diff tools/samtools/sam_merge_code.py @ 0:9071e359b9a3

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/samtools/sam_merge_code.py	Fri Mar 09 19:37:19 2012 -0500
@@ -0,0 +1,34 @@
+from galaxy.tools.parameters import DataToolParameter
+
+def validate_input( trans, error_map, param_values, page_param_map ):
+    dbkeys = set()
+    data_param_names = set()
+    data_params = 0
+    for name, param in page_param_map.iteritems():
+        if isinstance( param, DataToolParameter ):
+            # for each dataset parameter
+            if param_values.get(name, None) != None:
+                dbkeys.add( param_values[name].dbkey )
+                data_params += 1
+                # check meta data
+#                try:
+#                    param = param_values[name]
+#                    startCol = int( param.metadata.startCol )
+#                    endCol = int( param.metadata.endCol )
+#                    chromCol = int( param.metadata.chromCol )
+#                    if param.metadata.strandCol is not None:
+#                        strandCol = int ( param.metadata.strandCol )
+#                    else:
+#                        strandCol = 0
+#                except:
+#                    error_msg = "The attributes of this dataset are not properly set. " + \
+#                    "Click the pencil icon in the history item to set the chrom, start, end and strand columns."
+#                    error_map[name] = error_msg
+            data_param_names.add( name )
+    if len( dbkeys ) > 1:
+        for name in data_param_names:
+            error_map[name] = "All datasets must belong to same genomic build, " \
+                "this dataset is linked to build '%s'" % param_values[name].dbkey
+    if data_params != len(data_param_names):
+        for name in data_param_names:
+            error_map[name] = "A dataset of the appropriate type is required"