diff color_to_gray.py @ 6:f24c370e5ea4 draft default tip

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

--- a/color_to_gray.py	Fri Feb 26 14:12:26 2021 +0000
+++ b/color_to_gray.py	Sun Nov 05 09:35:54 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 = "ColorToGray"
 OUTPUT_FILENAME = "output.cppipe"
@@ -16,27 +15,38 @@
 
 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\\'Convert the color image to grayscale.\\'\\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\\'Convert the color image to grayscale.\\'\\x5D",
+            "batch_state:array(\\x5B\\x5D, dtype=uint8)",
+            "enabled:True",
+            "wants_pause:False]\n",
+        ]
+    )
     return result
 
 
 def build_main_block(input_params):
     """Creates the main block of the CP pipeline with the parameters that don't depend on conditional choices"""
-    result = INDENTATION.join([f"{INDENTATION}Select the input image:{get_json_value(input_params,'name_input_image')}\n",
-                               f"Conversion method:{get_json_value(input_params,'con_conversion_method.conversion_method')}\n",
-                               f"Image type:{get_json_value(input_params,'con_conversion_method.con_image_type.image_type')}\n",
-                               ])
+    result = INDENTATION.join(
+        [
+            f"{INDENTATION}Select the input image:{get_json_value(input_params,'name_input_image')}\n",
+            f"Conversion method:{get_json_value(input_params,'con_conversion_method.conversion_method')}\n",
+            f"Image type:{get_json_value(input_params,'con_conversion_method.con_image_type.image_type')}\n",
+        ]
+    )
 
-    conversion_method = get_json_value(input_params, 'con_conversion_method.conversion_method')
+    conversion_method = get_json_value(
+        input_params, "con_conversion_method.conversion_method"
+    )
 
-    image_type = get_json_value(input_params, 'con_conversion_method.con_image_type.image_type')
+    image_type = get_json_value(
+        input_params, "con_conversion_method.con_image_type.image_type"
+    )
     rgb_comb_name_out = "OrigGray"
     combine_w_red = 1.0
     combine_w_green = 1.0
@@ -59,88 +69,131 @@
     channel_count = 1
     if conversion_method == "Combine":
         if image_type == "RGB" or image_type == "HSV":
-            rgb_comb_name_out = get_json_value(input_params, 'con_conversion_method.name_output_image')
-            combine_w_red = get_json_value(input_params, 'con_conversion_method.con_image_type.weight_red_channel')
-            combine_w_green = get_json_value(input_params, 'con_conversion_method.con_image_type.weight_green_channel')
-            combine_w_blue = get_json_value(input_params, 'con_conversion_method.con_image_type.weight_blue_channel')
+            rgb_comb_name_out = get_json_value(
+                input_params, "con_conversion_method.name_output_image"
+            )
+            combine_w_red = get_json_value(
+                input_params, "con_conversion_method.con_image_type.weight_red_channel"
+            )
+            combine_w_green = get_json_value(
+                input_params,
+                "con_conversion_method.con_image_type.weight_green_channel",
+            )
+            combine_w_blue = get_json_value(
+                input_params, "con_conversion_method.con_image_type.weight_blue_channel"
+            )
     elif conversion_method == "Split":
         if image_type == "RGB":
-            split_red = get_json_value(input_params, 'con_conversion_method.con_image_type.con_convert_red.yes_no')
-            red_output_name = get_json_value(input_params, 'con_conversion_method.con_image_type.con_convert_red.name_output_image')
-            split_green = get_json_value(input_params, 'con_conversion_method.con_image_type.con_convert_green.yes_no')
-            green_output_name = get_json_value(input_params, 'con_conversion_method.con_image_type.con_convert_green.name_output_image')
-            split_blue = get_json_value(input_params, 'con_conversion_method.con_image_type.con_convert_blue.yes_no')
-            blue_output_name = get_json_value(input_params, 'con_conversion_method.con_image_type.con_convert_blue.name_output_image')
+            split_red = get_json_value(
+                input_params,
+                "con_conversion_method.con_image_type.con_convert_red.yes_no",
+            )
+            red_output_name = get_json_value(
+                input_params,
+                "con_conversion_method.con_image_type.con_convert_red.name_output_image",
+            )
+            split_green = get_json_value(
+                input_params,
+                "con_conversion_method.con_image_type.con_convert_green.yes_no",
+            )
+            green_output_name = get_json_value(
+                input_params,
+                "con_conversion_method.con_image_type.con_convert_green.name_output_image",
+            )
+            split_blue = get_json_value(
+                input_params,
+                "con_conversion_method.con_image_type.con_convert_blue.yes_no",
+            )
+            blue_output_name = get_json_value(
+                input_params,
+                "con_conversion_method.con_image_type.con_convert_blue.name_output_image",
+            )
         elif image_type == "HSV":
-            split_hue = get_json_value(input_params, 'con_conversion_method.con_image_type.con_convert_hue.yes_no')
-            hue_output_name = get_json_value(input_params, 'con_conversion_method.con_image_type.con_convert_hue.name_output_image')
-            split_saturation = get_json_value(input_params, 'con_conversion_method.con_image_type.con_convert_saturation.yes_no')
-            saturation_output_name = get_json_value(input_params, 'con_conversion_method.con_image_type.con_convert_saturation.name_output_image')
-            split_value = get_json_value(input_params, 'con_conversion_method.con_image_type.con_convert_value.yes_no')
-            value_output_name = get_json_value(input_params, 'con_conversion_method.con_image_type.con_convert_value.name_output_image')
+            split_hue = get_json_value(
+                input_params,
+                "con_conversion_method.con_image_type.con_convert_hue.yes_no",
+            )
+            hue_output_name = get_json_value(
+                input_params,
+                "con_conversion_method.con_image_type.con_convert_hue.name_output_image",
+            )
+            split_saturation = get_json_value(
+                input_params,
+                "con_conversion_method.con_image_type.con_convert_saturation.yes_no",
+            )
+            saturation_output_name = get_json_value(
+                input_params,
+                "con_conversion_method.con_image_type.con_convert_saturation.name_output_image",
+            )
+            split_value = get_json_value(
+                input_params,
+                "con_conversion_method.con_image_type.con_convert_value.yes_no",
+            )
+            value_output_name = get_json_value(
+                input_params,
+                "con_conversion_method.con_image_type.con_convert_value.name_output_image",
+            )
 
     result += INDENTATION.join(
-        [f"{INDENTATION}Name the output image:{rgb_comb_name_out}\n",
-         f"Relative weight of the red channel:{str(combine_w_red)}\n",
-         f"Relative weight of the green channel:{str(combine_w_green)}\n",
-         f"Relative weight of the blue channel:{str(combine_w_blue)}\n",
-
-         f"Convert red to gray?:{split_red}\n",
-         f"Name the output image:{red_output_name}\n",
-         f"Convert green to gray?:{split_green}\n",
-         f"Name the output image:{green_output_name}\n",
-         f"Convert blue to gray?:{split_blue}\n",
-         f"Name the output image:{blue_output_name}\n",
-
-         f"Convert hue to gray?:{split_hue}\n",
-         f"Name the output image:{hue_output_name}\n",
-         f"Convert saturation to gray?:{split_saturation}\n",
-         f"Name the output image:{saturation_output_name}\n",
-         f"Convert value to gray?:{split_value}\n",
-         f"Name the output image:{value_output_name}\n"
-         ])
+        [
+            f"{INDENTATION}Name the output image:{rgb_comb_name_out}\n",
+            f"Relative weight of the red channel:{str(combine_w_red)}\n",
+            f"Relative weight of the green channel:{str(combine_w_green)}\n",
+            f"Relative weight of the blue channel:{str(combine_w_blue)}\n",
+            f"Convert red to gray?:{split_red}\n",
+            f"Name the output image:{red_output_name}\n",
+            f"Convert green to gray?:{split_green}\n",
+            f"Name the output image:{green_output_name}\n",
+            f"Convert blue to gray?:{split_blue}\n",
+            f"Name the output image:{blue_output_name}\n",
+            f"Convert hue to gray?:{split_hue}\n",
+            f"Name the output image:{hue_output_name}\n",
+            f"Convert saturation to gray?:{split_saturation}\n",
+            f"Name the output image:{saturation_output_name}\n",
+            f"Convert value to gray?:{split_value}\n",
+            f"Name the output image:{value_output_name}\n",
+        ]
+    )
 
     channel_count = 1
     if image_type == "Channels":
-        channels = input_params['con_conversion_method']['con_image_type']['rpt_channel']
+        channels = input_params["con_conversion_method"]["con_image_type"][
+            "rpt_channel"
+        ]
         channel_count = len(channels)
-        result += INDENTATION.join(
-            [f"{INDENTATION}Channel count:{channel_count}\n"
-             ])
+        result += INDENTATION.join([f"{INDENTATION}Channel count:{channel_count}\n"])
 
         for ch in channels:
             rel_weight_ch = 1.0
             image_name = "Channel1"
             if conversion_method == "Combine":
-                rel_weight_ch = get_json_value(ch, 'weight_of_channel')
+                rel_weight_ch = get_json_value(ch, "weight_of_channel")
             else:
-                image_name = get_json_value(ch, 'image_name')
+                image_name = get_json_value(ch, "image_name")
             result += INDENTATION.join(
-                [f"{INDENTATION}Channel number:{get_json_value(ch,'channel_no')}\n",
-                 f"Relative weight of the channel:{str(rel_weight_ch)}\n",
-                 f"Image name:{image_name}\n"
-                 ])
+                [
+                    f"{INDENTATION}Channel number:{get_json_value(ch,'channel_no')}\n",
+                    f"Relative weight of the channel:{str(rel_weight_ch)}\n",
+                    f"Image name:{image_name}\n",
+                ]
+            )
     else:
         result += INDENTATION.join(
-            [f"{INDENTATION}Channel count:{channel_count}\n",
-             "Channel number:Red\\x3A 1\n",
-             "Relative weight of the channel:1.0\n",
-             "Image name:Channel1\n"
-             ])
+            [
+                f"{INDENTATION}Channel count:{channel_count}\n",
+                "Channel number:Red\\x3A 1\n",
+                "Relative weight of the channel:1.0\n",
+                "Image name:Channel1\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)