commit/galaxy-central: jgoecks: Set Cufflinks global model when upper quartile normalization is used.
by Bitbucket
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/21b645303c02/
changeset: 21b645303c02
user: jgoecks
date: 2011-12-22 19:54:33
summary: Set Cufflinks global model when upper quartile normalization is used.
affected #: 1 file
diff -r d6d62cb3cf7ea7b7a11a5ca4caf4a85c50a31a93 -r 21b645303c0221690a0114b021cd5e706b0c917a tools/ngs_rna/cufflinks_wrapper.py
--- a/tools/ngs_rna/cufflinks_wrapper.py
+++ b/tools/ngs_rna/cufflinks_wrapper.py
@@ -137,11 +137,11 @@
returncode = proc.wait()
tmp_stderr.close()
- # Read standard error to get total map mass.
+ # Read standard error to get total map/upper quartile mass.
total_map_mass = -1
tmp_stderr = open( tmp_name, 'r' )
for line in tmp_stderr:
- if line.lower().find( "total map mass") >= 0:
+ if line.lower().find( "total map mass" ) >= 0 or line.lower().find( "upper quartile" ) >= 0:
total_map_mass = float( line.split(":")[1].strip() )
break
tmp_stderr.close()
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: jgoecks: Trackster: when running tools, replace track with group.
by Bitbucket
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/d6d62cb3cf7e/
changeset: d6d62cb3cf7e
user: jgoecks
date: 2011-12-22 19:11:34
summary: Trackster: when running tools, replace track with group.
affected #: 1 file
diff -r 83756dd3d868aee6d319f0d1904a1dcdda12b5b9 -r d6d62cb3cf7ea7b7a11a5ca4caf4a85c50a31a93 static/scripts/trackster.js
--- a/static/scripts/trackster.js
+++ b/static/scripts/trackster.js
@@ -946,6 +946,20 @@
return false;
},
/**
+ * Replace one drawable with another.
+ */
+ replace_drawable: function(old_drawable, new_drawable, update_html) {
+ var index = this.drawables.indexOf(old_drawable);
+ if (index !== -1) {
+ this.drawables[index] = new_drawable;
+ if (update_html) {
+ old_drawable.container_div.replaceWith(new_drawable.container_div);
+ }
+ return true;
+ }
+ return false;
+ },
+ /**
* Remove drawable from this collection.
*/
remove_drawable: function(drawable) {
@@ -1002,7 +1016,11 @@
}
].concat(Drawable.prototype.action_icons_def),
build_container_div: function() {
- return $("<div/>").addClass("group").attr("id", "group_" + this.id).appendTo(this.container.content_div);
+ var container_div = $("<div/>").addClass("group").attr("id", "group_" + this.id);
+ if (this.container) {
+ this.container.content_div.append(container_div);
+ }
+ return container_div;
},
build_header_div: function() {
var header_div = $("<div/>").addClass("track-header");
@@ -1787,8 +1805,9 @@
// If track not in a group, create a group for it and add new track to group. If track
// already in group, add track to group.
if (current_track.container === view) {
- var group = new DrawableGroup(this.name, this.track.view, this.track.container);
- current_track.container.add_drawable(group);
+ // Create new group.
+ var group = new DrawableGroup(this.name, this.track.view);
+ current_track.container.replace_drawable(current_track, group, true);
// TODO: this is ugly way to move track from one container to another -- make this easier via
// a Drawable or DrawableCollection function.
current_track.container.remove_drawable(current_track);
@@ -1797,6 +1816,7 @@
container = group;
}
else {
+ // Use current group.
container = current_track.container;
}
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: jgoecks: Trackster: add support for including a global model when running tools in Trackster. This is done by using a new HiddenDataToolParameter and implementing 'set parameter' actions in a tool's trackster configuration. Cufflinks now uses a global model to produce correct output when run in Trackster.
by Bitbucket
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/356e8b9510a9/
changeset: 356e8b9510a9
user: jgoecks
date: 2011-12-21 23:04:23
summary: Trackster: add support for including a global model when running tools in Trackster. This is done by using a new HiddenDataToolParameter and implementing 'set parameter' actions in a tool's trackster configuration. Cufflinks now uses a global model to produce correct output when run in Trackster.
affected #: 6 files
diff -r 38fcdb8f0e63a8430bb80bac4500ad4faa7a4115 -r 356e8b9510a965d09226c450746dfa2ba267a42c lib/galaxy/tools/__init__.py
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -29,6 +29,7 @@
from cgi import FieldStorage
from galaxy.util.hash_util import *
from galaxy.util import listify
+from galaxy.visualization.tracks.visual_analytics import TracksterConfig
log = logging.getLogger( __name__ )
@@ -567,7 +568,11 @@
# Determine if this tool can be used in workflows
self.is_workflow_compatible = self.check_workflow_compatible()
# Trackster configuration.
- self.trackster_conf = ( root.find( "trackster_conf" ) is not None )
+ trackster_conf = root.find( "trackster_conf" )
+ if trackster_conf:
+ self.trackster_conf = TracksterConfig.parse( trackster_conf )
+ else:
+ self.trackster_conf = None
def parse_inputs( self, root ):
"""
diff -r 38fcdb8f0e63a8430bb80bac4500ad4faa7a4115 -r 356e8b9510a965d09226c450746dfa2ba267a42c lib/galaxy/tools/parameters/basic.py
--- a/lib/galaxy/tools/parameters/basic.py
+++ b/lib/galaxy/tools/parameters/basic.py
@@ -1549,6 +1549,22 @@
if call_attribute:
ref = ref()
return ref
+
+class HiddenDataToolParameter( HiddenToolParameter, DataToolParameter ):
+ """
+ Hidden parameter that behaves as a DataToolParameter. As with all hidden
+ parameters, this is a HACK.
+ """
+ def __init__( self, tool, elem ):
+ DataToolParameter.__init__( self, tool, elem )
+ self.value = "None"
+
+ def get_initial_value( self, trans, context ):
+ return None
+
+ def get_html_field( self, trans=None, value=None, other_values={} ):
+ return form_builder.HiddenField( self.name, self.value )
+
class LibraryDatasetToolParameter( ToolParameter ):
"""
@@ -1644,6 +1660,7 @@
select = SelectToolParameter,
data_column = ColumnListParameter,
hidden = HiddenToolParameter,
+ hidden_data = HiddenDataToolParameter,
baseurl = BaseURLToolParameter,
file = FileToolParameter,
ftpfile = FTPFileToolParameter,
diff -r 38fcdb8f0e63a8430bb80bac4500ad4faa7a4115 -r 356e8b9510a965d09226c450746dfa2ba267a42c lib/galaxy/visualization/tracks/visual_analytics.py
--- a/lib/galaxy/visualization/tracks/visual_analytics.py
+++ b/lib/galaxy/visualization/tracks/visual_analytics.py
@@ -3,6 +3,31 @@
from galaxy.tools.parameters.basic import IntegerToolParameter, FloatToolParameter, SelectToolParameter
from galaxy.tools.parameters.dynamic_options import DynamicOptions
+class TracksterConfig:
+ """ Trackster configuration encapsulation. """
+
+ def __init__( self, actions ):
+ self.actions = actions
+
+ @staticmethod
+ def parse( root ):
+ actions = []
+ for action_elt in root.findall( "action" ):
+ actions.append( SetParamAction.parse( action_elt ) )
+ return TracksterConfig( actions )
+
+class SetParamAction:
+ """ Set parameter action. """
+
+ def __init__( self, name, output_name ):
+ self.name = name
+ self.output_name = output_name
+
+ @staticmethod
+ def parse( elt ):
+ """ Parse action from element. """
+ return SetParamAction( elt.get( "name" ), elt.get( "output_name" ) )
+
def get_dataset_job( hda ):
# Get dataset's job.
job = None
diff -r 38fcdb8f0e63a8430bb80bac4500ad4faa7a4115 -r 356e8b9510a965d09226c450746dfa2ba267a42c lib/galaxy/web/controllers/tracks.py
--- a/lib/galaxy/web/controllers/tracks.py
+++ b/lib/galaxy/web/controllers/tracks.py
@@ -824,7 +824,7 @@
return to_json_string( msg )
#
- # Set tool parameters--except dataset parameters--using combination of
+ # Set tool parameters--except non-hidden dataset parameters--using combination of
# job's previous parameters and incoming parameters. Incoming parameters
# have priority.
#
@@ -872,15 +872,10 @@
else:
target_history = trans.get_history( create=True )
hda_permissions = trans.app.security_agent.history_get_default_permissions( target_history )
-
- #
- # Set input datasets for tool. If running on region, extract and use subset
- # when possible.
- #
def set_param_value( param_dict, param_name, param_value ):
"""
- Set new parameter value in a parameter dictionary.
+ Set new parameter value in a tool's parameter dictionary.
"""
# Recursive function to set param value.
@@ -913,8 +908,30 @@
group_index = int( group[ index + 1: ] )
return set_value( param_dict, group_name, group_index, param_name, param_value )
-
+
+ # Set parameters based tool's trackster config.
+ params_set = {}
+ for action in tool.trackster_conf.actions:
+ success = False
+ for joda in original_job.output_datasets:
+ if joda.name == action.output_name:
+ set_param_value( tool_params, action.name, joda.dataset )
+ params_set[ action.name ] = True
+ success = True
+ break
+
+ if not success:
+ return messages.ERROR
+
+ #
+ # Set input datasets for tool. If running on region, extract and use subset
+ # when possible.
+ #
for jida in original_job.input_datasets:
+ # If param set previously by config actions, do nothing.
+ if jida.name in params_set:
+ continue
+
input_dataset = jida.dataset
if input_dataset is None: #optional dataset and dataset wasn't selected
tool_params[ jida.name ] = None
diff -r 38fcdb8f0e63a8430bb80bac4500ad4faa7a4115 -r 356e8b9510a965d09226c450746dfa2ba267a42c tools/ngs_rna/cufflinks_wrapper.py
--- a/tools/ngs_rna/cufflinks_wrapper.py
+++ b/tools/ngs_rna/cufflinks_wrapper.py
@@ -1,6 +1,8 @@
#!/usr/bin/env python
import optparse, os, shutil, subprocess, sys, tempfile
+from galaxy import eggs
+from galaxy.datatypes.util.gff_util import parse_gff_attributes, gff_attributes_to_str
def stop_err( msg ):
sys.stderr.write( "%s\n" % msg )
@@ -51,6 +53,9 @@
parser.add_option( '', '--index_dir', dest='index_dir', help='GALAXY_DATA_INDEX_DIR' )
parser.add_option( '', '--ref_file', dest='ref_file', help='The reference dataset from the history' )
+ # Global model.
+ parser.add_option( '', '--global_model', dest='global_model_file', help='Global model used for computing on local data' )
+
(options, args) = parser.parse_args()
# output version # of tool
@@ -122,7 +127,9 @@
# Add input files.
cmd += " " + options.input
+ #
# Run command.
+ #
try:
tmp_name = tempfile.NamedTemporaryFile( dir="." ).name
tmp_stderr = open( tmp_name, 'wb' )
@@ -130,7 +137,60 @@
returncode = proc.wait()
tmp_stderr.close()
- # Get stderr, allowing for case where it's very large.
+ # Read standard error to get total map mass.
+ total_map_mass = -1
+ tmp_stderr = open( tmp_name, 'r' )
+ for line in tmp_stderr:
+ if line.lower().find( "total map mass") >= 0:
+ total_map_mass = float( line.split(":")[1].strip() )
+ break
+ tmp_stderr.close()
+
+ #
+ # If there's a global model provided, use model's total map mass
+ # to adjust FPKM + confidence intervals.
+ #
+ if options.global_model_file:
+ # Global model is simply total map mass from original run.
+ global_model_file = open( options.global_model_file, 'r' )
+ global_model_total_map_mass = float( global_model_file.readline() )
+ global_model_file.close()
+
+ # Ratio of global model's total map mass to original run's map mass is
+ # factor used to adjust FPKM.
+ fpkm_map_mass_ratio = total_map_mass / global_model_total_map_mass
+
+ # Update FPKM values in transcripts.gtf file.
+ transcripts_file = open( "transcripts.gtf", 'r' )
+ tmp_transcripts = tempfile.NamedTemporaryFile( dir="." ).name
+ new_transcripts_file = open( tmp_transcripts, 'w' )
+ for line in transcripts_file:
+ fields = line.split( '\t' )
+ attrs = parse_gff_attributes( fields[8] )
+ attrs[ "FPKM" ] = str( float( attrs[ "FPKM" ] ) * fpkm_map_mass_ratio )
+ attrs[ "conf_lo" ] = str( float( attrs[ "conf_lo" ] ) * fpkm_map_mass_ratio )
+ attrs[ "conf_hi" ] = str( float( attrs[ "conf_hi" ] ) * fpkm_map_mass_ratio )
+ fields[8] = gff_attributes_to_str( attrs, "GTF" )
+ new_transcripts_file.write( "%s\n" % '\t'.join( fields ) )
+ transcripts_file.close()
+ new_transcripts_file.close()
+ shutil.copyfile( tmp_transcripts, "transcripts.gtf" )
+
+ # TODO: update expression files as well.
+
+ # Set outputs. Transcript and gene expression handled by wrapper directives.
+ shutil.copyfile( "transcripts.gtf" , options.assembled_isoforms_output_file )
+ if total_map_mass > -1:
+ f = open( "global_model.txt", 'w' )
+ f.write( "%f\n" % total_map_mass )
+ f.close()
+
+ # Error checking.
+ if returncode != 0:
+ raise Exception, stderr
+ except Exception, e:
+ raise e
+ # Read stderr so that it can be reported:
tmp_stderr = open( tmp_name, 'rb' )
stderr = ''
buffsize = 1048576
@@ -142,14 +202,7 @@
except OverflowError:
pass
tmp_stderr.close()
-
- # Copy outputs.
- shutil.copyfile( "transcripts.gtf" , options.assembled_isoforms_output_file )
- # Error checking.
- if returncode != 0:
- raise Exception, stderr
- except Exception, e:
stop_err( 'Error running cufflinks. ' + str( e ) )
if __name__=="__main__": __main__()
diff -r 38fcdb8f0e63a8430bb80bac4500ad4faa7a4115 -r 356e8b9510a965d09226c450746dfa2ba267a42c tools/ngs_rna/cufflinks_wrapper.xml
--- a/tools/ngs_rna/cufflinks_wrapper.xml
+++ b/tools/ngs_rna/cufflinks_wrapper.xml
@@ -43,6 +43,11 @@
--dbkey=${input.metadata.dbkey}
--index_dir=${GALAXY_DATA_INDEX_DIR}
#end if
+
+ ## Include global model if available.
+ #if $global_model:
+ --global_model=$global_model
+ #end if
</command><inputs><param format="sam,bam" name="input" type="data" label="SAM or BAM file of aligned RNA-Seq reads" help=""/>
@@ -97,15 +102,20 @@
<param name="inner_distance_std_dev" type="integer" value="20" label="Standard Deviation for Inner Distance between Mate Pairs"/></when></conditional>
+ <param name="global_model" type="hidden_data" label="Global model (for use in Trackster)" optional="True"/></inputs><outputs><data format="tabular" name="genes_expression" label="${tool.name} on ${on_string}: gene expression" from_work_dir="genes.fpkm_tracking"/><data format="tabular" name="transcripts_expression" label="${tool.name} on ${on_string}: transcript expression" from_work_dir="isoforms.fpkm_tracking"/><data format="gtf" name="assembled_isoforms" label="${tool.name} on ${on_string}: assembled transcripts"/>
+ <data format="txt" name="total_map_mass" label="${tool.name} on ${on_string}: total map mass" hidden="true" from_work_dir="global_model.txt"/></outputs>
- <trackster_conf/>
+ <trackster_conf>
+ <action type="set_param" name="global_model" output_name="total_map_mass"/>
+ </trackster_conf>
+
<tests><!--
Simple test that uses test data included with cufflinks.
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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10 years, 9 months
commit/galaxy-central: clements: Updated "Example" images shown at the bottom of many
by Bitbucket
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/38fcdb8f0e63/
changeset: 38fcdb8f0e63
user: clements
date: 2011-12-19 11:44:31
summary: Updated "Example" images shown at the bottom of many
"Operate on Genomic Invervals" tool pages. Old onew were looking dated.
New ones look, well, newer, and cover more cases.
affected #: 20 files
diff -r bb5e05256c2997892f5cac6b1998bbe90896372d -r 38fcdb8f0e63a8430bb80bac4500ad4faa7a4115 static/operation_icons/gops_baseCoverage.gif
Binary file static/operation_icons/gops_baseCoverage.gif has changed
diff -r bb5e05256c2997892f5cac6b1998bbe90896372d -r 38fcdb8f0e63a8430bb80bac4500ad4faa7a4115 static/operation_icons/gops_clusterFind.gif
Binary file static/operation_icons/gops_clusterFind.gif has changed
diff -r bb5e05256c2997892f5cac6b1998bbe90896372d -r 38fcdb8f0e63a8430bb80bac4500ad4faa7a4115 static/operation_icons/gops_clusterMerge.gif
Binary file static/operation_icons/gops_clusterMerge.gif has changed
diff -r bb5e05256c2997892f5cac6b1998bbe90896372d -r 38fcdb8f0e63a8430bb80bac4500ad4faa7a4115 static/operation_icons/gops_complement.gif
Binary file static/operation_icons/gops_complement.gif has changed
diff -r bb5e05256c2997892f5cac6b1998bbe90896372d -r 38fcdb8f0e63a8430bb80bac4500ad4faa7a4115 static/operation_icons/gops_concatenate.gif
Binary file static/operation_icons/gops_concatenate.gif has changed
diff -r bb5e05256c2997892f5cac6b1998bbe90896372d -r 38fcdb8f0e63a8430bb80bac4500ad4faa7a4115 static/operation_icons/gops_intersectOverlappingIntervals.gif
Binary file static/operation_icons/gops_intersectOverlappingIntervals.gif has changed
diff -r bb5e05256c2997892f5cac6b1998bbe90896372d -r 38fcdb8f0e63a8430bb80bac4500ad4faa7a4115 static/operation_icons/gops_intersectOverlappingPieces.gif
Binary file static/operation_icons/gops_intersectOverlappingPieces.gif has changed
diff -r bb5e05256c2997892f5cac6b1998bbe90896372d -r 38fcdb8f0e63a8430bb80bac4500ad4faa7a4115 static/operation_icons/gops_joinFullOuter.gif
Binary file static/operation_icons/gops_joinFullOuter.gif has changed
diff -r bb5e05256c2997892f5cac6b1998bbe90896372d -r 38fcdb8f0e63a8430bb80bac4500ad4faa7a4115 static/operation_icons/gops_joinInner.gif
Binary file static/operation_icons/gops_joinInner.gif has changed
diff -r bb5e05256c2997892f5cac6b1998bbe90896372d -r 38fcdb8f0e63a8430bb80bac4500ad4faa7a4115 static/operation_icons/gops_joinLeftOuter.gif
Binary file static/operation_icons/gops_joinLeftOuter.gif has changed
diff -r bb5e05256c2997892f5cac6b1998bbe90896372d -r 38fcdb8f0e63a8430bb80bac4500ad4faa7a4115 static/operation_icons/gops_joinRecordsList.gif
Binary file static/operation_icons/gops_joinRecordsList.gif has changed
diff -r bb5e05256c2997892f5cac6b1998bbe90896372d -r 38fcdb8f0e63a8430bb80bac4500ad4faa7a4115 static/operation_icons/gops_joinRightOuter.gif
Binary file static/operation_icons/gops_joinRightOuter.gif has changed
diff -r bb5e05256c2997892f5cac6b1998bbe90896372d -r 38fcdb8f0e63a8430bb80bac4500ad4faa7a4115 static/operation_icons/gops_merge.gif
Binary file static/operation_icons/gops_merge.gif has changed
diff -r bb5e05256c2997892f5cac6b1998bbe90896372d -r 38fcdb8f0e63a8430bb80bac4500ad4faa7a4115 static/operation_icons/gops_subtractOverlappingIntervals.gif
Binary file static/operation_icons/gops_subtractOverlappingIntervals.gif has changed
diff -r bb5e05256c2997892f5cac6b1998bbe90896372d -r 38fcdb8f0e63a8430bb80bac4500ad4faa7a4115 static/operation_icons/gops_subtractOverlappingPieces.gif
Binary file static/operation_icons/gops_subtractOverlappingPieces.gif has changed
diff -r bb5e05256c2997892f5cac6b1998bbe90896372d -r 38fcdb8f0e63a8430bb80bac4500ad4faa7a4115 tools/new_operations/basecoverage.xml
--- a/tools/new_operations/basecoverage.xml
+++ b/tools/new_operations/basecoverage.xml
@@ -36,6 +36,10 @@
.. _Screencasts: http://wiki.g2.bx.psu.edu/Learn/Interval%20Operations
+**Example**
+
+.. image:: ./static/operation_icons/gops_baseCoverage.gif
+
</help>
-</tool>
\ No newline at end of file
+</tool>
diff -r bb5e05256c2997892f5cac6b1998bbe90896372d -r 38fcdb8f0e63a8430bb80bac4500ad4faa7a4115 tools/new_operations/cluster.xml
--- a/tools/new_operations/cluster.xml
+++ b/tools/new_operations/cluster.xml
@@ -82,9 +82,15 @@
-----
-**Example**
+**Examples**
-.. image:: ./static/operation_icons/gops_cluster.gif
+Find Clusters:
+
+.. image:: ./static/operation_icons/gops_clusterFind.gif
+
+Merge Clusters:
+
+.. image:: ./static/operation_icons/gops_clusterMerge.gif
</help>
-</tool>
\ No newline at end of file
+</tool>
diff -r bb5e05256c2997892f5cac6b1998bbe90896372d -r 38fcdb8f0e63a8430bb80bac4500ad4faa7a4115 tools/new_operations/intersect.xml
--- a/tools/new_operations/intersect.xml
+++ b/tools/new_operations/intersect.xml
@@ -129,9 +129,15 @@
-----
-**Example**
+**Examples**
-.. image:: ./static/operation_icons/gops_intersect.gif
+Overlapping Intervals:
+
+.. image:: ./static/operation_icons/gops_intersectOverlappingIntervals.gif
+
+Overlapping Pieces of Intervals:
+
+.. image:: ./static/operation_icons/gops_intersectOverlappingPieces.gif
</help>
-</tool>
\ No newline at end of file
+</tool>
diff -r bb5e05256c2997892f5cac6b1998bbe90896372d -r 38fcdb8f0e63a8430bb80bac4500ad4faa7a4115 tools/new_operations/join.xml
--- a/tools/new_operations/join.xml
+++ b/tools/new_operations/join.xml
@@ -92,48 +92,26 @@
-----
-**Example**
+**Examples**
-If **First dataset** is::
+.. image:: ./static/operation_icons/gops_joinRecordsList.gif
- chr1 10 100 Query1.1
- chr1 500 1000 Query1.2
- chr1 1100 1250 Query1.3
+Only records that are joined (inner join):
-and **Second dataset** is::
+.. image:: ./static/operation_icons/gops_joinInner.gif
- chr1 20 80 Query2.1
- chr1 2000 2204 Query2.2
- chr1 2500 3000 Query2.3
+All records of first dataset:
+.. image:: ./static/operation_icons/gops_joinLeftOuter.gif
-The four return options will generate:
+All records of second dataset:
+.. image:: ./static/operation_icons/gops_joinRightOuter.gif
-- **Return only records that are joined**::
+All records of both datasets:
- chr1 10 100 Query1.1 chr1 20 80 Query2.1
+.. image:: ./static/operation_icons/gops_joinFullOuter.gif
-- **Return all records of first dataset**::
-
- chr1 10 100 Query1.1 chr1 20 80 Query2.1
- chr1 500 1000 Query1.2 . . . .
- chr1 1100 1250 Query1.3 . . . .
-
-- **Return all records of second dataset**::
-
- chr1 10 100 Query1.1 chr1 20 80 Query2.1
- . . . . chr1 2000 2204 Query2.2
- . . . . chr1 2500 3000 Query2.3
-
-- **Return all records of both datasets**::
-
- chr1 10 100 Query1.1 chr1 20 80 Query2.1
- chr1 500 1000 Query1.2 . . . .
- chr1 1100 1250 Query1.3 . . . .
- . . . . chr1 2000 2204 Query2.2
- . . . . chr1 2500 3000 Query2.3
-
</help>
-</tool>
\ No newline at end of file
+</tool>
diff -r bb5e05256c2997892f5cac6b1998bbe90896372d -r 38fcdb8f0e63a8430bb80bac4500ad4faa7a4115 tools/new_operations/subtract.xml
--- a/tools/new_operations/subtract.xml
+++ b/tools/new_operations/subtract.xml
@@ -112,7 +112,13 @@
**Example**
-.. image:: ./static/operation_icons/gops_subtract.gif
+Intervals with no overlap:
+
+.. image:: ./static/operation_icons/gops_subtractOverlappingIntervals.gif
+
+Non-overlapping pieces of intervals:
+
+.. image:: ./static/operation_icons/gops_subtractOverlappingPieces.gif
</help>
-</tool>
\ No newline at end of file
+</tool>
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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10 years, 9 months
commit/galaxy-central: dan: Add UCSC VCF external display application.
by Bitbucket
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/bb5e05256c29/
changeset: bb5e05256c29
user: dan
date: 2011-12-20 21:40:07
summary: Add UCSC VCF external display application.
affected #: 2 files
diff -r f22a8a7bd077a118bcfa71430f345ff46873757f -r bb5e05256c2997892f5cac6b1998bbe90896372d datatypes_conf.xml.sample
--- a/datatypes_conf.xml.sample
+++ b/datatypes_conf.xml.sample
@@ -162,6 +162,7 @@
<converter file="vcf_to_vcf_bgzip_converter.xml" target_datatype="vcf_bgzip"/><converter file="vcf_to_tabix_converter.xml" target_datatype="tabix" depends_on="bgzip"/><converter file="vcf_to_summary_tree_converter.xml" target_datatype="summary_tree"/>
+ <display file="ucsc/vcf.xml" /><display file="igv/vcf.xml" /></datatype><datatype extension="bcf" type="galaxy.datatypes.binary:Binary" subclass="True"/>
diff -r f22a8a7bd077a118bcfa71430f345ff46873757f -r bb5e05256c2997892f5cac6b1998bbe90896372d display_applications/ucsc/vcf.xml
--- /dev/null
+++ b/display_applications/ucsc/vcf.xml
@@ -0,0 +1,17 @@
+<display id="ucsc_vcf" version="1.0.0" name="display at UCSC">
+ <!-- Load links from file: one line to one link -->
+ <dynamic_links from_file="tool-data/shared/ucsc/ucsc_build_sites.txt" skip_startswith="#" id="0" name="0">
+ <!-- Define parameters by column from file, allow splitting on builds -->
+ <dynamic_param name="site_id" value="0"/>
+ <dynamic_param name="ucsc_link" value="1"/>
+ <dynamic_param name="builds" value="2" split="True" separator="," />
+ <!-- Filter out some of the links based upon matching site_id to a Galaxy application configuration parameter and by dataset dbkey -->
+ <filter>${site_id in $APP.config.ucsc_display_sites}</filter>
+ <filter>${dataset.dbkey in $builds}</filter>
+ <!-- We define url and params as normal, but values defined in dynamic_param are available by specified name -->
+ <url>${ucsc_link}db=${qp($bgzip_file.dbkey)}&hgt.customText=${qp($track.url)}</url>
+ <param type="data" name="bgzip_file" url="galaxy_${DATASET_HASH}.vcf.gz" format="vcf_bgzip" />
+ <param type="data" name="tabix_file" dataset="bgzip_file" url="galaxy_${DATASET_HASH}.vcf.gz.tbi" format="tabix" />
+ <param type="template" name="track" viewable="True">track type="vcfTabix" name="${bgzip_file.name.replace( '\\', '\\\\' ).replace( '"', '\\"' )}" bigDataUrl="${bgzip_file.url}" db="${bgzip_file.dbkey}"</param>
+ </dynamic_links>
+</display>
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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10 years, 9 months
commit/galaxy-central: greg: Don't allow repository names to be changed if the repository has been cloned at least 1 time.
by Bitbucket
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/f22a8a7bd077/
changeset: f22a8a7bd077
user: greg
date: 2011-12-20 20:31:13
summary: Don't allow repository names to be changed if the repository has been cloned at least 1 time.
affected #: 1 file
diff -r 8458fa9dd5590e0890effaf04c50ba19013a280c -r f22a8a7bd077a118bcfa71430f345ff46873757f templates/webapps/community/repository/manage_repository.mako
--- a/templates/webapps/community/repository/manage_repository.mako
+++ b/templates/webapps/community/repository/manage_repository.mako
@@ -139,7 +139,14 @@
%endif
<div class="form-row"><label>Name:</label>
- <input name="repo_name" type="textfield" value="${repo_name}" size="40"/>
+ %if repository.times_downloaded > 0:
+ ${repo_name}
+ %else:
+ <input name="repo_name" type="textfield" value="${repo_name}" size="40"/>
+ %endif
+ <div class="toolParamHelp" style="clear: both;">
+ Repository names cannot be changed if the repository has been cloned.
+ </div><div style="clear: both"></div></div><div class="form-row">
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: greg: Make the tool_shed_install.xml.sample file ready for installing the correct versions of the emboss_5 and emboss_datatypes repositories from the main Galaxy tool shed.
by Bitbucket
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/8458fa9dd559/
changeset: 8458fa9dd559
user: greg
date: 2011-12-20 20:15:39
summary: Make the tool_shed_install.xml.sample file ready for installing the correct versions of the emboss_5 and emboss_datatypes repositories from the main Galaxy tool shed.
affected #: 1 file
diff -r 0497ba5576facae84f7b9a44092d0f67a61788ef -r 8458fa9dd5590e0890effaf04c50ba19013a280c tool_shed_install.xml.sample
--- a/tool_shed_install.xml.sample
+++ b/tool_shed_install.xml.sample
@@ -1,114 +1,116 @@
<?xml version="1.0"?><toolshed name="toolshed.g2.bx.psu.edu">
+ <!-- The following repository includes no tools, so nothing will be loaded into the tool panel. -->
+ <repository name="emboss_datatypes" description="Datatypes for Emboss tools" changeset_revision="a89163f31369" /><section name="EMBOSS" id="EMBOSSLite">
- <repository name="emboss_5" description="Galaxy wrappers for EMBOSS version 5 tools" changeset_revision="PlaceHereWhenKnown">
- <tool file="emboss_5/emboss_antigenic.xml" id="EMBOSS: antigenic1" version="5.0.0" />
- <tool file="emboss_5/emboss_backtranseq.xml" id="EMBOSS: backtranseq2" version="5.0.0" />
- <tool file="emboss_5/emboss_banana.xml" id="EMBOSS: banana3" version="5.0.0" />
- <tool file="emboss_5/emboss_biosed.xml" id="EMBOSS: biosed4" version="5.0.0" />
- <tool file="emboss_5/emboss_btwisted.xml" id="EMBOSS: btwisted5" version="5.0.0" />
- <tool file="emboss_5/emboss_cai_custom.xml" id="EMBOSS: cai_custom6" version="5.0.0" />
- <tool file="emboss_5/emboss_cai.xml" id="EMBOSS: cai6" version="5.0.0" />
- <tool file="emboss_5/emboss_chaos.xml" id="EMBOSS: chaos7" version="5.0.0" />
- <tool file="emboss_5/emboss_charge.xml" id="EMBOSS: charge8" version="5.0.0" />
- <tool file="emboss_5/emboss_checktrans.xml" id="EMBOSS: checktrans9" version="5.0.0" />
- <tool file="emboss_5/emboss_chips.xml" id="EMBOSS: chips10" version="5.0.0" />
- <tool file="emboss_5/emboss_cirdna.xml" id="EMBOSS: cirdna11" version="5.0.0" />
- <tool file="emboss_5/emboss_codcmp.xml" id="EMBOSS: codcmp12" version="5.0.0" />
- <tool file="emboss_5/emboss_coderet.xml" id="EMBOSS: coderet13" version="5.0.0" />
- <tool file="emboss_5/emboss_compseq.xml" id="EMBOSS: compseq14" version="5.0.0" />
- <tool file="emboss_5/emboss_cpgplot.xml" id="EMBOSS: cpgplot15" version="5.0.0" />
- <tool file="emboss_5/emboss_cpgreport.xml" id="EMBOSS: cpgreport16" version="5.0.0" />
- <tool file="emboss_5/emboss_cusp.xml" id="EMBOSS: cusp17" version="5.0.0" />
- <tool file="emboss_5/emboss_cutseq.xml" id="EMBOSS: cutseq18" version="5.0.0" />
- <tool file="emboss_5/emboss_dan.xml" id="EMBOSS: dan19" version="5.0.0" />
- <tool file="emboss_5/emboss_degapseq.xml" id="EMBOSS: degapseq20" version="5.0.0" />
- <tool file="emboss_5/emboss_descseq.xml" id="EMBOSS: descseq21" version="5.0.0" />
- <tool file="emboss_5/emboss_diffseq.xml" id="EMBOSS: diffseq22" version="5.0.0" />
- <tool file="emboss_5/emboss_digest.xml" id="EMBOSS: digest23" version="5.0.0" />
- <tool file="emboss_5/emboss_dotmatcher.xml" id="EMBOSS: dotmatcher24" version="5.0.0" />
- <tool file="emboss_5/emboss_dotpath.xml" id="EMBOSS: dotpath25" version="5.0.0" />
- <tool file="emboss_5/emboss_dottup.xml" id="EMBOSS: dottup26" version="5.0.0" />
- <tool file="emboss_5/emboss_dreg.xml" id="EMBOSS: dreg27" version="5.0.0" />
- <tool file="emboss_5/emboss_einverted.xml" id="EMBOSS: einverted28" version="5.0.0" />
- <tool file="emboss_5/emboss_epestfind.xml" id="EMBOSS: epestfind29" version="5.0.0" />
- <tool file="emboss_5/emboss_equicktandem.xml" id="EMBOSS: equicktandem31" version="5.0.0" />
- <tool file="emboss_5/emboss_est2genome.xml" id="EMBOSS: est2genome32" version="5.0.0" />
- <tool file="emboss_5/emboss_etandem.xml" id="EMBOSS: etandem33" version="5.0.0" />
- <tool file="emboss_5/emboss_extractfeat.xml" id="EMBOSS: extractfeat34" version="5.0.0" />
- <tool file="emboss_5/emboss_extractseq.xml" id="EMBOSS: extractseq35" version="5.0.0" />
- <tool file="emboss_5/emboss_freak.xml" id="EMBOSS: freak36" version="5.0.0" />
- <tool file="emboss_5/emboss_fuzznuc.xml" id="EMBOSS: fuzznuc37" version="5.0.0" />
- <tool file="emboss_5/emboss_fuzzpro.xml" id="EMBOSS: fuzzpro38" version="5.0.0" />
- <tool file="emboss_5/emboss_fuzztran.xml" id="EMBOSS: fuzztran39" version="5.0.0" />
- <tool file="emboss_5/emboss_garnier.xml" id="EMBOSS: garnier40" version="5.0.0" />
- <tool file="emboss_5/emboss_geecee.xml" id="EMBOSS: geecee41" version="5.0.0" />
- <tool file="emboss_5/emboss_getorf.xml" id="EMBOSS: getorf42" version="5.0.0" />
- <tool file="emboss_5/emboss_helixturnhelix.xml" id="EMBOSS: helixturnhelix43" version="5.0.0" />
- <tool file="emboss_5/emboss_hmoment.xml" id="EMBOSS: hmoment44" version="5.0.0" />
- <tool file="emboss_5/emboss_iep.xml" id="EMBOSS: iep45" version="5.0.0" />
- <tool file="emboss_5/emboss_infoseq.xml" id="EMBOSS: infoseq46" version="5.0.0" />
- <tool file="emboss_5/emboss_isochore.xml" id="EMBOSS: isochore47" version="5.0.0" />
- <tool file="emboss_5/emboss_lindna.xml" id="EMBOSS: lindna48" version="5.0.0" />
- <tool file="emboss_5/emboss_marscan.xml" id="EMBOSS: marscan49" version="5.0.0" />
- <tool file="emboss_5/emboss_maskfeat.xml" id="EMBOSS: maskfeat50" version="5.0.0" />
- <tool file="emboss_5/emboss_maskseq.xml" id="EMBOSS: maskseq51" version="5.0.0" />
- <tool file="emboss_5/emboss_matcher.xml" id="EMBOSS: matcher52" version="5.0.0" />
- <tool file="emboss_5/emboss_megamerger.xml" id="EMBOSS: megamerger53" version="5.0.0" />
- <tool file="emboss_5/emboss_merger.xml" id="EMBOSS: merger54" version="5.0.0" />
- <tool file="emboss_5/emboss_msbar.xml" id="EMBOSS: msbar55" version="5.0.0" />
- <tool file="emboss_5/emboss_needle.xml" id="EMBOSS: needle56" version="5.0.0" />
- <tool file="emboss_5/emboss_newcpgreport.xml" id="EMBOSS: newcpgreport57" version="5.0.0" />
- <tool file="emboss_5/emboss_newcpgseek.xml" id="EMBOSS: newcpgseek58" version="5.0.0" />
- <tool file="emboss_5/emboss_newseq.xml" id="EMBOSS: newseq59" version="5.0.0" />
- <tool file="emboss_5/emboss_noreturn.xml" id="EMBOSS: noreturn60" version="5.0.0" />
- <tool file="emboss_5/emboss_notseq.xml" id="EMBOSS: notseq61" version="5.0.0" />
- <tool file="emboss_5/emboss_nthseq.xml" id="EMBOSS: nthseq62" version="5.0.0" />
- <tool file="emboss_5/emboss_octanol.xml" id="EMBOSS: octanol63" version="5.0.0" />
- <tool file="emboss_5/emboss_oddcomp.xml" id="EMBOSS: oddcomp64" version="5.0.0" />
- <tool file="emboss_5/emboss_palindrome.xml" id="EMBOSS: palindrome65" version="5.0.0" />
- <tool file="emboss_5/emboss_pasteseq.xml" id="EMBOSS: pasteseq66" version="5.0.0" />
- <tool file="emboss_5/emboss_patmatdb.xml" id="EMBOSS: patmatdb67" version="5.0.0" />
- <tool file="emboss_5/emboss_pepcoil.xml" id="EMBOSS: pepcoil68" version="5.0.0" />
- <tool file="emboss_5/emboss_pepinfo.xml" id="EMBOSS: pepinfo69" version="5.0.0" />
- <tool file="emboss_5/emboss_pepnet.xml" id="EMBOSS: pepnet70" version="5.0.0" />
- <tool file="emboss_5/emboss_pepstats.xml" id="EMBOSS: pepstats71" version="5.0.0" />
- <tool file="emboss_5/emboss_pepwheel.xml" id="EMBOSS: pepwheel72" version="5.0.0" />
- <tool file="emboss_5/emboss_pepwindow.xml" id="EMBOSS: pepwindow73" version="5.0.0" />
- <tool file="emboss_5/emboss_pepwindowall.xml" id="EMBOSS: pepwindowall74" version="5.0.0" />
- <tool file="emboss_5/emboss_plotcon.xml" id="EMBOSS: plotcon75" version="5.0.0" />
- <tool file="emboss_5/emboss_plotorf.xml" id="EMBOSS: plotorf76" version="5.0.0" />
- <tool file="emboss_5/emboss_polydot.xml" id="EMBOSS: polydot77" version="5.0.0" />
- <tool file="emboss_5/emboss_preg.xml" id="EMBOSS: preg78" version="5.0.0" />
- <tool file="emboss_5/emboss_prettyplot.xml" id="EMBOSS: prettyplot79" version="5.0.0" />
- <tool file="emboss_5/emboss_prettyseq.xml" id="EMBOSS: prettyseq80" version="5.0.0" />
- <tool file="emboss_5/emboss_primersearch.xml" id="EMBOSS: primersearch81" version="5.0.0" />
- <tool file="emboss_5/emboss_revseq.xml" id="EMBOSS: revseq82" version="5.0.0" />
- <tool file="emboss_5/emboss_seqmatchall.xml" id="EMBOSS: seqmatchall83" version="5.0.0" />
- <tool file="emboss_5/emboss_seqret.xml" id="EMBOSS: seqret84" version="5.0.0" />
- <tool file="emboss_5/emboss_showfeat.xml" id="EMBOSS: showfeat85" version="5.0.0" />
- <tool file="emboss_5/emboss_shuffleseq.xml" id="EMBOSS: shuffleseq87" version="5.0.0" />
- <tool file="emboss_5/emboss_sigcleave.xml" id="EMBOSS: sigcleave88" version="5.0.0" />
- <tool file="emboss_5/emboss_sirna.xml" id="EMBOSS: sirna89" version="5.0.0" />
- <tool file="emboss_5/emboss_sixpack.xml" id="EMBOSS: sixpack90" version="5.0.0" />
- <tool file="emboss_5/emboss_skipseq.xml" id="EMBOSS: skipseq91" version="5.0.0" />
- <tool file="emboss_5/emboss_splitter.xml" id="EMBOSS: splitter92" version="5.0.0" />
- <tool file="emboss_5/emboss_supermatcher.xml" id="EMBOSS: supermatcher95" version="5.0.0" />
- <tool file="emboss_5/emboss_syco.xml" id="EMBOSS: syco96" version="5.0.0" />
- <tool file="emboss_5/emboss_tcode.xml" id="EMBOSS: tcode97" version="5.0.0" />
- <tool file="emboss_5/emboss_textsearch.xml" id="EMBOSS: textsearch98" version="5.0.0" />
- <tool file="emboss_5/emboss_tmap.xml" id="EMBOSS: tmap99" version="5.0.0" />
- <tool file="emboss_5/emboss_tranalign.xml" id="EMBOSS: tranalign100" version="5.0.0" />
- <tool file="emboss_5/emboss_transeq.xml" id="EMBOSS: transeq101" version="5.0.0" />
- <tool file="emboss_5/emboss_trimest.xml" id="EMBOSS: trimest102" version="5.0.0" />
- <tool file="emboss_5/emboss_trimseq.xml" id="EMBOSS: trimseq103" version="5.0.0" />
- <tool file="emboss_5/emboss_twofeat.xml" id="EMBOSS: twofeat104" version="5.0.0" />
- <tool file="emboss_5/emboss_union.xml" id="EMBOSS: union105" version="5.0.0" />
- <tool file="emboss_5/emboss_vectorstrip.xml" id="EMBOSS: vectorstrip106" version="5.0.0" />
- <tool file="emboss_5/emboss_water.xml" id="EMBOSS: water107" version="5.0.0" />
- <tool file="emboss_5/emboss_wobble.xml" id="EMBOSS: wobble108" version="5.0.0" />
- <tool file="emboss_5/emboss_wordcount.xml" id="EMBOSS: wordcount109" version="5.0.0" />
- <tool file="emboss_5/emboss_wordmatch.xml" id="EMBOSS: wordmatch110" version="5.0.0" />
+ <repository name="emboss_5" description="Galaxy wrappers for EMBOSS version 5.0.0 tools" changeset_revision="b94ca591877b">
+ <tool id="EMBOSS: antigenic1" version="5.0.0" />
+ <tool id="EMBOSS: backtranseq2" version="5.0.0" />
+ <tool id="EMBOSS: banana3" version="5.0.0" />
+ <tool id="EMBOSS: biosed4" version="5.0.0" />
+ <tool id="EMBOSS: btwisted5" version="5.0.0" />
+ <tool id="EMBOSS: cai_custom6" version="5.0.0" />
+ <tool id="EMBOSS: cai6" version="5.0.0" />
+ <tool id="EMBOSS: chaos7" version="5.0.0" />
+ <tool id="EMBOSS: charge8" version="5.0.0" />
+ <tool id="EMBOSS: checktrans9" version="5.0.0" />
+ <tool id="EMBOSS: chips10" version="5.0.0" />
+ <tool id="EMBOSS: cirdna11" version="5.0.0" />
+ <tool id="EMBOSS: codcmp12" version="5.0.0" />
+ <tool id="EMBOSS: coderet13" version="5.0.0" />
+ <tool id="EMBOSS: compseq14" version="5.0.0" />
+ <tool id="EMBOSS: cpgplot15" version="5.0.0" />
+ <tool id="EMBOSS: cpgreport16" version="5.0.0" />
+ <tool id="EMBOSS: cusp17" version="5.0.0" />
+ <tool id="EMBOSS: cutseq18" version="5.0.0" />
+ <tool id="EMBOSS: dan19" version="5.0.0" />
+ <tool id="EMBOSS: degapseq20" version="5.0.0" />
+ <tool id="EMBOSS: descseq21" version="5.0.0" />
+ <tool id="EMBOSS: diffseq22" version="5.0.0" />
+ <tool id="EMBOSS: digest23" version="5.0.0" />
+ <tool id="EMBOSS: dotmatcher24" version="5.0.0" />
+ <tool id="EMBOSS: dotpath25" version="5.0.0" />
+ <tool id="EMBOSS: dottup26" version="5.0.0" />
+ <tool id="EMBOSS: dreg27" version="5.0.0" />
+ <tool id="EMBOSS: einverted28" version="5.0.0" />
+ <tool id="EMBOSS: epestfind29" version="5.0.0" />
+ <tool id="EMBOSS: equicktandem31" version="5.0.0" />
+ <tool id="EMBOSS: est2genome32" version="5.0.0" />
+ <tool id="EMBOSS: etandem33" version="5.0.0" />
+ <tool id="EMBOSS: extractfeat34" version="5.0.0" />
+ <tool id="EMBOSS: extractseq35" version="5.0.0" />
+ <tool id="EMBOSS: freak36" version="5.0.0" />
+ <tool id="EMBOSS: fuzznuc37" version="5.0.0" />
+ <tool id="EMBOSS: fuzzpro38" version="5.0.0" />
+ <tool id="EMBOSS: fuzztran39" version="5.0.0" />
+ <tool id="EMBOSS: garnier40" version="5.0.0" />
+ <tool id="EMBOSS: geecee41" version="5.0.0" />
+ <tool id="EMBOSS: getorf42" version="5.0.0" />
+ <tool id="EMBOSS: helixturnhelix43" version="5.0.0" />
+ <tool id="EMBOSS: hmoment44" version="5.0.0" />
+ <tool id="EMBOSS: iep45" version="5.0.0" />
+ <tool id="EMBOSS: infoseq46" version="5.0.0" />
+ <tool id="EMBOSS: isochore47" version="5.0.0" />
+ <tool id="EMBOSS: lindna48" version="5.0.0" />
+ <tool id="EMBOSS: marscan49" version="5.0.0" />
+ <tool id="EMBOSS: maskfeat50" version="5.0.0" />
+ <tool id="EMBOSS: maskseq51" version="5.0.0" />
+ <tool id="EMBOSS: matcher52" version="5.0.0" />
+ <tool id="EMBOSS: megamerger53" version="5.0.0" />
+ <tool id="EMBOSS: merger54" version="5.0.0" />
+ <tool id="EMBOSS: msbar55" version="5.0.0" />
+ <tool id="EMBOSS: needle56" version="5.0.0" />
+ <tool id="EMBOSS: newcpgreport57" version="5.0.0" />
+ <tool id="EMBOSS: newcpgseek58" version="5.0.0" />
+ <tool id="EMBOSS: newseq59" version="5.0.0" />
+ <tool id="EMBOSS: noreturn60" version="5.0.0" />
+ <tool id="EMBOSS: notseq61" version="5.0.0" />
+ <tool id="EMBOSS: nthseq62" version="5.0.0" />
+ <tool id="EMBOSS: octanol63" version="5.0.0" />
+ <tool id="EMBOSS: oddcomp64" version="5.0.0" />
+ <tool id="EMBOSS: palindrome65" version="5.0.0" />
+ <tool id="EMBOSS: pasteseq66" version="5.0.0" />
+ <tool id="EMBOSS: patmatdb67" version="5.0.0" />
+ <tool id="EMBOSS: pepcoil68" version="5.0.0" />
+ <tool id="EMBOSS: pepinfo69" version="5.0.0" />
+ <tool id="EMBOSS: pepnet70" version="5.0.0" />
+ <tool id="EMBOSS: pepstats71" version="5.0.0" />
+ <tool id="EMBOSS: pepwheel72" version="5.0.0" />
+ <tool id="EMBOSS: pepwindow73" version="5.0.0" />
+ <tool id="EMBOSS: pepwindowall74" version="5.0.0" />
+ <tool id="EMBOSS: plotcon75" version="5.0.0" />
+ <tool id="EMBOSS: plotorf76" version="5.0.0" />
+ <tool id="EMBOSS: polydot77" version="5.0.0" />
+ <tool id="EMBOSS: preg78" version="5.0.0" />
+ <tool id="EMBOSS: prettyplot79" version="5.0.0" />
+ <tool id="EMBOSS: prettyseq80" version="5.0.0" />
+ <tool id="EMBOSS: primersearch81" version="5.0.0" />
+ <tool id="EMBOSS: revseq82" version="5.0.0" />
+ <tool id="EMBOSS: seqmatchall83" version="5.0.0" />
+ <tool id="EMBOSS: seqret84" version="5.0.0" />
+ <tool id="EMBOSS: showfeat85" version="5.0.0" />
+ <tool id="EMBOSS: shuffleseq87" version="5.0.0" />
+ <tool id="EMBOSS: sigcleave88" version="5.0.0" />
+ <tool id="EMBOSS: sirna89" version="5.0.0" />
+ <tool id="EMBOSS: sixpack90" version="5.0.0" />
+ <tool id="EMBOSS: skipseq91" version="5.0.0" />
+ <tool id="EMBOSS: splitter92" version="5.0.0" />
+ <tool id="EMBOSS: supermatcher95" version="5.0.0" />
+ <tool id="EMBOSS: syco96" version="5.0.0" />
+ <tool id="EMBOSS: tcode97" version="5.0.0" />
+ <tool id="EMBOSS: textsearch98" version="5.0.0" />
+ <tool id="EMBOSS: tmap99" version="5.0.0" />
+ <tool id="EMBOSS: tranalign100" version="5.0.0" />
+ <tool id="EMBOSS: transeq101" version="5.0.0" />
+ <tool id="EMBOSS: trimest102" version="5.0.0" />
+ <tool id="EMBOSS: trimseq103" version="5.0.0" />
+ <tool id="EMBOSS: twofeat104" version="5.0.0" />
+ <tool id="EMBOSS: union105" version="5.0.0" />
+ <tool id="EMBOSS: vectorstrip106" version="5.0.0" />
+ <tool id="EMBOSS: water107" version="5.0.0" />
+ <tool id="EMBOSS: wobble108" version="5.0.0" />
+ <tool id="EMBOSS: wordcount109" version="5.0.0" />
+ <tool id="EMBOSS: wordmatch110" version="5.0.0" /></repository></section></toolshed>
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: greg: Ensure that the integrated datatypes registry configs exist when needed.
by Bitbucket
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/0497ba5576fa/
changeset: 0497ba5576fa
user: greg
date: 2011-12-20 15:38:15
summary: Ensure that the integrated datatypes registry configs exist when needed.
affected #: 5 files
diff -r 166ea1ba55cbfbf768ec833ced5a10d3712dc998 -r 0497ba5576facae84f7b9a44092d0f67a61788ef lib/galaxy/app.py
--- a/lib/galaxy/app.py
+++ b/lib/galaxy/app.py
@@ -126,7 +126,7 @@
try:
# If the datatypes registry was persisted, attempt to
# remove the temporary file in which it was written.
- if self.datatypes_registry.xml_filename is not None:
- os.unlink( self.datatypes_registry.xml_filename )
+ if self.datatypes_registry.integrated_datatypes_configs is not None:
+ os.unlink( self.datatypes_registry.integrated_datatypes_configs )
except:
pass
diff -r 166ea1ba55cbfbf768ec833ced5a10d3712dc998 -r 0497ba5576facae84f7b9a44092d0f67a61788ef lib/galaxy/datatypes/registry.py
--- a/lib/galaxy/datatypes/registry.py
+++ b/lib/galaxy/datatypes/registry.py
@@ -434,6 +434,12 @@
if 'auto' not in rval and 'txt' in rval: #need to manually add 'auto' datatype
rval[ 'auto' ] = rval[ 'txt' ]
return rval
+ @property
+ def integrated_datatypes_configs( self ):
+ if self.xml_filename and os.path.isfile( self.xml_filename ):
+ return self.xml_filename
+ self.to_xml_file()
+ return self.xml_filename
def to_xml_file( self ):
if self.xml_filename is not None:
# If persisted previously, attempt to remove
diff -r 166ea1ba55cbfbf768ec833ced5a10d3712dc998 -r 0497ba5576facae84f7b9a44092d0f67a61788ef lib/galaxy/jobs/__init__.py
--- a/lib/galaxy/jobs/__init__.py
+++ b/lib/galaxy/jobs/__init__.py
@@ -868,7 +868,7 @@
if config_root is None:
config_root = self.app.config.root
if datatypes_config is None:
- datatypes_config = self.app.datatypes_registry.xml_filename
+ datatypes_config = self.app.datatypes_registry.integrated_datatypes_configs
return self.external_output_metadata.setup_external_metadata( [ output_dataset_assoc.dataset for output_dataset_assoc in job.output_datasets ],
self.sa_session,
exec_dir = exec_dir,
diff -r 166ea1ba55cbfbf768ec833ced5a10d3712dc998 -r 0497ba5576facae84f7b9a44092d0f67a61788ef lib/galaxy/tools/__init__.py
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -1674,7 +1674,7 @@
# For the upload tool, we need to know the root directory and the
# datatypes conf path, so we can load the datatypes registry
param_dict['__root_dir__'] = param_dict['GALAXY_ROOT_DIR'] = os.path.abspath( self.app.config.root )
- param_dict['__datatypes_config__'] = param_dict['GALAXY_DATATYPES_CONF_FILE'] = self.app.datatypes_registry.xml_filename
+ param_dict['__datatypes_config__'] = param_dict['GALAXY_DATATYPES_CONF_FILE'] = self.app.datatypes_registry.integrated_datatypes_configs
# Return the dictionary of parameters
return param_dict
diff -r 166ea1ba55cbfbf768ec833ced5a10d3712dc998 -r 0497ba5576facae84f7b9a44092d0f67a61788ef lib/galaxy/tools/actions/metadata.py
--- a/lib/galaxy/tools/actions/metadata.py
+++ b/lib/galaxy/tools/actions/metadata.py
@@ -51,7 +51,7 @@
dataset_files_path = trans.app.model.Dataset.file_path,
output_fnames = None,
config_root = None,
- datatypes_config = trans.app.datatypes_registry.xml_filename,
+ datatypes_config = trans.app.datatypes_registry.integrated_datatypes_configs,
job_metadata = None,
kwds = { 'overwrite' : overwrite } )
incoming[ '__SET_EXTERNAL_METADATA_COMMAND_LINE__' ] = cmd_line
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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10 years, 9 months
commit/galaxy-central: jgoecks: Clean up implementation in 303741fda0ec
by Bitbucket
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/166ea1ba55cb/
changeset: 166ea1ba55cb
user: jgoecks
date: 2011-12-19 21:00:53
summary: Clean up implementation in 303741fda0ec
affected #: 1 file
diff -r 303741fda0ec4ce0fc7b42a0334a6c84f44c7a1f -r 166ea1ba55cbfbf768ec833ced5a10d3712dc998 lib/galaxy/tools/__init__.py
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -678,7 +678,7 @@
output.count = int( data_elem.get("count", 1) )
output.filters = data_elem.findall( 'filter' )
output.from_work_dir = data_elem.get("from_work_dir", None)
- output.hidden = data_elem.get("hidden", None) in [ 'true', 'True' ]
+ output.hidden = util.string_as_bool( data_elem.get("hidden", "") )
output.tool = self
output.actions = ToolOutputActionGroup( output, data_elem.find( 'actions' ) )
self.outputs[ output.name ] = output
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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10 years, 9 months