Mercurial > repos > peterjc > mira4_assembler
diff tools/mira4_0/mira4_validator.py @ 4:1713289d9908 draft default tip
v0.0.11 tweak for use with bioconda dependencies
author | peterjc |
---|---|
date | Thu, 10 Aug 2017 11:09:10 -0400 |
parents | 4eb32a3d67d1 |
children |
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--- a/tools/mira4_0/mira4_validator.py Fri Oct 02 06:12:23 2015 -0400 +++ b/tools/mira4_0/mira4_validator.py Thu Aug 10 11:09:10 2017 -0400 @@ -1,5 +1,6 @@ -#Called from the Galaxy Tool XML file -#import sys +# Called from the Galaxy Tool XML file +# import sys + def validate_input(trans, error_map, param_values, page_param_map): """Validates the min_size/max_size user input, before execution.""" @@ -13,41 +14,41 @@ min_size = str(segments["min_size"]).strip() max_size = str(segments["max_size"]).strip() - #sys.stderr.write("DEBUG min_size=%r, max_size=%r\n" % (min_size, max_size)) + # sys.stderr.write("DEBUG min_size=%r, max_size=%r\n" % (min_size, max_size)) - #Somehow Galaxy seems to turn an empty field into string "None"... - if min_size=="None": + # Somehow Galaxy seems to turn an empty field into string "None"... + if min_size == "None": min_size = "" - if max_size=="None": + if max_size == "None": max_size = "" - if min_size=="" and max_size=="": - #Both missing is good + if min_size == "" and max_size == "": + # Both missing is good pass - elif min_size=="": + elif min_size == "": err["min_size"] = "Minimum size required if maximum size given" - elif max_size=="": + elif max_size == "": err["max_size"] = "Maximum size required if minimum size given" - + if min_size: try: min_size_int = int(min_size) if min_size_int < 0: err["min_size"] = "Minumum size must not be negative (%i)" % min_size_int - min_size = None # Avoid doing comparison below + min_size = None # Avoid doing comparison below except ValueError: err["min_size"] = "Minimum size is not an integer (%s)" % min_size - min_size = None # Avoid doing comparison below + min_size = None # Avoid doing comparison below if max_size: try: max_size_int = int(max_size) - if max_size_int< 0: + if max_size_int < 0: err["max_size"] = "Maximum size must not be negative (%i)" % max_size_int - max_size = None # Avoid doing comparison below + max_size = None # Avoid doing comparison below except ValueError: err["max_size"] = "Maximum size is not an integer (%s)" % max_size - max_size = None # Avoid doing comparison below + max_size = None # Avoid doing comparison below if min_size and max_size and min_size_int > max_size_int: msg = "Minimum size must be less than maximum size (%i vs %i)" % (min_size_int, max_size_int) @@ -55,10 +56,10 @@ err["max_size"] = msg if err: - err_list.append({"segments":err}) + err_list.append({"segments": err}) else: err_list.append(dict()) if any(err_list): - #Return an error map only if any readgroup gave errors + # Return an error map only if any readgroup gave errors error_map["read_group"] = err_list