1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/2790c2083719/
changeset: 2790c2083719
user: natefoo
date: 2011-09-02 16:16:07
summary: Bugfix for tool tests without attributes.
affected #: 1 file (15 bytes)
--- a/test/base/twilltestcase.py Fri Sep 02 08:57:55 2011 -0400
+++ b/test/base/twilltestcase.py Fri Sep 02 10:16:07 2011 -0400
@@ -655,10 +655,9 @@
self.home()
self.visit_page( "display?hid=" + hid )
data = self.last_page()
- assert_list = attributes["assert_list"]
- if assert_list is not None:
+ if attributes is not None and attributes.get( "assert_list", None ) is not None:
try:
- verify_assertions(data, assert_list)
+ verify_assertions(data, attributes["assert_list"])
except AssertionError, err:
errmsg = 'History item %s different than expected\n' % (hid)
errmsg += str( err )
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/ff7c8c0bef60/
changeset: ff7c8c0bef60
user: jgoecks
date: 2011-09-02 14:57:55
summary: Fix bug in setting Cufflinks' reference annotation.
affected #: 1 file (6 bytes)
--- a/tools/ngs_rna/cufflinks_wrapper.xml Thu Sep 01 14:01:00 2011 -0400
+++ b/tools/ngs_rna/cufflinks_wrapper.xml Fri Sep 02 08:57:55 2011 -0400
@@ -14,11 +14,11 @@
-j $pre_mrna_fraction
## Include reference annotation?
- #if $reference_annotation.use_ref == "use reference annotation":
+ #if $reference_annotation.use_ref == "Use reference annotation":
-G $reference_annotation.reference_annotation_file
#end if
- #if $reference_annotation.use_ref == "use reference annotation guide":
- -g $reference_annotation_guide.reference_annotation_guide_file
+ #if $reference_annotation.use_ref == "Use reference annotation guide":
+ -g $reference_annotation.reference_annotation_guide_file
#end if
## Set paired-end parameters?
@@ -63,7 +63,7 @@
<when value="Use reference annotation"><param format="gff3,gtf" name="reference_annotation_file" type="data" label="Reference Aonnotation" help="Make sure your annotation file is in GTF format and that Galaxy knows that your file is GTF--not GFF."/></when>
- <when value="Use reference annotation guide">
+ <when value="Use reference annotation guide"><param format="gff3,gtf" name="reference_annotation_guide_file" type="data" label="Reference Aonnotation" help="Make sure your annotation file is in GTF format and that Galaxy knows that your file is GTF--not GFF."/></when></conditional>
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/eae23586cb6a/
changeset: eae23586cb6a
user: jgoecks
date: 2011-09-01 18:35:20
summary: Improve GTF sniffing by doing proper parsing of attributes.
affected #: 1 file (687 bytes)
--- a/lib/galaxy/datatypes/interval.py Thu Sep 01 12:13:45 2011 -0400
+++ b/lib/galaxy/datatypes/interval.py Thu Sep 01 12:35:20 2011 -0400
@@ -939,23 +939,11 @@
return False
# Check attributes for gene_id, transcript_id
- attributes = hdr[8].split(";")
+ attributes = parse_gff_attributes( hdr[8] )
if len( attributes ) >= 2:
- try:
- # Imprecise: should check for a single space per the spec.
- # strip() needed b/c Ensembl GTF files include an (illegal)
- # space before attributes string.
- attr_name, attr_value = attributes[0].strip().split(" ")
- if attr_name != 'gene_id':
- return False
- except:
+ if 'gene_id' not in attributes:
return False
- try:
- # Imprecise: should check for a single space per the spec.
- attr_name, attr_value = attributes[1][1:].split(" ")
- if attr_name != 'transcript_id':
- return False
- except:
+ if 'transcript_id' not in attributes:
return False
else:
return False
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/63e15e4cc0aa/
changeset: 63e15e4cc0aa
user: jgoecks
date: 2011-09-01 18:13:45
summary: Fix Trackster dragging/moving bugs.
affected #: 1 file (79 bytes)
--- a/static/scripts/trackster.js Thu Sep 01 11:08:34 2011 -0400
+++ b/static/scripts/trackster.js Thu Sep 01 12:13:45 2011 -0400
@@ -145,11 +145,12 @@
/**
* Make `element` moveable within parent and sibling elements by dragging `handle` (a selector).
*/
-var moveable = function( element, handle, container_selector ) {
+var moveable = function( element, handle_class, container_selector ) {
// HACK: set default value for container selector.
container_selector = ".group";
var css_border_props = {};
- element.bind( "drag", { handle: handle, relative: true }, function ( e, d ) {
+ // Need to provide selector for handle, not class.
+ element.bind( "drag", { handle: "." + handle_class, relative: true }, function ( e, d ) {
var
parent = $(this).parent(),
children = parent.children(),
@@ -880,7 +881,7 @@
this.tracks.push(track);
if (track.init) { track.init(); }
track.container_div.attr('id', 'track_' + track.track_id);
- moveable(track.container_div, track.drag_handle);
+ moveable(track.container_div, track.drag_handle_class);
this.track_id_counter += 1;
this.num_tracks += 1;
this.has_changes = true;
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/20215fcf6da7/
changeset: 20215fcf6da7
user: dan
date: 2011-09-01 17:08:34
summary: Update existing GATK tools. Add 4 new GATK tools: VariantAnnotator, VariantFiltration, VariantRecalibrator, ApplyRecalibration, ValidateVariants, VariantEval and CombineVariants. All GATK tool wrappers are still considered BETA and (workflow/rerun/etc) backwards-incompatible changes should be expected.
affected #: 28 files (9.1 KB)
Diff too large to display.
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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