|
1
|
1 #Called from the Galaxy Tool XML file
|
|
|
2 #import sys
|
|
|
3
|
|
|
4 def validate_input(trans, error_map, param_values, page_param_map):
|
|
|
5 """Validates the min_size/max_size user input, before execution."""
|
|
|
6 err_list = []
|
|
|
7 for read_group in param_values["read_group"]:
|
|
|
8 err = dict()
|
|
|
9 segments = read_group["segments"]
|
|
|
10 if str(segments["type"]) != "paired":
|
|
|
11 err_list.append(dict())
|
|
|
12 continue
|
|
|
13
|
|
|
14 min_size = str(segments["min_size"]).strip()
|
|
|
15 max_size = str(segments["max_size"]).strip()
|
|
|
16 #sys.stderr.write("DEBUG min_size=%r, max_size=%r\n" % (min_size, max_size))
|
|
|
17
|
|
|
18 #Somehow Galaxy seems to turn an empty field into string "None"...
|
|
|
19 if min_size=="None":
|
|
|
20 min_size = ""
|
|
|
21 if max_size=="None":
|
|
|
22 max_size = ""
|
|
|
23
|
|
|
24 if min_size=="" and max_size=="":
|
|
|
25 #Both missing is good
|
|
|
26 pass
|
|
|
27 elif min_size=="":
|
|
|
28 err["min_size"] = "Minimum size required if maximum size given"
|
|
|
29 elif max_size=="":
|
|
|
30 err["max_size"] = "Maximum size required if minimum size given"
|
|
|
31
|
|
|
32 if min_size:
|
|
|
33 try:
|
|
|
34 min_size_int = int(min_size)
|
|
|
35 if min_size_int < 0:
|
|
|
36 err["min_size"] = "Minumum size must not be negative (%i)" % min_size_int
|
|
|
37 min_size = None # Avoid doing comparison below
|
|
|
38 except ValueError:
|
|
|
39 err["min_size"] = "Minimum size is not an integer (%s)" % min_size
|
|
|
40 min_size = None # Avoid doing comparison below
|
|
|
41
|
|
|
42 if max_size:
|
|
|
43 try:
|
|
|
44 max_size_int = int(max_size)
|
|
|
45 if max_size_int< 0:
|
|
|
46 err["max_size"] = "Maximum size must not be negative (%i)" % max_size_int
|
|
|
47 max_size = None # Avoid doing comparison below
|
|
|
48 except ValueError:
|
|
|
49 err["max_size"] = "Maximum size is not an integer (%s)" % max_size
|
|
|
50 max_size = None # Avoid doing comparison below
|
|
|
51
|
|
|
52 if min_size and max_size and min_size_int > max_size_int:
|
|
|
53 msg = "Minimum size must be less than maximum size (%i vs %i)" % (min_size_int, max_size_int)
|
|
|
54 err["min_size"] = msg
|
|
|
55 err["max_size"] = msg
|
|
|
56
|
|
|
57 if err:
|
|
|
58 err_list.append({"segments":err})
|
|
|
59 else:
|
|
|
60 err_list.append(dict())
|
|
|
61
|
|
|
62 if any(err_list):
|
|
|
63 #Return an error map only if any readgroup gave errors
|
|
|
64 error_map["read_group"] = err_list
|
