1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/commits/a87623b5f358/ Changeset: a87623b5f358 User: jgoecks Date: 2013-05-15 22:15:12 Summary: Viz framework: (a) add sam-to-bigwig converter and (b) Trackster bug fixes. Affected #: 2 files

diff -r 00ecd6a50591b108d3af3a2c6fd6f9389217d363 -r a87623b5f358a570718afc07d7a714269220db61 lib/galaxy/datatypes/converters/sam_to_bigwig_converter.xml --- /dev/null +++ b/lib/galaxy/datatypes/converters/sam_to_bigwig_converter.xml @@ -0,0 +1,20 @@ +<tool id="CONVERTER_sam_to_bigwig_0" name="Convert SAM to BigWig" version="1.0.0" hidden="true"> + <command> + samtools view -bh $input | bedtools genomecov -bg -split -ibam stdin -g $chromInfo + + ## Streaming the bedgraph file to wigToBigWig is fast but very memory intensive; hence, this + ## should only be used on systems with large RAM. + ## | wigToBigWig stdin $chromInfo $output + + ## This can be used anywhere. + > temp.bg ; bedGraphToBigWig temp.bg $chromInfo $output + </command> + <inputs> + <param format="bam" name="input" type="data" label="Choose BAM file"/> + </inputs> + <outputs> + <data format="bigwig" name="output"/> + </outputs> + <help> + </help> +</tool>

diff -r 00ecd6a50591b108d3af3a2c6fd6f9389217d363 -r a87623b5f358a570718afc07d7a714269220db61 static/scripts/viz/trackster/tracks.js --- a/static/scripts/viz/trackster/tracks.js +++ b/static/scripts/viz/trackster/tracks.js @@ -3026,7 +3026,7 @@ num_cols: 12, on_finish: function(new_val) { $(".bs-tooltip").remove(); - var new_val = parseFloat(new_val); + var new_val = round(parseFloat(new_val), 3); track.prefs[ pref_name ] = (!isNaN(new_val) ? new_val : null); on_change(); }, @@ -3134,14 +3134,14 @@ track.tile_cache.set_elt(key, tile_drawn); $.when.apply($, get_tile_data()).then( function() { var tile_data = get_tile_data(), - tracks_data = tile_data.slice(0, tile_data.length - 1), - seq_data = tile_data[tile_data.length - 1]; - + tracks_data = tile_data, + seq_data; + // If sequence data is available, subset to get only data in region. - if (seq_data) { - seq_data = view.reference_track.data_manager.subset_entry(seq_data, region); + if (view.reference_track) { + seq_data = view.reference_track.data_manager.subset_entry(tile_data.pop(), region); } - + // Get drawing modes, heights for all tracks. var drawing_modes = [], drawing_heights = []; @@ -3733,8 +3733,8 @@ */ postdraw_actions: function(tiles, width, w_scale, clear_after) { // Add min, max labels. - this._add_yaxis_label('max', round(this.prefs.max_value, 3), 'max_value'); - this._add_yaxis_label('min', round(this.prefs.min_value, 3), 'min_value'); + this._add_yaxis_label('max'); + this._add_yaxis_label('min'); } });

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

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