_img']['con_display_mode']['rpt_obj_to_display']:
-            obj_to_display = get_json_value(obj, 'obj_to_display')
+        for obj in input_params["con_blank_img"]["con_display_mode"][
+            "rpt_obj_to_display"
+        ]:
+            obj_to_display = get_json_value(obj, "obj_to_display")
             obj_outline_str += INDENTATION.join(
-                [f"{INDENTATION}Select outline color:{outline_color}\n",
-                 f"Select objects to display:{obj_to_display}\n"
-                 ])
+                [
+                    f"{INDENTATION}Select outline color:{outline_color}\n",
+                    f"Select objects to display:{obj_to_display}\n",
+                ]
+            )
     obj_outline_str = obj_outline_str.rstrip("\n")
     result += f"{obj_outline_str}"
 
@@ -83,14 +102,8 @@
 
 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)