--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/visualization/LAJ_code.py	Fri Mar 09 19:37:19 2012 -0500
@@ -0,0 +1,40 @@
+#post processing, add sequence and additional annoation info if available
+from urllib import urlencode
+from galaxy.datatypes.images import create_applet_tag_peek
+
+def exec_after_process(app, inp_data, out_data, param_dict, tool, stdout, stderr):
+    primary_data = out_data.items()[0][1]
+    
+    #default params for LAJ type
+    params = {
+    "alignfile1": "display?id=%s" % primary_data.id,
+    "buttonlabel": "Launch LAJ",
+    "title": "LAJ in Galaxy",
+    "posturl": "history_add_to?%s" % urlencode( { 'history_id': primary_data.history_id, 'ext': 'lav', 'name': 'LAJ Output', 'info': 'Added by LAJ', 'dbkey': primary_data.dbkey } )
+    }
+    for name,data in inp_data.items():
+        if name == "maf_input":
+            params["alignfile1"] = "display?id=%s" % data.id
+        elif name == "seq_file1" and data.state == data.states.OK and data.has_data():
+            params["file1seq1"] = "display?id=%s" % data.id
+        elif name == "seq_file2" and data.state == data.states.OK and data.has_data():
+            params["file1seq2"] = "display?id=%s" % data.id
+        elif name == "exonfile" and data.state == data.states.OK and data.has_data():
+            params["exonfile"] = "display?id=%s" % data.id
+        elif name == "repeatfile" and data.state == data.states.OK and data.has_data():
+            params["repeatfile"] = "display?id=%s" % data.id
+        elif name == "annotationfile" and data.state == data.states.OK and data.has_data():
+            params["annotationfile"] = "display?id=%s" % data.id
+        elif name == "underlayfile" and data.state == data.states.OK and data.has_data():
+            params["underlayfile"] = "display?id=%s" % data.id
+        elif name == "highlightfile" and data.state == data.states.OK and data.has_data():
+            params["highlightfile"] = "display?id=%s" % data.id
+    
+    if "file1seq1" not in params and "file1seq2" not in params:
+        params["noseq"] = "true"
+    
+    class_name = "edu.psu.cse.bio.laj.LajApplet.class"
+    archive = "/static/laj/laj.jar"
+    primary_data.peek = create_applet_tag_peek( class_name, archive, params )
+    app.model.context.add( primary_data )
+    app.model.context.flush()