3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f436b2313968/ Changeset: f436b2313968 User: jgoecks Date: 2013-07-26 01:45:29 Summary: Add --no-effective-length-correction parameter to Cufflinks wrapper Affected #: 2 files diff -r c55f7d1dc3a1e18b8f1b6e20157cc209caa647dd -r f436b23139681ae82b662a002e01b91ad87df21f tools/ngs_rna/cufflinks_wrapper.py --- a/tools/ngs_rna/cufflinks_wrapper.py +++ b/tools/ngs_rna/cufflinks_wrapper.py @@ -28,6 +28,7 @@ # Normalization options. parser.add_option( "-N", "--quartile-normalization", dest="do_normalization", action="store_true" ) + parser.add_option( "--no-effective-length-correction", dest="no_effective_length_correction", action="store_true" ) # Wrapper / Galaxy options. parser.add_option( '-A', '--assembled-isoforms-output', dest='assembled_isoforms_output_file', help='Assembled isoforms output file; formate is GTF.' ) @@ -110,6 +111,8 @@ cmd += ( " -N" ) if options.do_bias_correction: cmd += ( " -b %s" % seq_path ) + if options.no_effective_length_correction: + cmd += ( " --no-effective-length-correction" ) # Debugging. print cmd diff -r c55f7d1dc3a1e18b8f1b6e20157cc209caa647dd -r f436b23139681ae82b662a002e01b91ad87df21f tools/ngs_rna/cufflinks_wrapper.xml --- a/tools/ngs_rna/cufflinks_wrapper.xml +++ b/tools/ngs_rna/cufflinks_wrapper.xml @@ -1,4 +1,4 @@ -<tool id="cufflinks" name="Cufflinks" version="0.0.6"> +<tool id="cufflinks" name="Cufflinks" version="0.0.7"><!-- Wrapper supports Cufflinks versions v1.3.0 and newer --><description>transcript assembly and FPKM (RPKM) estimates for RNA-Seq data</description><requirements> @@ -12,6 +12,7 @@ -I $max_intron_len -F $min_isoform_fraction -j $pre_mrna_fraction + $effective_length_correction ## Include reference annotation? #if $reference_annotation.use_ref == "Use reference annotation": @@ -101,6 +102,11 @@ <option value="Yes">Yes</option></param> + <param name="effective_length_correction" type="select" label="Use effective length correction" help="Cufflinks will not employ its 'effective' length normalization to transcript FPKM."> + <option value="" selected="true">Yes</option> + <option value="--no-effective-length-correction">No</option> + </param> + <param name="global_model" type="hidden_data" label="Global model (for use in Trackster)" optional="True"/></inputs> @@ -128,6 +134,7 @@ <param name="do_normalization" value="No" /><param name="do_bias_correction" value="No"/><param name="multiread_correct" value="No"/> + <param name="effective_length_correction" value="Yes"/><output name="genes_expression" format="tabular" lines_diff="2" file="cufflinks_out3.fpkm_tracking"/><output name="transcripts_expression" format="tabular" lines_diff="2" file="cufflinks_out2.fpkm_tracking"/><output name="assembled_isoforms" file="cufflinks_out1.gtf"/> https://bitbucket.org/galaxy/galaxy-central/commits/32a48938fe77/ Changeset: 32a48938fe77 User: jgoecks Date: 2013-07-29 23:36:39 Summary: Add and document welcome_url config option. Affected #: 1 file diff -r f436b23139681ae82b662a002e01b91ad87df21f -r 32a48938fe771147abb64524f57d2adb65787ac5 universe_wsgi.ini.sample --- a/universe_wsgi.ini.sample +++ b/universe_wsgi.ini.sample @@ -228,6 +228,10 @@ # -- Display sites +# The URL of the page to display in Galaxy's middle pane when loaded. This can be +# an absolute or relative URL. +#welcome_url = /static/welcome.html + # Galaxy can display data at various external browsers. These options specify # which browsers should be available. URLs and builds available at these # browsers are defined in the specifield files. https://bitbucket.org/galaxy/galaxy-central/commits/4d4faedba9b6/ Changeset: 4d4faedba9b6 User: jgoecks Date: 2013-07-29 23:37:14 Summary: Automated merge Affected #: 4 files diff -r 32a48938fe771147abb64524f57d2adb65787ac5 -r 4d4faedba9b6caa555e3825e0f86a34c483e51ff lib/tool_shed/scripts/check_repositories_for_functional_tests.py --- a/lib/tool_shed/scripts/check_repositories_for_functional_tests.py +++ b/lib/tool_shed/scripts/check_repositories_for_functional_tests.py @@ -24,7 +24,7 @@ import galaxy.webapps.tool_shed.config as tool_shed_config import galaxy.webapps.tool_shed.model.mapping import sqlalchemy as sa -from galaxy.model.orm import and_, not_ +from galaxy.model.orm import and_, not_, select from galaxy.util.json import from_json_string, to_json_string from galaxy.web import url_for from galaxy.tools import parameters @@ -200,6 +200,7 @@ } ''' start = time.time() + skip_metadata_ids = [] checked_repository_ids = [] tool_count = 0 has_tests = 0 @@ -208,13 +209,16 @@ valid_revisions = 0 invalid_revisions = 0 records_checked = 0 + # Do not check metadata records that have an entry in the skip_tool_tests table, since they won't be tested anyway. + skip_metadata_ids = select( [ app.model.SkipToolTest.table.c.repository_metadata_id ] ) # Get the list of metadata records to check for functional tests and test data. Limit this to records that have not been flagged do_not_test, # since there's no need to check them again if they won't be tested anyway. Also filter out changeset revisions that are not downloadable, # because it's redundant to test a revision that a user can't install. for metadata_record in app.sa_session.query( app.model.RepositoryMetadata ) \ .filter( and_( app.model.RepositoryMetadata.table.c.downloadable == True, app.model.RepositoryMetadata.table.c.includes_tools == True, - app.model.RepositoryMetadata.table.c.do_not_test == False ) ): + app.model.RepositoryMetadata.table.c.do_not_test == False, + not_( app.model.RepositoryMetadata.table.c.id.in_( skip_metadata_ids ) ) ) ): records_checked += 1 # Initialize the repository_status dict with the test environment, but leave the test_errors empty. repository_status = {} diff -r 32a48938fe771147abb64524f57d2adb65787ac5 -r 4d4faedba9b6caa555e3825e0f86a34c483e51ff lib/tool_shed/util/commit_util.py --- a/lib/tool_shed/util/commit_util.py +++ b/lib/tool_shed/util/commit_util.py @@ -1,4 +1,5 @@ import cStringIO +import gzip import logging import os import pkg_resources diff -r 32a48938fe771147abb64524f57d2adb65787ac5 -r 4d4faedba9b6caa555e3825e0f86a34c483e51ff templates/webapps/tool_shed/repository/common.mako --- a/templates/webapps/tool_shed/repository/common.mako +++ b/templates/webapps/tool_shed/repository/common.mako @@ -445,18 +445,8 @@ parent="${parent}" %endif id="libraryItem-${encoded_id}"> - <style type="text/css"> - #failed_test_table{ table-layout:fixed; - width:100%; - overflow-wrap:normal; - overflow:hidden; - border:0px; - word-break:keep-all; - word-wrap:break-word; - line-break:strict; } - </style><td style="padding-left: ${pad+20}px;"> - <table id="failed_test_table"> + <table id="failed_test_table" class="tool_test_results"><tr><td bgcolor="#FFFFCC"><b>Tool id:</b> ${failed_test.tool_id | h}</td></tr><tr><td><b>Tool version:</b> ${failed_test.tool_id | h}</td></tr><tr><td><b>Test:</b> ${failed_test.test_id | h}</td></tr> @@ -573,18 +563,8 @@ parent="${parent}" %endif id="libraryItem-${encoded_id}"> - <style type="text/css"> - #missing_table{ table-layout:fixed; - width:100%; - overflow-wrap:normal; - overflow:hidden; - border:0px; - word-break:keep-all; - word-wrap:break-word; - line-break:strict; } - </style><td style="padding-left: ${pad+20}px;"> - <table id="missing_table"> + <table id="missing_table" class="tool_test_results"><tr><td bgcolor="#FFFFCC"><b>Tool id:</b> ${missing_test_component.tool_id | h}</td></tr><tr><td><b>Tool version:</b> ${missing_test_component.tool_version | h}</td></tr><tr><td><b>Tool guid:</b> ${missing_test_component.tool_guid | h}</td></tr> @@ -703,6 +683,19 @@ %></%def> +<%def name="render_tool_test_results_css()"> + <style type="text/css"> + table.tool_test_results{ table-layout:fixed; + width:100%; + overflow-wrap:normal; + overflow:hidden; + border:0px; + word-break:keep-all; + word-wrap:break-word; + line-break:strict; } + </style> +</%def> + <%def name="render_tool_dependency_installation_error( installation_error, pad, parent, row_counter, row_is_header=False )"><% encoded_id = trans.security.encode_id( installation_error.id ) %><tr class="datasetRow" @@ -710,18 +703,8 @@ parent="${parent}" %endif id="libraryItem-${encoded_id}"> - <style type="text/css"> - #td_install_error_table{ table-layout:fixed; - width:100%; - overflow-wrap:normal; - overflow:hidden; - border:0px; - word-break:keep-all; - word-wrap:break-word; - line-break:strict; } - </style><td style="padding-left: ${pad+20}px;"> - <table id="td_install_error_table"> + <table id="td_install_error_table" class="tool_test_results"><tr bgcolor="#FFFFCC"><th>Type</th><th>Name</th><th>Version</th></tr> @@ -748,18 +731,8 @@ parent="${parent}" %endif id="libraryItem-${encoded_id}"> - <style type="text/css"> - #rd_install_error_table{ table-layout:fixed; - width:100%; - overflow-wrap:normal; - overflow:hidden; - border:0px; - word-break:keep-all; - word-wrap:break-word; - line-break:strict; } - </style><td style="padding-left: ${pad+20}px;"> - <table id="rd_install_error_table"> + <table id="rd_install_error_table" class="tool_test_results"> %if not is_current_repository: <tr bgcolor="#FFFFCC"><th>Tool shed</th><th>Name</th><th>Owner</th><th>Changeset revision</th> @@ -789,18 +762,8 @@ parent="${parent}" %endif id="libraryItem-${encoded_id}"> - <style type="text/css"> - #not_tested_table{ table-layout:fixed; - width:100%; - overflow-wrap:normal; - overflow:hidden; - border:0px; - word-break:keep-all; - word-wrap:break-word; - line-break:strict; } - </style><td style="padding-left: ${pad+20}px;"> - <table id="not_tested_table"> + <table id="not_tested_table" class="tool_test_results"><tr><td>${not_tested.reason | h}</td></tr></table></td> @@ -818,18 +781,8 @@ parent="${parent}" %endif id="libraryItem-${encoded_id}"> - <style type="text/css"> - #passed_tests_table{ table-layout:fixed; - width:100%; - overflow-wrap:normal; - overflow:hidden; - border:0px; - word-break:keep-all; - word-wrap:break-word; - line-break:strict; } - </style><td style="padding-left: ${pad+20}px;"> - <table id="passed_tests_table"> + <table id="passed_tests_table" class="tool_test_results"><tr><td bgcolor="#FFFFCC"><b>Tool id:</b> ${passed_test.tool_id | h}</td></tr><tr><td><b>Tool version:</b> ${passed_test.tool_id | h}</td></tr><tr><td><b>Test:</b> ${passed_test.test_id | h}</td></tr> @@ -1206,6 +1159,7 @@ </div> %endif %if tool_test_results_root_folder: + ${render_tool_test_results_css()} <p/><div class="toolForm"><div class="toolFormTitle">Automated tool test results</div> diff -r 32a48938fe771147abb64524f57d2adb65787ac5 -r 4d4faedba9b6caa555e3825e0f86a34c483e51ff test/base/twilltestcase.py --- a/test/base/twilltestcase.py +++ b/test/base/twilltestcase.py @@ -1191,13 +1191,7 @@ # This loop gets the filename/label for the selected values. item_labels = [ item.attrs[ 'label' ] for item in control.get_items() if item.selected ] for value in kwd[ control.name ]: - # Galaxy truncates long file names in the dataset_collector in galaxy/tools/parameters/basic.py. - # This (and other places where this is done) should be refactored to use the HDA id. - if len( value ) > 30 and control.is_of_kind( 'singlelist' ): - field_value = '%s..%s' % ( value[:17], value[-11:] ) - else: - field_value = value - if field_value not in control.value and True not in [ field_value in item_label for item_label in item_labels ]: + if value not in control.value and True not in [ value in item_label for item_label in item_labels ]: changed = True break if changed: @@ -1205,11 +1199,7 @@ control.clear() # kwd[control.name] should be a singlelist for elem in kwd[ control.name ]: - if len( elem ) > 30 and control.is_of_kind( 'singlelist' ): - elem_name = '%s..%s' % ( elem[:17], elem[-11:] ) - else: - elem_name = elem - tc.fv( f.name, control.name, str( elem_name ) ) + tc.fv( f.name, control.name, str( elem ) ) # Create a new submit control, allows form to refresh, instead of going to next page control = ClientForm.SubmitControl( 'SubmitControl', '___refresh_grouping___', {'name':'refresh_grouping'} ) control.add_to_form( f ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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