1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/a6141e135830/
changeset: r5114:a6141e135830
user: natefoo
date: 2011-02-23 19:54:06
summary: Update bwa_wrapper to use the test data repository. bwa_color_wrapper will need to be done once the test data repository is updated to contain the data it uses.
affected #: 1 file (258 bytes)
--- a/tools/sr_mapping/bwa_wrapper.xml Wed Feb 23 11:56:16 2011 -0500
+++ b/tools/sr_mapping/bwa_wrapper.xml Wed Feb 23 13:54:06 2011 -0500
@@ -139,8 +139,7 @@
python -c "import sys; lines=file(sys.argv[1],'rb').readlines(); lines.sort(); file(sys.argv[2],'wb').write(''.join(lines))" bwa_wrapper_out1.u.sam bwa_wrapper_out1.sam
--><param name="refGenomeSource" value="indexed" />
- <!-- this is the backwards-compatible "unique value" for this index, not an actual path -->
- <param name="indices" value="/galaxy/data/phiX/bwa_index/phiX.fa" />
+ <param name="indices" value="phiX" /><param name="sPaired" value="single" /><param name="input1" value="bwa_wrapper_in1.fastqsanger" ftype="fastqsanger" /><param name="source_select" value="pre_set" />
@@ -195,8 +194,7 @@
python -c "import sys; lines=file(sys.argv[1],'rb').readlines(); lines.sort(); file(sys.argv[2],'wb').write(''.join(lines))" bwa_wrapper_out3.u.sam bwa_wrapper_out3.sam
--><param name="refGenomeSource" value="indexed" />
- <!-- this is the backwards-compatible "unique value" for this index, not an actual path -->
- <param name="indices" value="/galaxy/data/phiX/bwa_index/phiX.fa" />
+ <param name="indices" value="phiX" /><param name="sPaired" value="paired" /><param name="input1" value="bwa_wrapper_in2.fastqsanger" ftype="fastqsanger" /><param name="input2" value="bwa_wrapper_in3.fastqsanger" ftype="fastqsanger" />
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/4426265b87be/
changeset: r5112:4426265b87be
user: jgoecks
date: 2011-02-23 16:40:30
summary: Enhance GFF reader to handle headers and comments.
affected #: 1 file (308 bytes)
--- a/lib/galaxy/datatypes/util/gff_util.py Tue Feb 22 18:49:57 2011 -0500
+++ b/lib/galaxy/datatypes/util/gff_util.py Wed Feb 23 10:40:30 2011 -0500
@@ -3,6 +3,7 @@
"""
import pkg_resources; pkg_resources.require( "bx-python" )
from bx.intervals.io import *
+from bx.tabular.io import Header, Comment
class GFFInterval( GenomicInterval ):
"""
@@ -148,6 +149,12 @@
self.seed_interval = GenomicIntervalReader.next( self )
except ParseError, e:
handle_parse_error( e )
+
+ # If header or comment, clear seed interval and return it.
+ if isinstance( self.seed_interval, ( Header, Comment ) ):
+ return_val = self.seed_interval
+ self.seed_interval = None
+ return return_val
# Initialize feature name from seed.
feature_group = self.seed_interval.attributes.get( 'group', None ) # For GFF
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/6506489984e1/
changeset: r5110:6506489984e1
user: jgoecks
date: 2011-02-23 00:41:15
summary: Set output dataset type for 'Extract GFF features' tool to be input dataset type.
affected #: 1 file (26 bytes)
--- a/tools/filters/gff/extract_GFF_Features.xml Tue Feb 22 18:10:52 2011 -0500
+++ b/tools/filters/gff/extract_GFF_Features.xml Tue Feb 22 18:41:15 2011 -0500
@@ -59,7 +59,7 @@
</conditional></inputs><outputs>
- <data format="gff" name="out_file1" />
+ <data format="input" name="out_file1" metadata_source="input1"/></outputs><tests><test>
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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