1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/changeset/e4672c5b57b2/ changeset: e4672c5b57b2 user: carlfeberhard date: 2012-09-04 19:28:25 summary: Fix sniff.py blastxml doc/unittest, removal of func.test_get_data.py 0140 (megablast xml upload), increased lines_diff in cuffmerge_wrapper.xml to handle inconsistent oId assignment (cuffmerge.test_tool_000000) affected #: 3 files

diff -r 7182b04a32a7cb70411cbf07a5b10bf6bd59206e -r e4672c5b57b2234edc9f5e2c9d5abd6b7148fdca lib/galaxy/datatypes/sniff.py --- a/lib/galaxy/datatypes/sniff.py +++ b/lib/galaxy/datatypes/sniff.py @@ -231,7 +231,7 @@

>>> fname = get_test_fname('megablast_xml_parser_test1.blastxml') >>> guess_ext(fname) - 'blastxml' + 'xml' >>> fname = get_test_fname('interval.interval') >>> guess_ext(fname) 'interval'

diff -r 7182b04a32a7cb70411cbf07a5b10bf6bd59206e -r e4672c5b57b2234edc9f5e2c9d5abd6b7148fdca test/functional/test_get_data.py --- a/test/functional/test_get_data.py +++ b/test/functional/test_get_data.py @@ -360,16 +360,6 @@ self.check_history_for_string( '2,500 sequences format: <span class="csfasta">csfasta</span>, <td>&gt;2_14_26_F3,-1282216.0</td>' ) self.check_metadata_for_string( 'value="shrimp_cs_test1.csfasta" value="?" Change data type value="csfasta" selected="yes"' ) self.delete_history( id=self.security.encode_id( history.id ) ) - def test_0140_upload_file( self ): - """Test uploading megablast_xml_parser_test1.gz, NOT setting the file format""" - # Logged in as admin_user - self.check_history_for_string( 'Your history is empty' ) - history = get_latest_history_for_user( admin_user ) - self.upload_file( 'megablast_xml_parser_test1.gz' ) - hda = get_latest_hda() - assert hda is not None, "Problem retrieving hda from database" - self.check_history_for_string( 'NCBI Blast XML data format: <span class="blastxml">blastxml</span>' ) - self.delete_history( id=self.security.encode_id( history.id ) ) def test_0145_upload_file( self ): """Test uploading 1.axt, NOT setting the file format""" # Logged in as admin_user

diff -r 7182b04a32a7cb70411cbf07a5b10bf6bd59206e -r e4672c5b57b2234edc9f5e2c9d5abd6b7148fdca tools/ngs_rna/cuffmerge_wrapper.xml --- a/tools/ngs_rna/cuffmerge_wrapper.xml +++ b/tools/ngs_rna/cuffmerge_wrapper.xml @@ -87,7 +87,8 @@ <param name="use_ref_annotation" value="Yes"/><param name="reference_annotation" value="cuffcompare_in3.gtf" ftype="gtf"/><param name="use_seq_data" value="No"/> - <output name="merged_transcripts" file="cuffmerge_out1.gtf"/> + <!-- oId assignment differ/are non-deterministic --> + <output name="merged_transcripts" file="cuffmerge_out1.gtf" lines_diff="8"/></test></tests>

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

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