From 860bb2673c6a0324a6d0dc4738fe632d2e1a458b Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Fri, 17 Aug 2012 17:49:41 -0400
Subject: [PATCH] Converters enhancements: (a) ignore track lines in wiggle to
 bigwig converter and add clip option and (b) enable visualization of bedgraph
 datasets via a bedgraph to bigwig converter.

---
 .../converters/bedgraph_to_bigwig_converter.xml    | 14 ++++++++++++++
 .../converters/wig_to_bigwig_converter.xml         |  2 +-
 lib/galaxy/datatypes/interval.py                   |  5 +++--
 3 files changed, 18 insertions(+), 3 deletions(-)
 create mode 100644 lib/galaxy/datatypes/converters/bedgraph_to_bigwig_converter.xml

diff --git a/lib/galaxy/datatypes/converters/bedgraph_to_bigwig_converter.xml b/lib/galaxy/datatypes/converters/bedgraph_to_bigwig_converter.xml
new file mode 100644
index 00000000000..77d2c2a42e6
--- /dev/null
+++ b/lib/galaxy/datatypes/converters/bedgraph_to_bigwig_converter.xml
@@ -0,0 +1,14 @@
+<tool id="CONVERTER_bedgraph_to_bigwig" name="Convert BedGraph to BigWig" hidden="true">
+  <!-- Used internally to generate track indexes -->
+  <command>grep -v "^track" $input | wigToBigWig -clip stdin $chromInfo $output</command>
+  <inputs>
+    <page>
+      <param format="bedgraph" name="input" type="data" label="Choose wiggle"/>
+    </page>
+   </inputs>
+   <outputs>
+      <data format="bigwig" name="output"/>
+   </outputs>
+  <help>
+  </help>
+</tool>
\ No newline at end of file
diff --git a/lib/galaxy/datatypes/converters/wig_to_bigwig_converter.xml b/lib/galaxy/datatypes/converters/wig_to_bigwig_converter.xml
index e85c3a7b138..d90702efe78 100644
--- a/lib/galaxy/datatypes/converters/wig_to_bigwig_converter.xml
+++ b/lib/galaxy/datatypes/converters/wig_to_bigwig_converter.xml
@@ -1,6 +1,6 @@
 <tool id="CONVERTER_wig_to_bigwig" name="Convert Wiggle to BigWig" hidden="true">
   <!-- Used internally to generate track indexes -->
-  <command>wigToBigWig $input $chromInfo $output</command>
+  <command>grep -v "^track" $input | wigToBigWig -clip stdin $chromInfo $output</command>
   <inputs>
     <page>
       <param format="wig" name="input" type="data" label="Choose wiggle"/>
diff --git a/lib/galaxy/datatypes/interval.py b/lib/galaxy/datatypes/interval.py
index 69c77a553db..23c81cf48d2 100644
--- a/lib/galaxy/datatypes/interval.py
+++ b/lib/galaxy/datatypes/interval.py
@@ -338,7 +338,7 @@ class BedGraph( Interval ):
     file_ext = "bedgraph"
 
     def get_track_type( self ):
-        return "LineTrack", {"data": "array_tree"}
+        return "LineTrack", { "data": "bigwig", "index": "bigwig" }
         
     def as_ucsc_display_file( self, dataset, **kwd ):
         """
@@ -1141,8 +1141,9 @@ class Wiggle( Tabular, _RemoteCallMixin ):
         resolution = min( resolution, 100000 )
         resolution = max( resolution, 1 )
         return resolution
+        
     def get_track_type( self ):
-        return "LineTrack", {"data": "bigwig", "index": "bigwig"}
+        return "LineTrack", { "data": "bigwig", "index": "bigwig" }
 
 class CustomTrack ( Tabular ):
     """UCSC CustomTrack"""