Mercurial > repos > bgruening > cp_identify_primary_objects

comparison cp_common_functions.py @ 6:87d4d92d7487 draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
author bgruening
date Sun, 05 Nov 2023 09:32:24 +0000
parents 993faa34333b
children
comparison
equal deleted inserted replaced
5:b6eec6087271 6:87d4d92d7487
23 return f"{a}_{b}" 23 return f"{a}_{b}"
24 24
25 25
26 def get_total_number_of_modules(pipeline_lines): 26 def get_total_number_of_modules(pipeline_lines):
27 """Gets the number of modules from the header of the previous pipeline""" 27 """Gets the number of modules from the header of the previous pipeline"""
28 number_of_modules = pipeline_lines[LINE_NUM_MODULES].strip().split(':')[1] 28 number_of_modules = pipeline_lines[LINE_NUM_MODULES].strip().split(":")[1]
29 return int(number_of_modules) 29 return int(number_of_modules)
30 30
31 31
32 def get_pipeline_lines(input_pipeline): 32 def get_pipeline_lines(input_pipeline):
33 """Returns a list with the lines in the .cppipe file""" 33 """Returns a list with the lines in the .cppipe file"""
36 return lines 36 return lines
37 37
38 38
39 def update_module_count(pipeline_lines, count): 39 def update_module_count(pipeline_lines, count):
40 """Updates the number of modules in the .cppipe header""" 40 """Updates the number of modules in the .cppipe header"""
41 module_count_entry = pipeline_lines[LINE_NUM_MODULES].strip().split(':')[0] 41 module_count_entry = pipeline_lines[LINE_NUM_MODULES].strip().split(":")[0]
42 pipeline_lines[4] = f"{module_count_entry}:{count}\n" 42 pipeline_lines[4] = f"{module_count_entry}:{count}\n"
43 return pipeline_lines 43 return pipeline_lines
44 44
45 45
46 def write_pipeline(filename, lines_pipeline): 46 def write_pipeline(filename, lines_pipeline):
49 f.writelines(lines_pipeline) 49 f.writelines(lines_pipeline)
50 50
51 51
52 def build_header(module_name, module_number): 52 def build_header(module_name, module_number):
53 """Creates the first line of a module given the name and module number""" 53 """Creates the first line of a module given the name and module number"""
54 result = "|".join([f"{module_name}:[module_num:{module_number}", 54 result = "|".join(
55 "svn_version:\\'Unknown\\'", 55 [
56 "variable_revision_number:4", 56 f"{module_name}:[module_num:{module_number}",
57 "show_window:False", 57 "svn_version:\\'Unknown\\'",
58 "notes:\\x5B\\x5D", 58 "variable_revision_number:4",
59 "batch_state:array(\\x5B\\x5D, dtype=uint8)", 59 "show_window:False",
60 "enabled:True", 60 "notes:\\x5B\\x5D",
61 "wants_pause:False]\n"]) 61 "batch_state:array(\\x5B\\x5D, dtype=uint8)",
62 "enabled:True",
63 "wants_pause:False]\n",
64 ]
65 )
62 return result 66 return result