# HG changeset patch
# User cschu
# Date 1435160560 14400
# Node ID 9215ffe7d4d5e48a6095b76250edca18e928b58d
# Parent  28990f586370c2b80dfb784db6e3eeba87341810
Fixed issue with INDEL annotations. Changed output to iframe.

diff -r 28990f586370 -r 9215ffe7d4d5 candisnp.py
--- a/candisnp.py	Fri May 22 13:38:13 2015 -0400
+++ b/candisnp.py	Wed Jun 24 11:42:40 2015 -0400
@@ -119,7 +119,8 @@
         self.alternate_base = args[4]
      
         # info = dict([field.split('=') for field in args[7].strip().split(';')])
-        info = dict(field.split('=') for field in args[7].strip().split(';'))
+        # info = dict(field.split('=') for field in args[7].strip().split(';'))
+        info = dict(field.split('=') for field in args[7].strip().split(';') if len(field.split('=')) == 2)
         # self.log.write('***'+str(info.get('EFF', '@@@')+'***\n'))
         
         self.allele_frequency = float(info.get('AF', '0.0'))
@@ -199,9 +200,12 @@
         sys.stderr.write(str(e.reason) + '\n')
    
     if candiURL:
-        body = urllib2.urlopen(candiURL)
-        fo.write(body.read())
-        #fo.write('<iframe src="%s"></iframe>\n' % candiURL)
+        # body = urllib2.urlopen(candiURL)
+        # fo.write(body.read())
+        #fo.write('<iframe name="galaxy_main" id="galaxy_main" frameborder="0" style="position: absolute; width: 100%; height: 100%;" src="%s"></iframe>' % candiURL)
+        #fo.write('<iframe name="galaxy_main" id="galaxy_main" frameborder="0" style="position: absolute; width: 100%; height: 100%;" src="%s"></iframe>' % candiURL)     
+        fo.write('<iframe src="%s" frameborder="0" style="position: absolute; width: 100%%; height: 100%%;"></iframe>\n' % candiURL)
+        # fo.write('<iframe src="%s"></iframe>\n' % candiURL)
     else:
         fo.write('I am sorry. CandiSNP does not pick up. Maybe (<a href="%s" target="_blank">try it manually?</a>)\n' % CANDISNP_SERVER)
      
diff -r 28990f586370 -r 9215ffe7d4d5 candisnp.xml
--- a/candisnp.xml	Fri May 22 13:38:13 2015 -0400
+++ b/candisnp.xml	Wed Jun 24 11:42:40 2015 -0400
@@ -35,6 +35,6 @@
 	</outputs>
 
 	<help>
-	This tool is a testtool to issue POST requests from Galaxy.
+	A tool to pull in visualisation output from CandiSNP (candisnp.tsl.ac.uk).
 	</help>
 </tool>
diff -r 28990f586370 -r 9215ffe7d4d5 tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Wed Jun 24 11:42:40 2015 -0400
@@ -0,0 +1,6 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="snpeff" version="4.0">
+        <repository changeset_revision="92b80578fa22" name="snpeff" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
+</tool_dependency>