November 2011 - galaxy-commits - lists.galaxyproject.org

commit/galaxy-central: greg: Improve exception handling when loading and displaying tools in the tool shed, check content of files uploaded to a tool shed repository only when necessary, and clarify that borwsing repository files is only available for the repository tip.
by Bitbucket 16 Nov '11

16 Nov '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/537a42e5d265/ changeset: 537a42e5d265 user: greg date: 2011-11-16 17:03:14 summary: Improve exception handling when loading and displaying tools in the tool shed, check content of files uploaded to a tool shed repository only when necessary, and clarify that borwsing repository files is only available for the repository tip. affected #: 14 files diff -r 663a2a57ed4db4303661f3771c518b7611f9c85f -r 537a42e5d26578413f20b369643110404502b7c3 lib/galaxy/webapps/community/controllers/common.py --- a/lib/galaxy/webapps/community/controllers/common.py +++ b/lib/galaxy/webapps/community/controllers/common.py @@ -380,17 +380,19 @@ for name in files: # Find all tool configs. if name != 'datatypes_conf.xml' and name.endswith( '.xml' ): + full_path = os.path.abspath( os.path.join( root, name ) ) try: - full_path = os.path.abspath( os.path.join( root, name ) ) tool = load_tool( trans, full_path ) - if tool is not None: - can_set_metadata, invalid_files = check_tool_input_params( trans, name, tool, sample_files, invalid_files ) - if can_set_metadata: - # Update the list of metadata dictionaries for tools in metadata_dict. - tool_config = os.path.join( root, name ) - metadata_dict = generate_tool_metadata( trans, id, changeset_revision, tool_config, tool, metadata_dict ) + valid = True except Exception, e: + valid = False invalid_files.append( ( name, str( e ) ) ) + if valid and tool is not None: + can_set_metadata, invalid_files = check_tool_input_params( trans, name, tool, sample_files, invalid_files ) + if can_set_metadata: + # Update the list of metadata dictionaries for tools in metadata_dict. + tool_config = os.path.join( root, name ) + metadata_dict = generate_tool_metadata( trans, id, changeset_revision, tool_config, tool, metadata_dict ) # Find all exported workflows elif name.endswith( '.ga' ): try: @@ -427,17 +429,19 @@ fh.close() try: tool = load_tool( trans, tmp_filename ) - if tool is not None: - can_set_metadata, invalid_files = check_tool_input_params( trans, filename, tool, sample_files, invalid_files ) - if can_set_metadata: - # Update the list of metadata dictionaries for tools in metadata_dict. Note that filename - # here is the relative path to the config file within the change set context, something - # like filtering.xml, but when the change set was the repository tip, the value was - # something like database/community_files/000/repo_1/filtering.xml. This shouldn't break - # anything, but may result in a bit of confusion when maintaining the code / data over time. - metadata_dict = generate_tool_metadata( trans, id, changeset_revision, filename, tool, metadata_dict ) + valid = True except Exception, e: - invalid_files.append( ( name, str( e ) ) ) + invalid_files.append( ( filename, str( e ) ) ) + valid = False + if valid and tool is not None: + can_set_metadata, invalid_files = check_tool_input_params( trans, filename, tool, sample_files, invalid_files ) + if can_set_metadata: + # Update the list of metadata dictionaries for tools in metadata_dict. Note that filename + # here is the relative path to the config file within the change set context, something + # like filtering.xml, but when the change set was the repository tip, the value was + # something like database/community_files/000/repo_1/filtering.xml. This shouldn't break + # anything, but may result in a bit of confusion when maintaining the code / data over time. + metadata_dict = generate_tool_metadata( trans, id, changeset_revision, filename, tool, metadata_dict ) try: os.unlink( tmp_filename ) except: @@ -575,6 +579,17 @@ util.send_mail( frm, to, subject, body, trans.app.config ) except Exception, e: log.exception( "An error occurred sending a tool shed repository update alert by email." ) +def check_file_contents( trans ): + # See if any admin users have chosen to receive email alerts when a repository is updated. + # If so, the file contents of the update must be checked for inappropriate content. + admin_users = trans.app.config.get( "admin_users", "" ).split( "," ) + for repository in trans.sa_session.query( trans.model.Repository ) \ + .filter( trans.model.Repository.table.c.email_alerts != None ): + email_alerts = from_json_string( repository.email_alerts ) + for user_email in email_alerts: + if user_email in admin_users: + return True + return False def update_for_browsing( trans, repository, current_working_dir, commit_message='' ): # Make a copy of a repository's files for browsing, remove from disk all files that # are not tracked, and commit all added, modified or removed files that have not yet diff -r 663a2a57ed4db4303661f3771c518b7611f9c85f -r 537a42e5d26578413f20b369643110404502b7c3 lib/galaxy/webapps/community/controllers/repository.py --- a/lib/galaxy/webapps/community/controllers/repository.py +++ b/lib/galaxy/webapps/community/controllers/repository.py @@ -773,7 +773,7 @@ tool_guids = [] for filename in ctx: # Find all tool configs in this repository changeset_revision. - if filename.endswith( '.xml' ): + if filename != 'datatypes_conf.xml' and filename.endswith( '.xml' ): fctx = ctx[ filename ] # Write the contents of the old tool config to a temporary file. fh = tempfile.NamedTemporaryFile( 'w' ) @@ -784,11 +784,11 @@ fh.close() try: tool = load_tool( trans, tmp_filename ) - if tool is not None: - tool_guids.append( generate_tool_guid( trans, repository, tool ) ) + valid = True except: - # File must not be a valid tool config even though it has a .xml extension. - pass + valid = False + if valid and tool is not None: + tool_guids.append( generate_tool_guid( trans, repository, tool ) ) try: os.unlink( tmp_filename ) except: @@ -1614,39 +1614,49 @@ status = params.get( 'status', 'done' ) webapp = params.get( 'webapp', 'community' ) repository = get_repository( trans, repository_id ) - repo = hg.repository( get_configured_ui(), repository.repo_path ) + repo = hg.repository( get_configured_ui(), repository.repo_path ) + valid = True + if changeset_revision == repository.tip: + try: + tool = load_tool( trans, os.path.abspath( tool_config ) ) + except Exception, e: + tool = None + valid = False + message = "Error loading tool: %s. Clicking <b>Reset metadata</b> may correct this error." % str( e ) + else: + # Get the tool config file name from the hgweb url, something like: + # /repos/test/convert_chars1/file/e58dcf0026c7/convert_characters.xml + old_tool_config_file_name = tool_config.split( '/' )[ -1 ] + ctx = get_changectx_for_changeset( trans, repo, changeset_revision ) + fctx = None + for filename in ctx: + filename_head, filename_tail = os.path.split( filename ) + if filename_tail == old_tool_config_file_name: + fctx = ctx[ filename ] + break + if fctx: + # Write the contents of the old tool config to a temporary file. + fh = tempfile.NamedTemporaryFile( 'w' ) + tmp_filename = fh.name + fh.close() + fh = open( tmp_filename, 'w' ) + fh.write( fctx.data() ) + fh.close() + try: + tool = load_tool( trans, tmp_filename ) + except Exception, e: + tool = None + valid = False + message = "Error loading tool: %s. Clicking <b>Reset metadata</b> may correct this error." % str( e ) + try: + os.unlink( tmp_filename ) + except: + pass + else: + tool = None + tool_state = self.__new_state( trans ) + is_malicious = change_set_is_malicious( trans, repository_id, repository.tip ) try: - if changeset_revision == repository.tip: - # Get the tool config from the file system we use for browsing. - tool = load_tool( trans, os.path.abspath( tool_config ) ) - else: - # Get the tool config file name from the hgweb url, something like: - # /repos/test/convert_chars1/file/e58dcf0026c7/convert_characters.xml - old_tool_config_file_name = tool_config.split( '/' )[ -1 ] - ctx = get_changectx_for_changeset( trans, repo, changeset_revision ) - fctx = None - for filename in ctx: - filename_head, filename_tail = os.path.split( filename ) - if filename_tail == old_tool_config_file_name: - fctx = ctx[ filename ] - break - if fctx: - # Write the contents of the old tool config to a temporary file. - fh = tempfile.NamedTemporaryFile( 'w' ) - tmp_filename = fh.name - fh.close() - fh = open( tmp_filename, 'w' ) - fh.write( fctx.data() ) - fh.close() - tool = load_tool( trans, tmp_filename ) - try: - os.unlink( tmp_filename ) - except: - pass - else: - tool = None - tool_state = self.__new_state( trans ) - is_malicious = change_set_is_malicious( trans, repository_id, repository.tip ) return trans.fill_template( "/webapps/community/repository/tool_form.mako", repository=repository, changeset_revision=changeset_revision, @@ -1657,7 +1667,7 @@ message=message, status=status ) except Exception, e: - message = "Error loading tool: %s. Click <b>Reset metadata</b> to correct this error." % str( e ) + message = "Error displaying tool, probably due to a problem in the tool config. The exception is: %s." % str( e ) if webapp == 'galaxy': return trans.response.send_redirect( web.url_for( controller='repository', action='preview_tools_in_changeset', diff -r 663a2a57ed4db4303661f3771c518b7611f9c85f -r 537a42e5d26578413f20b369643110404502b7c3 lib/galaxy/webapps/community/controllers/upload.py --- a/lib/galaxy/webapps/community/controllers/upload.py +++ b/lib/galaxy/webapps/community/controllers/upload.py @@ -103,7 +103,10 @@ full_path = os.path.abspath( os.path.join( repo_dir, uploaded_file_filename ) ) # Move the uploaded file to the load_point within the repository hierarchy. shutil.move( uploaded_file_name, full_path ) - if os.path.isfile( full_path ): + # See if any admin users have chosen to receive email alerts when a repository is + # updated. If so, check every uploaded file to ensure content is appropriate. + check_contents = check_file_contents( trans ) + if check_contents and os.path.isfile( full_path ): content_alert_str = self.__check_file_content( full_path ) else: content_alert_str = '' @@ -238,9 +241,12 @@ except OSError, e: # The directory is not empty pass + # See if any admin users have chosen to receive email alerts when a repository is + # updated. If so, check every uploaded file to ensure content is appropriate. + check_contents = check_file_contents( trans ) for filename_in_archive in filenames_in_archive: # Check file content to ensure it is appropriate. - if os.path.isfile( filename_in_archive ): + if check_contents and os.path.isfile( filename_in_archive ): content_alert_str += self.__check_file_content( filename_in_archive ) commands.add( repo.ui, repo, filename_in_archive ) if filename_in_archive.endswith( 'tool_data_table_conf.xml.sample' ): diff -r 663a2a57ed4db4303661f3771c518b7611f9c85f -r 537a42e5d26578413f20b369643110404502b7c3 templates/webapps/community/repository/browse_repository.mako --- a/templates/webapps/community/repository/browse_repository.mako +++ b/templates/webapps/community/repository/browse_repository.mako @@ -97,7 +97,7 @@ %if can_browse_contents: <div class="toolForm"> - <div class="toolFormTitle">Browse ${repository.name}</div> + <div class="toolFormTitle">Browse ${repository.name} revision ${repository.tip} (repository tip)</div> %if can_download: <div class="form-row"><label>Clone this repository:</label> diff -r 663a2a57ed4db4303661f3771c518b7611f9c85f -r 537a42e5d26578413f20b369643110404502b7c3 templates/webapps/community/repository/contact_owner.mako --- a/templates/webapps/community/repository/contact_owner.mako +++ b/templates/webapps/community/repository/contact_owner.mako @@ -13,9 +13,9 @@ can_manage = is_admin or repository.user == trans.user can_view_change_log = not is_new if can_push: - browse_label = 'Browse or delete repository files' + browse_label = 'Browse or delete repository tip files' else: - browse_label = 'Browse repository files' + browse_label = 'Browse repository tip files' %><%! diff -r 663a2a57ed4db4303661f3771c518b7611f9c85f -r 537a42e5d26578413f20b369643110404502b7c3 templates/webapps/community/repository/manage_repository.mako --- a/templates/webapps/community/repository/manage_repository.mako +++ b/templates/webapps/community/repository/manage_repository.mako @@ -16,9 +16,9 @@ can_rate = not is_new and trans.user and repository.user != trans.user can_view_change_log = not is_new if can_push: - browse_label = 'Browse or delete repository files' + browse_label = 'Browse or delete repository tip files' else: - browse_label = 'Browse repository files' + browse_label = 'Browse repository tip files' can_set_malicious = metadata and can_set_metadata and is_admin and changeset_revision == repository.tip %> diff -r 663a2a57ed4db4303661f3771c518b7611f9c85f -r 537a42e5d26578413f20b369643110404502b7c3 templates/webapps/community/repository/preview_tools_in_changeset.mako --- a/templates/webapps/community/repository/preview_tools_in_changeset.mako +++ b/templates/webapps/community/repository/preview_tools_in_changeset.mako @@ -13,9 +13,9 @@ can_browse_contents = not is_new can_view_change_log = not is_new if can_push: - browse_label = 'Browse or delete repository files' + browse_label = 'Browse or delete repository tip files' else: - browse_label = 'Browse repository files' + browse_label = 'Browse repository tip files' %><%! diff -r 663a2a57ed4db4303661f3771c518b7611f9c85f -r 537a42e5d26578413f20b369643110404502b7c3 templates/webapps/community/repository/rate_repository.mako --- a/templates/webapps/community/repository/rate_repository.mako +++ b/templates/webapps/community/repository/rate_repository.mako @@ -16,9 +16,9 @@ can_manage = is_admin or repository.user == trans.user can_view_change_log = not is_new if can_push: - browse_label = 'Browse or delete repository files' + browse_label = 'Browse or delete repository tip files' else: - browse_label = 'Browse repository files' + browse_label = 'Browse repository tip files' %><%! diff -r 663a2a57ed4db4303661f3771c518b7611f9c85f -r 537a42e5d26578413f20b369643110404502b7c3 templates/webapps/community/repository/tool_form.mako --- a/templates/webapps/community/repository/tool_form.mako +++ b/templates/webapps/community/repository/tool_form.mako @@ -18,9 +18,9 @@ can_manage = is_admin or repository.user == trans.user can_view_change_log = not is_new if can_push: - browse_label = 'Browse or delete repository files' + browse_label = 'Browse or delete repository tip files' else: - browse_label = 'Browse repository files' + browse_label = 'Browse repository tip files' %><html> diff -r 663a2a57ed4db4303661f3771c518b7611f9c85f -r 537a42e5d26578413f20b369643110404502b7c3 templates/webapps/community/repository/view_changelog.mako --- a/templates/webapps/community/repository/view_changelog.mako +++ b/templates/webapps/community/repository/view_changelog.mako @@ -15,9 +15,9 @@ can_upload = can_push can_download = not is_new and ( not is_malicious or can_push ) if can_push: - browse_label = 'Browse or delete repository files' + browse_label = 'Browse or delete repository tip files' else: - browse_label = 'Browse repository files' + browse_label = 'Browse repository tip files' %><%! diff -r 663a2a57ed4db4303661f3771c518b7611f9c85f -r 537a42e5d26578413f20b369643110404502b7c3 templates/webapps/community/repository/view_changeset.mako --- a/templates/webapps/community/repository/view_changeset.mako +++ b/templates/webapps/community/repository/view_changeset.mako @@ -16,9 +16,9 @@ can_upload = can_push can_download = not is_new and ( not is_malicious or can_push ) if can_push: - browse_label = 'Browse or delete repository files' + browse_label = 'Browse or delete repository tip files' else: - browse_label = 'Browse repository files' + browse_label = 'Browse repository tip files' %><%! diff -r 663a2a57ed4db4303661f3771c518b7611f9c85f -r 537a42e5d26578413f20b369643110404502b7c3 templates/webapps/community/repository/view_repository.mako --- a/templates/webapps/community/repository/view_repository.mako +++ b/templates/webapps/community/repository/view_repository.mako @@ -14,9 +14,9 @@ can_browse_contents = webapp == 'community' and not is_new can_view_change_log = webapp == 'community' and not is_new if can_push: - browse_label = 'Browse or delete repository files' + browse_label = 'Browse or delete repository tip files' else: - browse_label = 'Browse repository files' + browse_label = 'Browse repository tip files' %><%! diff -r 663a2a57ed4db4303661f3771c518b7611f9c85f -r 537a42e5d26578413f20b369643110404502b7c3 templates/webapps/community/repository/view_tool_metadata.mako --- a/templates/webapps/community/repository/view_tool_metadata.mako +++ b/templates/webapps/community/repository/view_tool_metadata.mako @@ -17,9 +17,9 @@ can_manage = is_admin or repository.user == trans.user can_view_change_log = webapp == 'community' and not is_new if can_push: - browse_label = 'Browse or delete repository files' + browse_label = 'Browse or delete repository tip files' else: - browse_label = 'Browse repository files' + browse_label = 'Browse repository tip files' %><%! diff -r 663a2a57ed4db4303661f3771c518b7611f9c85f -r 537a42e5d26578413f20b369643110404502b7c3 templates/webapps/community/repository/view_workflow.mako --- a/templates/webapps/community/repository/view_workflow.mako +++ b/templates/webapps/community/repository/view_workflow.mako @@ -20,9 +20,9 @@ can_rate = in_tool_shed and not is_new and trans.user and repository.user != trans.user can_view_change_log = in_tool_shed and not is_new if can_push: - browse_label = 'Browse or delete repository files' + browse_label = 'Browse or delete repository tip files' else: - browse_label = 'Browse repository files' + browse_label = 'Browse repository tip files' %><%! Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: Add information for UCSC data to annotation profiler.
by Bitbucket 16 Nov '11

16 Nov '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/663a2a57ed4d/ changeset: 663a2a57ed4d user: dan date: 2011-11-16 16:40:55 summary: Add information for UCSC data to annotation profiler. affected #: 1 file diff -r 26e928ede562caaaebcbe56b172b84e88a639a2e -r 663a2a57ed4db4303661f3771c518b7611f9c85f tools/annotation_profiler/annotation_profiler.xml --- a/tools/annotation_profiler/annotation_profiler.xml +++ b/tools/annotation_profiler/annotation_profiler.xml @@ -136,6 +136,8 @@ **Citation** +For the underlying data, please see http://genome.ucsc.edu/cite.html for the proper citation. + If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.* </help> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: Add EMBOSS citation to EMBOSS tools.
by Bitbucket 16 Nov '11

16 Nov '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/26e928ede562/ changeset: 26e928ede562 user: dan date: 2011-11-16 15:50:34 summary: Add EMBOSS citation to EMBOSS tools. affected #: 107 files diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_antigenic.xml --- a/tools/emboss_5/emboss_antigenic.xml +++ b/tools/emboss_5/emboss_antigenic.xml @@ -48,8 +48,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help> diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_backtranseq.xml --- a/tools/emboss_5/emboss_backtranseq.xml +++ b/tools/emboss_5/emboss_backtranseq.xml @@ -219,8 +219,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_banana.xml --- a/tools/emboss_5/emboss_banana.xml +++ b/tools/emboss_5/emboss_banana.xml @@ -23,8 +23,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_biosed.xml --- a/tools/emboss_5/emboss_biosed.xml +++ b/tools/emboss_5/emboss_biosed.xml @@ -72,8 +72,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_btwisted.xml --- a/tools/emboss_5/emboss_btwisted.xml +++ b/tools/emboss_5/emboss_btwisted.xml @@ -23,8 +23,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_cai.xml --- a/tools/emboss_5/emboss_cai.xml +++ b/tools/emboss_5/emboss_cai.xml @@ -184,8 +184,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_cai_custom.xml --- a/tools/emboss_5/emboss_cai_custom.xml +++ b/tools/emboss_5/emboss_cai_custom.xml @@ -26,8 +26,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_chaos.xml --- a/tools/emboss_5/emboss_chaos.xml +++ b/tools/emboss_5/emboss_chaos.xml @@ -22,8 +22,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_charge.xml --- a/tools/emboss_5/emboss_charge.xml +++ b/tools/emboss_5/emboss_charge.xml @@ -34,8 +34,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_checktrans.xml --- a/tools/emboss_5/emboss_checktrans.xml +++ b/tools/emboss_5/emboss_checktrans.xml @@ -86,8 +86,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_chips.xml --- a/tools/emboss_5/emboss_chips.xml +++ b/tools/emboss_5/emboss_chips.xml @@ -29,8 +29,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_cirdna.xml --- a/tools/emboss_5/emboss_cirdna.xml +++ b/tools/emboss_5/emboss_cirdna.xml @@ -22,8 +22,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_codcmp.xml --- a/tools/emboss_5/emboss_codcmp.xml +++ b/tools/emboss_5/emboss_codcmp.xml @@ -329,8 +329,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_coderet.xml --- a/tools/emboss_5/emboss_coderet.xml +++ b/tools/emboss_5/emboss_coderet.xml @@ -72,8 +72,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_compseq.xml --- a/tools/emboss_5/emboss_compseq.xml +++ b/tools/emboss_5/emboss_compseq.xml @@ -41,8 +41,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_cpgplot.xml --- a/tools/emboss_5/emboss_cpgplot.xml +++ b/tools/emboss_5/emboss_cpgplot.xml @@ -32,8 +32,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_cpgreport.xml --- a/tools/emboss_5/emboss_cpgreport.xml +++ b/tools/emboss_5/emboss_cpgreport.xml @@ -48,8 +48,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_cusp.xml --- a/tools/emboss_5/emboss_cusp.xml +++ b/tools/emboss_5/emboss_cusp.xml @@ -29,8 +29,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_cutseq.xml --- a/tools/emboss_5/emboss_cutseq.xml +++ b/tools/emboss_5/emboss_cutseq.xml @@ -71,8 +71,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_dan.xml --- a/tools/emboss_5/emboss_dan.xml +++ b/tools/emboss_5/emboss_dan.xml @@ -83,8 +83,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_degapseq.xml --- a/tools/emboss_5/emboss_degapseq.xml +++ b/tools/emboss_5/emboss_degapseq.xml @@ -57,8 +57,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_descseq.xml --- a/tools/emboss_5/emboss_descseq.xml +++ b/tools/emboss_5/emboss_descseq.xml @@ -71,8 +71,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_diffseq.xml --- a/tools/emboss_5/emboss_diffseq.xml +++ b/tools/emboss_5/emboss_diffseq.xml @@ -63,8 +63,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_digest.xml --- a/tools/emboss_5/emboss_digest.xml +++ b/tools/emboss_5/emboss_digest.xml @@ -64,8 +64,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_dotmatcher.xml --- a/tools/emboss_5/emboss_dotmatcher.xml +++ b/tools/emboss_5/emboss_dotmatcher.xml @@ -28,8 +28,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_dotpath.xml --- a/tools/emboss_5/emboss_dotpath.xml +++ b/tools/emboss_5/emboss_dotpath.xml @@ -35,8 +35,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_dottup.xml --- a/tools/emboss_5/emboss_dottup.xml +++ b/tools/emboss_5/emboss_dottup.xml @@ -29,8 +29,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_dreg.xml --- a/tools/emboss_5/emboss_dreg.xml +++ b/tools/emboss_5/emboss_dreg.xml @@ -21,8 +21,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_einverted.xml --- a/tools/emboss_5/emboss_einverted.xml +++ b/tools/emboss_5/emboss_einverted.xml @@ -49,8 +49,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_epestfind.xml --- a/tools/emboss_5/emboss_epestfind.xml +++ b/tools/emboss_5/emboss_epestfind.xml @@ -64,8 +64,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_equicktandem.xml --- a/tools/emboss_5/emboss_equicktandem.xml +++ b/tools/emboss_5/emboss_equicktandem.xml @@ -59,8 +59,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_est2genome.xml --- a/tools/emboss_5/emboss_est2genome.xml +++ b/tools/emboss_5/emboss_est2genome.xml @@ -102,8 +102,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_etandem.xml --- a/tools/emboss_5/emboss_etandem.xml +++ b/tools/emboss_5/emboss_etandem.xml @@ -75,8 +75,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_extractfeat.xml --- a/tools/emboss_5/emboss_extractfeat.xml +++ b/tools/emboss_5/emboss_extractfeat.xml @@ -97,6 +97,8 @@ **Citation** +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_extractseq.xml --- a/tools/emboss_5/emboss_extractseq.xml +++ b/tools/emboss_5/emboss_extractseq.xml @@ -67,8 +67,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_freak.xml --- a/tools/emboss_5/emboss_freak.xml +++ b/tools/emboss_5/emboss_freak.xml @@ -35,8 +35,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_fuzznuc.xml --- a/tools/emboss_5/emboss_fuzznuc.xml +++ b/tools/emboss_5/emboss_fuzznuc.xml @@ -74,8 +74,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_fuzzpro.xml --- a/tools/emboss_5/emboss_fuzzpro.xml +++ b/tools/emboss_5/emboss_fuzzpro.xml @@ -43,8 +43,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_fuzztran.xml --- a/tools/emboss_5/emboss_fuzztran.xml +++ b/tools/emboss_5/emboss_fuzztran.xml @@ -94,8 +94,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_garnier.xml --- a/tools/emboss_5/emboss_garnier.xml +++ b/tools/emboss_5/emboss_garnier.xml @@ -57,8 +57,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_geecee.xml --- a/tools/emboss_5/emboss_geecee.xml +++ b/tools/emboss_5/emboss_geecee.xml @@ -23,8 +23,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_getorf.xml --- a/tools/emboss_5/emboss_getorf.xml +++ b/tools/emboss_5/emboss_getorf.xml @@ -128,8 +128,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_helixturnhelix.xml --- a/tools/emboss_5/emboss_helixturnhelix.xml +++ b/tools/emboss_5/emboss_helixturnhelix.xml @@ -62,8 +62,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_hmoment.xml --- a/tools/emboss_5/emboss_hmoment.xml +++ b/tools/emboss_5/emboss_hmoment.xml @@ -31,8 +31,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_iep.xml --- a/tools/emboss_5/emboss_iep.xml +++ b/tools/emboss_5/emboss_iep.xml @@ -37,8 +37,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_infoseq.xml --- a/tools/emboss_5/emboss_infoseq.xml +++ b/tools/emboss_5/emboss_infoseq.xml @@ -75,8 +75,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_isochore.xml --- a/tools/emboss_5/emboss_isochore.xml +++ b/tools/emboss_5/emboss_isochore.xml @@ -82,6 +82,8 @@ **Citation** +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help> diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_lindna.xml --- a/tools/emboss_5/emboss_lindna.xml +++ b/tools/emboss_5/emboss_lindna.xml @@ -98,8 +98,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_marscan.xml --- a/tools/emboss_5/emboss_marscan.xml +++ b/tools/emboss_5/emboss_marscan.xml @@ -44,8 +44,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_maskfeat.xml --- a/tools/emboss_5/emboss_maskfeat.xml +++ b/tools/emboss_5/emboss_maskfeat.xml @@ -71,8 +71,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_maskseq.xml --- a/tools/emboss_5/emboss_maskseq.xml +++ b/tools/emboss_5/emboss_maskseq.xml @@ -71,8 +71,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_matcher.xml --- a/tools/emboss_5/emboss_matcher.xml +++ b/tools/emboss_5/emboss_matcher.xml @@ -56,8 +56,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_megamerger.xml --- a/tools/emboss_5/emboss_megamerger.xml +++ b/tools/emboss_5/emboss_megamerger.xml @@ -62,8 +62,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_merger.xml --- a/tools/emboss_5/emboss_merger.xml +++ b/tools/emboss_5/emboss_merger.xml @@ -75,8 +75,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_msbar.xml --- a/tools/emboss_5/emboss_msbar.xml +++ b/tools/emboss_5/emboss_msbar.xml @@ -116,8 +116,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_needle.xml --- a/tools/emboss_5/emboss_needle.xml +++ b/tools/emboss_5/emboss_needle.xml @@ -125,8 +125,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_newcpgreport.xml --- a/tools/emboss_5/emboss_newcpgreport.xml +++ b/tools/emboss_5/emboss_newcpgreport.xml @@ -43,8 +43,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_newcpgseek.xml --- a/tools/emboss_5/emboss_newcpgseek.xml +++ b/tools/emboss_5/emboss_newcpgseek.xml @@ -34,8 +34,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_newseq.xml --- a/tools/emboss_5/emboss_newseq.xml +++ b/tools/emboss_5/emboss_newseq.xml @@ -71,8 +71,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_noreturn.xml --- a/tools/emboss_5/emboss_noreturn.xml +++ b/tools/emboss_5/emboss_noreturn.xml @@ -30,8 +30,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_notseq.xml --- a/tools/emboss_5/emboss_notseq.xml +++ b/tools/emboss_5/emboss_notseq.xml @@ -68,8 +68,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_nthseq.xml --- a/tools/emboss_5/emboss_nthseq.xml +++ b/tools/emboss_5/emboss_nthseq.xml @@ -68,8 +68,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_octanol.xml --- a/tools/emboss_5/emboss_octanol.xml +++ b/tools/emboss_5/emboss_octanol.xml @@ -39,6 +39,8 @@ **Citation** +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_oddcomp.xml --- a/tools/emboss_5/emboss_oddcomp.xml +++ b/tools/emboss_5/emboss_oddcomp.xml @@ -39,8 +39,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_palindrome.xml --- a/tools/emboss_5/emboss_palindrome.xml +++ b/tools/emboss_5/emboss_palindrome.xml @@ -52,8 +52,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_pasteseq.xml --- a/tools/emboss_5/emboss_pasteseq.xml +++ b/tools/emboss_5/emboss_pasteseq.xml @@ -72,8 +72,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_patmatdb.xml --- a/tools/emboss_5/emboss_patmatdb.xml +++ b/tools/emboss_5/emboss_patmatdb.xml @@ -48,8 +48,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_pepcoil.xml --- a/tools/emboss_5/emboss_pepcoil.xml +++ b/tools/emboss_5/emboss_pepcoil.xml @@ -45,8 +45,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_pepinfo.xml --- a/tools/emboss_5/emboss_pepinfo.xml +++ b/tools/emboss_5/emboss_pepinfo.xml @@ -27,8 +27,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_pepnet.xml --- a/tools/emboss_5/emboss_pepnet.xml +++ b/tools/emboss_5/emboss_pepnet.xml @@ -32,8 +32,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_pepstats.xml --- a/tools/emboss_5/emboss_pepstats.xml +++ b/tools/emboss_5/emboss_pepstats.xml @@ -29,8 +29,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_pepwheel.xml --- a/tools/emboss_5/emboss_pepwheel.xml +++ b/tools/emboss_5/emboss_pepwheel.xml @@ -44,8 +44,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_pepwindow.xml --- a/tools/emboss_5/emboss_pepwindow.xml +++ b/tools/emboss_5/emboss_pepwindow.xml @@ -21,8 +21,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_pepwindowall.xml --- a/tools/emboss_5/emboss_pepwindowall.xml +++ b/tools/emboss_5/emboss_pepwindowall.xml @@ -21,8 +21,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_plotcon.xml --- a/tools/emboss_5/emboss_plotcon.xml +++ b/tools/emboss_5/emboss_plotcon.xml @@ -21,8 +21,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_plotorf.xml --- a/tools/emboss_5/emboss_plotorf.xml +++ b/tools/emboss_5/emboss_plotorf.xml @@ -39,8 +39,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_polydot.xml --- a/tools/emboss_5/emboss_polydot.xml +++ b/tools/emboss_5/emboss_polydot.xml @@ -47,8 +47,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_preg.xml --- a/tools/emboss_5/emboss_preg.xml +++ b/tools/emboss_5/emboss_preg.xml @@ -20,8 +20,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_prettyplot.xml --- a/tools/emboss_5/emboss_prettyplot.xml +++ b/tools/emboss_5/emboss_prettyplot.xml @@ -112,8 +112,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_prettyseq.xml --- a/tools/emboss_5/emboss_prettyseq.xml +++ b/tools/emboss_5/emboss_prettyseq.xml @@ -52,8 +52,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_primersearch.xml --- a/tools/emboss_5/emboss_primersearch.xml +++ b/tools/emboss_5/emboss_primersearch.xml @@ -32,8 +32,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_revseq.xml --- a/tools/emboss_5/emboss_revseq.xml +++ b/tools/emboss_5/emboss_revseq.xml @@ -76,8 +76,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_seqmatchall.xml --- a/tools/emboss_5/emboss_seqmatchall.xml +++ b/tools/emboss_5/emboss_seqmatchall.xml @@ -53,8 +53,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_seqret.xml --- a/tools/emboss_5/emboss_seqret.xml +++ b/tools/emboss_5/emboss_seqret.xml @@ -69,8 +69,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_showfeat.xml --- a/tools/emboss_5/emboss_showfeat.xml +++ b/tools/emboss_5/emboss_showfeat.xml @@ -122,8 +122,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_shuffleseq.xml --- a/tools/emboss_5/emboss_shuffleseq.xml +++ b/tools/emboss_5/emboss_shuffleseq.xml @@ -61,8 +61,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_sigcleave.xml --- a/tools/emboss_5/emboss_sigcleave.xml +++ b/tools/emboss_5/emboss_sigcleave.xml @@ -54,8 +54,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_sirna.xml --- a/tools/emboss_5/emboss_sirna.xml +++ b/tools/emboss_5/emboss_sirna.xml @@ -117,8 +117,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_sixpack.xml --- a/tools/emboss_5/emboss_sixpack.xml +++ b/tools/emboss_5/emboss_sixpack.xml @@ -161,8 +161,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_skipseq.xml --- a/tools/emboss_5/emboss_skipseq.xml +++ b/tools/emboss_5/emboss_skipseq.xml @@ -58,8 +58,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_splitter.xml --- a/tools/emboss_5/emboss_splitter.xml +++ b/tools/emboss_5/emboss_splitter.xml @@ -78,8 +78,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_supermatcher.xml --- a/tools/emboss_5/emboss_supermatcher.xml +++ b/tools/emboss_5/emboss_supermatcher.xml @@ -63,8 +63,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_syco.xml --- a/tools/emboss_5/emboss_syco.xml +++ b/tools/emboss_5/emboss_syco.xml @@ -196,8 +196,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_tcode.xml --- a/tools/emboss_5/emboss_tcode.xml +++ b/tools/emboss_5/emboss_tcode.xml @@ -43,8 +43,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_textsearch.xml --- a/tools/emboss_5/emboss_textsearch.xml +++ b/tools/emboss_5/emboss_textsearch.xml @@ -57,8 +57,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_tmap.xml --- a/tools/emboss_5/emboss_tmap.xml +++ b/tools/emboss_5/emboss_tmap.xml @@ -38,8 +38,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_tranalign.xml --- a/tools/emboss_5/emboss_tranalign.xml +++ b/tools/emboss_5/emboss_tranalign.xml @@ -83,8 +83,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_transeq.xml --- a/tools/emboss_5/emboss_transeq.xml +++ b/tools/emboss_5/emboss_transeq.xml @@ -121,8 +121,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_trimest.xml --- a/tools/emboss_5/emboss_trimest.xml +++ b/tools/emboss_5/emboss_trimest.xml @@ -91,8 +91,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_trimseq.xml --- a/tools/emboss_5/emboss_trimseq.xml +++ b/tools/emboss_5/emboss_trimseq.xml @@ -96,8 +96,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_twofeat.xml --- a/tools/emboss_5/emboss_twofeat.xml +++ b/tools/emboss_5/emboss_twofeat.xml @@ -129,8 +129,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> \ No newline at end of file diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_union.xml --- a/tools/emboss_5/emboss_union.xml +++ b/tools/emboss_5/emboss_union.xml @@ -64,8 +64,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_vectorstrip.xml --- a/tools/emboss_5/emboss_vectorstrip.xml +++ b/tools/emboss_5/emboss_vectorstrip.xml @@ -81,8 +81,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_water.xml --- a/tools/emboss_5/emboss_water.xml +++ b/tools/emboss_5/emboss_water.xml @@ -65,8 +65,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_wobble.xml --- a/tools/emboss_5/emboss_wobble.xml +++ b/tools/emboss_5/emboss_wobble.xml @@ -39,8 +39,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_wordcount.xml --- a/tools/emboss_5/emboss_wordcount.xml +++ b/tools/emboss_5/emboss_wordcount.xml @@ -34,8 +34,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> diff -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f -r 26e928ede562caaaebcbe56b172b84e88a639a2e tools/emboss_5/emboss_wordmatch.xml --- a/tools/emboss_5/emboss_wordmatch.xml +++ b/tools/emboss_5/emboss_wordmatch.xml @@ -73,8 +73,10 @@ ------ -**Citation** - +**Citation** + +For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ + If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ </help></tool> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: jgoecks: Trackster: significant refactoring to unify Drawables' HTML structure and also facilitate customization. Groups now use icons and can show/hide content.
by Bitbucket 15 Nov '11

15 Nov '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/0d523eebeb0d/ changeset: 0d523eebeb0d user: jgoecks date: 2011-11-16 00:04:09 summary: Trackster: significant refactoring to unify Drawables' HTML structure and also facilitate customization. Groups now use icons and can show/hide content. affected #: 1 file diff -r 43a4ef4ec6d18dbbb50dc285afe01dfb8c6a29f8 -r 0d523eebeb0dd7f9c52f037b2ee9d6a7dfe3e73f static/scripts/trackster.js --- a/static/scripts/trackster.js +++ b/static/scripts/trackster.js @@ -650,8 +650,13 @@ */ /** - * Base interface for all drawable objects. Drawable objects have a name and are - * associated with a view and container. They optionally have a drag handle class. + * Base class for all drawable objects. Drawable objects are associated with a view and live in a + * container. They have the following HTML elements and structure: + * <container_div> + * <header_div> + * <content_div> + * + * They optionally have a drag handle class. */ var Drawable = function(name, view, container, prefs, drag_handle_class) { if (!Drawable.id_counter) { Drawable.id_counter = 0; } @@ -672,6 +677,33 @@ this.prefs = this.config.values; this.drag_handle_class = drag_handle_class; this.is_overview = false; + + // FIXME: this should be a saved setting + this.content_visible = true; + + // Build Drawable HTML and behaviors. + this.container_div = this.build_container_div(); + this.header_div = this.build_header_div(); + + if (this.header_div) { + this.container_div.append(this.header_div); + + this.icons_div = this.build_icons_div().hide(); + this.header_div.append(this.icons_div); + + // Suppress double clicks in header so that they do not impact viz. + this.header_div.dblclick( function(e) { e.stopPropagation(); } ); + + // Show icons when users is hovering over track. + var drawable = this; + this.container_div.hover( + function() { drawable.icons_div.show(); }, + function() { drawable.icons_div.hide(); } + ); + + // Needed for floating elts in header. + $("<div style='clear: both'/>").appendTo(this.container_div); + } }; extend(Drawable.prototype, { @@ -707,7 +739,31 @@ view.update_intro_div(); view.has_changes = true; }); - } + }, + /** + * Build drawable's container div; this is the parent div for all drawable's elements. + */ + build_container_div: function() {}, + /** + * Build drawable's header div. + */ + build_header_div: function() {}, + /** + * Build drawable's icons div. + */ + build_icons_div: function() {}, + /** + * Update icons. + */ + update_icons: function() {}, + /** + * Hide drawable's contents. + */ + hide_contents: function () {}, + /** + * Show drawable's contents. + */ + show_contents: function() {} }); /** @@ -805,36 +861,54 @@ var DrawableGroup = function(name, view, container, prefs) { DrawableCollection.call(this, "DrawableGroup", name, view, container, prefs, "group-handle"); - // HTML elements. - this.container_div = $("<div/>").addClass("group").attr("id", "group_" + this.id).appendTo(this.container.content_div); - this.header_div = $("<div/>").addClass("track-header").appendTo(this.container_div); - this.header_div.append($("<div/>").addClass(this.drag_handle_class)); - this.name_div = $("<div/>").addClass("group-name menubutton popup").text(this.name).appendTo(this.header_div); - this.content_div = $("<div/>").addClass("content-div").attr("id", "group_" + this.id + "_content_div").appendTo(this.container_div); - // Set up containers/moving for group: register both container_div and content div as container // because both are used as containers (container div to recognize container, content_div to // store elements). Group can be moved. + this.content_div = $("<div/>").addClass("content-div").attr("id", "group_" + this.id + "_content_div").appendTo(this.container_div); is_container(this.container_div, this); is_container(this.content_div, this); moveable(this.container_div, this.drag_handle_class, ".group", this); - - this.update_icons(); }; extend(DrawableGroup.prototype, Drawable.prototype, DrawableCollection.prototype, { - /** - * Make popup menu for group. - */ - update_icons: function() { + build_container_div: function() { + return $("<div/>").addClass("group").attr("id", "group_" + this.id).appendTo(this.container.content_div); + }, + build_header_div: function() { + var header_div = $("<div/>").addClass("track-header"); + header_div.append($("<div/>").addClass(this.drag_handle_class)); + this.name_div = $("<div/>").addClass("track-name").text(this.name).appendTo(header_div); + return header_div; + }, + build_icons_div: function() { + var icons_div = $("<div/>").css("float", "left"); + + this.toggle_icon = $("<a/>").attr("href", "javascript:void(0);").attr("title", "Hide/show group content") + .addClass("icon-button toggle").tipsy( {gravity: 's'} ) + .appendTo(icons_div); + this.settings_icon = $("<a/>").attr("href", "javascript:void(0);").attr("title", "Edit settings") + .addClass("icon-button settings-icon").tipsy( {gravity: 's'} ) + .appendTo(icons_div); + this.remove_icon = $("<a/>").attr("href", "javascript:void(0);").attr("title", "Remove") + .addClass("icon-button remove-icon").tipsy( {gravity: 's'} ) + .appendTo(icons_div); var group = this; - - var group_dropdown = {}; - - // - // Edit config option. - // - group_dropdown["Edit configuration"] = function() { + + // Toggle icon hides or shows the group content. + this.toggle_icon.click( function() { + if ( group.content_visible ) { + group.toggle_icon.addClass("toggle-expand").removeClass("toggle"); + group.hide_contents(); + group.content_visible = false; + } else { + group.toggle_icon.addClass("toggle").removeClass("toggle-expand"); + group.content_visible = true; + group.show_contents(); + } + }); + + // Clicking on settings icon opens group config. + this.settings_icon.click( function() { var cancel_fn = function() { hide_modal(); $(window).unbind("keypress.check_enter_esc"); }, ok_fn = function() { group.config.update_from_form( $(".dialog-box") ); @@ -854,16 +928,25 @@ "Cancel": cancel_fn, "OK": ok_fn }); - }; + }); - // - // Remove option. - // - group_dropdown.Remove = function() { + // Clicking on remove icon removes group. + this.remove_icon.click( function() { + // Tipsy for remove icon must be deleted when group is deleted. + $(".tipsy").remove(); group.remove(); - }; + }); - make_popupmenu(group.name_div, group_dropdown); + return icons_div; + }, + hide_contents : function () { + this.content_div.hide(); + }, + show_contents : function() { + // Show the contents div and labels (if present) + this.content_div.show(); + // Request a redraw of the content + this.request_draw(); } }); @@ -2356,7 +2439,7 @@ * -------> ReadTrack * -------> VcfTrack */ -var Track = function(name, view, container, show_header, prefs, data_url, data_query_wait) { +var Track = function(name, view, container, prefs, data_url, data_query_wait) { // For now, track's container is always view. Drawable.call(this, name, view, container, {}, "draghandle"); @@ -2368,58 +2451,59 @@ this.data_query_wait = (data_query_wait ? data_query_wait : DEFAULT_DATA_QUERY_WAIT); this.dataset_check_url = converted_datasets_state_url; - // FIXME: this should be a saved setting - this.content_visible = true; - if (!Track.id_counter) { Track.id_counter = 0; } this.id = Track.id_counter++; - + // - // Create HTML element structure for track. + // Create content div, which is where track is displayed. // - this.container_div = $("<div />").addClass('track').attr("id", "track_" + this.id).css("position", "relative"); - - // Create and initialize track header and icons. - if (show_header) { - this.header_div = $("<div class='track-header'/>").appendTo(this.container_div); - if (this.view.editor) { this.drag_div = $("<div/>").addClass(this.drag_handle_class).appendTo(this.header_div); } - this.name_div = $("<div/>").addClass("track-name").appendTo(this.header_div).text(this.name) + this.content_div = $("<div class='track-content'>").appendTo(this.container_div); + this.container.content_div.append(this.container_div); +}; +extend(Track.prototype, Drawable.prototype, { + build_container_div: function () { + return $("<div/>").addClass('track').attr("id", "track_" + this.id).css("position", "relative"); + }, + build_header_div: function() { + var header_div = $("<div class='track-header'/>"); + if (this.view.editor) { this.drag_div = $("<div/>").addClass(this.drag_handle_class).appendTo(header_div); } + this.name_div = $("<div/>").addClass("track-name").appendTo(header_div).text(this.name) .attr( "id", this.name.replace(/\s+/g,'-').replace(/[^a-zA-Z0-9\-]/g,'').toLowerCase() ); - this.icons_div = $("<div/>").css("float", "left").appendTo(this.header_div).hide(); - + return header_div; + }, + build_icons_div: function() { + var icons_div = $("<div/>").css("float", "left"); + // Track icons. this.mode_icon = $("<a/>").attr("href", "javascript:void(0);").attr("title", "Set display mode") - .addClass("icon-button chevron-expand").tipsy( {gravity: 's'} ).appendTo(this.icons_div); + .addClass("icon-button chevron-expand").tipsy( {gravity: 's'} ).appendTo(icons_div); this.toggle_icon = $("<a/>").attr("href", "javascript:void(0);").attr("title", "Hide/show track content") .addClass("icon-button toggle").tipsy( {gravity: 's'} ) - .appendTo(this.icons_div); + .appendTo(icons_div); this.settings_icon = $("<a/>").attr("href", "javascript:void(0);").attr("title", "Edit settings") .addClass("icon-button settings-icon").tipsy( {gravity: 's'} ) - .appendTo(this.icons_div); + .appendTo(icons_div); this.overview_icon = $("<a/>").attr("href", "javascript:void(0);").attr("title", "Set as overview") .addClass("icon-button overview-icon").tipsy( {gravity: 's'} ) - .appendTo(this.icons_div); + .appendTo(icons_div); this.filters_icon = $("<a/>").attr("href", "javascript:void(0);").attr("title", "Filters") .addClass("icon-button filters-icon").tipsy( {gravity: 's'} ) - .appendTo(this.icons_div).hide(); + .appendTo(icons_div).hide(); this.tools_icon = $("<a/>").attr("href", "javascript:void(0);").attr("title", "Tools") .addClass("icon-button tools-icon").tipsy( {gravity: 's'} ) - .appendTo(this.icons_div).hide(); + .appendTo(icons_div).hide(); this.remove_icon = $("<a/>").attr("href", "javascript:void(0);").attr("title", "Remove") .addClass("icon-button remove-icon").tipsy( {gravity: 's'} ) - .appendTo(this.icons_div); + .appendTo(icons_div); var track = this; - - // Suppress double clicks in header so that they do not impact viz. - this.header_div.dblclick( function(e) { e.stopPropagation(); } ); - + // Set up behavior for modes popup. if (track.display_modes !== undefined) { var init_mode = (track.config && track.config.values['mode'] ? track.config.values['mode'] : track.display_modes[0]); track.mode = init_mode; this.mode_icon.attr("title", "Set display mode (now: " + track.mode + ")"); - + var mode_mapping = {}; for (var i = 0, len = track.display_modes.length; i < len; i++) { var mode = track.display_modes[i]; @@ -2432,7 +2516,7 @@ track.container_div.mouseleave(function() { track.icons_div.hide(); } ); }; }(mode); } - + make_popupmenu(this.mode_icon, mode_mapping); } @@ -2448,7 +2532,7 @@ track.show_contents(); } }); - + // Clicking on settings icon opens track config. this.settings_icon.click( function() { var cancel_fn = function() { hide_modal(); $(window).unbind("keypress.check_enter_esc"); }, @@ -2471,22 +2555,22 @@ "OK": ok_fn }); }); - + this.overview_icon.click( function() { track.view.set_overview(track); }); - + this.filters_icon.click( function() { // TODO: update tipsy text. track.filters_div.toggle(); track.filters_manager.reset_filters(); }); - + this.tools_icon.click( function() { // TODO: update tipsy text. - + track.dynamic_tool_div.toggle(); - + // Update track name. if (track.dynamic_tool_div.is(":visible")) { track.set_name(track.name + track.tool_region_and_parameters_str()); @@ -2497,29 +2581,39 @@ // HACK: name change modifies icon placement, which leaves tooltip incorrectly placed. $(".tipsy").remove(); }); - + // Clicking on remove icon removes track. this.remove_icon.click( function() { // Tipsy for remove icon must be deleted when track is deleted. $(".tipsy").remove(); track.remove(); }); - - // Show icons when users is hovering over track. - this.container_div.hover( function() { track.icons_div.show(); }, function() { track.icons_div.hide(); } ); - // Needed for floating elts in header. - $("<div style='clear: both'/>").appendTo(this.container_div); - } - - // - // Create content div, which is where track is displayed. - // - this.content_div = $("<div class='track-content'>").appendTo(this.container_div); - this.container.content_div.append(this.container_div); -}; -extend(Track.prototype, Drawable.prototype, { - /** Returns track type. */ + return icons_div; + }, + /** + * Hide any elements that are part of the tracks contents area. Should + * remove as approprite, the track will be redrawn by show_contents. + */ + hide_contents : function () { + // Clear contents by removing any elements that are contained in + // the tracks content_div + this.content_div.children().remove(); + // Hide the content div + this.content_div.hide(); + // And any y axis labels (common to several track types) + this.container_div.find(".yaxislabel, .track-resize").hide() + }, + show_contents : function() { + // Show the contents div and labels (if present) + this.content_div.show(); + this.container_div.find(".yaxislabel, .track-resize").show() + // Request a redraw of the content + this.request_draw(); + }, + /** + * Returns track type. + */ get_type: function() { // Order is important: start with most-specific classes and go up the track hierarchy. if (this instanceof LabelTrack) { @@ -2612,33 +2706,13 @@ this.update_icons(); }, /** - * Hide any elements that are part of the tracks contents area. Should - * remove as approprite, the track will be redrawn by show_contents. - */ - hide_contents : function () { - // Clear contents by removing any elements that are contained in - // the tracks content_div - this.content_div.children().remove(); - // Hide the content div - this.content_div.hide(); - // And any y axis labels (common to several track types) - this.container_div.find(".yaxislabel, .track-resize").hide() - }, - show_contents : function() { - // Show the contents div and labels (if present) - this.content_div.show(); - this.container_div.find(".yaxislabel, .track-resize").show() - // Request a redraw of the content - this.request_draw(); - }, - /** * Additional initialization required before drawing track for the first time. */ predraw_init: function() {} }); -var TiledTrack = function(name, view, container, show_header, prefs, filters_list, tool_dict) { - Track.call(this, name, view, container, show_header, prefs); +var TiledTrack = function(name, view, container, prefs, filters_list, tool_dict) { + Track.call(this, name, view, container, prefs); var track = this, view = track.view; @@ -3031,6 +3105,7 @@ this.container_div.addClass( "label-track" ); }; extend(LabelTrack.prototype, Track.prototype, { + build_header_div: function() {}, init: function() { // Enable by default because there should always be data when drawing track. this.enabled = true; @@ -3057,7 +3132,7 @@ }); var ReferenceTrack = function (view) { - TiledTrack.call(this, "reference", view, { content_div: view.top_labeltrack }, false, {}); + TiledTrack.call(this, "reference", view, { content_div: view.top_labeltrack }, {}); view.reference_track = this; this.left_offset = 200; @@ -3072,6 +3147,7 @@ this.tile_cache = new Cache(CACHED_TILES_LINE); }; extend(ReferenceTrack.prototype, Drawable.prototype, TiledTrack.prototype, { + build_header_div: function() {}, init: function() { // Enable by default because there should always be data when drawing track. this.enabled = true; @@ -3109,7 +3185,7 @@ var track = this; this.display_modes = ["Histogram", "Line", "Filled", "Intensity"]; this.mode = "Histogram"; - TiledTrack.call( this, name, view, container, true, prefs ); + TiledTrack.call( this, name, view, container, prefs ); this.min_height_px = 16; this.max_height_px = 400; @@ -3269,7 +3345,7 @@ // // Initialization. // - TiledTrack.call(this, name, view, container, true, prefs, filters, tool); + TiledTrack.call(this, name, view, container, prefs, filters, tool); // Define and restore track configuration. this.config = new DrawableConfig( { Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: dan: Add VCF viewer for IGV. Add necessary datatypes and converters to support this view (vcf_bgzip; vcf_bgzip to tabix).
by Bitbucket 15 Nov '11

15 Nov '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/43a4ef4ec6d1/ changeset: 43a4ef4ec6d1 user: dan date: 2011-11-15 23:24:38 summary: Add VCF viewer for IGV. Add necessary datatypes and converters to support this view (vcf_bgzip; vcf_bgzip to tabix). affected #: 7 files diff -r 7897af491f07535915e2cd917afd0da981a1b45c -r 43a4ef4ec6d18dbbb50dc285afe01dfb8c6a29f8 datatypes_conf.xml.sample --- a/datatypes_conf.xml.sample +++ b/datatypes_conf.xml.sample @@ -9,7 +9,7 @@ <converter file="bam_to_summary_tree_converter.xml" target_datatype="summary_tree" depends_on="bai"/><display file="ucsc/bam.xml" /><display file="ensembl/ensembl_bam.xml" /> -  + <display file="igv/bam.xml" /></datatype><datatype extension="bed" type="galaxy.datatypes.interval:Bed" display_in_upload="true"><converter file="bed_to_gff_converter.xml" target_datatype="gff"/> @@ -154,8 +154,10 @@ <datatype extension="blastxml" type="galaxy.datatypes.xml:BlastXml" mimetype="application/xml" display_in_upload="true"/><datatype extension="vcf" type="galaxy.datatypes.tabular:Vcf" display_in_upload="true"><converter file="vcf_to_bgzip_converter.xml" target_datatype="bgzip"/> + <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="igv/vcf.xml" /></datatype><datatype extension="wsf" type="galaxy.datatypes.wsf:SnpFile" display_in_upload="true"/><datatype extension="velvet" type="galaxy.datatypes.assembly:Velvet" display_in_upload="false"/> @@ -168,6 +170,10 @@ <datatype extension="interval_index" type="galaxy.datatypes.binary:Binary" subclass="True" /><datatype extension="tabix" type="galaxy.datatypes.binary:Binary" subclass="True" /><datatype extension="bgzip" type="galaxy.datatypes.binary:Binary" subclass="True" /> + <datatype extension="vcf_bgzip" type_extension="bgzip" subclass="True" > + <display file="igv/vcf.xml" /> + <converter file="vcf_bgzip_to_tabix_converter.xml" target_datatype="tabix"/> + </datatype><datatype extension="acedb" type="galaxy.datatypes.data:Text"/><datatype extension="asn1" type="galaxy.datatypes.data:Text"/> diff -r 7897af491f07535915e2cd917afd0da981a1b45c -r 43a4ef4ec6d18dbbb50dc285afe01dfb8c6a29f8 display_applications/igv/bam.xml --- a/display_applications/igv/bam.xml +++ b/display_applications/igv/bam.xml @@ -1,12 +1,32 @@ +<?xml version="1.0"?><display id="igv_bam" version="1.0.0" name="display with IGV"> - <link id="web" name="web"> - <url>$jnlp.url</url> - <param type="data" name="bam_file" url="galaxy_${DATASET_HASH}.bam" strip_https="True" /> - <param type="data" name="bai_file" url="galaxy_${DATASET_HASH}.bam.bai" metadata="bam_index" strip_https="True" /> - <param type="template" name="jnlp" url="galaxy_${DATASET_HASH}.jnlp" viewable="True" strip_https="True" mimetype="application/x-java-jnlp-file"><?xml version="1.0" encoding="utf-8"?> + +  + <dynamic_links from_file="tool-data/shared/igv/igv_build_sites.txt" skip_startswith="#" id="0" name="1"> + +  + <dynamic_param name="site_id" value="0"/> + <dynamic_param name="site_name" value="1"/> + <dynamic_param name="site_link" value="2"/> + <dynamic_param name="site_dbkeys" value="3" split="True" separator="," /> + <dynamic_param name="site_organisms" value="4" split="True" separator="," /> + +  + <filter>${dataset.dbkey in $site_dbkeys}</filter> + +  + <url>${redirect_url}</url> + + <param type="data" name="bam_file" url="galaxy_${DATASET_HASH}.bam" /> + <param type="data" name="bai_file" url="galaxy_${DATASET_HASH}.bam.bai" metadata="bam_index" /> + <param type="template" name="site_organism" strip="True" > + $site_organisms[ $site_dbkeys.index( $bam_file.dbkey ) ] + </param> + + <param type="template" name="jnlp" url="galaxy_${DATASET_HASH}.jnlp" viewable="True" mimetype="application/x-java-jnlp-file"><?xml version="1.0" encoding="utf-8"?> <jnlp spec="1.0+" - codebase="http://www.broadinstitute.org/igvdata/jws/prod"> + codebase="${site_link}"> <information> <title>IGV 1.5</title> <vendor>The Broad Institute</vendor> @@ -54,17 +74,22 @@ <application-desc main-class="org.broad.igv.ui.IGVMainFrame"> <argument>-g</argument> - <argument>${bam_file.dbkey}</argument> + <argument>${site_organism}</argument> <argument>${bam_file.url}</argument> </application-desc> </jnlp> - </param> - </link> - - <link id="local" name="local"> - <url>http://localhost:60151/load?file=${qp($bam_file.url)}&genome=${qp($bam_…</url> - <param type="data" name="bam_file" url="galaxy_${DATASET_HASH}.bam" strip_https="True" /> - <param type="data" name="bai_file" url="galaxy_${DATASET_HASH}.bam.bai" metadata="bam_index" strip_https="True" /> - </link> + <param type="template" name="redirect_url" strip="True" > + #if $site_id.startswith( 'local_' ) + ${site_link}?file=${bam_file.qp}&genome=${site_organism}&merge=true + #elif $site_id.startswith( 'web_link_' ): + ${site_link}?sessionURL=${bam_file.qp}&genome=${site_organism}&merge=true + #else: + ${jnlp.url} + #end if + </param> + </dynamic_links> + + </display> + \ No newline at end of file diff -r 7897af491f07535915e2cd917afd0da981a1b45c -r 43a4ef4ec6d18dbbb50dc285afe01dfb8c6a29f8 display_applications/igv/vcf.xml --- /dev/null +++ b/display_applications/igv/vcf.xml @@ -0,0 +1,95 @@ +<?xml version="1.0"?> +<display id="igv_vcf" version="1.0.0" name="display with IGV"> + +  + <dynamic_links from_file="tool-data/shared/igv/igv_build_sites.txt" skip_startswith="#" id="0" name="1"> + +  + <dynamic_param name="site_id" value="0"/> + <dynamic_param name="site_name" value="1"/> + <dynamic_param name="site_link" value="2"/> + <dynamic_param name="site_dbkeys" value="3" split="True" separator="," /> + <dynamic_param name="site_organisms" value="4" split="True" separator="," /> + +  + <filter>${dataset.dbkey in $site_dbkeys}</filter> + +  + <url>${redirect_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="site_organism" strip="True" > + $site_organisms[ $site_dbkeys.index( $bgzip_file.dbkey ) ] + </param> + + <param type="template" name="jnlp" url="galaxy_${DATASET_HASH}.jnlp" viewable="True" mimetype="application/x-java-jnlp-file"><?xml version="1.0" encoding="utf-8"?> +<jnlp + spec="1.0+" + codebase="${site_link}"> + <information> + <title>IGV 1.5</title> + <vendor>The Broad Institute</vendor> + <homepage href="http://www.broadinstitute.org/igv"/> + <description>IGV Software</description> + <description kind="short">IGV</description> + </information> + <security> + <all-permissions/> + </security> + <resources> + +<j2se version="1.5+" initial-heap-size="256m" max-heap-size="1100m"/> + <jar href="igv.jar" download="eager" main="true"/> + <jar href="batik-codec.jar" download="eager"/> + <property name="apple.laf.useScreenMenuBar" value="true"/> + <property name="com.apple.mrj.application.growbox.intrudes" value="false"/> + <property name="com.apple.mrj.application.live-resize" value="true"/> + <property name="com.apple.macos.smallTabs" value="true"/> + </resources> + + <resources os="Mac" arch="i386"> + <property name="apple.awt.graphics.UseQuartz" value="false"/> + <nativelib href="hdfnative-macintel.jar"/> + </resources> + + <resources os="Mac" arch="ppc"> + <property name="apple.awt.graphics.UseQuartz" value="false"/> + <nativelib href="hdfnative-macppc.jar"/> + </resources> + + <resources os="Mac" arch="PowerPC"> + <property name="apple.awt.graphics.UseQuartz" value="false"/> + <nativelib href="hdfnative-macppc.jar"/> + </resources> + + <resources os="Windows"> + <property name="sun.java2d.noddraw" value="true"/> + <nativelib href="hdfnative-win.jar"/> + </resources> + + <resources os="Linux"> + <nativelib href="hdfnative-linux64.jar"/> + </resources> + + <application-desc main-class="org.broad.igv.ui.IGVMainFrame"> + <argument>-g</argument> + <argument>${site_organism}</argument> + <argument>${bgzip_file.url}</argument> + </application-desc> +</jnlp> + </param> + <param type="template" name="redirect_url" strip="True" > + #if $site_id.startswith( 'local_' ) + ${site_link}?file=${bgzip_file.qp}&genome=${site_organism}&merge=true + #elif $site_id.startswith( 'web_link_' ): + ${site_link}?sessionURL=${bgzip_file.qp}&genome=${site_organism}&merge=true + #else: + ${jnlp.url} + #end if + </param> + </dynamic_links> + + +</display> + \ No newline at end of file diff -r 7897af491f07535915e2cd917afd0da981a1b45c -r 43a4ef4ec6d18dbbb50dc285afe01dfb8c6a29f8 lib/galaxy/datatypes/converters/vcf_bgzip_to_tabix_converter.xml --- /dev/null +++ b/lib/galaxy/datatypes/converters/vcf_bgzip_to_tabix_converter.xml @@ -0,0 +1,14 @@ +<tool id="CONVERTER_vcf_bgzip_to_tabix_0" name="Convert BGZ VCF to tabix" version="1.0.0" hidden="true"> + + <command interpreter="python">interval_to_tabix_converter.py 'vcf' '' '$input1' '$output1'</command> + <inputs> + <page> + <param format="vcf_bgzip" name="input1" type="data" label="Choose BGZIP'd VCF file"/> + </page> + </inputs> + <outputs> + <data format="tabix" name="output1"/> + </outputs> + <help> + </help> +</tool> diff -r 7897af491f07535915e2cd917afd0da981a1b45c -r 43a4ef4ec6d18dbbb50dc285afe01dfb8c6a29f8 lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip_converter.xml --- /dev/null +++ b/lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip_converter.xml @@ -0,0 +1,14 @@ +<tool id="CONVERTER_vcf_to_vcf_bgzip_0" name="Convert VCF to VCF_BGZIP" version="1.0.0" hidden="true"> + + <command interpreter="python">bgzip.py vcf $input1 $output1</command> + <inputs> + <page> + <param format="vcf" name="input1" type="data" label="Choose Vcf file"/> + </page> + </inputs> + <outputs> + <data format="vcf_bgzip" name="output1"/> + </outputs> + <help> + </help> +</tool> diff -r 7897af491f07535915e2cd917afd0da981a1b45c -r 43a4ef4ec6d18dbbb50dc285afe01dfb8c6a29f8 run.sh --- a/run.sh +++ b/run.sh @@ -15,6 +15,7 @@ tool_sheds_conf.xml.sample universe_wsgi.ini.sample tool-data/shared/ucsc/builds.txt.sample + tool-data/shared/igv/igv_build_sites.txt.sample tool-data/*.sample static/welcome.html.sample " diff -r 7897af491f07535915e2cd917afd0da981a1b45c -r 43a4ef4ec6d18dbbb50dc285afe01dfb8c6a29f8 tool-data/shared/igv/igv_build_sites.txt.sample --- /dev/null +++ b/tool-data/shared/igv/igv_build_sites.txt.sample @@ -0,0 +1,4 @@ +#site_id site_name site_url dbkey ivg_build_name +web_link_main web current http://www.broadinstitute.org/igv/projects/current/igv.php hg19,hg_g1k_v37,hg18,1kg_ref,hg17,hg16,mm9,mm8,mm7,panTro2,rheMac2,rn4,canFam2,bosTau6,bosTau4,bosTau3,susScrofa,galGal3,cavPor3,monDom5,xenTro2,taeGut1,zebrafish,danRer6,danRer7,gasAcu1,Aplysia,Plasmodium_3D7_v2.1,Plasmodium_3D7_v5.5,Plasmodium_6.1,PlasmoDB_7.0,pvivax,GSM552910,sacCer1,sacCer2,sk1,Y55,sacCer62,spombe_709,spombe_1.55,candida,mg8,spur_2.1,spur_2.5,spur_3.0,WS201,ce6,ce4,dm3,dm2,dmel_5.9,dmel_r5.22,dmel_r5.33,tcas_2.0,tcas_3.0,ncrassa_v3,nc10,Glamblia_2.0,me49,tb927,tbgambi,lmjr,anidulans_4.1,NC_009012,U00096.2,NC_000913.2,NC_002655.2,CSavignyi_v2.1,tair8,tair9,tair10,O_Sativa_r6,osativa_6.1,B73,ZmB73_5a,ppatens_1.2,D.discoideum hg19,b37,hg18,1kg_ref,hg17,hg16,mm9,mm8,mm7,panTro2,rheMac2,rn4,canFam2,bosTau6,bosTau4,bosTau3,susScrofa,galGal3,cavPor3,monDom5,xenTro2,taeGut1,zebrafish,danRer6,danRer7,gasAcu1,Aplysia,Plasmodium_3D7_v2.1,Plasmodium_3D7_v5.5,Plasmodium_6.1,PlasmoDB_7.0,pvivax,GSM552910,sacCer1,sacCer2,sk1,Y55,sacCer62,spombe_709,spombe_1.55,candida,mg8,spur_2.1,spur_2.5,spur_3.0,WS201,ce6,ce4,dm3,dm2,dmel_5.9,dmel_r5.22,dmel_r5.33,tcas_2.0,tcas_3.0,ncrassa_v3,nc10,Glamblia_2.0,me49,tb927,tbgambi,lmjr,anidulans_4.1,NC_009012,U00096.2,NC_000913.2,NC_002655.2,CSavignyi_v2.1,tair8,tair9,tair10,O_Sativa_r6,osativa_6.1,B73,ZmB73_5a,ppatens_1.2,D.discoideum +#web_jnlp_1.5 web 1.5 http://www.broadinstitute.org/igvdata/jws/prod hg19,hg_g1k_v37,hg18,1kg_ref,hg17,hg16,mm9,mm8,mm7,panTro2,rheMac2,rn4,canFam2,bosTau6,bosTau4,bosTau3,susScrofa,galGal3,cavPor3,monDom5,xenTro2,taeGut1,zebrafish,danRer6,danRer7,gasAcu1,Aplysia,Plasmodium_3D7_v2.1,Plasmodium_3D7_v5.5,Plasmodium_6.1,PlasmoDB_7.0,pvivax,GSM552910,sacCer1,sacCer2,sk1,Y55,sacCer62,spombe_709,spombe_1.55,candida,mg8,spur_2.1,spur_2.5,spur_3.0,WS201,ce6,ce4,dm3,dm2,dmel_5.9,dmel_r5.22,dmel_r5.33,tcas_2.0,tcas_3.0,ncrassa_v3,nc10,Glamblia_2.0,me49,tb927,tbgambi,lmjr,anidulans_4.1,NC_009012,U00096.2,NC_000913.2,NC_002655.2,CSavignyi_v2.1,tair8,tair9,tair10,O_Sativa_r6,osativa_6.1,B73,ZmB73_5a,ppatens_1.2,D.discoideum hg19,b37,hg18,1kg_ref,hg17,hg16,mm9,mm8,mm7,panTro2,rheMac2,rn4,canFam2,bosTau6,bosTau4,bosTau3,susScrofa,galGal3,cavPor3,monDom5,xenTro2,taeGut1,zebrafish,danRer6,danRer7,gasAcu1,Aplysia,Plasmodium_3D7_v2.1,Plasmodium_3D7_v5.5,Plasmodium_6.1,PlasmoDB_7.0,pvivax,GSM552910,sacCer1,sacCer2,sk1,Y55,sacCer62,spombe_709,spombe_1.55,candida,mg8,spur_2.1,spur_2.5,spur_3.0,WS201,ce6,ce4,dm3,dm2,dmel_5.9,dmel_r5.22,dmel_r5.33,tcas_2.0,tcas_3.0,ncrassa_v3,nc10,Glamblia_2.0,me49,tb927,tbgambi,lmjr,anidulans_4.1,NC_009012,U00096.2,NC_000913.2,NC_002655.2,CSavignyi_v2.1,tair8,tair9,tair10,O_Sativa_r6,osativa_6.1,B73,ZmB73_5a,ppatens_1.2,D.discoideum +local_default local http://localhost:60151/load hg19,hg_g1k_v37,hg18,1kg_ref,hg17,hg16,mm9,mm8,mm7,panTro2,rheMac2,rn4,canFam2,bosTau6,bosTau4,bosTau3,susScrofa,galGal3,cavPor3,monDom5,xenTro2,taeGut1,zebrafish,danRer6,danRer7,gasAcu1,Aplysia,Plasmodium_3D7_v2.1,Plasmodium_3D7_v5.5,Plasmodium_6.1,PlasmoDB_7.0,pvivax,GSM552910,sacCer1,sacCer2,sk1,Y55,sacCer62,spombe_709,spombe_1.55,candida,mg8,spur_2.1,spur_2.5,spur_3.0,WS201,ce6,ce4,dm3,dm2,dmel_5.9,dmel_r5.22,dmel_r5.33,tcas_2.0,tcas_3.0,ncrassa_v3,nc10,Glamblia_2.0,me49,tb927,tbgambi,lmjr,anidulans_4.1,NC_009012,U00096.2,NC_000913.2,NC_002655.2,CSavignyi_v2.1,tair8,tair9,tair10,O_Sativa_r6,osativa_6.1,B73,ZmB73_5a,ppatens_1.2,D.discoideum hg19,b37,hg18,1kg_ref,hg17,hg16,mm9,mm8,mm7,panTro2,rheMac2,rn4,canFam2,bosTau6,bosTau4,bosTau3,susScrofa,galGal3,cavPor3,monDom5,xenTro2,taeGut1,zebrafish,danRer6,danRer7,gasAcu1,Aplysia,Plasmodium_3D7_v2.1,Plasmodium_3D7_v5.5,Plasmodium_6.1,PlasmoDB_7.0,pvivax,GSM552910,sacCer1,sacCer2,sk1,Y55,sacCer62,spombe_709,spombe_1.55,candida,mg8,spur_2.1,spur_2.5,spur_3.0,WS201,ce6,ce4,dm3,dm2,dmel_5.9,dmel_r5.22,dmel_r5.33,tcas_2.0,tcas_3.0,ncrassa_v3,nc10,Glamblia_2.0,me49,tb927,tbgambi,lmjr,anidulans_4.1,NC_009012,U00096.2,NC_000913.2,NC_002655.2,CSavignyi_v2.1,tair8,tair9,tair10,O_Sativa_r6,osativa_6.1,B73,ZmB73_5a,ppatens_1.2,D.discoideum \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Fix bug in Trackster's 'Add Datasets to Visualization' button.
by Bitbucket 15 Nov '11

15 Nov '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/7897af491f07/ changeset: 7897af491f07 user: jgoecks date: 2011-11-15 21:50:36 summary: Fix bug in Trackster's 'Add Datasets to Visualization' button. affected #: 1 file diff -r a87d7b85c5771372550bd786bd15606f8e29cf41 -r 7897af491f07535915e2cd917afd0da981a1b45c static/scripts/trackster.js --- a/static/scripts/trackster.js +++ b/static/scripts/trackster.js @@ -909,7 +909,7 @@ this.content_div = this.viewport_container; is_container(this.viewport_container, view); // Introduction div shown when there are no tracks. - this.intro_div = $("<div/>").addClass("intro"); + this.intro_div = $("<div/>").addClass("intro").appendTo(this.viewport_container).hide(); var add_tracks_button = $("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function () { add_tracks(); }); @@ -1077,10 +1077,10 @@ /** Add or remove intro div depending on view state. */ update_intro_div: function() { if (this.drawables.length === 0) { - this.intro_div.appendTo(this.viewport_container); + this.intro_div.show(); } else { - this.intro_div.remove(); + this.intro_div.hide(); } }, update_location: function(low, high) { Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: fubar: Fixes for the new horrible FastQC html layout. Now wastes a whole lot of space on the left
by Bitbucket 15 Nov '11

15 Nov '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/a87d7b85c577/ changeset: a87d7b85c577 user: fubar date: 2011-11-15 21:34:51 summary: Fixes for the new horrible FastQC html layout. Now wastes a whole lot of space on the left with a fancy TOC - ugh. Test updated also. affected #: 3 files diff -r e637518dada717ac2e1cde85c28d2de0f106fe8a -r a87d7b85c5771372550bd786bd15606f8e29cf41 test-data/fastqc_report.html --- a/test-data/fastqc_report.html +++ b/test-data/fastqc_report.html @@ -1,117 +1,224 @@ <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Strict//EN"><html> -<head><title>1000gsample.fastq FastQC Report</title> +<head><title>dataset_1.dat FastQC Report</title><style type="text/css"> - body { - font-family: sans-serif; - color: #000000; - background-color: #FFFFFF; - border: 0; - margin: 0; - padding: 0; - } + @media screen { + div.summary { + width: 18em; + position:fixed; + top: 3em; + margin:1em 0 0 1em; + } + + div.main { + display:block; + position:absolute; + overflow:auto; + height:auto; + width:auto; + top:4.5em; + bottom:2.3em; + left:18em; + right:0; + border-left: 1px solid #CCC; + padding:0 0 0 1em; + background-color: white; + z-index:1; + } + + div.header { + background-color: #EEE; + border:0; + margin:0; + padding: 0.5em; + font-size: 200%; + font-weight: bold; + position:fixed; + width:100%; + top:0; + left:0; + z-index:2; + } + + div.footer { + background-color: #EEE; + border:0; + margin:0; + padding:0.5em; + height: 1.3em; + overflow:hidden; + font-size: 100%; + font-weight: bold; + position:fixed; + bottom:0; + width:100%; + z-index:2; + } + + img.indented { + margin-left: 3em; + } + } + + @media print { + img { + max-width:100% !important; + page-break-inside: avoid; + } + h2, h3 { + page-break-after: avoid; + } + div.header { + background-color: #FFF; + } + + } + + body { + font-family: sans-serif; + color: #000; + background-color: #FFF; + border: 0; + margin: 0; + padding: 0; + } + + div.header { + border:0; + margin:0; + padding: 0.5em; + font-size: 200%; + font-weight: bold; + width:100%; + } + + #header_title { + display:inline-block; + float:left; + clear:left; + } + #header_filename { + display:inline-block; + float:right; + clear:right; + font-size: 50%; + margin-right:2em; + text-align: right; + } + + div.header h3 { + font-size: 50%; + margin-bottom: 0; + } + + div.summary ul { + padding-left:0; + list-style-type:none; + } + + div.summary ul li img { + margin-bottom:-0.5em; + margin-top:0.5em; + } + + div.main { + background-color: white; + } - div.header { - background-color: #EEEEEE; - border:0; - margin:0; - padding: 0.5em; - font-size: 200%; - font-weight: bold; - } + div.module { + padding-bottom:1.5em; + padding-top:1.5em; + } + + div.footer { + background-color: #EEE; + border:0; + margin:0; + padding: 0.5em; + font-size: 100%; + font-weight: bold; + width:100%; + } - div.footer { - background-color: #EEEEEE; - border:0; - margin:0; - padding: 0.5em; - font-size: 100%; - font-weight: bold; - } - div.main { - margin-left: 2em; - margin-right: 2em; - } + a { + color: #000080; + } + + a:hover { + color: #800000; + } - div.module { - padding-bottom:1.5em; - padding-top:1.5em; - } + h2 { + color: #800000; + padding-bottom: 0; + margin-bottom: 0; + clear:left; + } - a { - color: #000080; - } + table { + margin-left: 3em; + text-align: center; + } + + th { + text-align: center; + background-color: #000080; + color: #FFF; + padding: 0.4em; + } + + td { + font-family: monospace; + text-align: left; + background-color: #EEE; + color: #000; + padding: 0.4em; + } - a:hover { - color: #800000; - } - - h2 { - color: #800000; - padding-bottom: 0; - margin-bottom: 0; - } + img { + padding-top: 0; + margin-top: 0; + border-top: 0; + } - table { - margin-left: 3em; - text-align: center; - } - - th { - text-align: center; - background-color: #000080; - color: #FFFFFF; - padding: 0.4em; - } - - td { - font-family: monospace; - text-align: left; - background-color: #EEEEEE; - color: #000000; - padding: 0.4em; - } - - img { - padding-top: 0; - margin-top: 0; - border-top: 0; - } - - img.indented { - margin-left: 3em; - } - - p { - padding-top: 0; - margin-top: 0; - } + + p { + padding-top: 0; + margin-top: 0; + } + </style></head><body> -<div class="header"><img src="Icons/fastqc_icon.png">FastQC Report</div> +<div class="header"> +<div id="header_title"><img src="fastqc_icon.png" alt="FastQC">FastQC Report</div> +<div id="header_filename"> +Wed 16 Nov 2011<br /> +dataset_1.dat +</div> +</div> +<div class="summary"> +<h2>Summary</h2> +<ul> +<li><img src="tick.png" alt="[PASS]"><a href="#M0">Basic Statistics</a></li> +<li><img src="warning.png" alt="[WARNING]"><a href="#M1">Per base sequence quality</a></li> +<li><img src="warning.png" alt="[WARNING]"><a href="#M2">Per sequence quality scores</a></li> +<li><img src="warning.png" alt="[WARNING]"><a href="#M3">Per base sequence content</a></li> +<li><img src="tick.png" alt="[PASS]"><a href="#M4">Per base GC content</a></li> +<li><img src="warning.png" alt="[WARNING]"><a href="#M5">Per sequence GC content</a></li> +<li><img src="tick.png" alt="[PASS]"><a href="#M6">Per base N content</a></li> +<li><img src="tick.png" alt="[PASS]"><a href="#M7">Sequence Length Distribution</a></li> +<li><img src="tick.png" alt="[PASS]"><a href="#M8">Sequence Duplication Levels</a></li> +<li><img src="warning.png" alt="[WARNING]"><a href="#M9">Overrepresented sequences</a></li> +<li><img src="error.png" alt="[FAIL]"><a href="#M10">Kmer Content</a></li> +</ul> +</div><div class="main"> -<h3>Wed 27 Apr 2011</h3> -<h3>1000gsample.fastq</h3> -<h2 id="summary">Summary</h2> -<ul> -<li><img src="Icons/tick.png" alt="[PASS]"><a href="#M0">Basic Statistics</a></li> -<li><img src="Icons/warning.png" alt="[WARNING]"><a href="#M1">Per base sequence quality</a></li> -<li><img src="Icons/warning.png" alt="[WARNING]"><a href="#M2">Per sequence quality scores</a></li> -<li><img src="Icons/tick.png" alt="[PASS]"><a href="#M3">Per base sequence content</a></li> -<li><img src="Icons/tick.png" alt="[PASS]"><a href="#M4">Per base GC content</a></li> -<li><img src="Icons/warning.png" alt="[WARNING]"><a href="#M5">Per sequence GC content</a></li> -<li><img src="Icons/tick.png" alt="[PASS]"><a href="#M6">Per base N content</a></li> -<li><img src="Icons/tick.png" alt="[PASS]"><a href="#M7">Sequence Length Distribution</a></li> -<li><img src="Icons/tick.png" alt="[PASS]"><a href="#M8">Sequence Duplication Levels</a></li> -<li><img src="Icons/warning.png" alt="[WARNING]"><a href="#M9">Overrepresented sequences</a></li> -<li><img src="Icons/error.png" alt="[FAIL]"><a href="#M10">Kmer Content</a></li> -</ul> -<div class="module"><h2 id="M0"><img src="Icons/tick.png" alt="[FAIL]"> Basic Statistics</h2> +<div class="module"><h2 id="M0"><img src="tick.png" alt="[OK]"> Basic Statistics</h2><table><tr><th>Measure</th> @@ -119,7 +226,7 @@ </tr><tr><td>Filename</td> -<td>1000gsample.fastq</td> +<td>dataset_1.dat</td></tr><tr><td>File type</td> @@ -134,6 +241,10 @@ <td>5000</td></tr><tr> +<td>Filtered Sequences</td> +<td>0</td> +</tr> +<tr><td>Sequence length</td><td>54</td></tr> @@ -142,32 +253,32 @@ <td>43</td></tr></table> -<p><a href="#summary">Back to summary</a></div> -<div class="module"><h2 id="M1"><img src="Icons/warning.png" alt="[FAIL]"> Per base sequence quality</h2> -<p><img class="indented" src="Images/per_base_quality.png"></p> -<p><a href="#summary">Back to summary</a></div> -<div class="module"><h2 id="M2"><img src="Icons/warning.png" alt="[FAIL]"> Per sequence quality scores</h2> -<p><img class="indented" src="Images/per_sequence_quality.png"></p> -<p><a href="#summary">Back to summary</a></div> -<div class="module"><h2 id="M3"><img src="Icons/tick.png" alt="[FAIL]"> Per base sequence content</h2> -<p><img class="indented" src="Images/per_base_sequence_content.png"></p> -<p><a href="#summary">Back to summary</a></div> -<div class="module"><h2 id="M4"><img src="Icons/tick.png" alt="[FAIL]"> Per base GC content</h2> -<p><img class="indented" src="Images/per_base_gc_content.png"></p> -<p><a href="#summary">Back to summary</a></div> -<div class="module"><h2 id="M5"><img src="Icons/warning.png" alt="[FAIL]"> Per sequence GC content</h2> -<p><img class="indented" src="Images/per_sequence_gc_content.png"></p> -<p><a href="#summary">Back to summary</a></div> -<div class="module"><h2 id="M6"><img src="Icons/tick.png" alt="[FAIL]"> Per base N content</h2> -<p><img class="indented" src="Images/per_base_n_content.png"></p> -<p><a href="#summary">Back to summary</a></div> -<div class="module"><h2 id="M7"><img src="Icons/tick.png" alt="[FAIL]"> Sequence Length Distribution</h2> -<p><img class="indented" src="Images/sequence_length_distribution.png"></p> -<p><a href="#summary">Back to summary</a></div> -<div class="module"><h2 id="M8"><img src="Icons/tick.png" alt="[FAIL]"> Sequence Duplication Levels</h2> -<p><img class="indented" src="Images/duplication_levels.png"></p> -<p><a href="#summary">Back to summary</a></div> -<div class="module"><h2 id="M9"><img src="Icons/warning.png" alt="[FAIL]"> Overrepresented sequences</h2> +</div> +<div class="module"><h2 id="M1"><img src="warning.png" alt="[WARN]"> Per base sequence quality</h2> +<p><img class="indented" src="per_base_quality.png" alt="Per base quality graph"></p> +</div> +<div class="module"><h2 id="M2"><img src="warning.png" alt="[WARN]"> Per sequence quality scores</h2> +<p><img class="indented" src="per_sequence_quality.png" alt="Per Sequence quality graph"></p> +</div> +<div class="module"><h2 id="M3"><img src="warning.png" alt="[WARN]"> Per base sequence content</h2> +<p><img class="indented" src="per_base_sequence_content.png" alt="Per base sequence content"></p> +</div> +<div class="module"><h2 id="M4"><img src="tick.png" alt="[OK]"> Per base GC content</h2> +<p><img class="indented" src="per_base_gc_content.png" alt="Per base GC content graph"></p> +</div> +<div class="module"><h2 id="M5"><img src="warning.png" alt="[WARN]"> Per sequence GC content</h2> +<p><img class="indented" src="per_sequence_gc_content.png" alt="Per sequence GC content graph"></p> +</div> +<div class="module"><h2 id="M6"><img src="tick.png" alt="[OK]"> Per base N content</h2> +<p><img class="indented" src="per_base_n_content.png" alt="N content graph"></p> +</div> +<div class="module"><h2 id="M7"><img src="tick.png" alt="[OK]"> Sequence Length Distribution</h2> +<p><img class="indented" src="sequence_length_distribution.png" alt="Sequence length distribution"></p> +</div> +<div class="module"><h2 id="M8"><img src="tick.png" alt="[OK]"> Sequence Duplication Levels</h2> +<p><img class="indented" src="duplication_levels.png" alt="Duplication level graph"></p> +</div> +<div class="module"><h2 id="M9"><img src="warning.png" alt="[WARN]"> Overrepresented sequences</h2><table><tr><th>Sequence</th> @@ -188,9 +299,9 @@ <td>Illumina Paired End PCR Primer 2 (100% over 35bp)</td></tr></table> -<p><a href="#summary">Back to summary</a></div> -<div class="module"><h2 id="M10"><img src="Icons/error.png" alt="[FAIL]"> Kmer Content</h2> -<p><img class="indented" src="Images/kmer_profiles.png"></p> +</div> +<div class="module"><h2 id="M10"><img src="error.png" alt="[FAIL]"> Kmer Content</h2> +<p><img class="indented" src="kmer_profiles.png" alt="Kmer graph"></p><table><tr><th>Sequence</th> @@ -201,1132 +312,1498 @@ </tr><tr><td>CCCCC</td> -<td>1110</td> -<td>9.557241</td> -<td>23.193876</td> -<td>44</td> +<td>1180</td> +<td>9.957459</td> +<td>29.638031</td> +<td>50</td></tr><tr><td>AAAAA</td> -<td>2130</td> -<td>4.1300144</td> -<td>5.698024</td> -<td>7</td> +<td>2175</td> +<td>4.133217</td> +<td>7.129659</td> +<td>47</td></tr><tr><td>CTCCC</td> -<td>530</td> -<td>3.5749238</td> +<td>555</td> +<td>3.668942</td><td>11.56272</td><td>11</td></tr><tr><td>CCTCC</td> -<td>510</td> -<td>3.440021</td> +<td>525</td> +<td>3.4706206</td><td>11.56272</td><td>14</td></tr><tr><td>CTGGG</td><td>465</td> -<td>3.1575248</td> -<td>8.314476</td> -<td>45</td> +<td>3.0945942</td> +<td>8.331139</td> +<td>39</td> +</tr> +<tr> +<td>GGGGG</td> +<td>350</td> +<td>2.9865708</td> +<td>12.818572</td> +<td>41</td></tr><tr><td>TGGAA</td> -<td>785</td> -<td>2.929684</td> +<td>800</td> +<td>2.9261596</td><td>6.397646</td><td>17</td></tr><tr> -<td>GGGGG</td> -<td>335</td> -<td>2.9167063</td> -<td>10.660779</td> -<td>6</td> +<td>CCCAG</td> +<td>455</td> +<td>2.855999</td> +<td>9.429343</td> +<td>40</td></tr><tr><td>GAATG</td><td>775</td> -<td>2.8923633</td> +<td>2.8347175</td><td>10.053445</td><td>20</td></tr><tr> -<td>CCCAG</td> -<td>450</td> -<td>2.8820548</td> -<td>7.8420706</td> -<td>22</td> +<td>GTGTG</td> +<td>530</td> +<td>2.763172</td> +<td>7.8240557</td> +<td>33</td></tr><tr> -<td>GTGTG</td> -<td>520</td> -<td>2.7661672</td> -<td>6.513526</td> -<td>23</td> +<td>GGGAG</td> +<td>435</td> +<td>2.7487729</td> +<td>6.3220544</td> +<td>43</td></tr><tr><td>TGTGT</td> -<td>660</td> -<td>2.744307</td> +<td>670</td> +<td>2.7303638</td><td>6.109576</td><td>27</td></tr><tr> -<td>GGGAG</td> -<td>425</td> -<td>2.7401958</td> -<td>6.315732</td> -<td>6</td> -</tr> -<tr><td>ATGGA</td> -<td>730</td> -<td>2.7244196</td> +<td>735</td> +<td>2.688409</td><td>6.397646</td><td>20</td></tr><tr> -<td>GCTGG</td> -<td>395</td> -<td>2.6821985</td> -<td>6.651581</td> -<td>16</td> -</tr> -<tr> -<td>GGAGG</td> -<td>410</td> -<td>2.643483</td> -<td>7.894665</td> -<td>7</td> -</tr> -<tr><td>GGAAT</td> -<td>700</td> -<td>2.612457</td> +<td>730</td> +<td>2.6701207</td><td>7.3115954</td><td>19</td></tr><tr> +<td>GCTGG</td> +<td>400</td> +<td>2.6620166</td> +<td>8.322799</td> +<td>31</td> +</tr> +<tr> +<td>GGAGG</td> +<td>420</td> +<td>2.6539874</td> +<td>7.9104857</td> +<td>40</td> +</tr> +<tr><td>GCAGG</td> -<td>400</td> -<td>2.5732677</td> +<td>405</td> +<td>2.5535064</td><td>14.17877</td><td>16</td></tr><tr><td>CCTGG</td> -<td>370</td> -<td>2.5068476</td> +<td>375</td> +<td>2.4900866</td><td>6.6367774</td><td>7</td></tr><tr><td>CAGCC</td> -<td>380</td> -<td>2.4337354</td> -<td>6.273657</td> -<td>4</td> +<td>390</td> +<td>2.4479992</td> +<td>6.279937</td> +<td>38</td> +</tr> +<tr> +<td>GGCTG</td> +<td>365</td> +<td>2.4290898</td> +<td>9.97737</td> +<td>24</td></tr><tr><td>TGGGA</td> -<td>480</td> -<td>2.419065</td> +<td>490</td> +<td>2.4202447</td><td>7.40506</td><td>20</td></tr><tr> +<td>CCAGC</td> +<td>385</td> +<td>2.4166145</td> +<td>6.286229</td> +<td>41</td> +</tr> +<tr><td>AATGG</td> -<td>645</td> -<td>2.4071925</td> +<td>660</td> +<td>2.4140818</td><td>5.4836965</td><td>18</td></tr><tr> +<td>GCCTG</td> +<td>360</td> +<td>2.3904827</td> +<td>8.295971</td> +<td>5</td> +</tr> +<tr><td>GCCTC</td> -<td>355</td> -<td>2.3998654</td> -<td>6.622006</td> -<td>2</td> +<td>360</td> +<td>2.3851626</td> +<td>6.6286345</td> +<td>31</td></tr><tr><td>CCCTC</td> -<td>355</td> -<td>2.394524</td> -<td>8.259085</td> -<td>13</td> +<td>360</td> +<td>2.379854</td> +<td>8.267352</td> +<td>34</td></tr><tr> -<td>CCAGC</td> -<td>370</td> -<td>2.3696895</td> -<td>6.2736564</td> -<td>14</td> +<td>CTGTG</td> +<td>450</td> +<td>2.3408678</td> +<td>9.09864</td> +<td>44</td></tr><tr><td>GGAAG</td> -<td>495</td> -<td>2.3634295</td> +<td>500</td> +<td>2.3397229</td><td>14.031037</td><td>2</td></tr><tr> -<td>GGCTG</td> -<td>345</td> -<td>2.3426795</td> -<td>9.97737</td> -<td>24</td> +<td>CAGCA</td> +<td>500</td> +<td>2.32932</td> +<td>10.47649</td> +<td>14</td></tr><tr><td>CAGGA</td> -<td>490</td> -<td>2.3343499</td> +<td>495</td> +<td>2.3111706</td><td>13.99981</td><td>17</td></tr><tr> -<td>CCAGG</td> -<td>360</td> -<td>2.3107867</td> -<td>6.2876506</td> -<td>11</td> -</tr> -<tr> -<td>CTGTG</td> -<td>435</td> -<td>2.3088553</td> -<td>9.09864</td> -<td>44</td> -</tr> -<tr> -<td>GCCTG</td> -<td>340</td> -<td>2.3035896</td> -<td>8.295971</td> -<td>5</td> -</tr> -<tr><td>TCCCA</td> -<td>460</td> -<td>2.3028264</td> -<td>6.1297736</td> -<td>9</td> +<td>470</td> +<td>2.305994</td> +<td>7.370469</td> +<td>39</td></tr><tr><td>CTGCC</td> -<td>340</td> -<td>2.2984629</td> +<td>345</td> +<td>2.285781</td><td>8.277508</td><td>10</td></tr><tr> -<td>CAGCA</td> -<td>480</td> -<td>2.2816207</td> -<td>10.47649</td> -<td>14</td> +<td>GGTGG</td> +<td>340</td> +<td>2.2677608</td> +<td>5.009832</td> +<td>42</td> +</tr> +<tr> +<td>CCAGG</td> +<td>360</td> +<td>2.264732</td> +<td>6.300251</td> +<td>41</td></tr><tr><td>TTCCT</td> -<td>545</td> -<td>2.256056</td> +<td>555</td> +<td>2.2516627</td><td>7.0961456</td><td>1</td></tr><tr> +<td>TCCCC</td> +<td>335</td> +<td>2.2145865</td> +<td>8.267353</td> +<td>29</td> +</tr> +<tr> +<td>CAGGC</td> +<td>350</td> +<td>2.2018228</td> +<td>6.300251</td> +<td>42</td> +</tr> +<tr><td>CTCCT</td> -<td>415</td> -<td>2.1929073</td> +<td>425</td> +<td>2.2009897</td><td>6.4701333</td><td>15</td></tr><tr> -<td>TCCCC</td> -<td>325</td> -<td>2.1921701</td> -<td>6.6072683</td> -<td>28</td> -</tr> -<tr> -<td>CAGGC</td> -<td>335</td> -<td>2.1503155</td> -<td>6.2876506</td> -<td>14</td> +<td>GGCAG</td> +<td>340</td> +<td>2.1436844</td> +<td>6.301676</td> +<td>16</td></tr><tr><td>CCCCA</td> -<td>335</td> -<td>2.1407545</td> -<td>6.259694</td> -<td>20</td> +<td>340</td> +<td>2.129403</td> +<td>6.26596</td> +<td>31</td> +</tr> +<tr> +<td>CTCTG</td> +<td>410</td> +<td>2.1280441</td> +<td>5.1928453</td> +<td>48</td></tr><tr><td>TGGTG</td> -<td>400</td> -<td>2.127821</td> -<td>6.513526</td> -<td>9</td> +<td>405</td> +<td>2.1114805</td> +<td>6.520046</td> +<td>33</td> +</tr> +<tr> +<td>TTCCA</td> +<td>545</td> +<td>2.094778</td> +<td>6.7295837</td> +<td>33</td></tr><tr><td>CCCCT</td><td>315</td> -<td>2.1247187</td> +<td>2.0823722</td><td>6.607268</td><td>12</td></tr><tr> -<td>GGCAG</td> -<td>330</td> -<td>2.122946</td> -<td>6.301676</td> -<td>16</td> +<td>CTCAG</td> +<td>420</td> +<td>2.0652719</td> +<td>6.149596</td> +<td>46</td></tr><tr> -<td>CTCTG</td> -<td>400</td> -<td>2.1183603</td> -<td>5.187652</td> -<td>16</td> -</tr> -<tr> -<td>TTCCA</td> -<td>540</td> -<td>2.1177678</td> -<td>6.7228537</td> -<td>28</td> +<td>AGGGA</td> +<td>440</td> +<td>2.0589561</td> +<td>7.0225415</td> +<td>31</td></tr><tr><td>CAGAG</td><td>440</td> -<td>2.0961509</td> -<td>5.833255</td> -<td>28</td> +<td>2.054374</td> +<td>5.8390937</td> +<td>38</td> +</tr> +<tr> +<td>AGCAG</td> +<td>440</td> +<td>2.0543735</td> +<td>10.499857</td> +<td>15</td></tr><tr><td>CCCTG</td><td>310</td> -<td>2.095657</td> +<td>2.05389</td><td>6.622006</td><td>24</td></tr><tr> -<td>AGGGA</td> -<td>435</td> -<td>2.0769534</td> -<td>5.846266</td> -<td>1</td> -</tr> -<tr> -<td>CTCAG</td> -<td>410</td> -<td>2.0570977</td> -<td>6.143447</td> -<td>24</td> -</tr> -<tr><td>CTTCC</td> -<td>385</td> -<td>2.034384</td> +<td>390</td> +<td>2.0197318</td><td>6.4701333</td><td>17</td></tr><tr> -<td>AGCAG</td> -<td>425</td> -<td>2.0246909</td> -<td>10.499857</td> -<td>15</td> -</tr> -<tr><td>AGGAA</td> -<td>570</td> -<td>2.015381</td> +<td>580</td> +<td>2.0098667</td><td>10.390455</td><td>18</td></tr><tr> +<td>AGAGC</td> +<td>430</td> +<td>2.0076835</td> +<td>10.499858</td> +<td>5</td> +</tr> +<tr> +<td>TCTCC</td> +<td>385</td> +<td>1.9938378</td> +<td>5.181288</td> +<td>29</td> +</tr> +<tr><td>TCCTC</td> -<td>380</td> -<td>2.0079634</td> -<td>5.1761065</td> -<td>1</td> +<td>385</td> +<td>1.9938378</td> +<td>5.181288</td> +<td>48</td></tr><tr><td>TCAGC</td> -<td>400</td> -<td>2.0069244</td> +<td>405</td> +<td>1.9915122</td><td>12.286894</td><td>44</td></tr><tr> -<td>AGAGC</td> -<td>420</td> -<td>2.0008712</td> -<td>10.499858</td> -<td>5</td> +<td>TGCTG</td> +<td>380</td> +<td>1.9767327</td> +<td>6.5055346</td> +<td>47</td> +</tr> +<tr> +<td>CACCC</td> +<td>315</td> +<td>1.9728295</td> +<td>6.259694</td> +<td>9</td></tr><tr><td>TCCTG</td> -<td>375</td> -<td>1.9859626</td> +<td>380</td> +<td>1.9723336</td><td>6.4845653</td><td>8</td></tr><tr> -<td>TCTCC</td> -<td>375</td> -<td>1.9815428</td> -<td>5.1761065</td> -<td>8</td> -</tr> -<tr> -<td>CACCC</td> +<td>CAGGG</td><td>310</td> -<td>1.9809967</td> -<td>6.259694</td> -<td>9</td> -</tr> -<tr> -<td>TGTGG</td> -<td>370</td> -<td>1.9682345</td> -<td>5.210821</td> -<td>4</td> +<td>1.954536</td> +<td>6.3016763</td> +<td>21</td></tr><tr><td>GATGG</td> -<td>390</td> -<td>1.9654902</td> +<td>395</td> +<td>1.9510134</td><td>6.1708827</td><td>1</td></tr><tr><td>TGGCT</td> -<td>370</td> -<td>1.9638538</td> +<td>375</td> +<td>1.9507233</td><td>9.098641</td><td>45</td></tr><tr> -<td>TCCCT</td> -<td>370</td> -<td>1.9551222</td> -<td>5.1761065</td> -<td>37</td> -</tr> -<tr> -<td>CAGGG</td> -<td>300</td> -<td>1.9299511</td> -<td>6.3016763</td> -<td>21</td> -</tr> -<tr><td>AAGAG</td> -<td>545</td> -<td>1.9269869</td> +<td>560</td> +<td>1.9405607</td><td>9.524584</td><td>4</td></tr><tr> +<td>TGTGG</td> +<td>370</td> +<td>1.929007</td> +<td>6.5200467</td> +<td>30</td> +</tr> +<tr> +<td>CTGAG</td> +<td>390</td> +<td>1.9220302</td> +<td>6.163313</td> +<td>35</td> +</tr> +<tr> +<td>CCTGT</td> +<td>370</td> +<td>1.9204301</td> +<td>6.4845653</td> +<td>6</td> +</tr> +<tr><td>CAGAA</td> -<td>545</td> -<td>1.9226985</td> +<td>555</td> +<td>1.9189543</td><td>6.0476103</td><td>6</td></tr><tr> -<td>CTGAG</td> +<td>TCCCT</td> +<td>370</td> +<td>1.9161558</td> +<td>6.4766097</td> +<td>33</td> +</tr> +<tr> +<td>CCCAC</td> +<td>305</td> +<td>1.9101999</td> +<td>6.259694</td> +<td>4</td> +</tr> +<tr> +<td>CACCA</td> +<td>405</td> +<td>1.8825499</td> +<td>6.9757566</td> +<td>33</td> +</tr> +<tr> +<td>AAAGA</td> +<td>730</td> +<td>1.8732982</td> +<td>5.1399345</td> +<td>42</td> +</tr> +<tr> +<td>CAGTG</td><td>380</td> -<td>1.9108309</td> -<td>6.15715</td> -<td>11</td> +<td>1.8727474</td> +<td>6.163313</td> +<td>30</td> +</tr> +<tr> +<td>GAAGA</td> +<td>540</td> +<td>1.8712552</td> +<td>7.792842</td> +<td>26</td></tr><tr><td>TCTCT</td><td>460</td> -<td>1.9041945</td> +<td>1.8662432</td><td>5.068676</td><td>8</td></tr><tr> +<td>TTTCC</td> +<td>460</td> +<td>1.8662429</td> +<td>5.073749</td> +<td>38</td> +</tr> +<tr><td>GAGGC</td><td>295</td> -<td>1.897785</td> +<td>1.8599615</td><td>6.301676</td><td>22</td></tr><tr> -<td>CCCAC</td> -<td>295</td> -<td>1.885142</td> -<td>6.259694</td> -<td>4</td> +<td>TCTGT</td> +<td>455</td> +<td>1.8500755</td> +<td>5.0850673</td> +<td>49</td></tr><tr><td>CCTGC</td><td>275</td> -<td>1.8590509</td> +<td>1.8219992</td><td>9.93301</td><td>6</td></tr><tr> -<td>CCTGT</td> +<td>CCTCT</td><td>350</td> -<td>1.8535651</td> -<td>6.4845653</td> -<td>6</td> -</tr> -<tr> -<td>TTTCC</td> -<td>445</td> -<td>1.8421009</td> -<td>5.0686755</td> -<td>14</td> +<td>1.8125799</td> +<td>7.7641597</td> +<td>2</td></tr><tr><td>TGCCT</td><td>345</td> -<td>1.8270856</td> +<td>1.7906713</td><td>5.187652</td><td>12</td></tr><tr> -<td>CACAC</td> -<td>380</td> -<td>1.8022629</td> -<td>5.8073177</td> -<td>17</td> -</tr> -<tr> -<td>CCTCT</td> -<td>340</td> -<td>1.7965988</td> -<td>7.7641597</td> -<td>2</td> -</tr> -<tr><td>TTCCC</td> -<td>340</td> -<td>1.7965986</td> +<td>345</td> +<td>1.7866857</td><td>6.470133</td><td>18</td></tr><tr> -<td>GAAGA</td> -<td>500</td> -<td>1.767878</td> -<td>7.792842</td> -<td>26</td> +<td>GAGGG</td> +<td>280</td> +<td>1.769325</td> +<td>6.3283887</td> +<td>41</td> +</tr> +<tr> +<td>CACAC</td> +<td>380</td> +<td>1.7663432</td> +<td>5.813131</td> +<td>33</td> +</tr> +<tr> +<td>TCTGC</td> +<td>340</td> +<td>1.7647195</td> +<td>5.1980486</td> +<td>42</td></tr><tr><td>CTGGC</td> -<td>260</td> -<td>1.7615684</td> -<td>6.636777</td> -<td>8</td> +<td>265</td> +<td>1.7596608</td> +<td>6.6434207</td> +<td>43</td></tr><tr><td>TTCAG</td> -<td>440</td> -<td>1.7294377</td> +<td>455</td> +<td>1.7527524</td><td>9.6255</td><td>12</td></tr><tr> +<td>AGCCA</td> +<td>375</td> +<td>1.74699</td> +<td>5.8319354</td> +<td>39</td> +</tr> +<tr><td>CTCTC</td> -<td>325</td> -<td>1.717337</td> +<td>335</td> +<td>1.7348979</td><td>5.1761065</td><td>3</td></tr><tr> -<td>GTGGT</td> -<td>320</td> -<td>1.7022567</td> -<td>5.2108207</td> -<td>24</td> -</tr> -<tr><td>GGGTG</td> -<td>250</td> -<td>1.7013805</td> +<td>260</td> +<td>1.7341703</td><td>8.333022</td><td>28</td></tr><tr> -<td>TGCTT</td> -<td>410</td> -<td>1.7010024</td> -<td>5.0799813</td> -<td>4</td> +<td>TGGGG</td> +<td>260</td> +<td>1.7341703</td> +<td>8.349721</td> +<td>39</td> +</tr> +<tr> +<td>GTGGG</td> +<td>255</td> +<td>1.7008208</td> +<td>6.6730905</td> +<td>31</td> +</tr> +<tr> +<td>GGCCA</td> +<td>270</td> +<td>1.698549</td> +<td>6.293945</td> +<td>43</td> +</tr> +<tr> +<td>GCCCC</td> +<td>200</td> +<td>1.6914694</td> +<td>6.3460584</td> +<td>32</td></tr><tr><td>CTTTG</td> -<td>405</td> -<td>1.6802584</td> +<td>415</td> +<td>1.6874313</td><td>5.0799813</td><td>2</td></tr><tr> +<td>ACACA</td> +<td>485</td> +<td>1.6731915</td> +<td>5.1721287</td> +<td>14</td> +</tr> +<tr> +<td>GTGGT</td> +<td>320</td> +<td>1.6683302</td> +<td>5.216037</td> +<td>31</td> +</tr> +<tr> +<td>CTCAC</td> +<td>340</td> +<td>1.6681659</td> +<td>7.363092</td> +<td>31</td> +</tr> +<tr> +<td>TGCTT</td> +<td>410</td> +<td>1.6671008</td> +<td>5.090162</td> +<td>40</td> +</tr> +<tr> +<td>GGGGC</td> +<td>195</td> +<td>1.6602434</td> +<td>8.526694</td> +<td>40</td> +</tr> +<tr> +<td>AGTGG</td> +<td>335</td> +<td>1.654657</td> +<td>6.1708827</td> +<td>3</td> +</tr> +<tr> +<td>TTCTG</td> +<td>405</td> +<td>1.6467704</td> +<td>5.0850663</td> +<td>49</td> +</tr> +<tr><td>AGAAG</td><td>475</td> -<td>1.6794841</td> +<td>1.6460115</td><td>5.1952276</td><td>22</td></tr><tr><td>ACTCC</td> -<td>330</td> -<td>1.6520276</td> +<td>335</td> +<td>1.6436341</td><td>6.1297736</td><td>10</td></tr><tr> +<td>GGCTC</td> +<td>245</td> +<td>1.6268562</td> +<td>8.304275</td> +<td>46</td> +</tr> +<tr> +<td>TGGCA</td> +<td>330</td> +<td>1.6263331</td> +<td>8.637284</td> +<td>40</td> +</tr> +<tr> +<td>TCCTT</td> +<td>400</td> +<td>1.6228201</td> +<td>6.0946</td> +<td>40</td> +</tr> +<tr> +<td>TCTGG</td> +<td>310</td> +<td>1.612598</td> +<td>5.204428</td> +<td>43</td> +</tr> +<tr> +<td>GGGGA</td> +<td>255</td> +<td>1.6113497</td> +<td>6.3157325</td> +<td>7</td> +</tr> +<tr><td>CTGCT</td><td>310</td> -<td>1.6417291</td> +<td>1.609009</td><td>6.4845653</td><td>3</td></tr><tr> -<td>GCCCC</td> -<td>190</td> -<td>1.6395733</td> -<td>6.339712</td> -<td>37</td> +<td>CCCAA</td> +<td>345</td> +<td>1.6036536</td> +<td>5.8073177</td> +<td>10</td></tr><tr> -<td>AGTGG</td> -<td>325</td> -<td>1.6379085</td> -<td>6.1708827</td> -<td>3</td> +<td>TGGCC</td> +<td>240</td> +<td>1.5936551</td> +<td>6.6434207</td> +<td>49</td></tr><tr> -<td>TGGCA</td> -<td>325</td> -<td>1.6342632</td> -<td>6.1571493</td> -<td>16</td> -</tr> -<tr> -<td>GGCTC</td> -<td>240</td> -<td>1.626063</td> -<td>6.636776</td> -<td>25</td> -</tr> -<tr> -<td>ACACA</td> -<td>460</td> -<td>1.6192161</td> -<td>5.1721287</td> -<td>14</td> +<td>GTGCT</td> +<td>305</td> +<td>1.5865883</td> +<td>5.220104</td> +<td>50</td></tr><tr><td>GCTTT</td><td>390</td> -<td>1.6180266</td> -<td>5.0799813</td> -<td>5</td> +<td>1.5857788</td> +<td>6.1081944</td> +<td>41</td></tr><tr> -<td>TTCTG</td> -<td>390</td> -<td>1.6180266</td> -<td>5.0799813</td> -<td>3</td> +<td>CCACA</td> +<td>335</td> +<td>1.5571709</td> +<td>5.813131</td> +<td>30</td></tr><tr> -<td>TCCTT</td> -<td>390</td> -<td>1.6144258</td> -<td>6.0824113</td> -<td>16</td> +<td>CCTTC</td> +<td>300</td> +<td>1.5536399</td> +<td>6.4701333</td> +<td>17</td></tr><tr> -<td>CCCAA</td> -<td>335</td> -<td>1.588837</td> -<td>5.8073177</td> -<td>10</td> +<td>CCACT</td> +<td>315</td> +<td>1.5455065</td> +<td>6.135909</td> +<td>32</td> +</tr> +<tr> +<td>TCTTC</td> +<td>380</td> +<td>1.5416791</td> +<td>5.0737495</td> +<td>49</td> +</tr> +<tr> +<td>GTTCA</td> +<td>400</td> +<td>1.5408814</td> +<td>7.700401</td> +<td>11</td> +</tr> +<tr> +<td>AGGCA</td> +<td>330</td> +<td>1.5407803</td> +<td>5.8332543</td> +<td>6</td> +</tr> +<tr> +<td>AAAAG</td> +<td>600</td> +<td>1.5396972</td> +<td>5.782427</td> +<td>41</td></tr><tr><td>GCACA</td><td>330</td> -<td>1.5686142</td> +<td>1.5373511</td><td>5.8202715</td><td>18</td></tr><tr> -<td>GTTCA</td> -<td>395</td> -<td>1.5525635</td> -<td>7.700401</td> -<td>11</td> -</tr> -<tr> -<td>TCTTC</td> -<td>375</td> -<td>1.5523325</td> -<td>5.068676</td> -<td>4</td> -</tr> -<tr> -<td>AGGCA</td> -<td>325</td> -<td>1.5482932</td> -<td>5.8332543</td> -<td>6</td> -</tr> -<tr> -<td>GGGGA</td> -<td>240</td> -<td>1.5474048</td> -<td>6.3157325</td> -<td>7</td> -</tr> -<tr> -<td>CCTTC</td> -<td>290</td> -<td>1.5323931</td> -<td>6.4701333</td> -<td>17</td> -</tr> -<tr><td>ATGCC</td><td>305</td> -<td>1.5302798</td> +<td>1.4997808</td><td>12.286893</td><td>22</td></tr><tr><td>GAAGG</td><td>320</td> -<td>1.5278738</td> +<td>1.4974226</td><td>5.8462653</td><td>8</td></tr><tr> +<td>GAGAG</td> +<td>320</td> +<td>1.4974226</td> +<td>5.857981</td> +<td>41</td> +</tr> +<tr> +<td>TGTGC</td> +<td>285</td> +<td>1.4825499</td> +<td>5.2044287</td> +<td>29</td> +</tr> +<tr> +<td>TTGGC</td> +<td>285</td> +<td>1.4825495</td> +<td>5.199223</td> +<td>15</td> +</tr> +<tr><td>GGGAT</td> -<td>295</td> -<td>1.4867171</td> +<td>300</td> +<td>1.4817826</td><td>7.40506</td><td>21</td></tr><tr> -<td>TGTGC</td> -<td>280</td> -<td>1.4861598</td> -<td>5.199224</td> -<td>7</td> +<td>AGCTG</td> +<td>300</td> +<td>1.4784846</td> +<td>6.1633124</td> +<td>30</td></tr><tr><td>AACAG</td> -<td>420</td> -<td>1.4817125</td> +<td>425</td> +<td>1.4694693</td><td>5.1836653</td><td>10</td></tr><tr> +<td>GAGTG</td> +<td>295</td> +<td>1.4570862</td> +<td>6.1770606</td> +<td>33</td> +</tr> +<tr> +<td>GGGAC</td> +<td>230</td> +<td>1.4501395</td> +<td>6.3143044</td> +<td>40</td> +</tr> +<tr> +<td>GTGTT</td> +<td>355</td> +<td>1.4466851</td> +<td>6.134112</td> +<td>50</td> +</tr> +<tr> +<td>TTTGG</td> +<td>355</td> +<td>1.4466851</td> +<td>6.1095753</td> +<td>3</td> +</tr> +<tr><td>TCTTT</td><td>455</td> -<td>1.4755235</td> +<td>1.4461157</td><td>5.5590916</td><td>1</td></tr><tr> -<td>TTGGC</td> -<td>275</td> -<td>1.4596211</td> -<td>5.199223</td> -<td>15</td> -</tr> -<tr><td>GAGAT</td> -<td>385</td> -<td>1.4368514</td> +<td>395</td> +<td>1.4447913</td><td>6.397646</td><td>27</td></tr><tr> -<td>TTTGG</td> -<td>345</td> -<td>1.4345239</td> -<td>6.1095753</td> -<td>3</td> +<td>CAAAA</td> +<td>560</td> +<td>1.4338523</td> +<td>5.123362</td> +<td>31</td></tr><tr><td>GGTTC</td> -<td>270</td> -<td>1.4330826</td> +<td>275</td> +<td>1.4305303</td><td>10.398446</td><td>10</td></tr><tr> +<td>CCCTT</td> +<td>275</td> +<td>1.4241698</td> +<td>5.186479</td> +<td>39</td> +</tr> +<tr> +<td>CTGTT</td> +<td>350</td> +<td>1.4231348</td> +<td>5.0799813</td> +<td>10</td> +</tr> +<tr> +<td>ATGGT</td> +<td>365</td> +<td>1.4091904</td> +<td>6.7596393</td> +<td>47</td> +</tr> +<tr> +<td>TGTTG</td> +<td>345</td> +<td>1.4059336</td> +<td>5.1015162</td> +<td>40</td> +</tr> +<tr> +<td>CTGTC</td> +<td>270</td> +<td>1.4013947</td> +<td>5.198048</td> +<td>39</td> +</tr> +<tr> +<td>GAGAC</td> +<td>300</td> +<td>1.4007094</td> +<td>5.856681</td> +<td>50</td> +</tr> +<tr> +<td>CTTCT</td> +<td>345</td> +<td>1.3996824</td> +<td>7.1246448</td> +<td>50</td> +</tr> +<tr> +<td>GGCCC</td> +<td>165</td> +<td>1.398575</td> +<td>6.353853</td> +<td>2</td> +</tr> +<tr> +<td>TGAGT</td> +<td>360</td> +<td>1.3898867</td> +<td>5.7939773</td> +<td>32</td> +</tr> +<tr> +<td>GGCAC</td> +<td>220</td> +<td>1.3840029</td> +<td>6.2876506</td> +<td>17</td> +</tr> +<tr> +<td>CCTTT</td> +<td>340</td> +<td>1.3793972</td> +<td>5.068676</td> +<td>8</td> +</tr> +<tr><td>CCTTG</td><td>265</td> -<td>1.4034137</td> +<td>1.3754432</td><td>5.187652</td><td>18</td></tr><tr> -<td>CCCTT</td> -<td>265</td> -<td>1.4002901</td> -<td>5.176106</td> -<td>14</td> -</tr> -<tr> -<td>CTGTT</td> -<td>335</td> -<td>1.3898433</td> -<td>5.0799813</td> -<td>10</td> -</tr> -<tr> -<td>CCTTT</td> -<td>335</td> -<td>1.3867503</td> -<td>5.068676</td> -<td>8</td> -</tr> -<tr> -<td>GGCAC</td> -<td>215</td> -<td>1.3800533</td> -<td>6.2876506</td> -<td>17</td> -</tr> -<tr><td>TTGAA</td> -<td>465</td> -<td>1.3564935</td> +<td>475</td> +<td>1.3580486</td><td>6.4295163</td><td>7</td></tr><tr> -<td>CTTGG</td> -<td>255</td> -<td>1.3534669</td> -<td>5.1992235</td> -<td>18</td> +<td>GAGCG</td> +<td>215</td> +<td>1.3555653</td> +<td>12.603353</td> +<td>6</td></tr><tr> -<td>GTGTT</td> -<td>325</td> -<td>1.3513632</td> -<td>5.091313</td> -<td>28</td> -</tr> -<tr> -<td>GGCCC</td> -<td>155</td> -<td>1.3405302</td> -<td>6.353853</td> -<td>2</td> -</tr> -<tr> -<td>TGGTT</td> -<td>320</td> -<td>1.330573</td> -<td>5.091313</td> -<td>25</td> +<td>AAGGA</td> +<td>390</td> +<td>1.3514621</td> +<td>5.1952276</td> +<td>44</td></tr><tr><td>TTCTT</td> -<td>410</td> -<td>1.3295923</td> +<td>420</td> +<td>1.3348758</td><td>7.941558</td><td>4</td></tr><tr><td>GGGGT</td> -<td>195</td> -<td>1.327077</td> +<td>200</td> +<td>1.3339773</td><td>8.333022</td><td>45</td></tr><tr> -<td>AAGGA</td> -<td>375</td> -<td>1.3259085</td> -<td>5.1952276</td> -<td>44</td> +<td>CAGAT</td> +<td>365</td> +<td>1.3320893</td> +<td>5.4769697</td> +<td>34</td></tr><tr> -<td>CAGAT</td> -<td>350</td> -<td>1.3033215</td> -<td>5.471493</td> -<td>10</td> +<td>CTTGG</td> +<td>255</td> +<td>1.3264918</td> +<td>5.1992235</td> +<td>18</td> +</tr> +<tr> +<td>TGGTT</td> +<td>320</td> +<td>1.3040541</td> +<td>5.091313</td> +<td>25</td> +</tr> +<tr> +<td>TTGGG</td> +<td>250</td> +<td>1.3033829</td> +<td>6.5135255</td> +<td>6</td></tr><tr><td>CTGGT</td> -<td>245</td> -<td>1.3003898</td> -<td>5.1992235</td> -<td>12</td> +<td>250</td> +<td>1.3004823</td> +<td>5.204428</td> +<td>48</td> +</tr> +<tr> +<td>GCTCC</td> +<td>195</td> +<td>1.2919631</td> +<td>8.277508</td> +<td>26</td> +</tr> +<tr> +<td>TGATG</td> +<td>330</td> +<td>1.2740628</td> +<td>5.7939773</td> +<td>46</td></tr><tr><td>TGTCC</td><td>245</td> -<td>1.2974956</td> +<td>1.2716361</td><td>5.187652</td><td>21</td></tr><tr> -<td>GCTCC</td> -<td>190</td> -<td>1.2844352</td> -<td>8.277508</td> -<td>26</td> +<td>GGCTT</td> +<td>240</td> +<td>1.2484628</td> +<td>5.199223</td> +<td>4</td></tr><tr><td>GACAG</td><td>265</td> -<td>1.2624544</td> +<td>1.2372932</td><td>5.833254</td><td>27</td></tr><tr> -<td>GAGCG</td> -<td>195</td> -<td>1.2544682</td> -<td>12.603353</td> -<td>6</td> -</tr> -<tr> -<td>TTGGG</td> +<td>GGTGT</td><td>235</td> -<td>1.2500948</td> -<td>6.5135255</td> -<td>6</td> +<td>1.2251799</td> +<td>5.21082</td> +<td>27</td></tr><tr><td>AATGC</td><td>335</td> -<td>1.2474647</td> +<td>1.2226022</td><td>10.031068</td><td>21</td></tr><tr> -<td>GGCTT</td> -<td>235</td> -<td>1.2473125</td> -<td>5.199223</td> -<td>4</td> -</tr> -<tr><td>TTTGC</td> -<td>295</td> -<td>1.223892</td> +<td>300</td> +<td>1.2198299</td><td>5.0799813</td><td>9</td></tr><tr> -<td>GGTGT</td> +<td>GTCCT</td><td>230</td> -<td>1.223497</td> -<td>5.21082</td> -<td>27</td> +<td>1.1937809</td> +<td>5.1928453</td> +<td>47</td> +</tr> +<tr> +<td>GGGCC</td> +<td>140</td> +<td>1.1893166</td> +<td>6.3744006</td> +<td>43</td> +</tr> +<tr> +<td>ATCCC</td> +<td>240</td> +<td>1.1775287</td> +<td>6.135909</td> +<td>43</td> +</tr> +<tr> +<td>GCTCT</td> +<td>225</td> +<td>1.1678292</td> +<td>7.789268</td> +<td>47</td> +</tr> +<tr> +<td>AGCCC</td> +<td>185</td> +<td>1.1612303</td> +<td>6.2799363</td> +<td>31</td></tr><tr><td>GATCG</td><td>235</td> -<td>1.181698</td> -<td>6.1571493</td> -<td>45</td> +<td>1.1581463</td> +<td>6.1633124</td> +<td>29</td> +</tr> +<tr> +<td>ACCCT</td> +<td>230</td> +<td>1.128465</td> +<td>6.129773</td> +<td>10</td> +</tr> +<tr> +<td>GTTGG</td> +<td>215</td> +<td>1.1209095</td> +<td>5.2160373</td> +<td>47</td></tr><tr><td>AGCTC</td><td>225</td> -<td>1.1288949</td> +<td>1.1063956</td><td>6.1434464</td><td>25</td></tr><tr> -<td>ACCCT</td> +<td>CCCAT</td><td>225</td> -<td>1.1263824</td> +<td>1.1039332</td><td>6.129773</td> -<td>10</td> +<td>21</td></tr><tr><td>CGGAA</td><td>235</td> -<td>1.119535</td> +<td>1.0972222</td><td>9.333206</td><td>1</td></tr><tr> -<td>CCCAT</td> -<td>220</td> -<td>1.1013516</td> -<td>6.129773</td> -<td>21</td> -</tr> -<tr><td>TCTTG</td><td>265</td> -<td>1.0994283</td> +<td>1.0775164</td><td>5.0799813</td><td>21</td></tr><tr><td>ATGCA</td><td>295</td> -<td>1.0985136</td> +<td>1.0766199</td><td>5.4714913</td><td>37</td></tr><tr><td>GCTTG</td><td>205</td> -<td>1.0880812</td> +<td>1.0663953</td><td>5.199223</td><td>2</td></tr><tr><td>AGCGG</td><td>165</td> -<td>1.061473</td> +<td>1.0403174</td><td>12.603352</td><td>7</td></tr><tr> +<td>TTGCC</td> +<td>200</td> +<td>1.0380702</td> +<td>5.1876516</td> +<td>3</td> +</tr> +<tr> +<td>AACCT</td> +<td>285</td> +<td>1.0378094</td> +<td>5.4593143</td> +<td>13</td> +</tr> +<tr><td>AACCA</td><td>300</td> -<td>1.0560105</td> +<td>1.0349638</td><td>5.1721287</td><td>22</td></tr><tr> -<td>AACCT</td> -<td>280</td> -<td>1.0403365</td> -<td>5.4593143</td> -<td>13</td> -</tr> -<tr><td>CCGAG</td><td>160</td> -<td>1.0270164</td> +<td>1.0065476</td><td>12.575301</td><td>25</td></tr><tr> -<td>TTGCC</td> +<td>GTTCC</td><td>190</td> -<td>1.0062209</td> -<td>5.1876516</td> -<td>3</td> +<td>0.9861668</td> +<td>6.4845653</td> +<td>27</td></tr><tr><td>ACTCA</td> -<td>265</td> -<td>0.9846043</td> +<td>270</td> +<td>0.983188</td><td>5.4593153</td><td>11</td></tr><tr><td>CTCAT</td> -<td>250</td> -<td>0.98044825</td> +<td>255</td> +<td>0.9801258</td><td>5.7624474</td><td>4</td></tr><tr> -<td>GTTCC</td> -<td>185</td> -<td>0.9797416</td> -<td>6.4845653</td> -<td>27</td> -</tr> -<tr><td>GAACC</td> -<td>205</td> -<td>0.97444224</td> +<td>210</td> +<td>0.9783144</td><td>5.820272</td><td>25</td></tr><tr><td>GGCGG</td><td>110</td> -<td>0.9555928</td> +<td>0.93654746</td><td>10.637051</td><td>44</td></tr><tr> +<td>GCGGG</td> +<td>110</td> +<td>0.93654746</td> +<td>6.3886194</td> +<td>36</td> +</tr> +<tr> +<td>ATCGG</td> +<td>190</td> +<td>0.93637353</td> +<td>6.163312</td> +<td>30</td> +</tr> +<tr> +<td>GTCTG</td> +<td>180</td> +<td>0.9363471</td> +<td>5.2096424</td> +<td>41</td> +</tr> +<tr><td>GCGGT</td> -<td>130</td> -<td>0.8827489</td> +<td>140</td> +<td>0.93170583</td><td>13.303162</td><td>8</td></tr><tr> -<td>GCGGG</td> -<td>100</td> -<td>0.86872077</td> -<td>6.3822303</td> -<td>45</td> +<td>CGGGG</td> +<td>105</td> +<td>0.8939771</td> +<td>6.3886194</td> +<td>46</td> +</tr> +<tr> +<td>GGGCG</td> +<td>105</td> +<td>0.8939771</td> +<td>8.518159</td> +<td>43</td> +</tr> +<tr> +<td>TCGGA</td> +<td>170</td> +<td>0.83780795</td> +<td>7.395975</td> +<td>31</td> +</tr> +<tr> +<td>CTTGT</td> +<td>205</td> +<td>0.83355045</td> +<td>5.0850673</td> +<td>38</td></tr><tr><td>TGCCG</td><td>125</td> -<td>0.846908</td> +<td>0.83002883</td><td>14.93275</td><td>23</td></tr><tr><td>AGGCG</td> -<td>120</td> -<td>0.7719804</td> +<td>125</td> +<td>0.7881193</td><td>6.3016763</td><td>15</td></tr><tr><td>CGGTT</td> -<td>140</td> -<td>0.74307984</td> +<td>150</td> +<td>0.78028923</td><td>10.398446</td><td>9</td></tr><tr> +<td>GTGAC</td> +<td>150</td> +<td>0.7392424</td> +<td>6.163313</td> +<td>32</td> +</tr> +<tr><td>GCCGA</td><td>115</td> -<td>0.738168</td> +<td>0.723456</td><td>12.575301</td><td>24</td></tr><tr> +<td>CCCGC</td> +<td>85</td> +<td>0.7188745</td> +<td>6.3460584</td> +<td>30</td> +</tr> +<tr> +<td>CCCCG</td> +<td>85</td> +<td>0.7188745</td> +<td>10.576764</td> +<td>29</td> +</tr> +<tr><td>CGAGA</td> -<td>130</td> -<td>0.61931723</td> +<td>135</td> +<td>0.6303192</td><td>9.333206</td><td>26</td></tr><tr><td>CGGGA</td> -<td>85</td> -<td>0.5468194</td> +<td>90</td> +<td>0.5674459</td><td>6.301676</td><td>24</td></tr><tr><td>CACGG</td><td>85</td> -<td>0.54560244</td> +<td>0.5347284</td><td>6.2876506</td><td>37</td></tr> +<tr> +<td>CGCCT</td> +<td>80</td> +<td>0.5300361</td> +<td>6.6286345</td> +<td>30</td> +</tr> +<tr> +<td>CCGCA</td> +<td>75</td> +<td>0.47076905</td> +<td>6.2799363</td> +<td>36</td> +</tr> +<tr> +<td>CGTTG</td> +<td>40</td> +<td>0.20807713</td> +<td>5.2044277</td> +<td>46</td> +</tr></table> -<p><a href="#summary">Back to summary</a></div> -</div><div class="footer">Produced by <a href="http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/">FastQC</a> (version 0.9.1)</div> -</body></html> \ No newline at end of file +</div> +</body></html><div class="module"><h2>Files created by FastQC</h2><table cellspacing="2" cellpadding="2"> +<tr><td><a href="dataset_1.dat_fastqc.zip">dataset_1.dat_fastqc.zip (312.4 KB)</a></td></tr> +<tr><td><a href="duplication_levels.png">duplication_levels.png (14.5 KB)</a></td></tr> +<tr><td><a href="fastqc_data.txt">fastqc_data.txt (15.0 KB)</a></td></tr> +<tr><td><a href="fastqc_report.html">fastqc_report.html (25.2 KB)</a></td></tr> +<tr><td><a href="kmer_profiles.png">kmer_profiles.png (186.7 KB)</a></td></tr> +<tr><td><a href="per_base_gc_content.png">per_base_gc_content.png (12.1 KB)</a></td></tr> +<tr><td><a href="per_base_n_content.png">per_base_n_content.png (7.4 KB)</a></td></tr> +<tr><td><a href="per_base_quality.png">per_base_quality.png (9.6 KB)</a></td></tr> +<tr><td><a href="per_base_sequence_content.png">per_base_sequence_content.png (23.9 KB)</a></td></tr> +<tr><td><a href="per_sequence_gc_content.png">per_sequence_gc_content.png (29.6 KB)</a></td></tr> +<tr><td><a href="per_sequence_quality.png">per_sequence_quality.png (21.9 KB)</a></td></tr> +<tr><td><a href="sequence_length_distribution.png">sequence_length_distribution.png (18.9 KB)</a></td></tr> +<tr><td><a href="summary.txt">summary.txt (465 B)</a></td></tr> +</table> +<a href="http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/">FastQC documentation and full attribution is here</a><br/><hr/> +FastQC was run by Galaxy using the rgenetics rgFastQC wrapper - see http://rgenetics.org for details and licensing +</div></div><div class="footer">Produced by <a href="http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/">FastQC</a> (version 0.10.0)</div> diff -r e637518dada717ac2e1cde85c28d2de0f106fe8a -r a87d7b85c5771372550bd786bd15606f8e29cf41 tools/rgenetics/rgFastQC.py --- a/tools/rgenetics/rgFastQC.py +++ b/tools/rgenetics/rgFastQC.py @@ -91,21 +91,20 @@ def fix_fastqc(self,rep=[],flist=[],runlog=[]): """ add some of our stuff to the html """ - bs = '</body></html>\n' # hope they don't change this - try: - bodyindex = rep.index(bs) # hope they don't change this - except: - bodyindex = len(rep) - 1 - res = [] - res.append('<table>\n') + bodyindex = len(rep) -1 # hope they don't change this + footrow = bodyindex - 1 + footer = rep[footrow] + rep = rep[:footrow] + rep[footrow+1:] + res = ['<div class="module"><h2>Files created by FastQC</h2><table cellspacing="2" cellpadding="2">\n'] flist.sort() for i,f in enumerate(flist): if not(os.path.isdir(f)): fn = os.path.split(f)[-1] res.append('<tr><td><a href="%s">%s</a></td></tr>\n' % (fn,getFileString(fn, self.opts.outputdir))) - res.append('</table><p/>\n') + res.append('</table>\n') res.append('<a href="http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/">FastQC documentation and full attribution is here</a><br/><hr/>\n') - res.append('FastQC was run by Galaxy using the rgenetics rgFastQC wrapper - see http://rgenetics.org for details and licensing\n') + res.append('FastQC was run by Galaxy using the rgenetics rgFastQC wrapper - see http://rgenetics.org for details and licensing\n</div>') + res.append(footer) fixed = rep[:bodyindex] + res + rep[bodyindex:] return fixed # with our additions @@ -147,3 +146,4 @@ f.write(''.join(html)) f.close() + diff -r e637518dada717ac2e1cde85c28d2de0f106fe8a -r a87d7b85c5771372550bd786bd15606f8e29cf41 tools/rgenetics/rgFastQC.xml --- a/tools/rgenetics/rgFastQC.xml +++ b/tools/rgenetics/rgFastQC.xml @@ -1,4 +1,4 @@ -<tool name="Fastqc: Fastqc QC" id="fastqc" version="0.2"> +<tool name="Fastqc: Fastqc QC" id="fastqc" version="0.3"><description>using FastQC from Babraham</description><command interpreter="python"> rgFastQC.py -i $input_file -d $html_file.files_path -o $html_file -n "$out_prefix" -f $input_file.ext -e ${GALAXY_DATA_INDEX_DIR}/shared/jars/FastQC/fastqc Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jgoecks: Rename toggle-contract to toggle in CSS so that CSS class name matches icon file name.
by Bitbucket 15 Nov '11

15 Nov '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/e637518dada7/ changeset: e637518dada7 user: jgoecks date: 2011-11-15 21:29:25 summary: Rename toggle-contract to toggle in CSS so that CSS class name matches icon file name. affected #: 7 files diff -r 4412842dc7380ea74e03aba442fa9b655832bda1 -r e637518dada717ac2e1cde85c28d2de0f106fe8a static/june_2007_style/base.css.tmpl --- a/static/june_2007_style/base.css.tmpl +++ b/static/june_2007_style/base.css.tmpl @@ -865,7 +865,7 @@ -sprite-group: fugue; -sprite-image: fugue/toggle-expand.png; } -.icon-button.toggle-contract { +.icon-button.toggle { -sprite-group: fugue; -sprite-image: fugue/toggle.png; } diff -r 4412842dc7380ea74e03aba442fa9b655832bda1 -r e637518dada717ac2e1cde85c28d2de0f106fe8a static/june_2007_style/blue/base.css --- a/static/june_2007_style/blue/base.css +++ b/static/june_2007_style/blue/base.css @@ -153,8 +153,8 @@ .icon-button.tag--plus{background:url(fugue.png) no-repeat 0px -52px;} .icon-button.toggle-expand{background:transparent url(../images/fugue/toggle-expand-bw.png) no-repeat;} .icon-button.toggle-expand:hover{background:url(fugue.png) no-repeat 0px -78px;} -.icon-button.toggle-contract{background:transparent url(../images/fugue/toggle-bw.png) no-repeat;} -.icon-button.toggle-contract:hover{background:url(fugue.png) no-repeat 0px -104px;} +.icon-button.toggle{background:transparent url(../images/fugue/toggle-bw.png) no-repeat;} +.icon-button.toggle:hover{background:url(fugue.png) no-repeat 0px -104px;} .icon-button.arrow-circle{background:url(fugue.png) no-repeat 0px -130px;} .icon-button.chevron{background:url(fugue.png) no-repeat 0px -156px;} .icon-button.bug{background:url(fugue.png) no-repeat 0px -182px;} diff -r 4412842dc7380ea74e03aba442fa9b655832bda1 -r e637518dada717ac2e1cde85c28d2de0f106fe8a static/scripts/galaxy.base.js --- a/static/scripts/galaxy.base.js +++ b/static/scripts/galaxy.base.js @@ -555,7 +555,7 @@ }); // Generate 'collapse all' link - $("#top-links > a.toggle-contract").click( function() { + $("#top-links > a.toggle").click( function() { var prefs = $.jStorage.get("history_expand_state"); if (!prefs) { prefs = {}; } $( "div.historyItemBody:visible" ).each( function() { diff -r 4412842dc7380ea74e03aba442fa9b655832bda1 -r e637518dada717ac2e1cde85c28d2de0f106fe8a static/scripts/trackster.js --- a/static/scripts/trackster.js +++ b/static/scripts/trackster.js @@ -2391,7 +2391,7 @@ this.mode_icon = $("<a/>").attr("href", "javascript:void(0);").attr("title", "Set display mode") .addClass("icon-button chevron-expand").tipsy( {gravity: 's'} ).appendTo(this.icons_div); this.toggle_icon = $("<a/>").attr("href", "javascript:void(0);").attr("title", "Hide/show track content") - .addClass("icon-button toggle-contract").tipsy( {gravity: 's'} ) + .addClass("icon-button toggle").tipsy( {gravity: 's'} ) .appendTo(this.icons_div); this.settings_icon = $("<a/>").attr("href", "javascript:void(0);").attr("title", "Edit settings") .addClass("icon-button settings-icon").tipsy( {gravity: 's'} ) @@ -2439,11 +2439,11 @@ // Toggle icon hides or shows the track content. this.toggle_icon.click( function() { if ( track.content_visible ) { - track.toggle_icon.addClass("toggle-expand").removeClass("toggle-contract"); + track.toggle_icon.addClass("toggle-expand").removeClass("toggle"); track.hide_contents(); track.content_visible = false; } else { - track.toggle_icon.addClass("toggle-contract").removeClass("toggle-expand"); + track.toggle_icon.addClass("toggle").removeClass("toggle-expand"); track.content_visible = true; track.show_contents(); } diff -r 4412842dc7380ea74e03aba442fa9b655832bda1 -r e637518dada717ac2e1cde85c28d2de0f106fe8a templates/embed_base.mako --- a/templates/embed_base.mako +++ b/templates/embed_base.mako @@ -44,7 +44,7 @@ <div style="float: left"><a class="display_in_embed icon-button toggle-expand tooltip" item_id="${trans.security.encode_id( item.id )}" item_class="$item.__class__.__name__" href="${display_href}" title="Show ${item_display_name} content"></a> - <a class="toggle-contract icon-button tooltip" href="${display_href}" title="Hide ${item_display_name} content"></a> + <a class="toggle icon-button tooltip" href="${display_href}" title="Hide ${item_display_name} content"></a></div><div style="float: right;"> ${self.render_item_links( item )} diff -r 4412842dc7380ea74e03aba442fa9b655832bda1 -r e637518dada717ac2e1cde85c28d2de0f106fe8a templates/page/display.mako --- a/templates/page/display.mako +++ b/templates/page/display.mako @@ -26,7 +26,7 @@ container.find(".summary-content").hide("fast"); container.find(".item-content").html(item_content).show("fast"); container.find(".toggle-expand").hide(); - container.find(".toggle-contract").show(); + container.find(".toggle").show(); // Init needed for history items. init_history_items( container.find("div.historyItemWrapper"), "noinit", "nochanges" ); @@ -43,7 +43,7 @@ container.find(".summary-content").hide("fast"); container.find(".item-content").show("fast"); container.find(".toggle-expand").hide(); - container.find(".toggle-contract").show(); + container.find(".toggle").show(); } }; @@ -51,7 +51,7 @@ var hide_embedded_item = function() { container.find(".item-content").hide("fast"); container.find(".summary-content").show("fast"); - container.find(".toggle-contract").hide(); + container.find(".toggle").hide(); container.find(".toggle-expand").show(); }; @@ -63,7 +63,7 @@ }); // Setup toggle contract. - var toggle_contract = $(this).find('.toggle-contract'); + var toggle_contract = $(this).find('.toggle'); toggle_contract.click( function() { hide_embedded_item(); return false; @@ -89,7 +89,7 @@ ${parent.stylesheets()} ${h.css( "base", "history", "autocomplete_tagging" )} <style type="text/css"> - .toggle-contract { display: none; } + .toggle { display: none; } .embedded-item h4 { margin: 0px; } diff -r 4412842dc7380ea74e03aba442fa9b655832bda1 -r e637518dada717ac2e1cde85c28d2de0f106fe8a templates/root/history.mako --- a/templates/root/history.mako +++ b/templates/root/history.mako @@ -432,7 +432,7 @@ <div id="top-links" class="historyLinks"><a title="${_('refresh')}" class="icon-button arrow-circle tooltip" href="${h.url_for('history', show_deleted=show_deleted)}"></a> - <a title='${_('collapse all')}' class='icon-button toggle-contract tooltip' href='#' style="display: none"></a> + <a title='${_('collapse all')}' class='icon-button toggle tooltip' href='#' style="display: none"></a> %if trans.get_user(): <div style="width: 40px; float: right; white-space: nowrap;"> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: A tool shed admin will now receive content alerts (as part of the alert message) for each file uploaded to a repository that contains either image content or html content if the admin has chosen to receive email alerts for changes to the repository.
by Bitbucket 15 Nov '11

15 Nov '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/4412842dc738/ changeset: 4412842dc738 user: greg date: 2011-11-15 20:50:08 summary: A tool shed admin will now receive content alerts (as part of the alert message) for each file uploaded to a repository that contains either image content or html content if the admin has chosen to receive email alerts for changes to the repository. affected #: 3 files diff -r 3a49bca428c3f71a431a3d6f5a5c4397941aac55 -r 4412842dc7380ea74e03aba442fa9b655832bda1 lib/galaxy/webapps/community/controllers/common.py --- a/lib/galaxy/webapps/community/controllers/common.py +++ b/lib/galaxy/webapps/community/controllers/common.py @@ -26,6 +26,8 @@ Change description: ${description} +${content_alert_str} + ----------------------------------------------------------------------------- This change alert was sent from the Galaxy tool shed hosted on the server "${host}" @@ -520,7 +522,7 @@ def get_user( trans, id ): """Get a user from the database by id""" return trans.sa_session.query( trans.model.User ).get( trans.security.decode_id( id ) ) -def handle_email_alerts( trans, repository ): +def handle_email_alerts( trans, repository, content_alert_str='' ): repo_dir = repository.repo_path repo = hg.repository( get_configured_ui(), repo_dir ) smtp_server = trans.app.config.smtp_server @@ -541,14 +543,25 @@ username = ctx.user().split()[0] except: username = ctx.user() - # Build the email message + # We'll use 2 template bodies because we only want to send content + # alerts to tool shed admin users. + admin_body = string.Template( email_alert_template ) \ + .safe_substitute( host=trans.request.host, + repository_name=repository.name, + revision='%s:%s' %( str( ctx.rev() ), ctx ), + display_date=display_date, + description=ctx.description(), + username=username, + content_alert_str=content_alert_str ) body = string.Template( email_alert_template ) \ .safe_substitute( host=trans.request.host, repository_name=repository.name, revision='%s:%s' %( str( ctx.rev() ), ctx ), display_date=display_date, description=ctx.description(), - username=username ) + username=username, + content_alert_str='' ) + admin_users = trans.app.config.get( "admin_users", "" ).split( "," ) frm = email_from subject = "Galaxy tool shed repository update alert" email_alerts = from_json_string( repository.email_alerts ) @@ -556,7 +569,10 @@ to = email.strip() # Send it try: - util.send_mail( frm, to, subject, body, trans.app.config ) + if to in admin_users: + util.send_mail( frm, to, subject, admin_body, trans.app.config ) + else: + util.send_mail( frm, to, subject, body, trans.app.config ) except Exception, e: log.exception( "An error occurred sending a tool shed repository update alert by email." ) def update_for_browsing( trans, repository, current_working_dir, commit_message='' ): @@ -567,30 +583,20 @@ repo = hg.repository( get_configured_ui(), repo_dir ) # The following will delete the disk copy of only the files in the repository. #os.system( 'hg update -r null > /dev/null 2>&1' ) - repo.ui.pushbuffer() files_to_remove_from_disk = [] files_to_commit = [] - commands.status( repo.ui, repo, all=True ) - status_and_file_names = repo.ui.popbuffer().strip().split( "\n" ) - if status_and_file_names and status_and_file_names[ 0 ] not in [ '' ]: - # status_and_file_names looks something like: - # ['? README', '? tmap_tool/tmap-0.0.9.tar.gz', '? dna_filtering.py', 'C filtering.py', 'C filtering.xml'] - # The codes used to show the status of files are: - # M = modified - # A = added - # R = removed - # C = clean - # ! = deleted, but still tracked - # ? = not tracked - # I = ignored - for status_and_file_name in status_and_file_names: - if status_and_file_name.startswith( '?' ) or status_and_file_name.startswith( 'I' ): - files_to_remove_from_disk.append( os.path.abspath( os.path.join( repo_dir, status_and_file_name.split()[1] ) ) ) - elif status_and_file_name.startswith( 'M' ) or status_and_file_name.startswith( 'A' ) or status_and_file_name.startswith( 'R' ): - files_to_commit.append( os.path.abspath( os.path.join( repo_dir, status_and_file_name.split()[1] ) ) ) # We may have files on disk in the repo directory that aren't being tracked, so they must be removed. - # We'll use mercurial's purge extension to do this. Using this extension requires the following entry - # in the repository's hgrc file which was not required for some time, so we'll add it if it's missing. + # The codes used to show the status of files are as follows. + # M = modified + # A = added + # R = removed + # C = clean + # ! = deleted, but still tracked + # ? = not tracked + # I = ignored + # We'll use mercurial's purge extension to remove untracked file. Using this extension requires the + # following entry in the repository's hgrc file which was not required for some time, so we'll add it + # if it's missing. # [extensions] # hgext.purge= lines = repo.opener( 'hgrc', 'rb' ).readlines() @@ -624,9 +630,14 @@ commit_message = 'Committed changes to: %s' % ', '.join( files_to_commit ) repo.dirstate.write() repo.commit( user=trans.user.username, text=commit_message ) + cmd = 'hg update > /dev/null 2>&1' os.chdir( repo_dir ) - os.system( 'hg update > /dev/null 2>&1' ) + proc = subprocess.Popen( args=cmd, shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT ) + return_code = proc.wait() os.chdir( current_working_dir ) + if return_code != 0: + output = proc.stdout.read( 32768 ) + log.debug( 'hg update > /dev/null 2>&1 failed in repository directory %s, reason: %s' % ( repo_dir, output ) ) def load_tool( trans, config_file ): """ Load a single tool from the file named by `config_file` and return diff -r 3a49bca428c3f71a431a3d6f5a5c4397941aac55 -r 4412842dc7380ea74e03aba442fa9b655832bda1 lib/galaxy/webapps/community/controllers/upload.py --- a/lib/galaxy/webapps/community/controllers/upload.py +++ b/lib/galaxy/webapps/community/controllers/upload.py @@ -101,12 +101,12 @@ full_path = os.path.abspath( os.path.join( repo_dir, upload_point, uploaded_file_filename ) ) else: full_path = os.path.abspath( os.path.join( repo_dir, uploaded_file_filename ) ) - # TODO: enhance this method to set a flag and alert an admin to review content since - # the hard checks are too restrictive. - #ok, message = self.__check_file_content( uploaded_file_name ) - #if ok: # Move the uploaded file to the load_point within the repository hierarchy. shutil.move( uploaded_file_name, full_path ) + if os.path.isfile( full_path ): + content_alert_str = self.__check_file_content( full_path ) + else: + content_alert_str = '' commands.add( repo.ui, repo, full_path ) try: commands.commit( repo.ui, repo, full_path, user=trans.user.username, message=commit_message ) @@ -128,7 +128,7 @@ # Handle the special case where a xxx.loc.sample file is # being uploaded by copying it to ~/tool-data/xxx.loc. copy_sample_loc_file( trans, full_path ) - handle_email_alerts( trans, repository ) + handle_email_alerts( trans, repository, content_alert_str=content_alert_str ) if ok: # Update the repository files for browsing. update_for_browsing( trans, repository, current_working_dir, commit_message=commit_message ) @@ -194,18 +194,7 @@ tar.extractall( path=full_path ) tar.close() uploaded_file.close() - """ - # TODO: enhance this method to set a flag and alert an admin to review content since - # the hard checks are too restrictive. - for filename_in_archive in filenames_in_archive: - if os.path.isfile( filename_in_archive ): - ok, message = self.__check_file_content( filename_in_archive ) - if not ok: - # Refresh the repository files for browsing. - current_working_dir = os.getcwd() - update_for_browsing( trans, repository, current_working_dir ) - return False, message, [] - """ + content_alert_str = '' if remove_repo_files_not_in_tar and not repository.is_new: # We have a repository that is not new (it contains files), so discover # those files that are in the repository, but not in the uploaded archive. @@ -250,6 +239,9 @@ # The directory is not empty pass for filename_in_archive in filenames_in_archive: + # Check file content to ensure it is appropriate. + if os.path.isfile( filename_in_archive ): + content_alert_str += self.__check_file_content( filename_in_archive ) commands.add( repo.ui, repo, filename_in_archive ) if filename_in_archive.endswith( 'tool_data_table_conf.xml.sample' ): # Handle the special case where a tool_data_table_conf.xml.sample @@ -271,7 +263,7 @@ # exception. If this happens, we'll try the following. repo.dirstate.write() repo.commit( user=trans.user.username, text=commit_message ) - handle_email_alerts( trans, repository ) + handle_email_alerts( trans, repository, content_alert_str ) return True, '', files_to_remove def uncompress( self, repository, uploaded_file_name, uploaded_file_filename, isgzip, isbz2 ): if isgzip: @@ -349,15 +341,9 @@ return False, message return True, '' def __check_file_content( self, file_path ): - return True, '' message = '' - ok = True - head, tail = os.path.split( file_path ) if check_html( file_path ): - message = 'The file <b>%s</b> contains HTML content which cannot be uploaded to a Galaxy tool shed.' % str( tail ) - ok = False + message = 'The file "%s" contains HTML content.\n' % str( file_path ) elif check_image( file_path ): - # For now we won't allow images to be uploaded. - message = 'The file <b>%s</b> contains image content that cannot be uploaded to a Galaxy tool shed.' % str( tail ) - ok = False - return ok, message + message = 'The file "%s" contains image content.\n' % str( file_path ) + return message diff -r 3a49bca428c3f71a431a3d6f5a5c4397941aac55 -r 4412842dc7380ea74e03aba442fa9b655832bda1 templates/webapps/community/repository/upload.mako --- a/templates/webapps/community/repository/upload.mako +++ b/templates/webapps/community/repository/upload.mako @@ -64,7 +64,13 @@ <div class="toolForm"><div class="toolFormTitle">Upload a single file or a tarball</div><div class="toolFormBody"> - ## TODO: nginx + <div class="form-row"> + <div class="warningmessage"> + Uploading may take a while, depending upon the size of the file. Wait until a message is displayed in your + browser after clicking the <b>Upload</b> button below. + </div> + <div style="clear: both"></div> + </div><form id="upload_form" name="upload_form" action="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ) )}" enctype="multipart/form-data" method="post"><div class="form-row"><label>File:</label> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: Add 'type_extension' attribute to datatypes_conf.xml that allows creating a datatype from an earlier declared datatype by referencing extension. Make several datatypes that had been direct instantiations from Data become subclasses of Binary.
by Bitbucket 15 Nov '11

15 Nov '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/3a49bca428c3/ changeset: 3a49bca428c3 user: dan date: 2011-11-15 20:28:08 summary: Add 'type_extension' attribute to datatypes_conf.xml that allows creating a datatype from an earlier declared datatype by referencing extension. Make several datatypes that had been direct instantiations from Data become subclasses of Binary. affected #: 3 files diff -r 94a58c2fbf39ed76218d4af0ac30cb286b61541c -r 3a49bca428c3f71a431a3d6f5a5c4397941aac55 datatypes_conf.xml.sample --- a/datatypes_conf.xml.sample +++ b/datatypes_conf.xml.sample @@ -88,7 +88,7 @@ <datatype extension="gif" type="galaxy.datatypes.images:Gif" mimetype="image/gif"/><datatype extension="gmaj.zip" type="galaxy.datatypes.images:Gmaj" mimetype="application/zip"/><datatype extension="gtf" type="galaxy.datatypes.interval:Gtf" display_in_upload="true"/> - <datatype extension="h5" type="galaxy.datatypes.data:Data" mimetype="application/octet-stream"/> + <datatype extension="h5" type="galaxy.datatypes.binary:Binary" mimetype="application/octet-stream" subclass="True" /><datatype extension="html" type="galaxy.datatypes.images:Html" mimetype="text/html"/><datatype extension="interval" type="galaxy.datatypes.interval:Interval" display_in_upload="true"><converter file="interval_to_bed_converter.xml" target_datatype="bed"/> @@ -164,10 +164,10 @@ <converter file="wiggle_to_simple_converter.xml" target_datatype="interval"/></datatype> - <datatype extension="summary_tree" type="galaxy.datatypes.data:Data" /> - <datatype extension="interval_index" type="galaxy.datatypes.data:Data" /> - <datatype extension="tabix" type="galaxy.datatypes.data:Data" /> - <datatype extension="bgzip" type="galaxy.datatypes.data:Data" /> + <datatype extension="summary_tree" type="galaxy.datatypes.binary:Binary" subclass="True" /> + <datatype extension="interval_index" type="galaxy.datatypes.binary:Binary" subclass="True" /> + <datatype extension="tabix" type="galaxy.datatypes.binary:Binary" subclass="True" /> + <datatype extension="bgzip" type="galaxy.datatypes.binary:Binary" subclass="True" /><datatype extension="acedb" type="galaxy.datatypes.data:Text"/><datatype extension="asn1" type="galaxy.datatypes.data:Text"/> diff -r 94a58c2fbf39ed76218d4af0ac30cb286b61541c -r 3a49bca428c3f71a431a3d6f5a5c4397941aac55 lib/galaxy/datatypes/binary.py --- a/lib/galaxy/datatypes/binary.py +++ b/lib/galaxy/datatypes/binary.py @@ -26,7 +26,7 @@ """Set the peek and blurb text""" if not dataset.dataset.purged: dataset.peek = 'binary data' - dataset.blurb = 'data' + dataset.blurb = data.nice_size( dataset.get_size() ) else: dataset.peek = 'file does not exist' dataset.blurb = 'file purged from disk' diff -r 94a58c2fbf39ed76218d4af0ac30cb286b61541c -r 3a49bca428c3f71a431a3d6f5a5c4397941aac55 lib/galaxy/datatypes/registry.py --- a/lib/galaxy/datatypes/registry.py +++ b/lib/galaxy/datatypes/registry.py @@ -46,18 +46,22 @@ try: extension = elem.get( 'extension', None ) dtype = elem.get( 'type', None ) + type_extension = elem.get( 'type_extension', None ) mimetype = elem.get( 'mimetype', None ) display_in_upload = elem.get( 'display_in_upload', False ) make_subclass = galaxy.util.string_as_bool( elem.get( 'subclass', False ) ) - if extension and dtype: - fields = dtype.split( ':' ) - datatype_module = fields[0] - datatype_class_name = fields[1] - fields = datatype_module.split( '.' ) - module = __import__( fields.pop(0) ) - for mod in fields: - module = getattr( module, mod ) - datatype_class = getattr( module, datatype_class_name ) + if extension and ( dtype or type_extension ): + if dtype: + fields = dtype.split( ':' ) + datatype_module = fields[0] + datatype_class_name = fields[1] + fields = datatype_module.split( '.' ) + module = __import__( fields.pop(0) ) + for mod in fields: + module = getattr( module, mod ) + datatype_class = getattr( module, datatype_class_name ) + elif type_extension: + datatype_class = self.datatypes_by_extension[type_extension].__class__ if make_subclass: datatype_class = type( datatype_class_name, (datatype_class,), {} ) self.datatypes_by_extension[extension] = datatype_class() Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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