diff image_math.py @ 6:d3890df07463 draft default tip

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

--- a/image_math.py	Fri Feb 26 14:14:18 2021 +0000
+++ b/image_math.py	Sun Nov 05 09:29:39 2023 +0000
@@ -3,14 +3,11 @@
 import argparse
 import json
 
-from cp_common_functions import build_header
-from cp_common_functions import concat_conditional
-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 (build_header, concat_conditional,
+                                 get_json_value, get_pipeline_lines,
+                                 get_total_number_of_modules,
+                                 INDENTATION, update_module_count,
+                                 write_pipeline)
 
 MODULE_NAME = "ImageMath"
 OUTPUT_FILENAME = "output.cppipe"
@@ -29,33 +26,37 @@
     "and": "And",
     "or": "Or",
     "not": "Not",
-    "equals": "Equals"
+    "equals": "Equals",
 }
 
 
 def build_main_block(input_params):
     """Creates the main block of the CP pipeline with the parameters that don't depend on conditional choices"""
-    operation = operator_map[get_json_value(
-        input_params, 'operation.operation')]
-    result = INDENTATION.join([f"{INDENTATION}Operation:{operation}\n",
-                               f"Raise the power of the result by:{get_json_value(input_params,'operation.op_results.raise_the_power_of_the_result_by')}\n",
-                               f"Multiply the result by:{get_json_value(input_params,'operation.op_results.multiply_the_result_by')}\n",
-                               f"Add to result:{get_json_value(input_params,'operation.op_results.add_to_result')}\n",
-                               f"Set values less than 0 equal to 0?:{get_json_value(input_params,'operation.op_results.set_values_less_than_0_equal_to_0')}\n",
-                               f"Set values greater than 1 equal to 1?:{get_json_value(input_params,'operation.op_results.set_values_greater_than_1_equal_to_1')}\n",
-                               f"Ignore the image masks?:{get_json_value(input_params,'ignore_the_image_masks')}\n",
-                               f"Name the output image:{get_json_value(input_params,'name_output_image')}"
-                               ])
+    operation = operator_map[get_json_value(input_params, "operation.operation")]
+    result = INDENTATION.join(
+        [
+            f"{INDENTATION}Operation:{operation}\n",
+            f"Raise the power of the result by:{get_json_value(input_params,'operation.op_results.raise_the_power_of_the_result_by')}\n",
+            f"Multiply the result by:{get_json_value(input_params,'operation.op_results.multiply_the_result_by')}\n",
+            f"Add to result:{get_json_value(input_params,'operation.op_results.add_to_result')}\n",
+            f"Set values less than 0 equal to 0?:{get_json_value(input_params,'operation.op_results.set_values_less_than_0_equal_to_0')}\n",
+            f"Set values greater than 1 equal to 1?:{get_json_value(input_params,'operation.op_results.set_values_greater_than_1_equal_to_1')}\n",
+            f"Ignore the image masks?:{get_json_value(input_params,'ignore_the_image_masks')}\n",
+            f"Name the output image:{get_json_value(input_params,'name_output_image')}",
+        ]
+    )
     return result
 
 
 def build_variable_block(inputs_galaxy):
     result = ""
     first_image_block = build_first_image_block(
-        get_json_value(inputs_galaxy, 'operation.first_image'))
+        get_json_value(inputs_galaxy, "operation.first_image")
+    )
     result += f"\n{first_image_block}"
     second_image_block = build_second_image_block(
-        get_json_value(inputs_galaxy, 'operation.second_image'))
+        get_json_value(inputs_galaxy, "operation.second_image")
+    )
     result += f"\n{second_image_block}"
     return result
 
@@ -64,22 +65,27 @@
     """Creates the block of parameters for the first operator in operations"""
 
     value_select = get_json_value(
-        input_params, 'image_or_measurement_first.image_or_measurement_first')
+        input_params, "image_or_measurement_first.image_or_measurement_first"
+    )
     image_name = get_json_value(
-        input_params, 'image_or_measurement_first.select_the_first_image')
-    value_multiply = get_json_value(
-        input_params, 'multiply_the_first_image_by')
+        input_params, "image_or_measurement_first.select_the_first_image"
+    )
+    value_multiply = get_json_value(input_params, "multiply_the_first_image_by")
     category = get_json_value(
-        input_params, 'image_or_measurement_first.category_first.category_first')
+        input_params, "image_or_measurement_first.category_first.category_first"
+    )
     measurement = get_json_value(
-        input_params, 'image_or_measurement_first.category_first.measurement_first')
+        input_params, "image_or_measurement_first.category_first.measurement_first"
+    )
 
     result = INDENTATION.join(
-        [f"{INDENTATION}Image or measurement?:{value_select}\n",
-         f"Select the first image:{image_name}\n",
-         f"Multiply the first image by:{value_multiply}\n",
-         f"Measurement:{concat_conditional(category, measurement)}"
-         ])
+        [
+            f"{INDENTATION}Image or measurement?:{value_select}\n",
+            f"Select the first image:{image_name}\n",
+            f"Multiply the first image by:{value_multiply}\n",
+            f"Measurement:{concat_conditional(category, measurement)}",
+        ]
+    )
     return result
 
 
@@ -87,35 +93,34 @@
     """Creates the block of parameters for the second operator in binary operations"""
 
     value_select = get_json_value(
-        input_params, 'image_or_measurement_second.image_or_measurement_second')
+        input_params, "image_or_measurement_second.image_or_measurement_second"
+    )
     image_name = get_json_value(
-        input_params, 'image_or_measurement_second.select_the_second_image')
-    value_multiply = get_json_value(
-        input_params, 'multiply_the_second_image_by')
+        input_params, "image_or_measurement_second.select_the_second_image"
+    )
+    value_multiply = get_json_value(input_params, "multiply_the_second_image_by")
     category = get_json_value(
-        input_params, 'image_or_measurement_second.category_second.category_second')
+        input_params, "image_or_measurement_second.category_second.category_second"
+    )
     measurement = get_json_value(
-        input_params, 'image_or_measurement_second.category_second.measurement_second')
+        input_params, "image_or_measurement_second.category_second.measurement_second"
+    )
 
     result = INDENTATION.join(
-        [f"{INDENTATION}Image or measurement?:{value_select}\n",
-         f"Select the second image:{image_name}\n",
-         f"Multiply the second image by:{value_multiply}\n",
-         f"Measurement:{concat_conditional(category, measurement)}"
-         ])
+        [
+            f"{INDENTATION}Image or measurement?:{value_select}\n",
+            f"Select the second image:{image_name}\n",
+            f"Multiply the second image by:{value_multiply}\n",
+            f"Measurement:{concat_conditional(category, measurement)}",
+        ]
+    )
     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)