opensource/galaxy
3
0
Fork 0
mirror of https://github.com/galaxyproject/galaxy.git synced 2026-09-24 16:30:27 +08:00
Code Issues Packages Projects Releases Wiki Activity

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.

Browse Source
This commit is contained in:
Jeremy Goecks
2012-08-17 17:49:41 -04:00
parent dbc2c27a82
commit 860bb2673c
3 changed files with 18 additions and 3 deletions
Download Patch File Download Diff File Expand all files Collapse all files
lib/galaxy/datatypes/converters/bedgraph_to_bigwig_converter.xml
+14
View File
@@ -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>
lib/galaxy/datatypes/converters/wig_to_bigwig_converter.xml
+1 -1
View File
@@ -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"/>
lib/galaxy/datatypes/interval.py
+3 -2
View File
@@ -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"""