--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/mira4_0/mira4_validator.py	Wed Sep 02 07:46:29 2015 -0400
@@ -0,0 +1,64 @@
+#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."""
+    err_list = []
+    for read_group in param_values["read_group"]:
+        err = dict()
+        segments = read_group["segments"]
+        if str(segments["type"]) != "paired":
+            err_list.append(dict())
+            continue
+
+        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))
+
+        #Somehow Galaxy seems to turn an empty field into string "None"...
+        if min_size=="None":
+            min_size = ""
+        if max_size=="None":
+            max_size = ""
+
+        if min_size=="" and max_size=="":
+            #Both missing is good
+            pass
+        elif min_size=="":
+            err["min_size"] = "Minimum size required if maximum size given"
+        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
+            except ValueError:
+                err["min_size"] = "Minimum size is not an integer (%s)" % min_size
+                min_size = None # Avoid doing comparison below
+
+        if max_size:
+            try:
+                max_size_int = int(max_size)
+                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
+            except ValueError:
+                err["max_size"] = "Maximum size is not an integer (%s)" % max_size
+                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)
+            err["min_size"] = msg
+            err["max_size"] = msg
+
+        if 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
+        error_map["read_group"] = err_list