1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/d62d3c23a613/ changeset: d62d3c23a613 user: jgoecks date: 2012-08-17 23:49:41 summary: 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. affected #: 3 files diff -r e9587d2d241eeca42dae6280388152a0f062e71a -r d62d3c23a61377f3d7928b56e7af346d502aac73 lib/galaxy/datatypes/converters/bedgraph_to_bigwig_converter.xml --- /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 -r e9587d2d241eeca42dae6280388152a0f062e71a -r d62d3c23a61377f3d7928b56e7af346d502aac73 lib/galaxy/datatypes/converters/wig_to_bigwig_converter.xml --- 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 -r e9587d2d241eeca42dae6280388152a0f062e71a -r d62d3c23a61377f3d7928b56e7af346d502aac73 lib/galaxy/datatypes/interval.py --- a/lib/galaxy/datatypes/interval.py +++ b/lib/galaxy/datatypes/interval.py @@ -338,7 +338,7 @@ 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 @@ 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""" Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.