December 2012 - galaxy-commits - lists.galaxyproject.org

commit/galaxy-central: jgoecks: Trackster: remove unused var.
by Bitbucket 10 Dec '12

10 Dec '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/3ee0e5ee1b37/ changeset: 3ee0e5ee1b37 user: jgoecks date: 2012-12-10 21:38:57 summary: Trackster: remove unused var. affected #: 1 file diff -r 2fdc0270baad3b020118d05cc3429993a3d80207 -r 3ee0e5ee1b375c0fd580c26a93850f2fa44f93f0 static/scripts/viz/trackster/tracks.js --- a/static/scripts/viz/trackster/tracks.js +++ b/static/scripts/viz/trackster/tracks.js @@ -3278,7 +3278,6 @@ this.tile_predraw_init(); var canvas = track.view.canvas_manager.new_canvas(), - tile_bounds = track._get_tile_bounds(tile_index, resolution), tile_low = region.get('start'), tile_high = region.get('end'), all_data_index = 0, 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: Trackster: do not use width parameter in draw helper because it's not needed anymore.
by Bitbucket 10 Dec '12

10 Dec '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/2fdc0270baad/ changeset: 2fdc0270baad user: jgoecks date: 2012-12-10 21:31:38 summary: Trackster: do not use width parameter in draw helper because it's not needed anymore. affected #: 1 file diff -r 512c7561e1b95b381345296a0da3aa3effc05803 -r 2fdc0270baad3b020118d05cc3429993a3d80207 static/scripts/viz/trackster/tracks.js --- a/static/scripts/viz/trackster/tracks.js +++ b/static/scripts/viz/trackster/tracks.js @@ -2766,8 +2766,8 @@ * Generate a key for the tile cache. * TODO: create a TileCache object (like DataCache) and generate key internally. */ - _gen_tile_cache_key: function(width, w_scale, tile_index) { - return width + '_' + w_scale + '_' + tile_index; + _gen_tile_cache_key: function(w_scale, tile_index) { + return w_scale + '_' + tile_index; }, /** * Request that track be drawn. @@ -2826,7 +2826,7 @@ is_tile = function(o) { return (o && 'track' in o); }; // Draw tiles. while ( ( tile_index * TILE_SIZE * resolution ) < high ) { - var draw_result = this.draw_helper( force, width, tile_index, resolution, this.tiles_div, w_scale ); + var draw_result = this.draw_helper( force, tile_index, resolution, this.tiles_div, w_scale ); if ( is_tile(draw_result) ) { drawn_tiles.push( draw_result ); } else { @@ -2875,9 +2875,9 @@ * Retrieves from cache, draws, or sets up drawing for a single tile. Returns either a Tile object or a * jQuery.Deferred object that is fulfilled when tile can be drawn again. */ - draw_helper: function(force, width, tile_index, resolution, parent_element, w_scale, kwargs) { + draw_helper: function(force, tile_index, resolution, parent_element, w_scale, kwargs) { var track = this, - key = this._gen_tile_cache_key(width, w_scale, tile_index), + key = this._gen_tile_cache_key(w_scale, tile_index), region = this._get_tile_bounds(tile_index, resolution); // Init kwargs if necessary to avoid having to check if kwargs defined. @@ -3227,10 +3227,10 @@ this.action_icons.param_space_viz_icon.hide(); }, can_draw: Drawable.prototype.can_draw, - draw_helper: function(force, width, tile_index, resolution, parent_element, w_scale, kwargs) { + draw_helper: function(force, tile_index, resolution, parent_element, w_scale, kwargs) { // FIXME: this function is similar to TiledTrack.draw_helper -- can the two be merged/refactored? var track = this, - key = this._gen_tile_cache_key(width, w_scale, tile_index), + key = this._gen_tile_cache_key(w_scale, tile_index), region = this._get_tile_bounds(tile_index, resolution); // Init kwargs if necessary to avoid having to check if kwargs defined. @@ -3413,7 +3413,7 @@ for (var i = 0; i < tiles.length; i++) { var tile = tiles[i]; if (tile.html_elt.find("canvas").height() !== max_height) { - this.draw_helper(true, width, tile.index, tile.resolution, tile.html_elt.parent(), w_scale, { height: max_height } ); + this.draw_helper(true, tile.index, tile.resolution, tile.html_elt.parent(), w_scale, { height: max_height } ); tile.html_elt.remove(); } } @@ -3451,9 +3451,9 @@ /** * Only retrieves data and draws tile if reference data can be displayed. */ - draw_helper: function(force, width, tile_index, resolution, parent_element, w_scale, kwargs) { + draw_helper: function(force, tile_index, resolution, parent_element, w_scale, kwargs) { if (w_scale > this.view.canvas_manager.char_width_px) { - return TiledTrack.prototype.draw_helper.call(this, force, width, tile_index, resolution, parent_element, w_scale, kwargs); + return TiledTrack.prototype.draw_helper.call(this, force, tile_index, resolution, parent_element, w_scale, kwargs); } else { this.hide_contents(); @@ -3815,7 +3815,7 @@ var tile = tiles[i]; if (tile.max_val !== global_max) { tile.html_elt.remove(); - track.draw_helper(true, width, tile.index, tile.resolution, tile.html_elt.parent(), w_scale, { more_tile_data: { max: global_max } } ); + track.draw_helper(true, tile.index, tile.resolution, tile.html_elt.parent(), w_scale, { more_tile_data: { max: global_max } } ); } } } 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: inithello: More tool shed functional test enhancements.
by Bitbucket 10 Dec '12

10 Dec '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/512c7561e1b9/ changeset: 512c7561e1b9 user: inithello date: 2012-12-10 20:41:14 summary: More tool shed functional test enhancements. affected #: 8 files diff -r bd020b5aa5314718dbd7afe9e4e9e05bb3b53c7a -r 512c7561e1b95b381345296a0da3aa3effc05803 test/tool_shed/base/twilltestcase.py --- a/test/tool_shed/base/twilltestcase.py +++ b/test/tool_shed/base/twilltestcase.py @@ -15,6 +15,7 @@ self.hgweb_config_dir = os.environ.get( 'TEST_HG_WEB_CONFIG_DIR' ) self.hgweb_config_manager = galaxy.webapps.community.util.hgweb_config.HgWebConfigManager() self.hgweb_config_manager.hgweb_config_dir = self.hgweb_config_dir + self.tool_shed_test_tmp_dir = os.environ.get( 'TOOL_SHED_TEST_TMP_DIR', None) self.host = os.environ.get( 'TOOL_SHED_TEST_HOST' ) self.port = os.environ.get( 'TOOL_SHED_TEST_PORT' ) self.url = "http://%s:%s" % ( self.host, self.port ) @@ -213,6 +214,9 @@ string = string.replace( character, replacement ) return string def generate_repository_dependency_xml( self, repository, xml_filename, dependency_description='' ): + file_path = os.path.split( xml_filename )[0] + if not os.path.exists( file_path ): + os.makedirs( file_path ) changeset_revision = self.get_repository_tip( repository ) if dependency_description: description = ' description="%s"' % dependency_description @@ -226,6 +230,13 @@ description=description ) # Save the generated xml to the specified location. file( xml_filename, 'w' ).write( repository_dependency_xml ) + def generate_temp_path( self, test_script_path, additional_paths=[] ): + return os.path.join( self.tool_shed_test_tmp_dir, test_script_path, os.sep.join( additional_paths ) ) + def get_filename( self, filename, filepath=None ): + if filepath is not None: + return os.path.abspath( os.path.join( filepath, filename ) ) + else: + return os.path.abspath( os.path.join( self.file_dir, filename ) ) def get_latest_repository_metadata_for_repository( self, repository ): # TODO: This will not work as expected. Fix it. return repository.metadata_revisions[ 0 ] @@ -335,6 +346,7 @@ def upload_file( self, repository, filename, + filepath=None, valid_tools_only=True, strings_displayed=[], strings_not_displayed=[], @@ -344,6 +356,6 @@ strings_displayed.append( "has been successfully uploaded to the repository." ) for key in kwd: tc.fv( "1", key, kwd[ key ] ) - tc.formfile( "1", "file_data", self.get_filename( filename ) ) + tc.formfile( "1", "file_data", self.get_filename( filename, filepath ) ) tc.submit( "upload_button" ) self.check_for_strings( strings_displayed, strings_not_displayed ) diff -r bd020b5aa5314718dbd7afe9e4e9e05bb3b53c7a -r 512c7561e1b95b381345296a0da3aa3effc05803 test/tool_shed/functional/test_0000_basic_repository_features.py --- a/test/tool_shed/functional/test_0000_basic_repository_features.py +++ b/test/tool_shed/functional/test_0000_basic_repository_features.py @@ -1,7 +1,7 @@ from tool_shed.base.twilltestcase import ShedTwillTestCase, common, os from tool_shed.base.test_db_util import get_repository_by_name_and_owner, get_user, get_private_role -repository_name = 'filtering' +repository_name = 'filtering_0000' repository_description = "Galaxy's filtering tool" repository_long_description = "Long description of Galaxy's filtering tool" @@ -19,41 +19,48 @@ assert admin_user is not None, 'Problem retrieving user with email %s from the database' % common.admin_email admin_user_private_role = get_private_role( admin_user ) def test_0005_create_categories( self ): - """Create categories""" - self.create_category( 'Text Manipulation', 'Tools for manipulating text' ) - self.create_category( 'Text Analysis', 'Tools for analyzing text' ) + """Create categories for this test suite""" + self.create_category( 'Test 0000 Basic Repository Features 1', 'Test 0000 Basic Repository Features 1' ) + self.create_category( 'Test 0000 Basic Repository Features 2', 'Test 0000 Basic Repository Features 2' ) def test_0010_create_repository( self ): """Create the filtering repository""" + self.logout() + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + test_user_1 = get_user( common.test_user_1_email ) + assert test_user_1 is not None, 'Problem retrieving user with email %s from the database' % test_user_1_email + test_user_1_private_role = get_private_role( test_user_1 ) strings_displayed = [ 'Repository %s' % "'%s'" % repository_name, 'Repository %s has been created' % "'%s'" % repository_name ] self.create_repository( repository_name, repository_description, repository_long_description=repository_long_description, - categories=[ 'Text Manipulation' ], + categories=[ 'Test 0000 Basic Repository Features 1' ], strings_displayed=strings_displayed ) def test_0015_edit_repository( self ): """Edit the repository name, description, and long description""" - repository = get_repository_by_name_and_owner( repository_name, common.admin_username ) + repository = get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) new_name = "renamed_filtering" new_description = "Edited filtering tool" new_long_description = "Edited long description" self.edit_repository_information( repository, repo_name=new_name, description=new_description, long_description=new_long_description ) def test_0020_change_repository_category( self ): """Change the categories associated with the filtering repository""" - repository = get_repository_by_name_and_owner( repository_name, common.admin_username ) - self.edit_repository_categories( repository, categories_to_add=[ "Text Analysis" ], categories_to_remove=[ "Text Manipulation" ] ) + repository = get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) + self.edit_repository_categories( repository, + categories_to_add=[ "Test 0000 Basic Repository Features 2" ], + categories_to_remove=[ "Test 0000 Basic Repository Features 1" ] ) def test_0025_grant_write_access( self ): '''Grant write access to another user''' - repository = get_repository_by_name_and_owner( repository_name, common.admin_username ) - self.grant_write_access( repository, usernames=[ common.test_user_1_name ] ) - self.revoke_write_access( repository, common.test_user_1_name ) + repository = get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) + self.grant_write_access( repository, usernames=[ common.admin_username ] ) + self.revoke_write_access( repository, common.admin_username ) def test_0030_upload_filtering_1_1_0( self ): """Upload filtering_1.1.0.tar to the repository""" - repository = get_repository_by_name_and_owner( repository_name, common.admin_username ) + repository = get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) self.upload_file( repository, 'filtering/filtering_1.1.0.tar', commit_message="Uploaded filtering 1.1.0" ) def test_0035_verify_repository( self ): '''Display basic repository pages''' - repository = get_repository_by_name_and_owner( repository_name, common.admin_username ) + repository = get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) latest_changeset_revision = self.get_repository_tip( repository ) self.check_for_valid_tools( repository, strings_displayed=[ 'Filter1' ] ) self.check_count_of_metadata_revisions_associated_with_repository( repository, metadata_count=1 ) @@ -61,16 +68,20 @@ self.check_repository_tools_for_changeset_revision( repository, tip ) self.check_repository_metadata( repository, tip_only=False ) self.browse_repository( repository, strings_displayed=[ 'Browse %s revision' % repository.name, '(repository tip)' ] ) - self.display_repository_clone_page( common.admin_username, + self.display_repository_clone_page( common.test_user_1_name, repository_name, strings_displayed=[ 'Uploaded filtering 1.1.0', latest_changeset_revision ] ) def test_0040_alter_repository_states( self ): '''Test toggling the malicious and deprecated repository flags.''' - repository = get_repository_by_name_and_owner( repository_name, common.admin_username ) + repository = get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) + self.logout() + self.login( email=common.admin_email, username=common.admin_username ) self.set_repository_malicious( repository, set_malicious=True, strings_displayed=[ 'The repository tip has been defined as malicious.' ] ) self.set_repository_malicious( repository, set_malicious=False, strings_displayed=[ 'The repository tip has been defined as <b>not</b> malicious.' ] ) + self.logout() + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) self.set_repository_deprecated( repository, strings_displayed=[ 'has been marked as deprecated', 'Mark as not deprecated' ] ) self.display_manage_repository_page( repository, @@ -82,7 +93,7 @@ set_deprecated=False ) def test_0045_display_repository_tip_file( self ): '''Display the contents of filtering.xml in the repository tip revision''' - repository = get_repository_by_name_and_owner( repository_name, common.admin_username ) + repository = get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) self.display_repository_file_contents( repository=repository, filename='filtering.xml', filepath=None, @@ -90,16 +101,16 @@ strings_not_displayed=[] ) def test_0050_upload_filtering_txt_file( self ): '''Upload filtering.txt file associated with tool version 1.1.0.''' - repository = get_repository_by_name_and_owner( repository_name, common.admin_username ) + repository = get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) self.upload_file( repository, - 'filtering/filtering.txt', + 'filtering/filtering_0000.txt', commit_message="Uploaded filtering.txt", uncompress_file='No', remove_repo_files_not_in_tar='No' ) self.display_manage_repository_page( repository, strings_displayed=[ 'Readme file for filtering 1.1.0' ] ) def test_0055_upload_filtering_test_data( self ): '''Upload filtering test data.''' - repository = get_repository_by_name_and_owner( repository_name, common.admin_username ) + repository = get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) self.upload_file( repository, 'filtering/filtering_test_data.tar', commit_message="Uploaded filtering test data", remove_repo_files_not_in_tar='No' ) self.display_repository_file_contents( repository=repository, filename='1.bed', @@ -109,14 +120,14 @@ self.check_repository_metadata( repository, tip_only=True ) def test_0060_upload_filtering_2_2_0( self ): '''Upload filtering version 2.2.0''' - repository = get_repository_by_name_and_owner( repository_name, common.admin_username ) + repository = get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) self.upload_file( repository, 'filtering/filtering_2.2.0.tar', commit_message="Uploaded filtering 2.2.0", remove_repo_files_not_in_tar='No' ) def test_0065_verify_filtering_repository( self ): '''Verify the new tool versions and repository metadata.''' - repository = get_repository_by_name_and_owner( repository_name, common.admin_username ) + repository = get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) tip = self.get_repository_tip( repository ) self.check_for_valid_tools( repository ) strings_displayed = self.get_repository_metadata_revisions( repository ).append( 'Select a revision' ) @@ -126,7 +137,7 @@ self.check_repository_metadata( repository, tip_only=False ) def test_0070_upload_readme_txt_file( self ): '''Upload readme.txt file associated with tool version 2.2.0.''' - repository = get_repository_by_name_and_owner( repository_name, common.admin_username ) + repository = get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) self.upload_file( repository, 'readme.txt', commit_message="Uploaded readme.txt" ) self.display_manage_repository_page( repository, strings_displayed=[ 'This is a readme file.' ] ) # Verify that there is a different readme file for each metadata revision. @@ -134,13 +145,13 @@ self.display_manage_repository_page( repository, strings_displayed=[ 'Readme file for filtering 1.1.0', 'This is a readme file.' ] ) def test_0075_delete_readme_txt_file( self ): '''Delete the readme.txt file.''' - repository = get_repository_by_name_and_owner( repository_name, common.admin_username ) + repository = get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) self.delete_files_from_repository( repository, filenames=[ 'readme.txt' ] ) self.check_count_of_metadata_revisions_associated_with_repository( repository, metadata_count=2 ) self.display_manage_repository_page( repository, strings_displayed=[ 'Readme file for filtering 1.1.0' ] ) def test_0080_search_for_valid_filter_tool( self ): '''Search for the filtering tool by tool ID, name, and version.''' - repository = get_repository_by_name_and_owner( repository_name, common.admin_username ) + repository = get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) tip_changeset = self.get_repository_tip( repository ) search_fields = dict( tool_id='Filter1', tool_name='filter', tool_version='2.2.0' ) self.search_for_valid_tools( search_fields=search_fields, strings_displayed=[ tip_changeset ], strings_not_displayed=[] ) diff -r bd020b5aa5314718dbd7afe9e4e9e05bb3b53c7a -r 512c7561e1b95b381345296a0da3aa3effc05803 test/tool_shed/functional/test_0010_repository_with_tool_dependencies.py --- a/test/tool_shed/functional/test_0010_repository_with_tool_dependencies.py +++ b/test/tool_shed/functional/test_0010_repository_with_tool_dependencies.py @@ -1,7 +1,7 @@ from tool_shed.base.twilltestcase import ShedTwillTestCase, common, os from tool_shed.base.test_db_util import get_repository_by_name_and_owner, get_user, get_private_role -repository_name = 'freebayes' +repository_name = 'freebayes_0010' repository_description = "Galaxy's freebayes tool" repository_long_description = "Long description of Galaxy's freebayes tool" @@ -10,21 +10,28 @@ def test_0000_create_or_login_admin_user( self ): """Create necessary user accounts and login as an admin user.""" self.logout() + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + test_user_1 = get_user( common.test_user_1_email ) + assert test_user_1 is not None, 'Problem retrieving user with email %s from the database' % test_user_1_email + test_user_1_private_role = get_private_role( test_user_1 ) + self.logout() self.login( email=common.admin_email, username=common.admin_username ) admin_user = get_user( common.admin_email ) assert admin_user is not None, 'Problem retrieving user with email %s from the database' % admin_email admin_user_private_role = get_private_role( admin_user ) def test_0005_create_category( self ): - """Create SNP Analysis category.""" - self.create_category( 'SNP Analysis', 'Tools for single nucleotide polymorphism data such as WGA' ) + """Create a category for this test suite""" + self.create_category( 'Test 0010 Repository With Tool Dependencies', 'Tests for a repository with tool dependencies.' ) def test_0010_create_freebayes_repository_and_upload_tool_xml( self ): '''Create freebayes repository and upload freebayes.xml without tool_data_table_conf.xml.sample. This should result in an error message and invalid tool.''' + self.logout() + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) self.create_repository( repository_name, repository_description, repository_long_description=repository_long_description, - categories=[ 'SNP Analysis' ], + categories=[ 'Test 0010 Repository With Tool Dependencies' ], strings_displayed=[] ) - repository = get_repository_by_name_and_owner( repository_name, common.admin_username ) + repository = get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) self.upload_file( repository, 'freebayes/freebayes.xml', valid_tools_only=False, @@ -37,7 +44,7 @@ strings_displayed=[ 'requires an entry', 'tool_data_table_conf.xml' ] ) def test_0015_upload_missing_tool_data_table_conf_file( self ): '''Upload the missing tool_data_table_conf.xml.sample file to the repository.''' - repository = get_repository_by_name_and_owner( repository_name, common.admin_username ) + repository = get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) self.upload_file( repository, 'freebayes/tool_data_table_conf.xml.sample', valid_tools_only=False, @@ -50,27 +57,27 @@ strings_displayed=[ 'refers to a file', 'sam_fa_indices.loc' ] ) def test_0020_upload_missing_sample_loc_file( self ): '''Upload the missing sam_fa_indices.loc.sample file to the repository.''' - repository = get_repository_by_name_and_owner( repository_name, common.admin_username ) + repository = get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) self.upload_file( repository, 'freebayes/sam_fa_indices.loc.sample', strings_displayed=[], commit_message='Uploaded tool data table .loc file.' ) def test_0025_upload_invalid_tool_dependency_xml( self ): '''Upload tool_dependencies.xml defining version 0.9.5 of the freebayes package.''' - repository = get_repository_by_name_and_owner( repository_name, common.admin_username ) + repository = get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) self.upload_file( repository, os.path.join( 'freebayes', 'invalid_tool_dependencies', 'tool_dependencies.xml' ), strings_displayed=[ 'Name, version and type from a tool requirement tag does not match' ], commit_message='Uploaded invalid tool dependency XML.' ) def test_0030_upload_valid_tool_dependency_xml( self ): '''Upload tool_dependencies.xml defining version 0.9.4_9696d0ce8a962f7bb61c4791be5ce44312b81cf8 of the freebayes package.''' - repository = get_repository_by_name_and_owner( repository_name, common.admin_username ) + repository = get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) self.upload_file( repository, os.path.join( 'freebayes', 'tool_dependencies.xml' ), commit_message='Uploaded valid tool dependency XML.' ) def test_0035_verify_tool_dependencies( self ): '''Verify that the uploaded tool_dependencies.xml specifies the correct package versions.''' - repository = get_repository_by_name_and_owner( repository_name, common.admin_username ) + repository = get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) self.display_manage_repository_page( repository, strings_displayed=[ 'freebayes', '0.9.4_9696d0ce8a9', 'samtools', '0.1.18', 'Valid tools' ], strings_not_displayed=[ 'Invalid tools' ] ) diff -r bd020b5aa5314718dbd7afe9e4e9e05bb3b53c7a -r 512c7561e1b95b381345296a0da3aa3effc05803 test/tool_shed/functional/test_0020_basic_repository_dependencies.py --- a/test/tool_shed/functional/test_0020_basic_repository_dependencies.py +++ b/test/tool_shed/functional/test_0020_basic_repository_dependencies.py @@ -1,7 +1,7 @@ from tool_shed.base.twilltestcase import ShedTwillTestCase, common, os from tool_shed.base.test_db_util import get_repository_by_name_and_owner, get_user, get_private_role -datatypes_repository_name = 'emboss_datatypes' +datatypes_repository_name = 'emboss_datatypes_0020' datatypes_repository_description = "Galaxy applicable data formats used by Emboss tools." datatypes_repository_long_description = "Galaxy applicable data formats used by Emboss tools. This repository contains no tools." @@ -14,20 +14,18 @@ def test_0000_initiate_users( self ): """Create necessary user accounts and login as an admin user.""" self.logout() + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + test_user_1 = get_user( common.test_user_1_email ) + assert test_user_1 is not None, 'Problem retrieving user with email %s from the database' % common.test_user_1_email + test_user_1_private_role = get_private_role( test_user_1 ) + self.logout() self.login( email=common.admin_email, username=common.admin_username ) admin_user = get_user( common.admin_email ) assert admin_user is not None, 'Problem retrieving user with email %s from the database' % common.admin_email admin_user_private_role = get_private_role( admin_user ) - self.logout() - self.login( email=common.test_user_1_email, username=common.test_user_1_name ) - test_user_1 = get_user( common.test_user_1_email ) - assert test_user_1 is not None, 'Problem retrieving user with email %s from the database' % common.test_user_1_email - test_user_1_private_role = get_private_role( test_user_1 ) def test_0005_create_category( self ): - """Create Sequence Analysis category""" - self.logout() - self.login( email=common.admin_email, username=common.admin_username ) - self.create_category( 'Sequence Analysis', 'Tools for performing Protein and DNA/RNA analysis' ) + """Create a category for this test suite""" + self.create_category( 'Test 0020 Basic Repository Dependencies', 'Testing basic repository dependency features.' ) def test_0010_create_emboss_datatypes_repository_and_upload_tarball( self ): '''Create and populate the emboss_datatypes repository.''' self.logout() @@ -35,7 +33,7 @@ self.create_repository( datatypes_repository_name, datatypes_repository_description, repository_long_description=datatypes_repository_long_description, - categories=[ 'Sequence Analysis' ], + categories=[ 'Test 0020 Basic Repository Dependencies' ], strings_displayed=[] ) repository = get_repository_by_name_and_owner( datatypes_repository_name, common.test_user_1_name ) self.upload_file( repository, 'emboss/datatypes/datatypes_conf.xml', commit_message='Uploaded datatypes_conf.xml.' ) @@ -48,7 +46,7 @@ self.create_repository( emboss_repository_name, emboss_repository_description, repository_long_description=emboss_repository_long_description, - categories=[ 'Text Manipulation' ], + categories=[ 'Test 0020 Basic Repository Dependencies' ], strings_displayed=[] ) repository = get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name ) self.upload_file( repository, 'emboss/emboss.tar', commit_message='Uploaded emboss_5.tar' ) @@ -56,8 +54,13 @@ '''Generate and upload the repository_dependencies.xml file''' repository = get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name ) datatypes_repository = get_repository_by_name_and_owner( datatypes_repository_name, common.test_user_1_name ) - self.generate_repository_dependency_xml( datatypes_repository, self.get_filename( 'emboss/5/repository_dependencies.xml' ) ) - self.upload_file( repository, 'emboss/5/repository_dependencies.xml', commit_message='Uploaded repository_dependencies.xml' ) + repository_dependencies_path = self.generate_temp_path( 'test_0020', additional_paths=[ 'emboss', '5' ] ) + self.generate_repository_dependency_xml( datatypes_repository, + self.get_filename( 'repository_dependencies.xml', filepath=repository_dependencies_path ) ) + self.upload_file( repository, + 'repository_dependencies.xml', + filepath=repository_dependencies_path, + commit_message='Uploaded repository_dependencies.xml' ) def test_0030_verify_emboss_5_repository_dependency_on_emboss_datatypes( self ): '''Verify that the emboss_5 repository now depends on the emboss_datatypes repository with correct name, owner, and changeset revision.''' repository = get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name ) @@ -65,7 +68,3 @@ changeset_revision = self.get_repository_tip( datatypes_repository ) strings_displayed = [ datatypes_repository_name, common.test_user_1_name, changeset_revision, 'Repository dependencies' ] self.display_manage_repository_page( repository, strings_displayed=strings_displayed ) - def test_0035_cleanup( self ): - '''Clean up generated test data.''' - if os.path.exists( self.get_filename( 'emboss/5/repository_dependencies.xml' ) ): - os.remove( self.get_filename( 'emboss/5/repository_dependencies.xml' ) ) diff -r bd020b5aa5314718dbd7afe9e4e9e05bb3b53c7a -r 512c7561e1b95b381345296a0da3aa3effc05803 test/tool_shed/functional/test_0030_repository_dependency_revisions.py --- a/test/tool_shed/functional/test_0030_repository_dependency_revisions.py +++ b/test/tool_shed/functional/test_0030_repository_dependency_revisions.py @@ -5,7 +5,7 @@ datatypes_repository_description = "Galaxy applicable data formats used by Emboss tools." datatypes_repository_long_description = "Galaxy applicable data formats used by Emboss tools. This repository contains no tools." -emboss_repository_name = 'emboss' +emboss_repository_name = 'emboss_0030' emboss_5_repository_name = 'emboss_5_0030' emboss_6_repository_name = 'emboss_6_0030' emboss_repository_description = 'Galaxy wrappers for Emboss version 5.0.0 tools' @@ -13,38 +13,31 @@ class TestRepositoryDependencyRevisions( ShedTwillTestCase ): '''Test dependencies on different revisions of a repository.''' - ''' - create repository emboss_5_0030 - create repository emboss_6_0030 - create repository emboss_datatypes if necessary - create repository emboss - emboss_5 has repository_dependency.xml file that defines emboss_datatypes - emboss_6 has repository_dependency.xml file that defines emboss_datatypes - get information to create repository dependency imformation for emboss - emboss depends on emboss_5 - then emboss depends on emboss_6 - verify per-changeset dependencies - ''' def test_0000_initiate_users( self ): """Create necessary user accounts.""" self.logout() + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + test_user_1 = get_user( common.test_user_1_email ) + assert test_user_1 is not None, 'Problem retrieving user with email %s from the database' % regular_email + test_user_1_private_role = get_private_role( test_user_1 ) + self.logout() self.login( email=common.admin_email, username=common.admin_username ) admin_user = get_user( common.admin_email ) assert admin_user is not None, 'Problem retrieving user with email %s from the database' % admin_email admin_user_private_role = get_private_role( admin_user ) + def test_0005_create_category( self ): + """Create a category for this test suite""" + self.create_category( 'Test 0030 Repository Dependency Revisions', 'Testing repository dependencies by revision.' ) + def test_0005_create_repositories( self ): + '''Create the emboss_5_0030, emboss_6_0030, emboss_datatypes, and emboss repositories and populate the emboss_datatypes repository.''' self.logout() self.login( email=common.test_user_1_email, username=common.test_user_1_name ) - test_user_1 = get_user( common.test_user_1_email ) - assert test_user_1 is not None, 'Problem retrieving user with email %s from the database' % regular_email - test_user_1_private_role = get_private_role( test_user_1 ) - def test_0005_create_repositories( self ): - '''Create the emboss_5_0030, emboss_6_0030, emboss_datatypes, and emboss repositories and populate the emboss_datatypes repository.''' emboss_5_repository = get_repository_by_name_and_owner( emboss_5_repository_name, common.test_user_1_name ) if emboss_5_repository is None: self.create_repository( emboss_5_repository_name, emboss_repository_description, repository_long_description=emboss_repository_long_description, - categories=[ 'Sequence Analysis' ], + categories=[ 'Test 0030 Repository Dependency Revisions' ], strings_displayed=[] ) emboss_5_repository = get_repository_by_name_and_owner( emboss_5_repository_name, common.test_user_1_name ) self.upload_file( emboss_5_repository, 'emboss/emboss.tar', commit_message='Uploaded tool tarball.' ) @@ -53,7 +46,7 @@ self.create_repository( emboss_6_repository_name, emboss_repository_description, repository_long_description=emboss_repository_long_description, - categories=[ 'Sequence Analysis' ], + categories=[ 'Test 0030 Repository Dependency Revisions' ], strings_displayed=[] ) emboss_6_repository = get_repository_by_name_and_owner( emboss_6_repository_name, common.test_user_1_name ) self.upload_file( emboss_6_repository, 'emboss/emboss.tar', commit_message='Uploaded tool tarball..' ) @@ -62,7 +55,7 @@ self.create_repository( datatypes_repository_name, datatypes_repository_description, repository_long_description=datatypes_repository_long_description, - categories=[ 'Sequence Analysis' ], + categories=[ 'Test 0030 Repository Dependency Revisions' ], strings_displayed=[] ) datatypes_repository = get_repository_by_name_and_owner( datatypes_repository_name, common.test_user_1_name ) if self.repository_is_new( datatypes_repository ): @@ -72,45 +65,56 @@ self.create_repository( emboss_repository_name, emboss_repository_description, repository_long_description=emboss_repository_long_description, - categories=[ 'Sequence Analysis' ], + categories=[ 'Test 0030 Repository Dependency Revisions' ], strings_displayed=[] ) emboss_repository = get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name ) self.upload_file( emboss_5_repository, 'emboss/emboss.tar', commit_message='Uploaded tool tarball.' ) def test_0010_generate_repository_dependencies_for_emboss_5( self ): '''Generate a repository_dependencies.xml file specifying emboss_datatypes and upload it to the emboss_5 repository.''' datatypes_repository = get_repository_by_name_and_owner( datatypes_repository_name, common.test_user_1_name ) - self.generate_repository_dependency_xml( datatypes_repository, self.get_filename( 'emboss/repository_dependencies.xml' ) ) + repository_dependencies_path = self.generate_temp_path( 'test_0030', additional_paths=[ 'emboss' ] ) + self.generate_repository_dependency_xml( datatypes_repository, + self.get_filename( 'repository_dependencies.xml', filepath=repository_dependencies_path ) ) emboss_5_repository = get_repository_by_name_and_owner( emboss_5_repository_name, common.test_user_1_name ) - self.upload_file( emboss_5_repository, 'emboss/repository_dependencies.xml', commit_message='Uploaded repository_depepndencies.xml.' ) + self.upload_file( emboss_5_repository, + 'repository_dependencies.xml', + filepath=repository_dependencies_path, + commit_message='Uploaded repository_depepndencies.xml.' ) def test_0015_generate_repository_dependencies_for_emboss_6( self ): '''Generate a repository_dependencies.xml file specifying emboss_datatypes and upload it to the emboss_6 repository.''' emboss_6_repository = get_repository_by_name_and_owner( emboss_6_repository_name, common.test_user_1_name ) - self.upload_file( emboss_6_repository, 'emboss/repository_dependencies.xml', commit_message='Uploaded repository_depepndencies.xml.' ) + repository_dependencies_path = self.generate_temp_path( 'test_0030', additional_paths=[ 'emboss' ] ) + self.upload_file( emboss_6_repository, + 'repository_dependencies.xml', + filepath=repository_dependencies_path, + commit_message='Uploaded repository_depepndencies.xml.' ) def test_0020_generate_repository_dependency_on_emboss_5( self ): '''Create and upload repository_dependencies.xml for the emboss_5_0030 repository.''' emboss_repository = get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name ) emboss_5_repository = get_repository_by_name_and_owner( emboss_5_repository_name, common.test_user_1_name ) + repository_dependencies_path = self.generate_temp_path( 'test_0030', additional_paths=[ 'emboss', '5' ] ) self.generate_repository_dependency_xml( emboss_5_repository, - self.get_filename( 'emboss/5/repository_dependencies.xml' ), + self.get_filename( 'repository_dependencies.xml', filepath=repository_dependencies_path ), dependency_description='Emboss requires the Emboss 5 repository.' ) self.upload_file( emboss_repository, - 'emboss/5/repository_dependencies.xml', + 'repository_dependencies.xml', + filepath=repository_dependencies_path, commit_message='Uploaded dependency configuration specifying emboss_5' ) def test_0025_generate_repository_dependency_on_emboss_6( self ): '''Create and upload repository_dependencies.xml for the emboss_6_0030 repository.''' emboss_repository = get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name ) emboss_6_repository = get_repository_by_name_and_owner( emboss_6_repository_name, common.test_user_1_name ) + repository_dependencies_path = self.generate_temp_path( 'test_0030', additional_paths=[ 'emboss', '6' ] ) self.generate_repository_dependency_xml( emboss_6_repository, - self.get_filename( 'emboss/6/repository_dependencies.xml' ), + self.get_filename( 'repository_dependencies.xml', filepath=repository_dependencies_path ), dependency_description='Emboss requires the Emboss 6 repository.' ) self.upload_file( emboss_repository, - 'emboss/6/repository_dependencies.xml', + 'repository_dependencies.xml', + filepath=repository_dependencies_path, commit_message='Uploaded dependency configuration specifying emboss_6' ) def test_0030_verify_repository_dependency_revisions( self ): '''Verify that different metadata revisions of the emboss repository have different repository dependencies.''' repository = get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name ) - # Reset emboss metadata to pick up the repository dependency changes. -# self.reset_repository_metadata( repository ) repository_metadata = [ ( metadata.metadata, metadata.changeset_revision ) for metadata in self.get_repository_metadata( repository ) ] datatypes_repository = get_repository_by_name_and_owner( datatypes_repository_name, common.test_user_1_name ) datatypes_tip = self.get_repository_tip( datatypes_repository ) @@ -127,8 +131,3 @@ self.display_manage_repository_page( repository, changeset_revision=changeset_revision, strings_displayed=[ str( metadata ) for metadata in repository_dependency_metadata ] ) - def test_0035_cleanup( self ): - '''Clean up generated repository dependency XML files.''' - for filename in [ 'emboss/5/repository_dependencies.xml', 'emboss/6/repository_dependencies.xml', 'emboss/repository_dependencies.xml' ]: - if os.path.exists( self.get_filename( filename ) ): - os.remove( self.get_filename( filename ) ) diff -r bd020b5aa5314718dbd7afe9e4e9e05bb3b53c7a -r 512c7561e1b95b381345296a0da3aa3effc05803 test/tool_shed/functional_tests.py --- a/test/tool_shed/functional_tests.py +++ b/test/tool_shed/functional_tests.py @@ -10,6 +10,7 @@ # the hgweb.config file, the database, new repositories, etc. Since the tool shed browses repository contents via HTTP, # the full path to the temporary directroy wher eht repositories are located cannot contain invalid url characters. tool_shed_test_tmp_dir = os.path.join( tool_shed_home_directory, 'tmp' ) +os.environ[ 'TOOL_SHED_TEST_TMP_DIR' ] = tool_shed_test_tmp_dir new_path = [ os.path.join( cwd, "lib" ) ] new_path.extend( sys.path[1:] ) sys.path = new_path @@ -270,7 +271,7 @@ for dir in [ tool_shed_test_tmp_dir ]: if os.path.exists( dir ): log.info( "Cleaning up temporary files in %s" % dir ) - #shutil.rmtree( dir ) + shutil.rmtree( dir ) except: pass if success: diff -r bd020b5aa5314718dbd7afe9e4e9e05bb3b53c7a -r 512c7561e1b95b381345296a0da3aa3effc05803 test/tool_shed/test_data/filtering/filtering.txt --- a/test/tool_shed/test_data/filtering/filtering.txt +++ /dev/null @@ -1,1 +0,0 @@ -Readme file for filtering 1.1.0 diff -r bd020b5aa5314718dbd7afe9e4e9e05bb3b53c7a -r 512c7561e1b95b381345296a0da3aa3effc05803 test/tool_shed/test_data/filtering/filtering_0000.txt --- /dev/null +++ b/test/tool_shed/test_data/filtering/filtering_0000.txt @@ -0,0 +1,1 @@ +Readme file for filtering 1.1.0 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: Fix for SelectToolParameter rerun, workflow when multiple="true", submited by Jim Johnson.
by Bitbucket 10 Dec '12

10 Dec '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/bd020b5aa531/ changeset: bd020b5aa531 user: dan date: 2012-12-10 18:48:58 summary: Fix for SelectToolParameter rerun,workflow when multiple="true", submited by Jim Johnson. affected #: 1 file diff -r 0042b30216fc5dc4f92b314c93a3aa9a0d810d77 -r bd020b5aa5314718dbd7afe9e4e9e05bb3b53c7a lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -714,7 +714,12 @@ else: if value not in legal_values: raise ValueError( "An invalid option was selected, please verify" ) - return value + return value + def to_html_value( self, value, app ): + if isinstance( value, list ): + return value + else: + return str( value ) def to_param_dict_string( self, value, other_values={} ): if value is None: return "None" 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: clements: Added boilerplate for Sphinx doc home page.
by Bitbucket 07 Dec '12

07 Dec '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/0042b30216fc/ changeset: 0042b30216fc user: clements date: 2012-11-06 20:14:22 summary: Added boilerplate for Sphinx doc home page. affected #: 1 file diff -r c8f0ea550d51b2c203f5f60568817164c62220fd -r 0042b30216fc5dc4f92b314c93a3aa9a0d810d77 doc/source/index.rst --- a/doc/source/index.rst +++ b/doc/source/index.rst @@ -1,12 +1,41 @@ Galaxy Code Documentation ************************* -Galaxy is an open, web-based platform for accessible, reproducible, and +Galaxy_ is an open, web-based platform for accessible, reproducible, and transparent computational biomedical research. -- Accessible: Users without programming experience can easily specify parameters and run tools and workflows. -- Reproducible: Galaxy captures information so that any user can repeat and understand a complete computational analysis. -- Transparent: Users share and publish analyses via the web and create Pages, interactive, web-based documents that describe a complete analysis. +- *Accessible:* Users without programming experience can easily specify parameters and run tools and workflows. +- *Reproducible:* Galaxy captures information so that any user can repeat and understand a complete computational analysis. +- *Transparent:* Users share and publish analyses via the web and create Pages, interactive, web-based documents that describe a complete analysis. + +Two copies of the Galaxy code doumentation are published by the Galaxy Project + +- Galaxy-Dist_: This describes the code in the `most recent official release`_ of Galaxy. +- Galaxy-Central_: Describes the `current code in the development branch`_ of Galaxy. This is the latest checkin, bleeding edge version of the code. The documentation should never be more than an hour behind the code. + +Both copies are hosted at ReadTheDocs_, a publicly supported web site for hosting project documentation. + +If you have your own copy of the Galaxy source code, you can also generate your own version of this documentation: + +:: + + $ cd doc + $ make html + +The generated documentation will be in ``doc/build/html/`` and can be viewed with a web browser. Note that you will need to install Sphinx and a fair number of module dependencies before this will produce output. + +.. _Galaxy: http://galaxyproject.org/ +.. _Galaxy-Dist: https://galaxy-dist.readthedocs.org/ +.. _most recent official release: https://bitbucket.org/galaxy/galaxy-dist +.. _Galaxy-Central: https://galaxy-central.readthedocs.org/ +.. _current code in the development branch: https://bitbucket.org/galaxy/galaxy-central +.. _ReadTheDocs: https://readthedocs.org/ + + +For more on the Galaxy Project, please visit the `project home page`_. + +.. _project home page: http://galaxyproject.org/ + Contents ======== 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: 2 new changesets
by Bitbucket 07 Dec '12

07 Dec '12

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/8cb49d27d1a4/ changeset: 8cb49d27d1a4 user: lance_parsons date: 2012-12-07 23:22:48 summary: Fix for finding test-data for installed tools See bug: https://trello.com/c/Z0vhJEq6 affected #: 1 file diff -r 2f45da781f926f667dd90ad23d23fd123716a535 -r 8cb49d27d1a4c681eb774ac020d524258709ce20 scripts/functional_tests.py --- a/scripts/functional_tests.py +++ b/scripts/functional_tests.py @@ -57,8 +57,10 @@ last_galaxy_test_file_dir = None last_tested_repository_name = None last_tested_changeset_revision = None + tool_path = None tree = util.parse_xml( config ) root = tree.getroot() + tool_path = root.get('tool_path') for elem in root: if elem.tag == 'tool': galaxy_test_file_dir, \ @@ -66,7 +68,8 @@ last_tested_changeset_revision = get_installed_repository_info( elem, last_galaxy_test_file_dir, last_tested_repository_name, - last_tested_changeset_revision ) + last_tested_changeset_revision, + tool_path ) if galaxy_test_file_dir: if galaxy_test_file_dir != last_galaxy_test_file_dir: if not os.path.isabs( galaxy_test_file_dir ): @@ -82,7 +85,8 @@ last_tested_changeset_revision = get_installed_repository_info( section_elem, last_galaxy_test_file_dir, last_tested_repository_name, - last_tested_changeset_revision ) + last_tested_changeset_revision, + tool_path ) if galaxy_test_file_dir: if galaxy_test_file_dir != last_galaxy_test_file_dir: if not os.path.isabs( galaxy_test_file_dir ): @@ -92,7 +96,7 @@ last_galaxy_test_file_dir = galaxy_test_file_dir return shed_tools_dict -def get_installed_repository_info( elem, last_galaxy_test_file_dir, last_tested_repository_name, last_tested_changeset_revision ): +def get_installed_repository_info( elem, last_galaxy_test_file_dir, last_tested_repository_name, last_tested_changeset_revision, tool_path ): """ Return the GALAXY_TEST_FILE_DIR, the containing repository name and the change set revision for the tool elem. This only happens when testing tools installed from the tool shed. @@ -107,7 +111,7 @@ if repository_name != last_tested_repository_name or changeset_revision != last_tested_changeset_revision: # Locate the test-data directory. installed_tool_path = os.path.join( installed_tool_path_items[ 0 ], 'repos', repository_owner, repository_name, changeset_revision ) - for root, dirs, files in os.walk( installed_tool_path ): + for root, dirs, files in os.walk( os.path.join(tool_path, installed_tool_path )): if 'test-data' in dirs: return os.path.join( root, 'test-data' ), repository_name, changeset_revision return None, repository_name, changeset_revision https://bitbucket.org/galaxy/galaxy-central/changeset/c8f0ea550d51/ changeset: c8f0ea550d51 user: greg date: 2012-12-08 01:09:00 summary: Merged in lance_parsons/galaxy-central_installed-tools-functional-tests-fix (pull request #95) affected #: 1 file diff -r 6f3266a589e397cbdbe8efe4f4d26b7dcdc8924c -r c8f0ea550d51b2c203f5f60568817164c62220fd scripts/functional_tests.py --- a/scripts/functional_tests.py +++ b/scripts/functional_tests.py @@ -57,8 +57,10 @@ last_galaxy_test_file_dir = None last_tested_repository_name = None last_tested_changeset_revision = None + tool_path = None tree = util.parse_xml( config ) root = tree.getroot() + tool_path = root.get('tool_path') for elem in root: if elem.tag == 'tool': galaxy_test_file_dir, \ @@ -66,7 +68,8 @@ last_tested_changeset_revision = get_installed_repository_info( elem, last_galaxy_test_file_dir, last_tested_repository_name, - last_tested_changeset_revision ) + last_tested_changeset_revision, + tool_path ) if galaxy_test_file_dir: if galaxy_test_file_dir != last_galaxy_test_file_dir: if not os.path.isabs( galaxy_test_file_dir ): @@ -82,7 +85,8 @@ last_tested_changeset_revision = get_installed_repository_info( section_elem, last_galaxy_test_file_dir, last_tested_repository_name, - last_tested_changeset_revision ) + last_tested_changeset_revision, + tool_path ) if galaxy_test_file_dir: if galaxy_test_file_dir != last_galaxy_test_file_dir: if not os.path.isabs( galaxy_test_file_dir ): @@ -92,7 +96,7 @@ last_galaxy_test_file_dir = galaxy_test_file_dir return shed_tools_dict -def get_installed_repository_info( elem, last_galaxy_test_file_dir, last_tested_repository_name, last_tested_changeset_revision ): +def get_installed_repository_info( elem, last_galaxy_test_file_dir, last_tested_repository_name, last_tested_changeset_revision, tool_path ): """ Return the GALAXY_TEST_FILE_DIR, the containing repository name and the change set revision for the tool elem. This only happens when testing tools installed from the tool shed. @@ -107,7 +111,7 @@ if repository_name != last_tested_repository_name or changeset_revision != last_tested_changeset_revision: # Locate the test-data directory. installed_tool_path = os.path.join( installed_tool_path_items[ 0 ], 'repos', repository_owner, repository_name, changeset_revision ) - for root, dirs, files in os.walk( installed_tool_path ): + for root, dirs, files in os.walk( os.path.join(tool_path, installed_tool_path )): if 'test-data' in dirs: return os.path.join( root, 'test-data' ), repository_name, changeset_revision return None, repository_name, changeset_revision 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: clements: Added numpy to mock modules list. Readthedocs of galaxy-central is broken, and it's complaining about numpy. So, try adding it to mock modules list and see if that helps.
by Bitbucket 07 Dec '12

07 Dec '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/6f3266a589e3/ changeset: 6f3266a589e3 user: clements date: 2012-11-06 18:31:28 summary: Added numpy to mock modules list. Readthedocs of galaxy-central is broken, and it's complaining about numpy. So, try adding it to mock modules list and see if that helps. affected #: 1 file diff -r 6d86fa9ca5977060372704346a1e9a2b6308a292 -r 6f3266a589e397cbdbe8efe4f4d26b7dcdc8924c doc/source/conf.py --- a/doc/source/conf.py +++ b/doc/source/conf.py @@ -274,6 +274,6 @@ return Mock() # adding pbs_python, DRMAA_python, markupsafe, and drmaa here had no effect. -MOCK_MODULES = ['tables', 'decorator'] +MOCK_MODULES = ['tables', 'decorator', 'numpy'] for mod_name in MOCK_MODULES: sys.modules[mod_name] = Mock() 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: greg: Handle somce cases of circular dependencies and other corner case siturations with repository dependency definitions.
by Bitbucket 07 Dec '12

07 Dec '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/6d86fa9ca597/ changeset: 6d86fa9ca597 user: greg date: 2012-12-07 22:47:24 summary: Handle somce cases of circular dependencies and other corner case siturations with repository dependency definitions. affected #: 3 files diff -r facdd387b85e814df7428ca8cbb71828d0ec48a2 -r 6d86fa9ca5977060372704346a1e9a2b6308a292 lib/galaxy/util/shed_util_common.py --- a/lib/galaxy/util/shed_util_common.py +++ b/lib/galaxy/util/shed_util_common.py @@ -2,12 +2,12 @@ from galaxy import util from galaxy.tools import parameters from galaxy.util import inflector -from galaxy.util.json import * +from galaxy.util import json from galaxy.web import url_for from galaxy.web.form_builder import SelectField -from galaxy.webapps.community.util.container_util import * -from galaxy.datatypes.checkers import * -from galaxy.model.orm import * +from galaxy.webapps.community.util import container_util +from galaxy.datatypes import checkers +from galaxy.model.orm import and_ from galaxy.tools.parameters import dynamic_options from galaxy import eggs @@ -124,45 +124,49 @@ # Datatypes container. if metadata and 'datatypes' in metadata: datatypes = metadata[ 'datatypes' ] - folder_id, datatypes_root_folder = build_datatypes_folder( folder_id, datatypes ) + folder_id, datatypes_root_folder = container_util.build_datatypes_folder( folder_id, datatypes ) containers_dict[ 'datatypes' ] = datatypes_root_folder # Invalid tools container. if metadata and 'invalid_tools' in metadata: invalid_tool_configs = metadata[ 'invalid_tools' ] - folder_id, invalid_tools_root_folder = build_invalid_tools_folder( folder_id, - invalid_tool_configs, - changeset_revision, - repository=repository, - label='Invalid tools' ) + folder_id, invalid_tools_root_folder = container_util.build_invalid_tools_folder( folder_id, + invalid_tool_configs, + changeset_revision, + repository=repository, + label='Invalid tools' ) containers_dict[ 'invalid_tools' ] = invalid_tools_root_folder # Readme files container. readme_files_dict = build_readme_files_dict( repository_metadata ) - folder_id, readme_files_root_folder = build_readme_files_folder( folder_id, readme_files_dict ) + folder_id, readme_files_root_folder = container_util.build_readme_files_folder( folder_id, readme_files_dict ) containers_dict[ 'readme_files' ] = readme_files_root_folder # Repository dependencies container. toolshed_base_url = str( url_for( '/', qualified=True ) ).rstrip( '/' ) - folder_id, repository_dependencies_root_folder = build_repository_dependencies_folder( toolshed_base_url=toolshed_base_url, - repository_name=repository.name, - repository_owner=repository.user.username, - changeset_revision=changeset_revision, - folder_id=folder_id, - repository_dependencies=repository_dependencies ) + folder_id, repository_dependencies_root_folder = container_util.build_repository_dependencies_folder( toolshed_base_url=toolshed_base_url, + repository_name=repository.name, + repository_owner=repository.user.username, + changeset_revision=changeset_revision, + folder_id=folder_id, + repository_dependencies=repository_dependencies ) if repository_dependencies_root_folder: containers_dict[ 'repository_dependencies' ] = repository_dependencies_root_folder # Tool dependencies container. if metadata and 'tool_dependencies' in metadata: tool_dependencies = metadata[ 'tool_dependencies' ] - folder_id, tool_dependencies_root_folder = build_tool_dependencies_folder( folder_id, tool_dependencies, for_galaxy=False ) + folder_id, tool_dependencies_root_folder = container_util.build_tool_dependencies_folder( folder_id, tool_dependencies, for_galaxy=False ) containers_dict[ 'tool_dependencies' ] = tool_dependencies_root_folder # Valid tools container. if metadata and 'tools' in metadata: valid_tools = metadata[ 'tools' ] - folder_id, valid_tools_root_folder = build_tools_folder( folder_id, valid_tools, repository, changeset_revision, label='Valid tools' ) + folder_id, valid_tools_root_folder = container_util.build_tools_folder( folder_id, + valid_tools, + repository, + changeset_revision, + label='Valid tools' ) containers_dict[ 'valid_tools' ] = valid_tools_root_folder # Workflows container. if metadata and 'workflows' in metadata: workflows = metadata[ 'workflows' ] - folder_id, workflows_root_folder = build_workflows_folder( folder_id, workflows, repository_metadata, label='Workflows' ) + folder_id, workflows_root_folder = container_util.build_workflows_folder( folder_id, workflows, repository_metadata, label='Workflows' ) containers_dict[ 'workflows' ] = workflows_root_folder except Exception, e: log.debug( "Exception in build_repository_containers_for_tool_shed: %s" % str( e ) ) @@ -190,6 +194,29 @@ option_value = trans.security.encode_id( repository.id ) repositories_select_field.add_option( option_label, option_value ) return repositories_select_field +def can_add_entry_to_all_repository_dependencies( current_repository_key, repository_dependency, all_repository_dependencies ): + """ + Handle circular repository dependencies that could result in an infinite loop by determining if it is safe to add an entry to the + repository dependencies container. + """ + # First check for an exact match - if this is true, the changeset revision was not updated. + repository_dependency_as_key = container_util.generate_repository_dependencies_key_for_repository( repository_dependency[ 0 ], + repository_dependency[ 1 ], + repository_dependency[ 2 ], + repository_dependency[ 3] ) + current_repository_key_as_repository_dependency = current_repository_key.split( container_util.STRSEP ) + if repository_dependency_as_key in all_repository_dependencies: + val = all_repository_dependencies[ repository_dependency_as_key ] + if current_repository_key_as_repository_dependency in val: + return False + # Now handle the case where an update to the changeset revision was done, so everything will match except the changeset_revision. + repository_dependency_as_partial_key = container_util.STRSEP.join( [ repository_dependency[ 0 ], repository_dependency[ 1 ], repository_dependency[ 2 ] ] ) + for key in all_repository_dependencies: + if key.startswith( repository_dependency_as_partial_key ): + val = all_repository_dependencies[ key ] + if current_repository_key_as_repository_dependency in val: + return False + return True def can_generate_tool_dependency_metadata( root, metadata_dict ): """ Make sure the combination of name, version and type (the type will be the value of elem.tag) of each root element tag in the tool_dependencies.xml @@ -736,8 +763,8 @@ elif name not in NOT_TOOL_CONFIGS and name.endswith( '.xml' ): full_path = str( os.path.abspath( os.path.join( root, name ) ) ) if os.path.getsize( full_path ) > 0: - if not ( check_binary( full_path ) or check_image( full_path ) or check_gzip( full_path )[ 0 ] - or check_bz2( full_path )[ 0 ] or check_zip( full_path ) ): + if not ( checkers.check_binary( full_path ) or checkers.check_image( full_path ) or checkers.check_gzip( full_path )[ 0 ] + or checkers.check_bz2( full_path )[ 0 ] or checkers.check_zip( full_path ) ): try: # Make sure we're looking at a tool config and not a display application config or something else. element_tree = util.parse_xml( full_path ) @@ -779,7 +806,7 @@ fp = open( relative_path, 'rb' ) workflow_text = fp.read() fp.close() - exported_workflow_dict = from_json_string( workflow_text ) + exported_workflow_dict = json.from_json_string( workflow_text ) if 'a_galaxy_workflow' in exported_workflow_dict and exported_workflow_dict[ 'a_galaxy_workflow' ] == 'true': metadata_dict = generate_workflow_metadata( relative_path, exported_workflow_dict, metadata_dict ) if readme_files: @@ -1189,106 +1216,112 @@ repository_dependencies_dict = metadata[ 'repository_dependencies' ] # The repository_dependencies entry in the metadata is a dictionary that may have a value for a 'description' key. We want to # store the value of this key only once, the first time through this recursive method. - repository_dependencies_root_key = generate_repository_dependencies_key_for_repository( toolshed_base_url=toolshed_base_url, - repository_name=repository.name, - repository_owner=repository.user.username, - changeset_revision=repository_metadata.changeset_revision ) + current_repository_key = container_util.generate_repository_dependencies_key_for_repository( toolshed_base_url=toolshed_base_url, + repository_name=repository.name, + repository_owner=repository.user.username, + changeset_revision=repository_metadata.changeset_revision ) if not all_repository_dependencies: - # Initialize the all_repository_dependencies dictionary. - all_repository_dependencies[ 'root_key' ] = repository_dependencies_root_key - all_repository_dependencies[ repository_dependencies_root_key ] = [] + # Initialize the all_repository_dependencies dictionary. It's safe to assume that current_repository_key in this case will have a value. + all_repository_dependencies[ 'root_key' ] = current_repository_key + all_repository_dependencies[ current_repository_key ] = [] if 'description' not in all_repository_dependencies: description = repository_dependencies_dict.get( 'description', None ) all_repository_dependencies[ 'description' ] = description # The next key of interest in repository_dependencies_dict is 'repository_dependencies', which is a list of tuples. repository_dependencies_tups = repository_dependencies_dict[ 'repository_dependencies' ] + if repository_dependencies_tups and current_repository_key: + # Remove all repository dependencies that point to a revision within its own repository. + repository_dependencies_tups = remove_ropository_dependency_reference_to_self( repository_dependencies_tups, current_repository_key ) for repository_dependency in repository_dependencies_tups: - # Skip repository dependencies that point to the root repository. - check_key = generate_repository_dependencies_key_for_repository( toolshed_base_url=repository_dependency[ 0 ], - repository_name=repository_dependency[ 1 ], - repository_owner=repository_dependency[ 2 ], - changeset_revision=repository_dependency[ 3 ] ) - if check_key == repository_dependencies_root_key: - handled.append( repository_dependency ) - elif repository_dependency not in handled and repository_dependency not in repository_dependencies: + if repository_dependency not in handled and repository_dependency not in repository_dependencies: + # The following if statement handles repositories dependencies that are circular in nature. + if current_repository_key: + if current_repository_key in all_repository_dependencies: + # Add all repository dependencies for the current repository into it's entry in all_repository_dependencies. + all_repository_dependencies_val = all_repository_dependencies[ current_repository_key ] + if repository_dependency not in all_repository_dependencies_val: + all_repository_dependencies_val.append( repository_dependency ) + all_repository_dependencies[ current_repository_key ] = all_repository_dependencies_val + elif can_add_entry_to_all_repository_dependencies( current_repository_key, repository_dependency, all_repository_dependencies ): + # We don't have a circular dependency that could result in an infinite loop. + all_repository_dependencies[ current_repository_key ] = [ repository_dependency ] repository_dependencies.append( repository_dependency ) else: - repository_dependencies_root_key = None - if repository_dependencies: - repository_dependency = repository_dependencies.pop( 0 ) - # Cast unicode to string. - repository_dependency = [ str( item ) for item in repository_dependency ] - tool_shed, name, owner, changeset_revision = repository_dependency - if repository_dependencies_root_key: - if repository_dependencies_root_key in all_repository_dependencies: - # See if this repository_dependency is contained in the list associated with the repository_dependencies_root_key. - all_repository_dependencies_val = all_repository_dependencies[ repository_dependencies_root_key ] - if repository_dependency not in all_repository_dependencies_val: - all_repository_dependencies_val.append( repository_dependency ) - all_repository_dependencies[ repository_dependencies_root_key ] = all_repository_dependencies_val - handled.append( repository_dependency ) - else: - # Insert this repository_dependency. - all_repository_dependencies[ repository_dependencies_root_key ] = [ repository_dependency ] + # The current repository does not have repository dependencies defined for it. + current_repository_key = None + # The following if statement handles repositories dependencies that are circular in nature. + if current_repository_key and current_repository_key in all_repository_dependencies: + repository_dependencies_tups = [ rd for rd in all_repository_dependencies[ current_repository_key ] ] + if repository_dependencies_tups: + repository_dependency = repository_dependencies_tups.pop( 0 ) + if repository_dependency not in handled: handled.append( repository_dependency ) - if tool_shed_is_this_tool_shed( tool_shed ): - # The repository is in the current tool shed. - required_repository = get_repository_by_name_and_owner( trans, name, owner ) - required_repository_metadata = get_repository_metadata_by_repository_id_changset_revision( trans, - trans.security.encode_id( required_repository.id ), - changeset_revision ) - if required_repository_metadata: - required_repo_dir = required_repository.repo_path( trans.app ) - required_repo = hg.repository( get_configured_ui(), required_repo_dir ) - else: - # The repository changeset_revision is no longer installable, so see if there's been an update. - required_repo_dir = required_repository.repo_path( trans.app ) - required_repo = hg.repository( get_configured_ui(), required_repo_dir ) - required_changeset_revision = get_next_downloadable_changeset_revision( required_repository, required_repo, changeset_revision ) + if repository_dependency in repository_dependencies: + repository_dependencies.remove( repository_dependency ) + toolshed, name, owner, changeset_revision = repository_dependency + if tool_shed_is_this_tool_shed( toolshed ): + required_repository = get_repository_by_name_and_owner( trans, name, owner ) required_repository_metadata = get_repository_metadata_by_repository_id_changset_revision( trans, trans.security.encode_id( required_repository.id ), - required_changeset_revision ) + changeset_revision ) if required_repository_metadata: - # The changeset_revision defined in a repository_dependencies.xml file is outdated, so we need to fix appropriate - # entries in our all_repository_dependencies dictionary. - updated_repository_dependency = [ tool_shed, name, owner, required_changeset_revision ] - for k, v in all_repository_dependencies.items(): - if k in [ 'root_key', 'description' ]: - continue - for i, current_repository_dependency in enumerate( v ): - current_tool_shed, current_name, current_owner, current_changeset_revision = current_repository_dependency - if tool_shed == current_tool_shed and name == current_name and owner == current_owner and changeset_revision == current_changeset_revision: - if updated_repository_dependency in v: - # We've already stored the updated repository_dependency, so remove the outdated one. - v = v.remove( repository_dependency ) - else: - # Store the updated repository_dependency. - v[ i ] = updated_repository_dependency - all_repository_dependencies[ k ] = v - if required_repository_metadata: - # The required_repository_metadata changeset_revision is installable. - required_metadata = required_repository_metadata.metadata - if required_metadata: - return get_repository_dependencies_for_changeset_revision( trans=trans, - repo=required_repo, - repository=required_repository, - repository_metadata=required_repository_metadata, - toolshed_base_url=tool_shed, - repository_dependencies=repository_dependencies, - all_repository_dependencies=all_repository_dependencies, - handled=handled ) - else: - # The repository is in a different tool shed, so build an url and send a request. - raise Exception( "Repository dependencies that refer to repositories in other tool sheds is not yet supported." ) + required_repo_dir = required_repository.repo_path( trans.app ) + required_repo = hg.repository( get_configured_ui(), required_repo_dir ) + else: + # The repository changeset_revision is no longer installable, so see if there's been an update. + required_repo_dir = required_repository.repo_path( trans.app ) + required_repo = hg.repository( get_configured_ui(), required_repo_dir ) + required_changeset_revision = get_next_downloadable_changeset_revision( required_repository, required_repo, changeset_revision ) + required_repository_metadata = get_repository_metadata_by_repository_id_changset_revision( trans, + trans.security.encode_id( required_repository.id ), + required_changeset_revision ) + if required_repository_metadata: + # The changeset_revision defined in a repository_dependencies.xml file is outdated, so we need to fix appropriate + # entries in our all_repository_dependencies dictionary. + updated_repository_dependency = [ toolshed, name, owner, required_changeset_revision ] + for k, v in all_repository_dependencies.items(): + if k in [ 'root_key', 'description' ]: + continue + for i, current_repository_dependency in enumerate( v ): + cts, cn, co, ccr = current_repository_dependency + if toolshed == cts and name == cn and owner == co and changeset_revision == ccr: + if updated_repository_dependency in v: + # We've already stored the updated repository_dependency, so remove the outdated one. + v = v.remove( repository_dependency ) + all_repository_dependencies[ k ] = v + else: + # Store the updated repository_dependency. + v[ i ] = updated_repository_dependency + all_repository_dependencies[ k ] = v + if required_repository_metadata: + # The required_repository_metadata changeset_revision is installable. + required_metadata = required_repository_metadata.metadata + if required_metadata: + for repository_dependency in repository_dependencies_tups: + if repository_dependency not in repository_dependencies: + repository_dependencies.append( repository_dependency ) + return get_repository_dependencies_for_changeset_revision( trans=trans, + repo=required_repo, + repository=required_repository, + repository_metadata=required_repository_metadata, + toolshed_base_url=toolshed, + repository_dependencies=repository_dependencies, + all_repository_dependencies=all_repository_dependencies, + handled=handled ) + else: + # The repository is in a different tool shed, so build an url and send a request. + error_message = "Repository dependencies are currently supported only within the same tool shed. Ignoring repository dependency definition " + error_message += "for tool shed %s, name %s, owner %s, changeset revision %s" % ( toolshed, name, owner, changeset_revision ) + log.debug( error_message ) return all_repository_dependencies def get_repository_file_contents( file_path ): - if is_gzip( file_path ): + if checkers.is_gzip( file_path ): safe_str = to_safe_string( '\ngzip compressed file\n' ) - elif is_bz2( file_path ): + elif checkers.is_bz2( file_path ): safe_str = to_safe_string( '\nbz2 compressed file\n' ) - elif check_zip( file_path ): + elif checkers.check_zip( file_path ): safe_str = to_safe_string( '\nzip compressed file\n' ) - elif check_binary( file_path ): + elif checkers.check_binary( file_path ): safe_str = to_safe_string( '\nBinary file\n' ) else: safe_str = '' @@ -1526,6 +1559,18 @@ shutil.rmtree( dir ) except: pass +def remove_ropository_dependency_reference_to_self( repository_dependencies, repository_key ): + """Remove all repository dependencies that point to a revision within its own repository.""" + clean_repository_dependencies = [] + repository_tup = repository_key.split( container_util.STRSEP ) + rd_toolshed, rd_name, rd_owner, rd_changeset_revision = repository_tup + for repository_dependency in repository_dependencies: + toolshed, name, owner, changeset_revision = repository_dependency + if rd_toolshed == toolshed and rd_name == name and rd_owner == owner: + log.debug( "Removing repository dependency for repository %s owned by %s since it refers to a revision within itself." % ( name, owner ) ) + else: + clean_repository_dependencies.append( repository_dependency ) + return clean_repository_dependencies def remove_tool_dependency_installation_directory( dependency_install_dir ): if os.path.exists( dependency_install_dir ): try: diff -r facdd387b85e814df7428ca8cbb71828d0ec48a2 -r 6d86fa9ca5977060372704346a1e9a2b6308a292 lib/galaxy/webapps/community/controllers/upload.py --- a/lib/galaxy/webapps/community/controllers/upload.py +++ b/lib/galaxy/webapps/community/controllers/upload.py @@ -188,7 +188,7 @@ else: metadata_dict = {} if 'tool_dependencies' not in metadata_dict: - message += 'Name, version and type from a tool requirement tag does not match the information in the "tool_dependencies.xml". ' + message += 'Name, version and type from a tool requirement tag does not match the information in the "tool_dependencies.xml file". ' status = 'warning' log.debug( 'Error in tool dependencies for repository %s: %s.' % ( repository.id, repository.name ) ) # Reset the tool_data_tables by loading the empty tool_data_table_conf.xml file. diff -r facdd387b85e814df7428ca8cbb71828d0ec48a2 -r 6d86fa9ca5977060372704346a1e9a2b6308a292 lib/galaxy/webapps/community/util/container_util.py --- a/lib/galaxy/webapps/community/util/container_util.py +++ b/lib/galaxy/webapps/community/util/container_util.py @@ -212,7 +212,7 @@ repository_dependencies_folder.description = repository_dependencies.get( 'description', None ) repository_dependencies_root_folder.folders.append( repository_dependencies_folder ) del repository_dependencies[ 'description' ] - # The remaining keys in repository_dependencies should all be folders. + # The current keys in repository_dependencies should all be folders. folder_keys = repository_dependencies.keys() # If repository_dependencies_folder_key is an entry in repository_dependencies, process it first. if repository_dependencies_folder_key in repository_dependencies: @@ -404,7 +404,7 @@ STRSEP, str( changeset_revision ) ) def get_folder( folder, key ): - if folder and folder.key == key: + if folder.key == key: return folder for sub_folder in folder.folders: return get_folder( sub_folder, key ) @@ -421,25 +421,30 @@ folder_keys, folder_id, repository_dependency_id, repository_name, repository_owner, changeset_revision, key, val ): # Only create a new folder object if necessary. - folder = get_folder( repository_dependencies_root_folder, key ) + folder = get_folder( repository_dependencies_folder, key ) if not folder: folder_id += 1 label = generate_repository_dependencies_folder_label_from_key( repository_name, repository_owner, changeset_revision, key ) folder = Folder( id=folder_id, key=key, label=label, parent=repository_dependencies_folder ) for repository_dependency_tup in val: toolshed, name, owner, changeset_revision = repository_dependency_tup - if is_root_repository( repository_dependencies_folder_key, toolshed, name, owner ): - # Do not include repository dependencies that point to a revision within the same repository. - continue if is_or_should_be_folder( folder_keys, toolshed, name, owner, changeset_revision ): check_folder_key = generate_repository_dependencies_key_for_repository( toolshed, name, owner, changeset_revision ) - if get_folder( repository_dependencies_root_folder, check_folder_key ): - continue + check_folder = get_folder( repository_dependencies_folder, check_folder_key ) + if check_folder: + repository_dependency_id += 1 + repository_dependency = RepositoryDependency( id=repository_dependency_id, + toolshed=toolshed, + repository_name=name, + repository_owner=owner, + changeset_revision=changeset_revision ) + if not check_folder.contains_repository_dependency( repository_dependency ): + check_folder.repository_dependencies.append( repository_dependency ) else: # Create a new folder, which may be populated later. folder_id += 1 label = generate_repository_dependencies_folder_label_from_key( name, owner, changeset_revision, key ) - sub_folder = Folder( id=folder_id, key=check_folder_key, label=label, parent=repository_dependencies_folder ) + sub_folder = Folder( id=folder_id, key=check_folder_key, label=label, parent=folder ) folder.folders.append( sub_folder ) else: repository_dependency_id += 1 @@ -458,11 +463,6 @@ def is_or_should_be_folder( folder_keys, toolshed, repository_name, repository_owner, changeset_revision ): key = '%s%s%s%s%s%s%s' % ( toolshed, STRSEP, repository_name, STRSEP, repository_owner, STRSEP, changeset_revision ) return key in folder_keys -def is_root_repository( repository_dependencies_folder_key, toolshed, repository_name, repository_owner ): - # Return True if a repository dependency points to a revision within it's own repository. - repository_dependencies_folder_tup = repository_dependencies_folder_key.split( STRSEP ) - rdf_toolshed, rdf_repository_name, rdf_repository_owner, rdf_changeset_revision = repository_dependencies_folder_tup - return rdf_toolshed == toolshed and rdf_repository_name == repository_name and rdf_repository_owner == repository_owner def key_is_current_repositorys_key( repository_name, repository_owner, changeset_revision, key ): toolshed_base_url, key_name, key_owner, key_changeset_revision = get_components_from_key( key ) return repository_name == key_name and repository_owner == key_owner and changeset_revision == key_changeset_revision Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 2 new changesets
by Bitbucket 07 Dec '12

07 Dec '12

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/659392eae2a8/ changeset: 659392eae2a8 user: inithello date: 2012-12-07 22:38:26 summary: Revert tool migration. affected #: 35 files diff -r 2f45da781f926f667dd90ad23d23fd123716a535 -r 659392eae2a8946ea6d2f2c5534d5c51c1dc28f3 lib/galaxy/tool_shed/migrate/versions/0008_tools.py --- a/lib/galaxy/tool_shed/migrate/versions/0008_tools.py +++ /dev/null @@ -1,21 +0,0 @@ -""" -The following tools have been eliminated from the distribution: -Add column to an existing dataset, Change Case of selected columns, -Condense consecutive characters, Convert delimiters to TAB, -Cut columns from a table, Merge Columns together, Remove beginning of a file, -Select first lines from a dataset, Select last lines from a dataset, -and Trim leading or trailing characters. The tools are now available in the -repositories named add_value, change_case, condense_characters, -convert_characters, cut_columns, merge_cols, remove_beginning, -show_beginning, show_tail, and trimmer from the main Galaxy tool shed at -http://toolshed.g2.bx.psu.edu, and will be installed into your -local Galaxy instance at the location discussed above by running -the following command. -""" - -import sys - -def upgrade(): - print __doc__ -def downgrade(): - pass diff -r 2f45da781f926f667dd90ad23d23fd123716a535 -r 659392eae2a8946ea6d2f2c5534d5c51c1dc28f3 scripts/migrate_tools/0008_tools.sh --- a/scripts/migrate_tools/0008_tools.sh +++ /dev/null @@ -1,4 +0,0 @@ -#!/bin/sh - -cd `dirname $0`/../.. -python ./scripts/migrate_tools/migrate_tools.py 0008_tools.xml $@ diff -r 2f45da781f926f667dd90ad23d23fd123716a535 -r 659392eae2a8946ea6d2f2c5534d5c51c1dc28f3 scripts/migrate_tools/0008_tools.xml --- a/scripts/migrate_tools/0008_tools.xml +++ /dev/null @@ -1,33 +0,0 @@ -<?xml version="1.0"?> -<toolshed name="toolshed.g2.bx.psu.edu"> - <repository name="add_value" description="Add a value as a new column." changeset_revision="181dd378275c"> - <tool id="addValue" version="1.0.0" file="fixedValueColumn.xml" /> - </repository> - <repository name="change_case" description="Change the case of a column." changeset_revision="e6f966602870"> - <tool id="ChangeCase" version="1.0.0" file="changeCase.xml" /> - </repository> - <repository name="condense_characters" description="Condense repeated characters." changeset_revision="2c08781560de"> - <tool id="Condense characters1" version="1.0.0" file="condense_characters.xml" /> - </repository> - <repository name="convert_characters" description="Convert delimiters to TAB." changeset_revision="64d46676a13e"> - <tool id="Convert characters1" version="1.0.0" file="convert_characters.xml" /> - </repository> - <repository name="cut_columns" description="Remove or rearrange columns." changeset_revision="34c29e183ef7"> - <tool id="Cut1" version="1.0.1" file="cutWrapper.xml" /> - </repository> - <repository name="merge_cols" description="Merge columns together." changeset_revision="28ca7552e884"> - <tool id="mergeCols1" version="1.0.1" file="mergeCols.xml" /> - </repository> - <repository name="remove_beginning" description="Remove lines from the beginning of a file." changeset_revision="d9b82504a321"> - <tool id="Remove beginning1" version="1.0.0" file="remove_beginning.xml" /> - </repository> - <repository name="show_beginning" description="Select lines from the beginning of a file." changeset_revision="ecca14446e6a"> - <tool id="Show beginning1" version="1.0.0" file="headWrapper.xml" /> - </repository> - <repository name="show_tail" description="Select lines from the end of a file." changeset_revision="8bb4d908a523"> - <tool id="Show tail1" version="1.0.0" file="tailWrapper.xml" /> - </repository> - <repository name="trimmer" description="Trim trailing characters from each line or column." changeset_revision="f862a6e4d096"> - <tool id="trimmer" version="0.0.1" file="trimmer.xml" /> - </repository> -</toolshed> diff -r 2f45da781f926f667dd90ad23d23fd123716a535 -r 659392eae2a8946ea6d2f2c5534d5c51c1dc28f3 test-data/a.txt --- /dev/null +++ b/test-data/a.txt @@ -0,0 +1,15 @@ + CHR SNP BP A1 TEST NMISS BETA STAT P + 1 rs1181876 3671541 T DOMDEV 958 -1.415 -3.326 0.0009161 + 1 rs10492923 5092886 C ADD 1007 5.105 4.368 1.382e-05 + 1 rs10492923 5092886 C DOMDEV 1007 -5.612 -4.249 2.35e-05 + 1 rs10492923 5092886 C GENO_2DF 1007 NA 19.9 4.775e-05 + 1 rs1801133 11778965 T ADD 1022 1.23 3.97 7.682e-05 + 1 rs1801133 11778965 T GENO_2DF 1022 NA 16.07 0.0003233 + 1 rs1361912 12663121 A ADD 1021 12.69 4.093 4.596e-05 + 1 rs1361912 12663121 A DOMDEV 1021 -12.37 -3.945 8.533e-05 + 1 rs1361912 12663121 A GENO_2DF 1021 NA 17.05 0.0001982 + 1 rs1009806 19373138 G ADD 1021 -1.334 -3.756 0.0001826 + 1 rs1009806 19373138 G GENO_2DF 1021 NA 19.36 6.244e-05 + 1 rs873654 29550948 A DOMDEV 1012 1.526 3.6 0.0003339 + 1 rs10489527 36800027 C ADD 1016 12.67 4.114 4.211e-05 + 1 rs10489527 36800027 C DOMDEV 1016 -13.05 -4.02 6.249e-05 \ No newline at end of file diff -r 2f45da781f926f667dd90ad23d23fd123716a535 -r 659392eae2a8946ea6d2f2c5534d5c51c1dc28f3 test-data/changeCase_out1.tabular --- /dev/null +++ b/test-data/changeCase_out1.tabular @@ -0,0 +1,10 @@ +CHR1 4225 19670 +CHR10 6 8 +CHR1 24417 24420 +CHR6_HLA_HAP2 0 150 +CHR2 1 5 +CHR10 2 10 +CHR1 30 55 +CHRY 1 20 +CHR1 1225979 42287290 +CHR10 7 8 diff -r 2f45da781f926f667dd90ad23d23fd123716a535 -r 659392eae2a8946ea6d2f2c5534d5c51c1dc28f3 test-data/changeCase_out2.tabular --- /dev/null +++ b/test-data/changeCase_out2.tabular @@ -0,0 +1,65 @@ +CHR1 147962192 147962580 CCDS989.1_cds_0_0_chr1_147962193_r 0 - +CHR1 147984545 147984630 CCDS990.1_cds_0_0_chr1_147984546_f 0 + +CHR1 148078400 148078582 CCDS993.1_cds_0_0_chr1_148078401_r 0 - +CHR1 148185136 148185276 CCDS996.1_cds_0_0_chr1_148185137_f 0 + +CHR10 55251623 55253124 CCDS7248.1_cds_0_0_chr10_55251624_r 0 - +CHR11 116124407 116124501 CCDS8374.1_cds_0_0_chr11_116124408_r 0 - +CHR11 116206508 116206563 CCDS8377.1_cds_0_0_chr11_116206509_f 0 + +CHR11 116211733 116212337 CCDS8378.1_cds_0_0_chr11_116211734_r 0 - +CHR11 1812377 1812407 CCDS7726.1_cds_0_0_chr11_1812378_f 0 + +CHR12 38440094 38440321 CCDS8736.1_cds_0_0_chr12_38440095_r 0 - +CHR13 112381694 112381953 CCDS9526.1_cds_0_0_chr13_112381695_f 0 + +CHR14 98710240 98712285 CCDS9949.1_cds_0_0_chr14_98710241_r 0 - +CHR15 41486872 41487060 CCDS10096.1_cds_0_0_chr15_41486873_r 0 - +CHR15 41673708 41673857 CCDS10097.1_cds_0_0_chr15_41673709_f 0 + +CHR15 41679161 41679250 CCDS10098.1_cds_0_0_chr15_41679162_r 0 - +CHR15 41826029 41826196 CCDS10101.1_cds_0_0_chr15_41826030_f 0 + +CHR16 142908 143003 CCDS10397.1_cds_0_0_chr16_142909_f 0 + +CHR16 179963 180135 CCDS10401.1_cds_0_0_chr16_179964_r 0 - +CHR16 244413 244681 CCDS10402.1_cds_0_0_chr16_244414_f 0 + +CHR16 259268 259383 CCDS10403.1_cds_0_0_chr16_259269_r 0 - +CHR18 23786114 23786321 CCDS11891.1_cds_0_0_chr18_23786115_r 0 - +CHR18 59406881 59407046 CCDS11985.1_cds_0_0_chr18_59406882_f 0 + +CHR18 59455932 59456337 CCDS11986.1_cds_0_0_chr18_59455933_r 0 - +CHR18 59600586 59600754 CCDS11988.1_cds_0_0_chr18_59600587_f 0 + +CHR19 59068595 59069564 CCDS12866.1_cds_0_0_chr19_59068596_f 0 + +CHR19 59236026 59236146 CCDS12872.1_cds_0_0_chr19_59236027_r 0 - +CHR19 59297998 59298008 CCDS12877.1_cds_0_0_chr19_59297999_f 0 + +CHR19 59302168 59302288 CCDS12878.1_cds_0_0_chr19_59302169_r 0 - +CHR2 118288583 118288668 CCDS2120.1_cds_0_0_chr2_118288584_f 0 + +CHR2 118394148 118394202 CCDS2121.1_cds_0_0_chr2_118394149_r 0 - +CHR2 220190202 220190242 CCDS2441.1_cds_0_0_chr2_220190203_f 0 + +CHR2 220229609 220230869 CCDS2443.1_cds_0_0_chr2_220229610_r 0 - +CHR20 33330413 33330423 CCDS13249.1_cds_0_0_chr20_33330414_r 0 - +CHR20 33513606 33513792 CCDS13255.1_cds_0_0_chr20_33513607_f 0 + +CHR20 33579500 33579527 CCDS13256.1_cds_0_0_chr20_33579501_r 0 - +CHR20 33593260 33593348 CCDS13257.1_cds_0_0_chr20_33593261_f 0 + +CHR21 32707032 32707192 CCDS13614.1_cds_0_0_chr21_32707033_f 0 + +CHR21 32869641 32870022 CCDS13615.1_cds_0_0_chr21_32869642_r 0 - +CHR21 33321040 33322012 CCDS13620.1_cds_0_0_chr21_33321041_f 0 + +CHR21 33744994 33745040 CCDS13625.1_cds_0_0_chr21_33744995_r 0 - +CHR22 30120223 30120265 CCDS13897.1_cds_0_0_chr22_30120224_f 0 + +CHR22 30160419 30160661 CCDS13898.1_cds_0_0_chr22_30160420_r 0 - +CHR22 30665273 30665360 CCDS13901.1_cds_0_0_chr22_30665274_f 0 + +CHR22 30939054 30939266 CCDS13903.1_cds_0_0_chr22_30939055_r 0 - +CHR5 131424298 131424460 CCDS4149.1_cds_0_0_chr5_131424299_f 0 + +CHR5 131556601 131556672 CCDS4151.1_cds_0_0_chr5_131556602_r 0 - +CHR5 131621326 131621419 CCDS4152.1_cds_0_0_chr5_131621327_f 0 + +CHR5 131847541 131847666 CCDS4155.1_cds_0_0_chr5_131847542_r 0 - +CHR6 108299600 108299744 CCDS5061.1_cds_0_0_chr6_108299601_r 0 - +CHR6 108594662 108594687 CCDS5063.1_cds_0_0_chr6_108594663_f 0 + +CHR6 108640045 108640151 CCDS5064.1_cds_0_0_chr6_108640046_r 0 - +CHR6 108722976 108723115 CCDS5067.1_cds_0_0_chr6_108722977_f 0 + +CHR7 113660517 113660685 CCDS5760.1_cds_0_0_chr7_113660518_f 0 + +CHR7 116512159 116512389 CCDS5771.1_cds_0_0_chr7_116512160_r 0 - +CHR7 116714099 116714152 CCDS5773.1_cds_0_0_chr7_116714100_f 0 + +CHR7 116945541 116945787 CCDS5774.1_cds_0_0_chr7_116945542_r 0 - +CHR8 118881131 118881317 CCDS6324.1_cds_0_0_chr8_118881132_r 0 - +CHR9 128764156 128764189 CCDS6914.1_cds_0_0_chr9_128764157_f 0 + +CHR9 128787519 128789136 CCDS6915.1_cds_0_0_chr9_128787520_r 0 - +CHR9 128882427 128882523 CCDS6917.1_cds_0_0_chr9_128882428_f 0 + +CHR9 128937229 128937445 CCDS6919.1_cds_0_0_chr9_128937230_r 0 - +CHRX 122745047 122745924 CCDS14606.1_cds_0_0_chrX_122745048_f 0 + +CHRX 152648964 152649196 CCDS14733.1_cds_0_0_chrX_152648965_r 0 - +CHRX 152691446 152691471 CCDS14735.1_cds_0_0_chrX_152691447_f 0 + +CHRX 152694029 152694263 CCDS14736.1_cds_0_0_chrX_152694030_r 0 - diff -r 2f45da781f926f667dd90ad23d23fd123716a535 -r 659392eae2a8946ea6d2f2c5534d5c51c1dc28f3 test-data/eq-addvalue.dat --- /dev/null +++ b/test-data/eq-addvalue.dat @@ -0,0 +1,65 @@ +chr1 147962192 147962580 CCDS989.1_cds_0_0_chr1_147962193_r 0 - 1 +chr1 147984545 147984630 CCDS990.1_cds_0_0_chr1_147984546_f 0 + 1 +chr1 148078400 148078582 CCDS993.1_cds_0_0_chr1_148078401_r 0 - 1 +chr1 148185136 148185276 CCDS996.1_cds_0_0_chr1_148185137_f 0 + 1 +chr10 55251623 55253124 CCDS7248.1_cds_0_0_chr10_55251624_r 0 - 1 +chr11 116124407 116124501 CCDS8374.1_cds_0_0_chr11_116124408_r 0 - 1 +chr11 116206508 116206563 CCDS8377.1_cds_0_0_chr11_116206509_f 0 + 1 +chr11 116211733 116212337 CCDS8378.1_cds_0_0_chr11_116211734_r 0 - 1 +chr11 1812377 1812407 CCDS7726.1_cds_0_0_chr11_1812378_f 0 + 1 +chr12 38440094 38440321 CCDS8736.1_cds_0_0_chr12_38440095_r 0 - 1 +chr13 112381694 112381953 CCDS9526.1_cds_0_0_chr13_112381695_f 0 + 1 +chr14 98710240 98712285 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CCDS10402.1_cds_0_0_chr16_244414_f 244413 244681 +chr16 CCDS10403.1_cds_0_0_chr16_259269_r 259268 259383 +chr18 CCDS11891.1_cds_0_0_chr18_23786115_r 23786114 23786321 +chr18 CCDS11985.1_cds_0_0_chr18_59406882_f 59406881 59407046 +chr18 CCDS11986.1_cds_0_0_chr18_59455933_r 59455932 59456337 +chr18 CCDS11988.1_cds_0_0_chr18_59600587_f 59600586 59600754 +chr19 CCDS12866.1_cds_0_0_chr19_59068596_f 59068595 59069564 +chr19 CCDS12872.1_cds_0_0_chr19_59236027_r 59236026 59236146 +chr19 CCDS12877.1_cds_0_0_chr19_59297999_f 59297998 59298008 +chr19 CCDS12878.1_cds_0_0_chr19_59302169_r 59302168 59302288 +chr2 CCDS2120.1_cds_0_0_chr2_118288584_f 118288583 118288668 +chr2 CCDS2121.1_cds_0_0_chr2_118394149_r 118394148 118394202 +chr2 CCDS2441.1_cds_0_0_chr2_220190203_f 220190202 220190242 +chr2 CCDS2443.1_cds_0_0_chr2_220229610_r 220229609 220230869 +chr20 CCDS13249.1_cds_0_0_chr20_33330414_r 33330413 33330423 +chr20 CCDS13255.1_cds_0_0_chr20_33513607_f 33513606 33513792 +chr20 CCDS13256.1_cds_0_0_chr20_33579501_r 33579500 33579527 +chr20 CCDS13257.1_cds_0_0_chr20_33593261_f 33593260 33593348 +chr21 CCDS13614.1_cds_0_0_chr21_32707033_f 32707032 32707192 +chr21 CCDS13615.1_cds_0_0_chr21_32869642_r 32869641 32870022 +chr21 CCDS13620.1_cds_0_0_chr21_33321041_f 33321040 33322012 +chr21 CCDS13625.1_cds_0_0_chr21_33744995_r 33744994 33745040 +chr22 CCDS13897.1_cds_0_0_chr22_30120224_f 30120223 30120265 +chr22 CCDS13898.1_cds_0_0_chr22_30160420_r 30160419 30160661 +chr22 CCDS13901.1_cds_0_0_chr22_30665274_f 30665273 30665360 +chr22 CCDS13903.1_cds_0_0_chr22_30939055_r 30939054 30939266 +chr5 CCDS4149.1_cds_0_0_chr5_131424299_f 131424298 131424460 +chr5 CCDS4151.1_cds_0_0_chr5_131556602_r 131556601 131556672 +chr5 CCDS4152.1_cds_0_0_chr5_131621327_f 131621326 131621419 +chr5 CCDS4155.1_cds_0_0_chr5_131847542_r 131847541 131847666 +chr6 CCDS5061.1_cds_0_0_chr6_108299601_r 108299600 108299744 +chr6 CCDS5063.1_cds_0_0_chr6_108594663_f 108594662 108594687 +chr6 CCDS5064.1_cds_0_0_chr6_108640046_r 108640045 108640151 +chr6 CCDS5067.1_cds_0_0_chr6_108722977_f 108722976 108723115 +chr7 CCDS5760.1_cds_0_0_chr7_113660518_f 113660517 113660685 +chr7 CCDS5771.1_cds_0_0_chr7_116512160_r 116512159 116512389 +chr7 CCDS5773.1_cds_0_0_chr7_116714100_f 116714099 116714152 +chr7 CCDS5774.1_cds_0_0_chr7_116945542_r 116945541 116945787 +chr8 CCDS6324.1_cds_0_0_chr8_118881132_r 118881131 118881317 +chr9 CCDS6914.1_cds_0_0_chr9_128764157_f 128764156 128764189 +chr9 CCDS6915.1_cds_0_0_chr9_128787520_r 128787519 128789136 +chr9 CCDS6917.1_cds_0_0_chr9_128882428_f 128882427 128882523 +chr9 CCDS6919.1_cds_0_0_chr9_128937230_r 128937229 128937445 +chrX CCDS14606.1_cds_0_0_chrX_122745048_f 122745047 122745924 +chrX CCDS14733.1_cds_0_0_chrX_152648965_r 152648964 152649196 +chrX CCDS14735.1_cds_0_0_chrX_152691447_f 152691446 152691471 +chrX CCDS14736.1_cds_0_0_chrX_152694030_r 152694029 152694263 diff -r 2f45da781f926f667dd90ad23d23fd123716a535 -r 659392eae2a8946ea6d2f2c5534d5c51c1dc28f3 test-data/mergeCols.dat --- /dev/null +++ b/test-data/mergeCols.dat @@ -0,0 +1,65 @@ +chr1 147962192 147962580 CCDS989.1_cds_0_0_chr1_147962193_r 0 - CCDS989.1_cds_0_0_chr1_147962193_rchr1- +chr1 147984545 147984630 CCDS990.1_cds_0_0_chr1_147984546_f 0 + CCDS990.1_cds_0_0_chr1_147984546_fchr1+ +chr1 148078400 148078582 CCDS993.1_cds_0_0_chr1_148078401_r 0 - CCDS993.1_cds_0_0_chr1_148078401_rchr1- +chr1 148185136 148185276 CCDS996.1_cds_0_0_chr1_148185137_f 0 + CCDS996.1_cds_0_0_chr1_148185137_fchr1+ +chr10 55251623 55253124 CCDS7248.1_cds_0_0_chr10_55251624_r 0 - CCDS7248.1_cds_0_0_chr10_55251624_rchr10- +chr11 116124407 116124501 CCDS8374.1_cds_0_0_chr11_116124408_r 0 - CCDS8374.1_cds_0_0_chr11_116124408_rchr11- +chr11 116206508 116206563 CCDS8377.1_cds_0_0_chr11_116206509_f 0 + CCDS8377.1_cds_0_0_chr11_116206509_fchr11+ +chr11 116211733 116212337 CCDS8378.1_cds_0_0_chr11_116211734_r 0 - CCDS8378.1_cds_0_0_chr11_116211734_rchr11- +chr11 1812377 1812407 CCDS7726.1_cds_0_0_chr11_1812378_f 0 + CCDS7726.1_cds_0_0_chr11_1812378_fchr11+ +chr12 38440094 38440321 CCDS8736.1_cds_0_0_chr12_38440095_r 0 - CCDS8736.1_cds_0_0_chr12_38440095_rchr12- +chr13 112381694 112381953 CCDS9526.1_cds_0_0_chr13_112381695_f 0 + CCDS9526.1_cds_0_0_chr13_112381695_fchr13+ +chr14 98710240 98712285 CCDS9949.1_cds_0_0_chr14_98710241_r 0 - CCDS9949.1_cds_0_0_chr14_98710241_rchr14- +chr15 41486872 41487060 CCDS10096.1_cds_0_0_chr15_41486873_r 0 - CCDS10096.1_cds_0_0_chr15_41486873_rchr15- +chr15 41673708 41673857 CCDS10097.1_cds_0_0_chr15_41673709_f 0 + CCDS10097.1_cds_0_0_chr15_41673709_fchr15+ +chr15 41679161 41679250 CCDS10098.1_cds_0_0_chr15_41679162_r 0 - CCDS10098.1_cds_0_0_chr15_41679162_rchr15- +chr15 41826029 41826196 CCDS10101.1_cds_0_0_chr15_41826030_f 0 + CCDS10101.1_cds_0_0_chr15_41826030_fchr15+ +chr16 142908 143003 CCDS10397.1_cds_0_0_chr16_142909_f 0 + CCDS10397.1_cds_0_0_chr16_142909_fchr16+ +chr16 179963 180135 CCDS10401.1_cds_0_0_chr16_179964_r 0 - CCDS10401.1_cds_0_0_chr16_179964_rchr16- +chr16 244413 244681 CCDS10402.1_cds_0_0_chr16_244414_f 0 + CCDS10402.1_cds_0_0_chr16_244414_fchr16+ +chr16 259268 259383 CCDS10403.1_cds_0_0_chr16_259269_r 0 - CCDS10403.1_cds_0_0_chr16_259269_rchr16- +chr18 23786114 23786321 CCDS11891.1_cds_0_0_chr18_23786115_r 0 - CCDS11891.1_cds_0_0_chr18_23786115_rchr18- +chr18 59406881 59407046 CCDS11985.1_cds_0_0_chr18_59406882_f 0 + CCDS11985.1_cds_0_0_chr18_59406882_fchr18+ +chr18 59455932 59456337 CCDS11986.1_cds_0_0_chr18_59455933_r 0 - CCDS11986.1_cds_0_0_chr18_59455933_rchr18- +chr18 59600586 59600754 CCDS11988.1_cds_0_0_chr18_59600587_f 0 + CCDS11988.1_cds_0_0_chr18_59600587_fchr18+ +chr19 59068595 59069564 CCDS12866.1_cds_0_0_chr19_59068596_f 0 + CCDS12866.1_cds_0_0_chr19_59068596_fchr19+ +chr19 59236026 59236146 CCDS12872.1_cds_0_0_chr19_59236027_r 0 - CCDS12872.1_cds_0_0_chr19_59236027_rchr19- +chr19 59297998 59298008 CCDS12877.1_cds_0_0_chr19_59297999_f 0 + CCDS12877.1_cds_0_0_chr19_59297999_fchr19+ +chr19 59302168 59302288 CCDS12878.1_cds_0_0_chr19_59302169_r 0 - CCDS12878.1_cds_0_0_chr19_59302169_rchr19- +chr2 118288583 118288668 CCDS2120.1_cds_0_0_chr2_118288584_f 0 + CCDS2120.1_cds_0_0_chr2_118288584_fchr2+ +chr2 118394148 118394202 CCDS2121.1_cds_0_0_chr2_118394149_r 0 - CCDS2121.1_cds_0_0_chr2_118394149_rchr2- +chr2 220190202 220190242 CCDS2441.1_cds_0_0_chr2_220190203_f 0 + CCDS2441.1_cds_0_0_chr2_220190203_fchr2+ +chr2 220229609 220230869 CCDS2443.1_cds_0_0_chr2_220229610_r 0 - CCDS2443.1_cds_0_0_chr2_220229610_rchr2- +chr20 33330413 33330423 CCDS13249.1_cds_0_0_chr20_33330414_r 0 - CCDS13249.1_cds_0_0_chr20_33330414_rchr20- +chr20 33513606 33513792 CCDS13255.1_cds_0_0_chr20_33513607_f 0 + CCDS13255.1_cds_0_0_chr20_33513607_fchr20+ +chr20 33579500 33579527 CCDS13256.1_cds_0_0_chr20_33579501_r 0 - CCDS13256.1_cds_0_0_chr20_33579501_rchr20- +chr20 33593260 33593348 CCDS13257.1_cds_0_0_chr20_33593261_f 0 + CCDS13257.1_cds_0_0_chr20_33593261_fchr20+ +chr21 32707032 32707192 CCDS13614.1_cds_0_0_chr21_32707033_f 0 + CCDS13614.1_cds_0_0_chr21_32707033_fchr21+ +chr21 32869641 32870022 CCDS13615.1_cds_0_0_chr21_32869642_r 0 - CCDS13615.1_cds_0_0_chr21_32869642_rchr21- +chr21 33321040 33322012 CCDS13620.1_cds_0_0_chr21_33321041_f 0 + CCDS13620.1_cds_0_0_chr21_33321041_fchr21+ +chr21 33744994 33745040 CCDS13625.1_cds_0_0_chr21_33744995_r 0 - CCDS13625.1_cds_0_0_chr21_33744995_rchr21- +chr22 30120223 30120265 CCDS13897.1_cds_0_0_chr22_30120224_f 0 + CCDS13897.1_cds_0_0_chr22_30120224_fchr22+ +chr22 30160419 30160661 CCDS13898.1_cds_0_0_chr22_30160420_r 0 - CCDS13898.1_cds_0_0_chr22_30160420_rchr22- +chr22 30665273 30665360 CCDS13901.1_cds_0_0_chr22_30665274_f 0 + CCDS13901.1_cds_0_0_chr22_30665274_fchr22+ +chr22 30939054 30939266 CCDS13903.1_cds_0_0_chr22_30939055_r 0 - CCDS13903.1_cds_0_0_chr22_30939055_rchr22- +chr5 131424298 131424460 CCDS4149.1_cds_0_0_chr5_131424299_f 0 + CCDS4149.1_cds_0_0_chr5_131424299_fchr5+ +chr5 131556601 131556672 CCDS4151.1_cds_0_0_chr5_131556602_r 0 - CCDS4151.1_cds_0_0_chr5_131556602_rchr5- +chr5 131621326 131621419 CCDS4152.1_cds_0_0_chr5_131621327_f 0 + CCDS4152.1_cds_0_0_chr5_131621327_fchr5+ +chr5 131847541 131847666 CCDS4155.1_cds_0_0_chr5_131847542_r 0 - CCDS4155.1_cds_0_0_chr5_131847542_rchr5- +chr6 108299600 108299744 CCDS5061.1_cds_0_0_chr6_108299601_r 0 - CCDS5061.1_cds_0_0_chr6_108299601_rchr6- +chr6 108594662 108594687 CCDS5063.1_cds_0_0_chr6_108594663_f 0 + CCDS5063.1_cds_0_0_chr6_108594663_fchr6+ +chr6 108640045 108640151 CCDS5064.1_cds_0_0_chr6_108640046_r 0 - CCDS5064.1_cds_0_0_chr6_108640046_rchr6- +chr6 108722976 108723115 CCDS5067.1_cds_0_0_chr6_108722977_f 0 + CCDS5067.1_cds_0_0_chr6_108722977_fchr6+ +chr7 113660517 113660685 CCDS5760.1_cds_0_0_chr7_113660518_f 0 + CCDS5760.1_cds_0_0_chr7_113660518_fchr7+ +chr7 116512159 116512389 CCDS5771.1_cds_0_0_chr7_116512160_r 0 - CCDS5771.1_cds_0_0_chr7_116512160_rchr7- +chr7 116714099 116714152 CCDS5773.1_cds_0_0_chr7_116714100_f 0 + CCDS5773.1_cds_0_0_chr7_116714100_fchr7+ +chr7 116945541 116945787 CCDS5774.1_cds_0_0_chr7_116945542_r 0 - CCDS5774.1_cds_0_0_chr7_116945542_rchr7- +chr8 118881131 118881317 CCDS6324.1_cds_0_0_chr8_118881132_r 0 - CCDS6324.1_cds_0_0_chr8_118881132_rchr8- +chr9 128764156 128764189 CCDS6914.1_cds_0_0_chr9_128764157_f 0 + CCDS6914.1_cds_0_0_chr9_128764157_fchr9+ +chr9 128787519 128789136 CCDS6915.1_cds_0_0_chr9_128787520_r 0 - CCDS6915.1_cds_0_0_chr9_128787520_rchr9- +chr9 128882427 128882523 CCDS6917.1_cds_0_0_chr9_128882428_f 0 + CCDS6917.1_cds_0_0_chr9_128882428_fchr9+ +chr9 128937229 128937445 CCDS6919.1_cds_0_0_chr9_128937230_r 0 - CCDS6919.1_cds_0_0_chr9_128937230_rchr9- +chrX 122745047 122745924 CCDS14606.1_cds_0_0_chrX_122745048_f 0 + CCDS14606.1_cds_0_0_chrX_122745048_fchrX+ +chrX 152648964 152649196 CCDS14733.1_cds_0_0_chrX_152648965_r 0 - CCDS14733.1_cds_0_0_chrX_152648965_rchrX- +chrX 152691446 152691471 CCDS14735.1_cds_0_0_chrX_152691447_f 0 + CCDS14735.1_cds_0_0_chrX_152691447_fchrX+ +chrX 152694029 152694263 CCDS14736.1_cds_0_0_chrX_152694030_r 0 - CCDS14736.1_cds_0_0_chrX_152694030_rchrX- diff -r 2f45da781f926f667dd90ad23d23fd123716a535 -r 659392eae2a8946ea6d2f2c5534d5c51c1dc28f3 test-data/trimmer_a_f_c0_s1_e13_i62.dat --- /dev/null +++ b/test-data/trimmer_a_f_c0_s1_e13_i62.dat @@ -0,0 +1,5 @@ +12345 abcdef +67890 ghjkl g +>assa lljlj ljlj +sasas hghg hg +@dgf gfgf gfg diff -r 2f45da781f926f667dd90ad23d23fd123716a535 -r 659392eae2a8946ea6d2f2c5534d5c51c1dc28f3 test-data/trimmer_a_f_c2_s1_e2_i62.dat --- /dev/null +++ b/test-data/trimmer_a_f_c2_s1_e2_i62.dat @@ -0,0 +1,5 @@ +12345 ab xyz +67890 gh ghjt +>assa lljlj ljlj +sasas hg hghg +@dgf gf gfgf diff -r 2f45da781f926f667dd90ad23d23fd123716a535 -r 659392eae2a8946ea6d2f2c5534d5c51c1dc28f3 test-data/trimmer_tab_delimited.dat --- /dev/null +++ b/test-data/trimmer_tab_delimited.dat @@ -0,0 +1,5 @@ +12345 abcdef xyz +67890 ghjkl ghjt +>assa lljlj ljlj +sasas hghg hghg +@dgf gfgf gfgf diff -r 2f45da781f926f667dd90ad23d23fd123716a535 -r 659392eae2a8946ea6d2f2c5534d5c51c1dc28f3 tool_conf.xml.sample --- a/tool_conf.xml.sample +++ b/tool_conf.xml.sample @@ -44,12 +44,21 @@ <tool file="extract/liftOver_wrapper.xml" /></section><section name="Text Manipulation" id="textutil"> + <tool file="filters/fixedValueColumn.xml" /><tool file="stats/column_maker.xml" /><tool file="filters/catWrapper.xml" /><tool file="filters/cutWrapper.xml" /> + <tool file="filters/mergeCols.xml" /> + <tool file="filters/convert_characters.xml" /><tool file="filters/CreateInterval.xml" /> + <tool file="filters/cutWrapper.xml" /> + <tool file="filters/changeCase.xml" /><tool file="filters/pasteWrapper.xml" /> + <tool file="filters/remove_beginning.xml" /><tool file="filters/randomlines.xml" /> + <tool file="filters/headWrapper.xml" /> + <tool file="filters/tailWrapper.xml" /> + <tool file="filters/trimmer.xml" /><tool file="filters/wc_gnu.xml" /><tool file="filters/secure_hash_message_digest.xml" /><tool file="stats/dna_filtering.xml" /> diff -r 2f45da781f926f667dd90ad23d23fd123716a535 -r 659392eae2a8946ea6d2f2c5534d5c51c1dc28f3 tools/filters/changeCase.pl --- /dev/null +++ b/tools/filters/changeCase.pl @@ -0,0 +1,58 @@ +#! /usr/bin/perl -w + +use strict; +use warnings; + +my $columns = {}; +my $del = ""; +my @in = (); +my @out = (); +my $command = ""; +my $field = 0; + +# a wrapper for changing the case of columns from within galaxy +# isaChangeCase.pl [filename] [columns] [delim] [casing] [output] + +die "Check arguments: $0 [filename] [columns] [delim] [casing] [output]\n" unless @ARGV == 5; + +# process column input +$ARGV[1] =~ s/\s+//g; +foreach ( split /,/, $ARGV[1] ) { + if (m/^c\d{1,}$/i) { + s/c//ig; + $columns->{$_} = --$_; + } +} + +die "No columns specified, columns are not preceeded with 'c', or commas are not used to separate column numbers: $ARGV[1]\n" if keys %$columns == 0; + +my $column_delimiters_href = { + 'TAB' => q{\t}, + 'COMMA' => ",", + 'DASH' => "-", + 'UNDERSCORE' => "_", + 'PIPE' => q{\|}, + 'DOT' => q{\.}, + 'SPACE' => q{\s+} +}; + +$del = $column_delimiters_href->{$ARGV[2]}; + +open (OUT, ">$ARGV[4]") or die "Cannot create $ARGV[4]:$!\n"; +open (IN, "<$ARGV[0]") or die "Cannot open $ARGV[0]:$!\n"; +while (<IN>) { + chop; + @in = split /$del/; + for ( my $i = 0; $i <= $#in; ++$i) { + if (exists $columns->{$i}) { + push(@out, $ARGV[3] eq 'up' ? uc($in[$i]) : lc($in[$i])); + } else { + push(@out, $in[$i]); + } + } + print OUT join("\t",@out), "\n"; + @out = (); +} +close IN; + +close OUT; diff -r 2f45da781f926f667dd90ad23d23fd123716a535 -r 659392eae2a8946ea6d2f2c5534d5c51c1dc28f3 tools/filters/changeCase.xml --- /dev/null +++ b/tools/filters/changeCase.xml @@ -0,0 +1,77 @@ +<tool id="ChangeCase" name="Change Case"> + <description> of selected columns</description> + <stdio> + <exit_code range="1:" err_level="fatal" /> + </stdio> + <command interpreter="perl">changeCase.pl $input "$cols" $delimiter $casing $out_file1</command> + <inputs> + <param name="input" format="txt" type="data" label="From"/> + <param name="cols" size="10" type="text" value="c1,c2" label="Change case of columns"/> + <param name="delimiter" type="select" label="Delimited by"> + <option value="TAB">Tab</option> + <option value="SPACE">Whitespace</option> + <option value="DOT">Dot</option> + <option value="COMMA">Comma</option> + <option value="DASH">Dash</option> + <option value="UNDERSCORE">Underscore</option> + <option value="PIPE">Pipe</option> + </param> + <param name="casing" type="select" label="To"> + <option value="up">Upper case</option> + <option value="lo">Lower case</option> + </param> + </inputs> + <outputs> + <data format="tabular" name="out_file1" /> + </outputs> + <tests> + <test> + <param name="input" value="1.txt" ftype="txt"/> + <param name="cols" value="c1"/> + <param name="delimiter" value="SPACE"/> + <param name="casing" value="up"/> + <output name="out_file1" file="changeCase_out1.tabular"/> + </test> + <test> + <param name="input" value="1.bed" ftype="bed"/> + <param name="cols" value="c1"/> + <param name="delimiter" value="TAB"/> + <param name="casing" value="up"/> + <output name="out_file1" file="changeCase_out2.tabular"/> + </test> + </tests> + <help> + +.. class:: warningmark + +**This tool breaks column assignments.** To re-establish column assignments run the tool and click on the pencil icon in the resulting history item. + +.. class:: warningmark + +The format of the resulting dataset from this tool is always tabular. + +----- + +**What it does** + +This tool selects specified columns from a dataset and converts the values of those columns to upper or lower case. + +- Columns are specified as **c1**, **c2**, and so on. +- Columns can be specified in any order (e.g., **c2,c1,c6**) + +----- + +**Example** + +Changing columns 1 and 3 ( delimited by Comma ) to upper case in:: + + apple,is,good + windows,is,bad + +will result in:: + + APPLE is GOOD + WINDOWS is BAD + + </help> +</tool> diff -r 2f45da781f926f667dd90ad23d23fd123716a535 -r 659392eae2a8946ea6d2f2c5534d5c51c1dc28f3 tools/filters/condense_characters.pl --- /dev/null +++ b/tools/filters/condense_characters.pl @@ -0,0 +1,105 @@ +#! /usr/bin/perl -w + +use strict; +use warnings; + +# condenses all consecutive characters of one type +# convert_characters.pl [input] [character] [output] + +die "Check arguments" unless @ARGV == 3; + +my $inputfile = $ARGV[0]; +my $character = $ARGV[1]; +my $outputfile = $ARGV[2]; + + +my $convert_from; +my $convert_to; + + +if ($character eq "s") +{ + $convert_from = '\s'; +} +elsif ($character eq "T") +{ + $convert_from = '\t'; +} +elsif ($character eq "Sp") +{ + $convert_from = " "; +} +elsif ($character eq "Dt") +{ + $convert_from = '\.'; +} +elsif ($character eq "C") +{ + $convert_from = ","; +} +elsif ($character eq "D") +{ + $convert_from = "-"; +} +elsif ($character eq "U") +{ + $convert_from = "_"; +} +elsif ($character eq "P") +{ + $convert_from = '\|'; +} +else +{ + die "Invalid value specified for convert from\n"; +} + + +if ($character eq "T") +{ + $convert_to = "\t"; +} +elsif ($character eq "Sp") +{ + $convert_to = " "; +} +elsif ($character eq "Dt") +{ + $convert_to = "\."; +} +elsif ($character eq "C") +{ + $convert_to = ","; +} +elsif ($character eq "D") +{ + $convert_to = "-"; +} +elsif ($character eq "U") +{ + $convert_to = "_"; +} +elsif ($character eq "P") +{ + $convert_to = "|"; +} +else +{ + die "Invalid value specified for Convert to\n"; +} + +my $fhIn; +open ($fhIn, "< $inputfile") or die "Cannot open source file"; + +my $fhOut; +open ($fhOut, "> $outputfile"); + +while (<$fhIn>) +{ + my $thisLine = $_; + chomp $thisLine; + $thisLine =~ s/${convert_from}+/$convert_to/g; + print $fhOut $thisLine,"\n"; +} +close ($fhIn) or die "Cannot close source file"; +close ($fhOut) or die "Cannot close output file"; diff -r 2f45da781f926f667dd90ad23d23fd123716a535 -r 659392eae2a8946ea6d2f2c5534d5c51c1dc28f3 tools/filters/condense_characters.xml --- /dev/null +++ b/tools/filters/condense_characters.xml @@ -0,0 +1,48 @@ +<tool id="Condense characters1" name="Condense"> + <description>consecutive characters</description> + <command interpreter="perl">condense_characters.pl $input $character $out_file1</command> + <inputs> + + <param name="character" type="select" label="Condense all consecutive"> + <option value="T">Tabs</option> + <option value="Sp">Spaces</option> + <option value="Dt">Dots</option> + <option value="C">Commas</option> + <option value="D">Dashes</option> + <option value="U">Underscores</option> + <option value="P">Pipes</option> + </param> + <param format="txt" name="input" type="data" label="in this Query"/> + </inputs> + <outputs> + <data format="input" name="out_file1" metadata_source="input" /> + </outputs> + <tests> + <test> + <param name="character" value="T"/> + <param name="input" value="1.bed"/> + <output name="out_file1" file="eq-condense.dat"/> + </test> + </tests> + <help> + +**What it does** + +This tool condenses all consecutive characters of a specified type. + +----- + +**Example** + +- Input file:: + + geneX,,,10,,,,,20 + geneY,,5,,,,,12,15,9, + +- Condense all consecutive commas. The above file will be converted into:: + + geneX,10,20 + geneY,5,12,15,9 + +</help> +</tool> diff -r 2f45da781f926f667dd90ad23d23fd123716a535 -r 659392eae2a8946ea6d2f2c5534d5c51c1dc28f3 tools/filters/convert_characters.py --- /dev/null +++ b/tools/filters/convert_characters.py @@ -0,0 +1,42 @@ +#!/usr/bin/env python +#By, Guruprasad Ananda. + +from galaxy import eggs +import sys, re + +def stop_err(msg): + sys.stderr.write(msg) + sys.exit() + +def main(): + if len(sys.argv) != 4: + stop_err("usage: convert_characters infile from_char outfile") + + try: + fin = open(sys.argv[1],'r') + except: + stop_err("Input file cannot be opened for reading.") + + from_char = sys.argv[2] + + try: + fout = open(sys.argv[3],'w') + except: + stop_err("Output file cannot be opened for writing.") + + char_dict = {'T':'\t','s':'\s','Dt':'\.','C':',','D':'-','U':'_','P':'\|','Co':':'} + from_ch = char_dict[from_char] + '+' #making an RE to match 1 or more occurences. + skipped = 0 + + for line in fin: + line = line.strip() + try: + fout.write("%s\n" %(re.sub(from_ch,'\t',line))) + except: + skipped += 1 + + if skipped: + print "Skipped %d lines as invalid." %skipped + +if __name__ == "__main__": + main() \ No newline at end of file diff -r 2f45da781f926f667dd90ad23d23fd123716a535 -r 659392eae2a8946ea6d2f2c5534d5c51c1dc28f3 tools/filters/convert_characters.xml --- /dev/null +++ b/tools/filters/convert_characters.xml @@ -0,0 +1,58 @@ +<tool id="Convert characters1" name="Convert"> + <description>delimiters to TAB</description> + <command interpreter="python">convert_characters.py $input $convert_from $out_file1</command> + <inputs> + <param name="convert_from" type="select" label="Convert all"> + <option value="s">Whitespaces</option> + <option value="T">Tabs</option> +  + <option value="Dt">Dots</option> + <option value="C">Commas</option> + <option value="D">Dashes</option> + <option value="U">Underscores</option> + <option value="P">Pipes</option> + <option value="Co">Colons</option> + </param> + <param format="txt" name="input" type="data" label="in Query"/> + </inputs> + <outputs> + <data format="tabular" name="out_file1" /> + </outputs> + <tests> + <test> + <param name="convert_from" value="s"/> + <param name="input" value="1.bed"/> + <output name="out_file1" file="eq-convert.dat"/> + </test> + <test> + <param name="convert_from" value="s"/> + <param name="input" value="a.txt"/> + <output name="out_file1" file="a.tab"/> + </test> + </tests> + <help> + +**What it does** + +Converts all delimiters of a specified type into TABs. Consecutive characters are condensed. For example, if columns are separated by 5 spaces they will converted into 1 tab. + +----- + +**Example** + +- Input file:: + + chrX||151283558|151283724|NM_000808_exon_8_0_chrX_151283559_r|0|- + chrX|151370273|151370486|NM_000808_exon_9_0_chrX_151370274_r|0|- + chrX|151559494|151559583|NM_018558_exon_1_0_chrX_151559495_f|0|+ + chrX|151564643|151564711|NM_018558_exon_2_0_chrX_151564644_f||||0|+ + +- Converting all pipe delimiters of the above file to TABs will get:: + + chrX 151283558 151283724 NM_000808_exon_8_0_chrX_151283559_r 0 - + chrX 151370273 151370486 NM_000808_exon_9_0_chrX_151370274_r 0 - + chrX 151559494 151559583 NM_018558_exon_1_0_chrX_151559495_f 0 + + chrX 151564643 151564711 NM_018558_exon_2_0_chrX_151564644_f 0 + + +</help> +</tool> diff -r 2f45da781f926f667dd90ad23d23fd123716a535 -r 659392eae2a8946ea6d2f2c5534d5c51c1dc28f3 tools/filters/cutWrapper.pl --- /dev/null +++ b/tools/filters/cutWrapper.pl @@ -0,0 +1,77 @@ +#!/usr/bin/perl -w + +use strict; +use warnings; + +my @columns = (); +my $del = ""; +my @in = (); +my @out = (); +my $command = ""; +my $field = 0; + +# a wrapper for cut for use in galaxy +# cutWrapper.pl [filename] [columns] [delim] [output] + +die "Check arguments\n" unless @ARGV == 4; + +$ARGV[1] =~ s/\s+//g; +foreach ( split /,/, $ARGV[1] ) { + if (m/^c\d{1,}$/i) { + push (@columns, $_); + $columns[@columns-1] =~s/c//ig; + } +} + +die "No columns specified, columns are not preceded with 'c', or commas are not used to separate column numbers: $ARGV[1]\n" if @columns == 0; + +my $column_delimiters_href = { + 'T' => q{\t}, + 'C' => ",", + 'D' => "-", + 'U' => "_", + 'P' => q{\|}, + 'Dt' => q{\.}, + 'Sp' => q{\s+} +}; + +$del = $column_delimiters_href->{$ARGV[2]}; + +open (OUT, ">$ARGV[3]") or die "Cannot create $ARGV[2]:$!\n"; +open (IN, "<$ARGV[0]") or die "Cannot open $ARGV[0]:$!\n"; + +while (my $line=<IN>) { + if ($line =~ /^#/) { + #Ignore comment lines + } else { + chop($line); + @in = split(/$del/, $line); + foreach $field (@columns) { + if (defined($in[$field-1])) { + push(@out, $in[$field-1]); + } else { + push(@out, "."); + } + } + print OUT join("\t",@out), "\n"; + @out = (); + } +} + +#while (<IN>) { +# chop; +# @in = split /$del/; +# foreach $field (@columns) { +# if (defined($in[$field-1])) { +# push(@out, $in[$field-1]); +# } else { +# push(@out, "."); +# } +# } +# print OUT join("\t",@out), "\n"; +# @out = (); +#} +close IN; + +close OUT; + diff -r 2f45da781f926f667dd90ad23d23fd123716a535 -r 659392eae2a8946ea6d2f2c5534d5c51c1dc28f3 tools/filters/cutWrapper.xml --- /dev/null +++ b/tools/filters/cutWrapper.xml @@ -0,0 +1,202 @@ +<tool id="Cut1" name="Cut" version="1.0.1"> + <description>columns from a table</description> + <command interpreter="perl">cutWrapper.pl $input "$columnList" $delimiter $out_file1</command> + <inputs> + <param name="columnList" size="10" type="text" value="c1,c2" label="Cut columns"/> + <param name="delimiter" type="select" label="Delimited by"> + <option value="T">Tab</option> + <option value="Sp">Whitespace</option> + <option value="Dt">Dot</option> + <option value="C">Comma</option> + <option value="D">Dash</option> + <option value="U">Underscore</option> + <option value="P">Pipe</option> + </param> + <param format="txt" name="input" type="data" label="From"/> + </inputs> + <outputs> + <data format="tabular" name="out_file1" > + <actions> + <conditional name="delimiter"> + <when value="T"> + <conditional name="input"> + <when datatype_isinstance="interval"> + <action type="format" default="tabular"> + <option type="from_param" name="columnList" column="0" offset="0"> + + <filter type="insert_column" column="0" value="interval"/> + + <filter type="insert_column" ref="columnList" /> + + <filter type="insert_column" ref="columnList" /> + + <filter type="multiple_splitter" column="1" separator=","/> + <filter type="column_strip" column="1"/> + <filter type="string_function" column="1" name="lower" /> + <filter type="param_value" column="1" value="^c\d{1,}$" compare="re_search" keep="True"/> + <filter type="column_strip" column="1" strip="c"/> + <filter type="boolean" column="1" cast="int" /> + + <filter type="multiple_splitter" column="2" separator=","/> + <filter type="column_strip" column="2"/> + <filter type="string_function" column="2" name="lower" /> + <filter type="param_value" column="2" value="^c\d{1,}$" compare="re_search" keep="True"/> + <filter type="column_strip" column="2" strip="c"/> + <filter type="boolean" column="2" cast="int" /> + + <filter type="multiple_splitter" column="3" separator=","/> + <filter type="column_strip" column="3"/> + <filter type="string_function" column="3" name="lower" /> + <filter type="param_value" column="3" value="^c\d{1,}$" compare="re_search" keep="True"/> + <filter type="column_strip" column="3" strip="c"/> + <filter type="boolean" column="3" cast="int" /> + + <filter type="metadata_value" ref="input" name="chromCol" column="1" /> + <filter type="metadata_value" ref="input" name="startCol" column="2" /> + <filter type="metadata_value" ref="input" name="endCol" column="3" /> + + </option> + </action> + + <conditional name="out_file1"> + <when datatype_isinstance="interval"> + <action type="metadata" name="chromCol"> + <option type="from_param" name="columnList" column="0" offset="0"> + <filter type="multiple_splitter" column="0" separator=","/> + <filter type="column_strip" column="0"/> + <filter type="string_function" column="0" name="lower" /> + <filter type="param_value" column="0" value="^c\d{1,}$" compare="re_search" keep="True"/> + <filter type="column_strip" column="0" strip="c"/> + <filter type="insert_column" value="1" iterate="True" column="0"/> + <filter type="boolean" column="1" cast="int" /> + <filter type="metadata_value" ref="input" name="chromCol" column="1" /> + </option> + </action> + + <action type="metadata" name="startCol"> + <option type="from_param" name="columnList" column="0" offset="0"> + <filter type="multiple_splitter" column="0" separator=","/> + <filter type="column_strip" column="0"/> + <filter type="string_function" column="0" name="lower" /> + <filter type="param_value" column="0" value="^c\d{1,}$" compare="re_search" keep="True"/> + <filter type="column_strip" column="0" strip="c"/> + <filter type="insert_column" value="1" iterate="True" column="0"/> + <filter type="boolean" column="1" cast="int" /> + <filter type="metadata_value" ref="input" name="startCol" column="1" /> + </option> + </action> + + <action type="metadata" name="endCol"> + <option type="from_param" name="columnList" column="0" offset="0"> + <filter type="multiple_splitter" column="0" separator=","/> + <filter type="column_strip" column="0"/> + <filter type="string_function" column="0" name="lower" /> + <filter type="param_value" column="0" value="^c\d{1,}$" compare="re_search" keep="True"/> + <filter type="column_strip" column="0" strip="c"/> + <filter type="insert_column" value="1" iterate="True" column="0"/> + <filter type="boolean" column="1" cast="int" /> + <filter type="metadata_value" ref="input" name="endCol" column="1" /> + </option> + </action> + + <action type="metadata" name="nameCol" default="0"> + <option type="from_param" name="columnList" column="0" offset="0"> + <filter type="multiple_splitter" column="0" separator=","/> + <filter type="column_strip" column="0"/> + <filter type="string_function" column="0" name="lower" /> + <filter type="param_value" column="0" value="^c\d{1,}$" compare="re_search" keep="True"/> + <filter type="column_strip" column="0" strip="c"/> + <filter type="insert_column" value="1" iterate="True" column="0"/> + <filter type="boolean" column="1" cast="int" /> + <filter type="metadata_value" ref="input" name="nameCol" column="1" /> + </option> + </action> + + <action type="metadata" name="strandCol" default="0"> + <option type="from_param" name="columnList" column="0" offset="0"> + <filter type="multiple_splitter" column="0" separator=","/> + <filter type="column_strip" column="0"/> + <filter type="string_function" column="0" name="lower" /> + <filter type="param_value" column="0" value="^c\d{1,}$" compare="re_search" keep="True"/> + <filter type="column_strip" column="0" strip="c"/> + <filter type="insert_column" value="1" iterate="True" column="0"/> + <filter type="boolean" column="1" cast="int" /> + <filter type="metadata_value" ref="input" name="strandCol" column="1" /> + </option> + </action> + </when> + </conditional> + + </when> + </conditional> + </when> + </conditional> + </actions> + </data> + </outputs> + <tests> + <test> + <param name="columnList" value="c1,c4,c2,c3"/> + <param name="delimiter" value="T"/> + <param name="input" value="1.bed"/> + <output name="out_file1" file="eq-cut.dat"/> + </test> + </tests> + <help> + +.. class:: warningmark + +**WARNING: This tool breaks column assignments.** To re-establish column assignments run the tools and click on the pencil icon in the latest history item. + +.. class:: infomark + +The output of this tool is always in tabular format (e.g., if your original delimiters are commas, they will be replaced with tabs). For example: + + Cutting columns 1 and 3 from:: + + apple,is,good + windows,is,bad + + will give:: + + apple good + windows bad + +----- + +**What it does** + +This tool selects (cuts out) specified columns from the dataset. + +- Columns are specified as **c1**, **c2**, and so on. Column count begins with **1** +- Columns can be specified in any order (e.g., **c2,c1,c6**) +- If you specify more columns than actually present - empty spaces will be filled with dots + +----- + +**Example** + +Input dataset (six columns: c1, c2, c3, c4, c5, and c6):: + + chr1 10 1000 gene1 0 + + chr2 100 1500 gene2 0 + + +**cut** on columns "**c1,c4,c6**" will return:: + + chr1 gene1 + + chr2 gene2 + + +**cut** on columns "**c6,c5,c4,c1**" will return:: + + + 0 gene1 chr1 + + 0 gene2 chr2 + + +**cut** on columns "**c8,c7,c4**" will return:: + + . . gene1 + . . gene2 + + +</help> +</tool> diff -r 2f45da781f926f667dd90ad23d23fd123716a535 -r 659392eae2a8946ea6d2f2c5534d5c51c1dc28f3 tools/filters/fixedValueColumn.pl --- /dev/null +++ b/tools/filters/fixedValueColumn.pl @@ -0,0 +1,34 @@ +#! /usr/bin/perl -w + +use strict; +use warnings; + +# fixedValueColumn.pl $input $out_file1 "expression" "iterate [yes|no]" + +my ($input, $out_file1, $expression, $iterate) = @ARGV; +my $i = 0; +my $numeric = 0; + +die "Check arguments\n" unless @ARGV == 4; + +open (DATA, "<$input") or die "Cannot open $input:$!\n"; +open (OUT, ">$out_file1") or die "Cannot create $out_file1:$!\n"; + +if ($expression =~ m/^\d+$/) { + $numeric = 1; + $i = $expression; +} + +while (<DATA>) { + chop; + if ($iterate eq "no") { + print OUT "$_\t$expression\n"; + } else { + print OUT "$_\t$i\n" if $numeric == 1; + print OUT "$_\t$expression-$i\n" if $numeric == 0; + ++$i; + } +} + +close DATA; +close OUT; diff -r 2f45da781f926f667dd90ad23d23fd123716a535 -r 659392eae2a8946ea6d2f2c5534d5c51c1dc28f3 tools/filters/fixedValueColumn.xml --- /dev/null +++ b/tools/filters/fixedValueColumn.xml @@ -0,0 +1,61 @@ +<tool id="addValue" name="Add column"> + <description>to an existing dataset</description> + <command interpreter="perl">fixedValueColumn.pl $input $out_file1 "$exp" $iterate</command> + <inputs> + <param name="exp" size="20" type="text" value="1" label="Add this value"/> + <param format="tabular" name="input" type="data" label="to Dataset" help="Dataset missing? See TIP below" /> + <param name="iterate" type="select" label="Iterate?"> + <option value="no">NO</option> + <option value="yes">YES</option> + </param> + </inputs> + <outputs> + <data format="input" name="out_file1" metadata_source="input"/> + </outputs> + <tests> + <test> + <param name="exp" value="1"/> + <param name="input" value="1.bed"/> + <param name="iterate" value="no"/> + <output name="out_file1" file="eq-addvalue.dat"/> + </test> + </tests> + <help> + +.. class:: infomark + +**TIP:** If your data is not TAB delimited, use *Text Manipulation->Convert* + +----- + +**What it does** + +You can enter any value and it will be added as a new column to your dataset + +----- + +**Example** + +If you original data looks like this:: + + chr1 10 100 geneA + chr2 200 300 geneB + chr2 400 500 geneC + +Typing **+** in the text box will generate:: + + chr1 10 100 geneA + + chr2 200 300 geneB + + chr2 400 500 geneC + + + +You can also add line numbers by selecting **Iterate: YES**. In this case if you enter **1** in the text box you will get:: + + chr1 10 100 geneA 1 + chr2 200 300 geneB 2 + chr2 400 500 geneC 3 + + + +</help> +</tool> diff -r 2f45da781f926f667dd90ad23d23fd123716a535 -r 659392eae2a8946ea6d2f2c5534d5c51c1dc28f3 tools/filters/headWrapper.pl --- /dev/null +++ b/tools/filters/headWrapper.pl @@ -0,0 +1,19 @@ +#! /usr/bin/perl -w + +use strict; +use warnings; + +# a wrapper for head for use in galaxy +# headWrapper.pl [filename] [# lines to show] [output] + +die "Check arguments" unless @ARGV == 3; +die "Line number must be an integer\n" unless $ARGV[1]=~ m/^\d+$/; + +open (OUT, ">$ARGV[2]") or die "Cannot create $ARGV[2]:$!\n"; +open (HEAD, "head -n $ARGV[1] $ARGV[0]|") or die "Cannot run head:$!\n"; +while (<HEAD>) { + print OUT; +} +close OUT; +close HEAD; + diff -r 2f45da781f926f667dd90ad23d23fd123716a535 -r 659392eae2a8946ea6d2f2c5534d5c51c1dc28f3 tools/filters/headWrapper.xml --- /dev/null +++ b/tools/filters/headWrapper.xml @@ -0,0 +1,42 @@ +<tool id="Show beginning1" name="Select first"> + <description>lines from a dataset</description> + <command interpreter="perl">headWrapper.pl $input $lineNum $out_file1</command> + <inputs> + <param name="lineNum" size="5" type="integer" value="10" label="Select first" help="lines"/> + <param format="txt" name="input" type="data" label="from"/> + </inputs> + <outputs> + <data format="input" name="out_file1" metadata_source="input"/> + </outputs> + <tests> + <test> + <param name="lineNum" value="10"/> + <param name="input" value="1.bed"/> + <output name="out_file1" file="eq-showbeginning.dat"/> + </test> + </tests> + <help> + +**What it does** + +This tool outputs specified number of lines from the **beginning** of a dataset + +----- + +**Example** + +Selecting 2 lines from this:: + + chr7 56632 56652 D17003_CTCF_R6 310 + + chr7 56736 56756 D17003_CTCF_R7 354 + + chr7 56761 56781 D17003_CTCF_R4 220 + + chr7 56772 56792 D17003_CTCF_R7 372 + + chr7 56775 56795 D17003_CTCF_R4 207 + + +will produce:: + + chr7 56632 56652 D17003_CTCF_R6 310 + + chr7 56736 56756 D17003_CTCF_R7 354 + + + </help> +</tool> diff -r 2f45da781f926f667dd90ad23d23fd123716a535 -r 659392eae2a8946ea6d2f2c5534d5c51c1dc28f3 tools/filters/mergeCols.py --- /dev/null +++ b/tools/filters/mergeCols.py @@ -0,0 +1,37 @@ +import sys, re + +def stop_err( msg ): + sys.stderr.write( msg ) + sys.exit() + +def __main__(): + try: + infile = open ( sys.argv[1], 'r') + outfile = open ( sys.argv[2], 'w') + except: + stop_err( 'Cannot open or create a file\n' ) + + if len( sys.argv ) < 4: + stop_err( 'No columns to merge' ) + else: + cols = sys.argv[3:] + + skipped_lines = 0 + + for line in infile: + line = line.rstrip( '\r\n' ) + if line and not line.startswith( '#' ): + fields = line.split( '\t' ) + line += '\t' + for col in cols: + try: + line += fields[ int( col ) -1 ] + except: + skipped_lines += 1 + + print >>outfile, line + + if skipped_lines > 0: + print 'Skipped %d invalid lines' % skipped_lines + +if __name__ == "__main__" : __main__() \ No newline at end of file diff -r 2f45da781f926f667dd90ad23d23fd123716a535 -r 659392eae2a8946ea6d2f2c5534d5c51c1dc28f3 tools/filters/mergeCols.xml --- /dev/null +++ b/tools/filters/mergeCols.xml @@ -0,0 +1,63 @@ +<tool id="mergeCols1" name="Merge Columns" version="1.0.1"> + <description>together</description> + <command interpreter="python"> + mergeCols.py + $input1 + $out_file1 + $col1 + $col2 + #for $col in $columns + ${col.datacol} + #end for + </command> + <inputs> + <param format="tabular" name="input1" type="data" label="Select data" help="Dataset missing? See TIP below."/> + <param name="col1" label="Merge column" type="data_column" data_ref="input1" /> + <param name="col2" label="with column" type="data_column" data_ref="input1" help="Need to add more columns? Use controls below."/> + <repeat name="columns" title="Columns"> + <param name="datacol" label="Add column" type="data_column" data_ref="input1" /> + </repeat> + </inputs> + <outputs> + <data format="tabular" name="out_file1" /> + </outputs> + <tests> + <test> + <param name="input1" value="1.bed"/> + <param name="col1" value="4" /> + <param name="col2" value="1" /> + <param name="datacol" value="6" /> + <output name="out_file1" file="mergeCols.dat"/> + </test> + </tests> +<help> + +.. class:: infomark + +**TIP:** If your data is not TAB delimited, use *Text Manipulation->Convert* + +----- + +**What it does** + +This tool merges columns together. Any number of valid columns can be merged in any order. + +----- + +**Example** + +Input dataset (five columns: c1, c2, c3, c4, and c5):: + + 1 10 1000 gene1 chr + 2 100 1500 gene2 chr + +merging columns "**c5,c1**" will return:: + + 1 10 1000 gene1 chr chr1 + 2 100 1500 gene2 chr chr2 + +.. class:: warningmark + +Note that all original columns are preserved and the result of merge is added as the rightmost column. + </help> +</tool> diff -r 2f45da781f926f667dd90ad23d23fd123716a535 -r 659392eae2a8946ea6d2f2c5534d5c51c1dc28f3 tools/filters/remove_beginning.pl --- /dev/null +++ b/tools/filters/remove_beginning.pl @@ -0,0 +1,33 @@ +#! /usr/bin/perl -w + +use strict; +use warnings; + +# Removes the specified number of lines from the beginning of the file. +# remove_beginning.pl [input] [num_lines] [output] + +die "Check arguments" unless @ARGV == 3; + +my $inputfile = $ARGV[0]; +my $num_lines = $ARGV[1]; +my $outputfile = $ARGV[2]; + +my $curCount=0; + +my $fhIn; +open ($fhIn, "< $inputfile") or die "Cannot open source file"; + +my $fhOut; +open ($fhOut, "> $outputfile"); + +while (<$fhIn>) +{ + $curCount++; + if ($curCount<=$num_lines) + { + next; + } + print $fhOut $_; +} +close ($fhIn) or die "Cannot close source file"; +close ($fhOut) or die "Cannot close output file"; diff -r 2f45da781f926f667dd90ad23d23fd123716a535 -r 659392eae2a8946ea6d2f2c5534d5c51c1dc28f3 tools/filters/remove_beginning.xml --- /dev/null +++ b/tools/filters/remove_beginning.xml @@ -0,0 +1,42 @@ +<tool id="Remove beginning1" name="Remove beginning"> + <description>of a file</description> + <command interpreter="perl">remove_beginning.pl $input $num_lines $out_file1</command> + <inputs> + <param name="num_lines" size="5" type="integer" value="1" label="Remove first" help="lines"/> + <param format="txt" name="input" type="data" label="from"/> + </inputs> + <outputs> + <data format="input" name="out_file1" metadata_source="input"/> + </outputs> + <tests> + <test> + <param name="num_lines" value="5"/> + <param name="input" value="1.bed"/> + <output name="out_file1" file="eq-removebeginning.dat"/> + </test> + </tests> + <help> + +**What it does** + +This tool removes a specified number of lines from the beginning of a dataset. + +----- + +**Example** + +Input File:: + + chr7 56632 56652 D17003_CTCF_R6 310 + + chr7 56736 56756 D17003_CTCF_R7 354 + + chr7 56761 56781 D17003_CTCF_R4 220 + + chr7 56772 56792 D17003_CTCF_R7 372 + + chr7 56775 56795 D17003_CTCF_R4 207 + + +After removing the first 3 lines the dataset will look like this:: + + chr7 56772 56792 D17003_CTCF_R7 372 + + chr7 56775 56795 D17003_CTCF_R4 207 + + +</help> +</tool> diff -r 2f45da781f926f667dd90ad23d23fd123716a535 -r 659392eae2a8946ea6d2f2c5534d5c51c1dc28f3 tools/filters/tailWrapper.pl --- /dev/null +++ b/tools/filters/tailWrapper.pl @@ -0,0 +1,19 @@ +#! /usr/bin/perl -w + +use strict; +use warnings; + +# a wrapper for tail for use in galaxy +# lessWrapper.pl [filename] [# lines to show] [output] + +die "Check arguments" unless @ARGV == 3; +die "Line number should be an integer\n" unless $ARGV[1]=~ m/^\d+$/; + +open (OUT, ">$ARGV[2]") or die "Cannot create $ARGV[2]:$!\n"; +open (TAIL, "tail -n $ARGV[1] $ARGV[0]|") or die "Cannot run tail:$!\n"; +while (<TAIL>) { + print OUT; +} +close OUT; +close TAIL; + diff -r 2f45da781f926f667dd90ad23d23fd123716a535 -r 659392eae2a8946ea6d2f2c5534d5c51c1dc28f3 tools/filters/tailWrapper.xml --- /dev/null +++ b/tools/filters/tailWrapper.xml @@ -0,0 +1,42 @@ +<tool id="Show tail1" name="Select last"> + <description>lines from a dataset</description> + <command interpreter="perl">tailWrapper.pl $input $lineNum $out_file1</command> + <inputs> + <param name="lineNum" size="5" type="integer" value="10" label="Select last" help="lines"/> + <param format="txt" name="input" type="data" label="from"/> + </inputs> + <outputs> + <data format="input" name="out_file1" metadata_source="input"/> + </outputs> + <tests> + <test> + <param name="lineNum" value="10"/> + <param name="input" value="1.bed"/> + <output name="out_file1" file="eq-showtail.dat"/> + </test> + </tests> + <help> + +**What it does** + +This tool outputs specified number of lines from the **end** of a dataset + +----- + +**Example** + +- Input File:: + + chr7 57134 57154 D17003_CTCF_R7 356 - + chr7 57247 57267 D17003_CTCF_R4 207 + + chr7 57314 57334 D17003_CTCF_R5 269 + + chr7 57341 57361 D17003_CTCF_R7 375 + + chr7 57457 57477 D17003_CTCF_R3 188 + + +- Show last two lines of above file. The result is:: + + chr7 57341 57361 D17003_CTCF_R7 375 + + chr7 57457 57477 D17003_CTCF_R3 188 + + + </help> +</tool> diff -r 2f45da781f926f667dd90ad23d23fd123716a535 -r 659392eae2a8946ea6d2f2c5534d5c51c1dc28f3 tools/filters/trimmer.py --- /dev/null +++ b/tools/filters/trimmer.py @@ -0,0 +1,106 @@ +#!/usr/bin/env python + +import sys +import optparse + +def stop_err( msg ): + sys.stderr.write( msg ) + sys.exit() + +def main(): + usage = """%prog [options] + +options (listed below) default to 'None' if omitted + """ + parser = optparse.OptionParser(usage=usage) + + parser.add_option( + '-a','--ascii', + dest='ascii', + action='store_true', + default = False, + help='Use ascii codes to defined ignored beginnings instead of raw characters') + + parser.add_option( + '-q','--fastq', + dest='fastq', + action='store_true', + default = False, + help='The input data in fastq format. It selected the script skips every even line since they contain sequence ids') + + parser.add_option( + '-i','--ignore', + dest='ignore', + help='A comma separated list on ignored beginnings (e.g., ">,@"), or its ascii codes (e.g., "60,42") if option -a is enabled') + + parser.add_option( + '-s','--start', + dest='start', + default = '0', + help='Trim from beginning to here (1-based)') + + parser.add_option( + '-e','--end', + dest='end', + default = '0', + help='Trim from here to the ned (1-based)') + + parser.add_option( + '-f','--file', + dest='input_txt', + default = False, + help='Name of file to be chopped. STDIN is default') + + parser.add_option( + '-c','--column', + dest='col', + default = '0', + help='Column to chop. If 0 = chop the whole line') + + + options, args = parser.parse_args() + invalid_starts = [] + + if options.input_txt: + infile = open ( options.input_txt, 'r') + else: + infile = sys.stdin + + if options.ignore and options.ignore != "None": + invalid_starts = options.ignore.split(',') + + if options.ascii and options.ignore and options.ignore != "None": + for i, item in enumerate( invalid_starts ): + invalid_starts[i] = chr( int( item ) ) + + col = int( options.col ) + + for i, line in enumerate( infile ): + line = line.rstrip( '\r\n' ) + if line: + + if options.fastq and i % 2 == 0: + print line + continue + + + if line[0] not in invalid_starts: + if col == 0: + if int( options.end ) > 0: + line = line[ int( options.start )-1 : int( options.end ) ] + else: + line = line[ int( options.start )-1 : ] + else: + fields = line.split( '\t' ) + if col-1 > len( fields ): + stop_err('Column %d does not exist. Check input parameters\n' % col) + + if int( options.end ) > 0: + fields[col - 1] = fields[col - 1][ int( options.start )-1 : int( options.end ) ] + else: + fields[col - 1] = fields[col - 1][ int( options.start )-1 : ] + line = '\t'.join(fields) + print line + +if __name__ == "__main__": main() + diff -r 2f45da781f926f667dd90ad23d23fd123716a535 -r 659392eae2a8946ea6d2f2c5534d5c51c1dc28f3 tools/filters/trimmer.xml --- /dev/null +++ b/tools/filters/trimmer.xml @@ -0,0 +1,120 @@ +<tool id="trimmer" name="Trim" version="0.0.1"> + <description>leading or trailing characters</description> + <command interpreter="python"> + trimmer.py -a -f $input1 -c $col -s $start -e $end -i $ignore $fastq > $out_file1 + </command> + <inputs> + <param format="tabular,txt" name="input1" type="data" label="this dataset"/> + <param name="col" type="integer" value="0" label="Trim this column only" help="0 = process entire line" /> + <param name="start" type="integer" size="10" value="1" label="Trim from the beginning to this position" help="1 = do not trim the beginning"/> + <param name="end" type="integer" size="10" value="0" label="Remove everything from this position to the end" help="0 = do not trim the end"/> + <param name="fastq" type="select" label="Is input dataset in fastq format?" help="If set to YES, the tool will not trim evenly numbered lines (0, 2, 4, etc...)"> + <option selected="true" value="">No</option> + <option value="-q">Yes</option> + </param> + <param name="ignore" type="select" display="checkboxes" multiple="True" label="Ignore lines beginning with these characters" help="lines beginning with these are not trimmed"> + <option value="62">></option> + <option value="64">@</option> + <option value="43">+</option> + <option value="60"><</option> + <option value="42">*</option> + <option value="45">-</option> + <option value="61">=</option> + <option value="124">|</option> + <option value="63">?</option> + <option value="36">$</option> + <option value="46">.</option> + <option value="58">:</option> + <option value="38">&</option> + <option value="37">%</option> + <option value="94">^</option> + <option value="35">#</option> + </param> + </inputs> + <outputs> + <data name="out_file1" format="input" metadata_source="input1"/> + </outputs> + <tests> + <test> + <param name="input1" value="trimmer_tab_delimited.dat"/> + <param name="col" value="0"/> + <param name="start" value="1"/> + <param name="end" value="13"/> + <param name="ignore" value="62"/> + <param name="fastq" value="No"/> + <output name="out_file1" file="trimmer_a_f_c0_s1_e13_i62.dat"/> + </test> + <test> + <param name="input1" value="trimmer_tab_delimited.dat"/> + <param name="col" value="2"/> + <param name="start" value="1"/> + <param name="end" value="2"/> + <param name="ignore" value="62"/> + <param name="fastq" value="No"/> + <output name="out_file1" file="trimmer_a_f_c2_s1_e2_i62.dat"/> + </test> + + </tests> + + <help> + + +**What it does** + +Trims specified number of characters from a dataset or its field (if dataset is tab-delimited). + +----- + +**Example 1** + +Trimming this dataset:: + + 1234567890 + abcdefghijk + +by setting **Trim from the beginning to this position** to *2* and **Remove everything from this position to the end** to *6* will produce:: + + 23456 + bcdef + +----- + +**Example 2** + +Trimming column 2 of this dataset:: + + abcde 12345 fghij 67890 + fghij 67890 abcde 12345 + +by setting **Trim content of this column only** to *2*, **Trim from the beginning to this position** to *2*, and **Remove everything from this position to the end** to *4* will produce:: + + abcde 234 fghij 67890 + fghij 789 abcde 12345 + +----- + +**Trimming FASTQ datasets** + +This tool can be used to trim sequences and quality strings in fastq datasets. This is done by selected *Yes* from the **Is input dataset in fastq format?** dropdown. If set to *Yes*, the tool will skip all even numbered lines (see warning below). For example, trimming last 5 bases of this dataset:: + + @081017-and-081020:1:1:1715:1759 + GGACTCAGATAGTAATCCACGCTCCTTTAAAATATC + + + II#IIIIIII$5+.(9IIIIIII$%*$G$A31I&&B + +cab done by setting **Remove everything from this position to the end** to 31:: + + @081017-and-081020:1:1:1715:1759 + GGACTCAGATAGTAATCCACGCTCCTTTAAA + + + II#IIIIIII$5+.(9IIIIIII$%*$G$A3 + +**Note** that headers are skipped. + +.. class:: warningmark + +**WARNING:** This tool will only work on properly formatted fastq datasets where (1) each read and quality string occupy one line and (2) '@' (read header) and "+" (quality header) lines are evenly numbered like in the above example. + + + </help> +</tool> https://bitbucket.org/galaxy/galaxy-central/changeset/facdd387b85e/ changeset: facdd387b85e user: inithello date: 2012-12-07 22:39:17 summary: Updated tool_conf.xml.main with reverted migration. affected #: 1 file diff -r 659392eae2a8946ea6d2f2c5534d5c51c1dc28f3 -r facdd387b85e814df7428ca8cbb71828d0ec48a2 tool_conf.xml.main --- a/tool_conf.xml.main +++ b/tool_conf.xml.main @@ -33,11 +33,21 @@ <tool file="extract/liftOver_wrapper.xml" /></section><section name="Text Manipulation" id="textutil"> + <tool file="filters/fixedValueColumn.xml" /><tool file="stats/column_maker.xml" /><tool file="filters/catWrapper.xml" /> + <tool file="filters/condense_characters.xml" /> + <tool file="filters/convert_characters.xml" /> + <tool file="filters/mergeCols.xml" /><tool file="filters/CreateInterval.xml" /> + <tool file="filters/cutWrapper.xml" /> + <tool file="filters/changeCase.xml" /><tool file="filters/pasteWrapper.xml" /> + <tool file="filters/remove_beginning.xml" /><tool file="filters/randomlines.xml" /> + <tool file="filters/headWrapper.xml" /> + <tool file="filters/tailWrapper.xml" /> + <tool file="filters/trimmer.xml" /><tool file="filters/wc_gnu.xml" /><tool file="filters/secure_hash_message_digest.xml" /></section> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 2 new changesets
by Bitbucket 07 Dec '12

07 Dec '12

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/c68762fcb5a5/ changeset: c68762fcb5a5 user: inithello date: 2012-12-07 22:08:40 summary: Migrate tools to tool shed: addValue, ChangeCase, Condense characters1, Convert characters1, Cut1, mergeCols1, Remove beginning1, Show beginning1, Show tail1, trimmer affected #: 35 files diff -r 63fc9cbe381d2719134f87c019911565e3a934a1 -r c68762fcb5a521007d89cb01455a0ad409011528 lib/galaxy/tool_shed/migrate/versions/0008_tools.py --- /dev/null +++ b/lib/galaxy/tool_shed/migrate/versions/0008_tools.py @@ -0,0 +1,21 @@ +""" +The following tools have been eliminated from the distribution: +Add column to an existing dataset, Change Case of selected columns, +Condense consecutive characters, Convert delimiters to TAB, +Cut columns from a table, Merge Columns together, Remove beginning of a file, +Select first lines from a dataset, Select last lines from a dataset, +and Trim leading or trailing characters. The tools are now available in the +repositories named add_value, change_case, condense_characters, +convert_characters, cut_columns, merge_cols, remove_beginning, +show_beginning, show_tail, and trimmer from the main Galaxy tool shed at +http://toolshed.g2.bx.psu.edu, and will be installed into your +local Galaxy instance at the location discussed above by running +the following command. +""" + +import sys + +def upgrade(): + print __doc__ +def downgrade(): + pass diff -r 63fc9cbe381d2719134f87c019911565e3a934a1 -r c68762fcb5a521007d89cb01455a0ad409011528 scripts/migrate_tools/0008_tools.sh --- /dev/null +++ b/scripts/migrate_tools/0008_tools.sh @@ -0,0 +1,4 @@ +#!/bin/sh + +cd `dirname $0`/../.. +python ./scripts/migrate_tools/migrate_tools.py 0008_tools.xml $@ diff -r 63fc9cbe381d2719134f87c019911565e3a934a1 -r c68762fcb5a521007d89cb01455a0ad409011528 scripts/migrate_tools/0008_tools.xml --- /dev/null +++ b/scripts/migrate_tools/0008_tools.xml @@ -0,0 +1,33 @@ +<?xml version="1.0"?> +<toolshed name="toolshed.g2.bx.psu.edu"> + <repository name="add_value" description="Add a value as a new column." changeset_revision="181dd378275c"> + <tool id="addValue" version="1.0.0" file="fixedValueColumn.xml" /> + </repository> + <repository name="change_case" description="Change the case of a column." changeset_revision="e6f966602870"> + <tool id="ChangeCase" version="1.0.0" file="changeCase.xml" /> + </repository> + <repository name="condense_characters" description="Condense repeated characters." changeset_revision="2c08781560de"> + <tool id="Condense characters1" version="1.0.0" file="condense_characters.xml" /> + </repository> + <repository name="convert_characters" description="Convert delimiters to TAB." changeset_revision="64d46676a13e"> + <tool id="Convert characters1" version="1.0.0" file="convert_characters.xml" /> + </repository> + <repository name="cut_columns" description="Remove or rearrange columns." changeset_revision="34c29e183ef7"> + <tool id="Cut1" version="1.0.1" file="cutWrapper.xml" /> + </repository> + <repository name="merge_cols" description="Merge columns together." changeset_revision="28ca7552e884"> + <tool id="mergeCols1" version="1.0.1" file="mergeCols.xml" /> + </repository> + <repository name="remove_beginning" description="Remove lines from the beginning of a file." changeset_revision="d9b82504a321"> + <tool id="Remove beginning1" version="1.0.0" file="remove_beginning.xml" /> + </repository> + <repository name="show_beginning" description="Select lines from the beginning of a file." changeset_revision="ecca14446e6a"> + <tool id="Show beginning1" version="1.0.0" file="headWrapper.xml" /> + </repository> + <repository name="show_tail" description="Select lines from the end of a file." changeset_revision="8bb4d908a523"> + <tool id="Show tail1" version="1.0.0" file="tailWrapper.xml" /> + </repository> + <repository name="trimmer" description="Trim trailing characters from each line or column." changeset_revision="f862a6e4d096"> + <tool id="trimmer" version="0.0.1" file="trimmer.xml" /> + </repository> +</toolshed> diff -r 63fc9cbe381d2719134f87c019911565e3a934a1 -r c68762fcb5a521007d89cb01455a0ad409011528 test-data/a.txt --- a/test-data/a.txt +++ /dev/null @@ -1,15 +0,0 @@ - CHR SNP BP A1 TEST NMISS BETA STAT P - 1 rs1181876 3671541 T DOMDEV 958 -1.415 -3.326 0.0009161 - 1 rs10492923 5092886 C ADD 1007 5.105 4.368 1.382e-05 - 1 rs10492923 5092886 C DOMDEV 1007 -5.612 -4.249 2.35e-05 - 1 rs10492923 5092886 C GENO_2DF 1007 NA 19.9 4.775e-05 - 1 rs1801133 11778965 T ADD 1022 1.23 3.97 7.682e-05 - 1 rs1801133 11778965 T GENO_2DF 1022 NA 16.07 0.0003233 - 1 rs1361912 12663121 A ADD 1021 12.69 4.093 4.596e-05 - 1 rs1361912 12663121 A DOMDEV 1021 -12.37 -3.945 8.533e-05 - 1 rs1361912 12663121 A GENO_2DF 1021 NA 17.05 0.0001982 - 1 rs1009806 19373138 G ADD 1021 -1.334 -3.756 0.0001826 - 1 rs1009806 19373138 G GENO_2DF 1021 NA 19.36 6.244e-05 - 1 rs873654 29550948 A DOMDEV 1012 1.526 3.6 0.0003339 - 1 rs10489527 36800027 C ADD 1016 12.67 4.114 4.211e-05 - 1 rs10489527 36800027 C DOMDEV 1016 -13.05 -4.02 6.249e-05 \ No newline at end of file diff -r 63fc9cbe381d2719134f87c019911565e3a934a1 -r c68762fcb5a521007d89cb01455a0ad409011528 test-data/changeCase_out1.tabular --- a/test-data/changeCase_out1.tabular +++ /dev/null @@ -1,10 +0,0 @@ -CHR1 4225 19670 -CHR10 6 8 -CHR1 24417 24420 -CHR6_HLA_HAP2 0 150 -CHR2 1 5 -CHR10 2 10 -CHR1 30 55 -CHRY 1 20 -CHR1 1225979 42287290 -CHR10 7 8 diff -r 63fc9cbe381d2719134f87c019911565e3a934a1 -r c68762fcb5a521007d89cb01455a0ad409011528 test-data/changeCase_out2.tabular --- a/test-data/changeCase_out2.tabular +++ /dev/null @@ -1,65 +0,0 @@ -CHR1 147962192 147962580 CCDS989.1_cds_0_0_chr1_147962193_r 0 - -CHR1 147984545 147984630 CCDS990.1_cds_0_0_chr1_147984546_f 0 + -CHR1 148078400 148078582 CCDS993.1_cds_0_0_chr1_148078401_r 0 - -CHR1 148185136 148185276 CCDS996.1_cds_0_0_chr1_148185137_f 0 + -CHR10 55251623 55253124 CCDS7248.1_cds_0_0_chr10_55251624_r 0 - -CHR11 116124407 116124501 CCDS8374.1_cds_0_0_chr11_116124408_r 0 - -CHR11 116206508 116206563 CCDS8377.1_cds_0_0_chr11_116206509_f 0 + -CHR11 116211733 116212337 CCDS8378.1_cds_0_0_chr11_116211734_r 0 - -CHR11 1812377 1812407 CCDS7726.1_cds_0_0_chr11_1812378_f 0 + -CHR12 38440094 38440321 CCDS8736.1_cds_0_0_chr12_38440095_r 0 - -CHR13 112381694 112381953 CCDS9526.1_cds_0_0_chr13_112381695_f 0 + -CHR14 98710240 98712285 CCDS9949.1_cds_0_0_chr14_98710241_r 0 - -CHR15 41486872 41487060 CCDS10096.1_cds_0_0_chr15_41486873_r 0 - -CHR15 41673708 41673857 CCDS10097.1_cds_0_0_chr15_41673709_f 0 + -CHR15 41679161 41679250 CCDS10098.1_cds_0_0_chr15_41679162_r 0 - -CHR15 41826029 41826196 CCDS10101.1_cds_0_0_chr15_41826030_f 0 + -CHR16 142908 143003 CCDS10397.1_cds_0_0_chr16_142909_f 0 + -CHR16 179963 180135 CCDS10401.1_cds_0_0_chr16_179964_r 0 - -CHR16 244413 244681 CCDS10402.1_cds_0_0_chr16_244414_f 0 + -CHR16 259268 259383 CCDS10403.1_cds_0_0_chr16_259269_r 0 - -CHR18 23786114 23786321 CCDS11891.1_cds_0_0_chr18_23786115_r 0 - -CHR18 59406881 59407046 CCDS11985.1_cds_0_0_chr18_59406882_f 0 + -CHR18 59455932 59456337 CCDS11986.1_cds_0_0_chr18_59455933_r 0 - -CHR18 59600586 59600754 CCDS11988.1_cds_0_0_chr18_59600587_f 0 + -CHR19 59068595 59069564 CCDS12866.1_cds_0_0_chr19_59068596_f 0 + -CHR19 59236026 59236146 CCDS12872.1_cds_0_0_chr19_59236027_r 0 - -CHR19 59297998 59298008 CCDS12877.1_cds_0_0_chr19_59297999_f 0 + -CHR19 59302168 59302288 CCDS12878.1_cds_0_0_chr19_59302169_r 0 - -CHR2 118288583 118288668 CCDS2120.1_cds_0_0_chr2_118288584_f 0 + -CHR2 118394148 118394202 CCDS2121.1_cds_0_0_chr2_118394149_r 0 - -CHR2 220190202 220190242 CCDS2441.1_cds_0_0_chr2_220190203_f 0 + -CHR2 220229609 220230869 CCDS2443.1_cds_0_0_chr2_220229610_r 0 - -CHR20 33330413 33330423 CCDS13249.1_cds_0_0_chr20_33330414_r 0 - -CHR20 33513606 33513792 CCDS13255.1_cds_0_0_chr20_33513607_f 0 + -CHR20 33579500 33579527 CCDS13256.1_cds_0_0_chr20_33579501_r 0 - -CHR20 33593260 33593348 CCDS13257.1_cds_0_0_chr20_33593261_f 0 + -CHR21 32707032 32707192 CCDS13614.1_cds_0_0_chr21_32707033_f 0 + -CHR21 32869641 32870022 CCDS13615.1_cds_0_0_chr21_32869642_r 0 - -CHR21 33321040 33322012 CCDS13620.1_cds_0_0_chr21_33321041_f 0 + -CHR21 33744994 33745040 CCDS13625.1_cds_0_0_chr21_33744995_r 0 - -CHR22 30120223 30120265 CCDS13897.1_cds_0_0_chr22_30120224_f 0 + -CHR22 30160419 30160661 CCDS13898.1_cds_0_0_chr22_30160420_r 0 - -CHR22 30665273 30665360 CCDS13901.1_cds_0_0_chr22_30665274_f 0 + -CHR22 30939054 30939266 CCDS13903.1_cds_0_0_chr22_30939055_r 0 - -CHR5 131424298 131424460 CCDS4149.1_cds_0_0_chr5_131424299_f 0 + -CHR5 131556601 131556672 CCDS4151.1_cds_0_0_chr5_131556602_r 0 - -CHR5 131621326 131621419 CCDS4152.1_cds_0_0_chr5_131621327_f 0 + -CHR5 131847541 131847666 CCDS4155.1_cds_0_0_chr5_131847542_r 0 - -CHR6 108299600 108299744 CCDS5061.1_cds_0_0_chr6_108299601_r 0 - -CHR6 108594662 108594687 CCDS5063.1_cds_0_0_chr6_108594663_f 0 + -CHR6 108640045 108640151 CCDS5064.1_cds_0_0_chr6_108640046_r 0 - -CHR6 108722976 108723115 CCDS5067.1_cds_0_0_chr6_108722977_f 0 + -CHR7 113660517 113660685 CCDS5760.1_cds_0_0_chr7_113660518_f 0 + -CHR7 116512159 116512389 CCDS5771.1_cds_0_0_chr7_116512160_r 0 - -CHR7 116714099 116714152 CCDS5773.1_cds_0_0_chr7_116714100_f 0 + -CHR7 116945541 116945787 CCDS5774.1_cds_0_0_chr7_116945542_r 0 - -CHR8 118881131 118881317 CCDS6324.1_cds_0_0_chr8_118881132_r 0 - -CHR9 128764156 128764189 CCDS6914.1_cds_0_0_chr9_128764157_f 0 + -CHR9 128787519 128789136 CCDS6915.1_cds_0_0_chr9_128787520_r 0 - -CHR9 128882427 128882523 CCDS6917.1_cds_0_0_chr9_128882428_f 0 + -CHR9 128937229 128937445 CCDS6919.1_cds_0_0_chr9_128937230_r 0 - -CHRX 122745047 122745924 CCDS14606.1_cds_0_0_chrX_122745048_f 0 + -CHRX 152648964 152649196 CCDS14733.1_cds_0_0_chrX_152648965_r 0 - -CHRX 152691446 152691471 CCDS14735.1_cds_0_0_chrX_152691447_f 0 + -CHRX 152694029 152694263 CCDS14736.1_cds_0_0_chrX_152694030_r 0 - diff -r 63fc9cbe381d2719134f87c019911565e3a934a1 -r c68762fcb5a521007d89cb01455a0ad409011528 test-data/eq-addvalue.dat --- a/test-data/eq-addvalue.dat +++ /dev/null @@ -1,65 +0,0 @@ -chr1 147962192 147962580 CCDS989.1_cds_0_0_chr1_147962193_r 0 - 1 -chr1 147984545 147984630 CCDS990.1_cds_0_0_chr1_147984546_f 0 + 1 -chr1 148078400 148078582 CCDS993.1_cds_0_0_chr1_148078401_r 0 - 1 -chr1 148185136 148185276 CCDS996.1_cds_0_0_chr1_148185137_f 0 + 1 -chr10 55251623 55253124 CCDS7248.1_cds_0_0_chr10_55251624_r 0 - 1 -chr11 116124407 116124501 CCDS8374.1_cds_0_0_chr11_116124408_r 0 - 1 -chr11 116206508 116206563 CCDS8377.1_cds_0_0_chr11_116206509_f 0 + 1 -chr11 116211733 116212337 CCDS8378.1_cds_0_0_chr11_116211734_r 0 - 1 -chr11 1812377 1812407 CCDS7726.1_cds_0_0_chr11_1812378_f 0 + 1 -chr12 38440094 38440321 CCDS8736.1_cds_0_0_chr12_38440095_r 0 - 1 -chr13 112381694 112381953 CCDS9526.1_cds_0_0_chr13_112381695_f 0 + 1 -chr14 98710240 98712285 CCDS9949.1_cds_0_0_chr14_98710241_r 0 - 1 -chr15 41486872 41487060 CCDS10096.1_cds_0_0_chr15_41486873_r 0 - 1 -chr15 41673708 41673857 CCDS10097.1_cds_0_0_chr15_41673709_f 0 + 1 -chr15 41679161 41679250 CCDS10098.1_cds_0_0_chr15_41679162_r 0 - 1 -chr15 41826029 41826196 CCDS10101.1_cds_0_0_chr15_41826030_f 0 + 1 -chr16 142908 143003 CCDS10397.1_cds_0_0_chr16_142909_f 0 + 1 -chr16 179963 180135 CCDS10401.1_cds_0_0_chr16_179964_r 0 - 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-chr9 128882427 128882523 CCDS6917.1_cds_0_0_chr9_128882428_f 0 + -chr9 128937229 128937445 CCDS6919.1_cds_0_0_chr9_128937230_r 0 - -chrX 122745047 122745924 CCDS14606.1_cds_0_0_chrX_122745048_f 0 + -chrX 152648964 152649196 CCDS14733.1_cds_0_0_chrX_152648965_r 0 - -chrX 152691446 152691471 CCDS14735.1_cds_0_0_chrX_152691447_f 0 + -chrX 152694029 152694263 CCDS14736.1_cds_0_0_chrX_152694030_r 0 - diff -r 63fc9cbe381d2719134f87c019911565e3a934a1 -r c68762fcb5a521007d89cb01455a0ad409011528 test-data/eq-cut.dat --- a/test-data/eq-cut.dat +++ /dev/null @@ -1,65 +0,0 @@ -chr1 CCDS989.1_cds_0_0_chr1_147962193_r 147962192 147962580 -chr1 CCDS990.1_cds_0_0_chr1_147984546_f 147984545 147984630 -chr1 CCDS993.1_cds_0_0_chr1_148078401_r 148078400 148078582 -chr1 CCDS996.1_cds_0_0_chr1_148185137_f 148185136 148185276 -chr10 CCDS7248.1_cds_0_0_chr10_55251624_r 55251623 55253124 -chr11 CCDS8374.1_cds_0_0_chr11_116124408_r 116124407 116124501 -chr11 CCDS8377.1_cds_0_0_chr11_116206509_f 116206508 116206563 -chr11 CCDS8378.1_cds_0_0_chr11_116211734_r 116211733 116212337 -chr11 CCDS7726.1_cds_0_0_chr11_1812378_f 1812377 1812407 -chr12 CCDS8736.1_cds_0_0_chr12_38440095_r 38440094 38440321 -chr13 CCDS9526.1_cds_0_0_chr13_112381695_f 112381694 112381953 -chr14 CCDS9949.1_cds_0_0_chr14_98710241_r 98710240 98712285 -chr15 CCDS10096.1_cds_0_0_chr15_41486873_r 41486872 41487060 -chr15 CCDS10097.1_cds_0_0_chr15_41673709_f 41673708 41673857 -chr15 CCDS10098.1_cds_0_0_chr15_41679162_r 41679161 41679250 -chr15 CCDS10101.1_cds_0_0_chr15_41826030_f 41826029 41826196 -chr16 CCDS10397.1_cds_0_0_chr16_142909_f 142908 143003 -chr16 CCDS10401.1_cds_0_0_chr16_179964_r 179963 180135 -chr16 CCDS10402.1_cds_0_0_chr16_244414_f 244413 244681 -chr16 CCDS10403.1_cds_0_0_chr16_259269_r 259268 259383 -chr18 CCDS11891.1_cds_0_0_chr18_23786115_r 23786114 23786321 -chr18 CCDS11985.1_cds_0_0_chr18_59406882_f 59406881 59407046 -chr18 CCDS11986.1_cds_0_0_chr18_59455933_r 59455932 59456337 -chr18 CCDS11988.1_cds_0_0_chr18_59600587_f 59600586 59600754 -chr19 CCDS12866.1_cds_0_0_chr19_59068596_f 59068595 59069564 -chr19 CCDS12872.1_cds_0_0_chr19_59236027_r 59236026 59236146 -chr19 CCDS12877.1_cds_0_0_chr19_59297999_f 59297998 59298008 -chr19 CCDS12878.1_cds_0_0_chr19_59302169_r 59302168 59302288 -chr2 CCDS2120.1_cds_0_0_chr2_118288584_f 118288583 118288668 -chr2 CCDS2121.1_cds_0_0_chr2_118394149_r 118394148 118394202 -chr2 CCDS2441.1_cds_0_0_chr2_220190203_f 220190202 220190242 -chr2 CCDS2443.1_cds_0_0_chr2_220229610_r 220229609 220230869 -chr20 CCDS13249.1_cds_0_0_chr20_33330414_r 33330413 33330423 -chr20 CCDS13255.1_cds_0_0_chr20_33513607_f 33513606 33513792 -chr20 CCDS13256.1_cds_0_0_chr20_33579501_r 33579500 33579527 -chr20 CCDS13257.1_cds_0_0_chr20_33593261_f 33593260 33593348 -chr21 CCDS13614.1_cds_0_0_chr21_32707033_f 32707032 32707192 -chr21 CCDS13615.1_cds_0_0_chr21_32869642_r 32869641 32870022 -chr21 CCDS13620.1_cds_0_0_chr21_33321041_f 33321040 33322012 -chr21 CCDS13625.1_cds_0_0_chr21_33744995_r 33744994 33745040 -chr22 CCDS13897.1_cds_0_0_chr22_30120224_f 30120223 30120265 -chr22 CCDS13898.1_cds_0_0_chr22_30160420_r 30160419 30160661 -chr22 CCDS13901.1_cds_0_0_chr22_30665274_f 30665273 30665360 -chr22 CCDS13903.1_cds_0_0_chr22_30939055_r 30939054 30939266 -chr5 CCDS4149.1_cds_0_0_chr5_131424299_f 131424298 131424460 -chr5 CCDS4151.1_cds_0_0_chr5_131556602_r 131556601 131556672 -chr5 CCDS4152.1_cds_0_0_chr5_131621327_f 131621326 131621419 -chr5 CCDS4155.1_cds_0_0_chr5_131847542_r 131847541 131847666 -chr6 CCDS5061.1_cds_0_0_chr6_108299601_r 108299600 108299744 -chr6 CCDS5063.1_cds_0_0_chr6_108594663_f 108594662 108594687 -chr6 CCDS5064.1_cds_0_0_chr6_108640046_r 108640045 108640151 -chr6 CCDS5067.1_cds_0_0_chr6_108722977_f 108722976 108723115 -chr7 CCDS5760.1_cds_0_0_chr7_113660518_f 113660517 113660685 -chr7 CCDS5771.1_cds_0_0_chr7_116512160_r 116512159 116512389 -chr7 CCDS5773.1_cds_0_0_chr7_116714100_f 116714099 116714152 -chr7 CCDS5774.1_cds_0_0_chr7_116945542_r 116945541 116945787 -chr8 CCDS6324.1_cds_0_0_chr8_118881132_r 118881131 118881317 -chr9 CCDS6914.1_cds_0_0_chr9_128764157_f 128764156 128764189 -chr9 CCDS6915.1_cds_0_0_chr9_128787520_r 128787519 128789136 -chr9 CCDS6917.1_cds_0_0_chr9_128882428_f 128882427 128882523 -chr9 CCDS6919.1_cds_0_0_chr9_128937230_r 128937229 128937445 -chrX CCDS14606.1_cds_0_0_chrX_122745048_f 122745047 122745924 -chrX CCDS14733.1_cds_0_0_chrX_152648965_r 152648964 152649196 -chrX CCDS14735.1_cds_0_0_chrX_152691447_f 152691446 152691471 -chrX CCDS14736.1_cds_0_0_chrX_152694030_r 152694029 152694263 diff -r 63fc9cbe381d2719134f87c019911565e3a934a1 -r c68762fcb5a521007d89cb01455a0ad409011528 test-data/mergeCols.dat --- a/test-data/mergeCols.dat +++ /dev/null @@ -1,65 +0,0 @@ -chr1 147962192 147962580 CCDS989.1_cds_0_0_chr1_147962193_r 0 - CCDS989.1_cds_0_0_chr1_147962193_rchr1- -chr1 147984545 147984630 CCDS990.1_cds_0_0_chr1_147984546_f 0 + CCDS990.1_cds_0_0_chr1_147984546_fchr1+ -chr1 148078400 148078582 CCDS993.1_cds_0_0_chr1_148078401_r 0 - CCDS993.1_cds_0_0_chr1_148078401_rchr1- -chr1 148185136 148185276 CCDS996.1_cds_0_0_chr1_148185137_f 0 + CCDS996.1_cds_0_0_chr1_148185137_fchr1+ -chr10 55251623 55253124 CCDS7248.1_cds_0_0_chr10_55251624_r 0 - CCDS7248.1_cds_0_0_chr10_55251624_rchr10- -chr11 116124407 116124501 CCDS8374.1_cds_0_0_chr11_116124408_r 0 - CCDS8374.1_cds_0_0_chr11_116124408_rchr11- -chr11 116206508 116206563 CCDS8377.1_cds_0_0_chr11_116206509_f 0 + CCDS8377.1_cds_0_0_chr11_116206509_fchr11+ -chr11 116211733 116212337 CCDS8378.1_cds_0_0_chr11_116211734_r 0 - CCDS8378.1_cds_0_0_chr11_116211734_rchr11- -chr11 1812377 1812407 CCDS7726.1_cds_0_0_chr11_1812378_f 0 + CCDS7726.1_cds_0_0_chr11_1812378_fchr11+ -chr12 38440094 38440321 CCDS8736.1_cds_0_0_chr12_38440095_r 0 - CCDS8736.1_cds_0_0_chr12_38440095_rchr12- -chr13 112381694 112381953 CCDS9526.1_cds_0_0_chr13_112381695_f 0 + CCDS9526.1_cds_0_0_chr13_112381695_fchr13+ -chr14 98710240 98712285 CCDS9949.1_cds_0_0_chr14_98710241_r 0 - CCDS9949.1_cds_0_0_chr14_98710241_rchr14- -chr15 41486872 41487060 CCDS10096.1_cds_0_0_chr15_41486873_r 0 - CCDS10096.1_cds_0_0_chr15_41486873_rchr15- -chr15 41673708 41673857 CCDS10097.1_cds_0_0_chr15_41673709_f 0 + CCDS10097.1_cds_0_0_chr15_41673709_fchr15+ -chr15 41679161 41679250 CCDS10098.1_cds_0_0_chr15_41679162_r 0 - CCDS10098.1_cds_0_0_chr15_41679162_rchr15- -chr15 41826029 41826196 CCDS10101.1_cds_0_0_chr15_41826030_f 0 + CCDS10101.1_cds_0_0_chr15_41826030_fchr15+ -chr16 142908 143003 CCDS10397.1_cds_0_0_chr16_142909_f 0 + CCDS10397.1_cds_0_0_chr16_142909_fchr16+ -chr16 179963 180135 CCDS10401.1_cds_0_0_chr16_179964_r 0 - CCDS10401.1_cds_0_0_chr16_179964_rchr16- -chr16 244413 244681 CCDS10402.1_cds_0_0_chr16_244414_f 0 + CCDS10402.1_cds_0_0_chr16_244414_fchr16+ -chr16 259268 259383 CCDS10403.1_cds_0_0_chr16_259269_r 0 - CCDS10403.1_cds_0_0_chr16_259269_rchr16- -chr18 23786114 23786321 CCDS11891.1_cds_0_0_chr18_23786115_r 0 - CCDS11891.1_cds_0_0_chr18_23786115_rchr18- -chr18 59406881 59407046 CCDS11985.1_cds_0_0_chr18_59406882_f 0 + CCDS11985.1_cds_0_0_chr18_59406882_fchr18+ -chr18 59455932 59456337 CCDS11986.1_cds_0_0_chr18_59455933_r 0 - CCDS11986.1_cds_0_0_chr18_59455933_rchr18- -chr18 59600586 59600754 CCDS11988.1_cds_0_0_chr18_59600587_f 0 + CCDS11988.1_cds_0_0_chr18_59600587_fchr18+ -chr19 59068595 59069564 CCDS12866.1_cds_0_0_chr19_59068596_f 0 + CCDS12866.1_cds_0_0_chr19_59068596_fchr19+ -chr19 59236026 59236146 CCDS12872.1_cds_0_0_chr19_59236027_r 0 - CCDS12872.1_cds_0_0_chr19_59236027_rchr19- -chr19 59297998 59298008 CCDS12877.1_cds_0_0_chr19_59297999_f 0 + CCDS12877.1_cds_0_0_chr19_59297999_fchr19+ -chr19 59302168 59302288 CCDS12878.1_cds_0_0_chr19_59302169_r 0 - CCDS12878.1_cds_0_0_chr19_59302169_rchr19- -chr2 118288583 118288668 CCDS2120.1_cds_0_0_chr2_118288584_f 0 + CCDS2120.1_cds_0_0_chr2_118288584_fchr2+ -chr2 118394148 118394202 CCDS2121.1_cds_0_0_chr2_118394149_r 0 - CCDS2121.1_cds_0_0_chr2_118394149_rchr2- -chr2 220190202 220190242 CCDS2441.1_cds_0_0_chr2_220190203_f 0 + CCDS2441.1_cds_0_0_chr2_220190203_fchr2+ -chr2 220229609 220230869 CCDS2443.1_cds_0_0_chr2_220229610_r 0 - CCDS2443.1_cds_0_0_chr2_220229610_rchr2- -chr20 33330413 33330423 CCDS13249.1_cds_0_0_chr20_33330414_r 0 - CCDS13249.1_cds_0_0_chr20_33330414_rchr20- -chr20 33513606 33513792 CCDS13255.1_cds_0_0_chr20_33513607_f 0 + CCDS13255.1_cds_0_0_chr20_33513607_fchr20+ -chr20 33579500 33579527 CCDS13256.1_cds_0_0_chr20_33579501_r 0 - CCDS13256.1_cds_0_0_chr20_33579501_rchr20- -chr20 33593260 33593348 CCDS13257.1_cds_0_0_chr20_33593261_f 0 + CCDS13257.1_cds_0_0_chr20_33593261_fchr20+ -chr21 32707032 32707192 CCDS13614.1_cds_0_0_chr21_32707033_f 0 + CCDS13614.1_cds_0_0_chr21_32707033_fchr21+ -chr21 32869641 32870022 CCDS13615.1_cds_0_0_chr21_32869642_r 0 - CCDS13615.1_cds_0_0_chr21_32869642_rchr21- -chr21 33321040 33322012 CCDS13620.1_cds_0_0_chr21_33321041_f 0 + CCDS13620.1_cds_0_0_chr21_33321041_fchr21+ -chr21 33744994 33745040 CCDS13625.1_cds_0_0_chr21_33744995_r 0 - CCDS13625.1_cds_0_0_chr21_33744995_rchr21- -chr22 30120223 30120265 CCDS13897.1_cds_0_0_chr22_30120224_f 0 + CCDS13897.1_cds_0_0_chr22_30120224_fchr22+ -chr22 30160419 30160661 CCDS13898.1_cds_0_0_chr22_30160420_r 0 - CCDS13898.1_cds_0_0_chr22_30160420_rchr22- -chr22 30665273 30665360 CCDS13901.1_cds_0_0_chr22_30665274_f 0 + CCDS13901.1_cds_0_0_chr22_30665274_fchr22+ -chr22 30939054 30939266 CCDS13903.1_cds_0_0_chr22_30939055_r 0 - CCDS13903.1_cds_0_0_chr22_30939055_rchr22- -chr5 131424298 131424460 CCDS4149.1_cds_0_0_chr5_131424299_f 0 + CCDS4149.1_cds_0_0_chr5_131424299_fchr5+ -chr5 131556601 131556672 CCDS4151.1_cds_0_0_chr5_131556602_r 0 - CCDS4151.1_cds_0_0_chr5_131556602_rchr5- -chr5 131621326 131621419 CCDS4152.1_cds_0_0_chr5_131621327_f 0 + CCDS4152.1_cds_0_0_chr5_131621327_fchr5+ -chr5 131847541 131847666 CCDS4155.1_cds_0_0_chr5_131847542_r 0 - CCDS4155.1_cds_0_0_chr5_131847542_rchr5- -chr6 108299600 108299744 CCDS5061.1_cds_0_0_chr6_108299601_r 0 - CCDS5061.1_cds_0_0_chr6_108299601_rchr6- -chr6 108594662 108594687 CCDS5063.1_cds_0_0_chr6_108594663_f 0 + CCDS5063.1_cds_0_0_chr6_108594663_fchr6+ -chr6 108640045 108640151 CCDS5064.1_cds_0_0_chr6_108640046_r 0 - CCDS5064.1_cds_0_0_chr6_108640046_rchr6- -chr6 108722976 108723115 CCDS5067.1_cds_0_0_chr6_108722977_f 0 + CCDS5067.1_cds_0_0_chr6_108722977_fchr6+ -chr7 113660517 113660685 CCDS5760.1_cds_0_0_chr7_113660518_f 0 + CCDS5760.1_cds_0_0_chr7_113660518_fchr7+ -chr7 116512159 116512389 CCDS5771.1_cds_0_0_chr7_116512160_r 0 - CCDS5771.1_cds_0_0_chr7_116512160_rchr7- -chr7 116714099 116714152 CCDS5773.1_cds_0_0_chr7_116714100_f 0 + CCDS5773.1_cds_0_0_chr7_116714100_fchr7+ -chr7 116945541 116945787 CCDS5774.1_cds_0_0_chr7_116945542_r 0 - CCDS5774.1_cds_0_0_chr7_116945542_rchr7- -chr8 118881131 118881317 CCDS6324.1_cds_0_0_chr8_118881132_r 0 - CCDS6324.1_cds_0_0_chr8_118881132_rchr8- -chr9 128764156 128764189 CCDS6914.1_cds_0_0_chr9_128764157_f 0 + CCDS6914.1_cds_0_0_chr9_128764157_fchr9+ -chr9 128787519 128789136 CCDS6915.1_cds_0_0_chr9_128787520_r 0 - CCDS6915.1_cds_0_0_chr9_128787520_rchr9- -chr9 128882427 128882523 CCDS6917.1_cds_0_0_chr9_128882428_f 0 + CCDS6917.1_cds_0_0_chr9_128882428_fchr9+ -chr9 128937229 128937445 CCDS6919.1_cds_0_0_chr9_128937230_r 0 - CCDS6919.1_cds_0_0_chr9_128937230_rchr9- -chrX 122745047 122745924 CCDS14606.1_cds_0_0_chrX_122745048_f 0 + CCDS14606.1_cds_0_0_chrX_122745048_fchrX+ -chrX 152648964 152649196 CCDS14733.1_cds_0_0_chrX_152648965_r 0 - CCDS14733.1_cds_0_0_chrX_152648965_rchrX- -chrX 152691446 152691471 CCDS14735.1_cds_0_0_chrX_152691447_f 0 + CCDS14735.1_cds_0_0_chrX_152691447_fchrX+ -chrX 152694029 152694263 CCDS14736.1_cds_0_0_chrX_152694030_r 0 - CCDS14736.1_cds_0_0_chrX_152694030_rchrX- diff -r 63fc9cbe381d2719134f87c019911565e3a934a1 -r c68762fcb5a521007d89cb01455a0ad409011528 test-data/trimmer_a_f_c0_s1_e13_i62.dat --- a/test-data/trimmer_a_f_c0_s1_e13_i62.dat +++ /dev/null @@ -1,5 +0,0 @@ -12345 abcdef -67890 ghjkl g ->assa lljlj ljlj -sasas hghg hg -@dgf gfgf gfg diff -r 63fc9cbe381d2719134f87c019911565e3a934a1 -r c68762fcb5a521007d89cb01455a0ad409011528 test-data/trimmer_a_f_c2_s1_e2_i62.dat --- a/test-data/trimmer_a_f_c2_s1_e2_i62.dat +++ /dev/null @@ -1,5 +0,0 @@ -12345 ab xyz -67890 gh ghjt ->assa lljlj ljlj -sasas hg hghg -@dgf gf gfgf diff -r 63fc9cbe381d2719134f87c019911565e3a934a1 -r c68762fcb5a521007d89cb01455a0ad409011528 test-data/trimmer_tab_delimited.dat --- a/test-data/trimmer_tab_delimited.dat +++ /dev/null @@ -1,5 +0,0 @@ -12345 abcdef xyz -67890 ghjkl ghjt ->assa lljlj ljlj -sasas hghg hghg -@dgf gfgf gfgf diff -r 63fc9cbe381d2719134f87c019911565e3a934a1 -r c68762fcb5a521007d89cb01455a0ad409011528 tool_conf.xml.sample --- a/tool_conf.xml.sample +++ b/tool_conf.xml.sample @@ -44,21 +44,12 @@ <tool file="extract/liftOver_wrapper.xml" /></section><section name="Text Manipulation" id="textutil"> - <tool file="filters/fixedValueColumn.xml" /><tool file="stats/column_maker.xml" /><tool file="filters/catWrapper.xml" /><tool file="filters/cutWrapper.xml" /> - <tool file="filters/mergeCols.xml" /> - <tool file="filters/convert_characters.xml" /><tool file="filters/CreateInterval.xml" /> - <tool file="filters/cutWrapper.xml" /> - <tool file="filters/changeCase.xml" /><tool file="filters/pasteWrapper.xml" /> - <tool file="filters/remove_beginning.xml" /><tool file="filters/randomlines.xml" /> - <tool file="filters/headWrapper.xml" /> - <tool file="filters/tailWrapper.xml" /> - <tool file="filters/trimmer.xml" /><tool file="filters/wc_gnu.xml" /><tool file="filters/secure_hash_message_digest.xml" /><tool file="stats/dna_filtering.xml" /> diff -r 63fc9cbe381d2719134f87c019911565e3a934a1 -r c68762fcb5a521007d89cb01455a0ad409011528 tools/filters/changeCase.pl --- a/tools/filters/changeCase.pl +++ /dev/null @@ -1,58 +0,0 @@ -#! /usr/bin/perl -w - -use strict; -use warnings; - -my $columns = {}; -my $del = ""; -my @in = (); -my @out = (); -my $command = ""; -my $field = 0; - -# a wrapper for changing the case of columns from within galaxy -# isaChangeCase.pl [filename] [columns] [delim] [casing] [output] - -die "Check arguments: $0 [filename] [columns] [delim] [casing] [output]\n" unless @ARGV == 5; - -# process column input -$ARGV[1] =~ s/\s+//g; -foreach ( split /,/, $ARGV[1] ) { - if (m/^c\d{1,}$/i) { - s/c//ig; - $columns->{$_} = --$_; - } -} - -die "No columns specified, columns are not preceeded with 'c', or commas are not used to separate column numbers: $ARGV[1]\n" if keys %$columns == 0; - -my $column_delimiters_href = { - 'TAB' => q{\t}, - 'COMMA' => ",", - 'DASH' => "-", - 'UNDERSCORE' => "_", - 'PIPE' => q{\|}, - 'DOT' => q{\.}, - 'SPACE' => q{\s+} -}; - -$del = $column_delimiters_href->{$ARGV[2]}; - -open (OUT, ">$ARGV[4]") or die "Cannot create $ARGV[4]:$!\n"; -open (IN, "<$ARGV[0]") or die "Cannot open $ARGV[0]:$!\n"; -while (<IN>) { - chop; - @in = split /$del/; - for ( my $i = 0; $i <= $#in; ++$i) { - if (exists $columns->{$i}) { - push(@out, $ARGV[3] eq 'up' ? uc($in[$i]) : lc($in[$i])); - } else { - push(@out, $in[$i]); - } - } - print OUT join("\t",@out), "\n"; - @out = (); -} -close IN; - -close OUT; diff -r 63fc9cbe381d2719134f87c019911565e3a934a1 -r c68762fcb5a521007d89cb01455a0ad409011528 tools/filters/changeCase.xml --- a/tools/filters/changeCase.xml +++ /dev/null @@ -1,77 +0,0 @@ -<tool id="ChangeCase" name="Change Case"> - <description> of selected columns</description> - <stdio> - <exit_code range="1:" err_level="fatal" /> - </stdio> - <command interpreter="perl">changeCase.pl $input "$cols" $delimiter $casing $out_file1</command> - <inputs> - <param name="input" format="txt" type="data" label="From"/> - <param name="cols" size="10" type="text" value="c1,c2" label="Change case of columns"/> - <param name="delimiter" type="select" label="Delimited by"> - <option value="TAB">Tab</option> - <option value="SPACE">Whitespace</option> - <option value="DOT">Dot</option> - <option value="COMMA">Comma</option> - <option value="DASH">Dash</option> - <option value="UNDERSCORE">Underscore</option> - <option value="PIPE">Pipe</option> - </param> - <param name="casing" type="select" label="To"> - <option value="up">Upper case</option> - <option value="lo">Lower case</option> - </param> - </inputs> - <outputs> - <data format="tabular" name="out_file1" /> - </outputs> - <tests> - <test> - <param name="input" value="1.txt" ftype="txt"/> - <param name="cols" value="c1"/> - <param name="delimiter" value="SPACE"/> - <param name="casing" value="up"/> - <output name="out_file1" file="changeCase_out1.tabular"/> - </test> - <test> - <param name="input" value="1.bed" ftype="bed"/> - <param name="cols" value="c1"/> - <param name="delimiter" value="TAB"/> - <param name="casing" value="up"/> - <output name="out_file1" file="changeCase_out2.tabular"/> - </test> - </tests> - <help> - -.. class:: warningmark - -**This tool breaks column assignments.** To re-establish column assignments run the tool and click on the pencil icon in the resulting history item. - -.. class:: warningmark - -The format of the resulting dataset from this tool is always tabular. - ------ - -**What it does** - -This tool selects specified columns from a dataset and converts the values of those columns to upper or lower case. - -- Columns are specified as **c1**, **c2**, and so on. -- Columns can be specified in any order (e.g., **c2,c1,c6**) - ------ - -**Example** - -Changing columns 1 and 3 ( delimited by Comma ) to upper case in:: - - apple,is,good - windows,is,bad - -will result in:: - - APPLE is GOOD - WINDOWS is BAD - - </help> -</tool> diff -r 63fc9cbe381d2719134f87c019911565e3a934a1 -r c68762fcb5a521007d89cb01455a0ad409011528 tools/filters/condense_characters.pl --- a/tools/filters/condense_characters.pl +++ /dev/null @@ -1,105 +0,0 @@ -#! /usr/bin/perl -w - -use strict; -use warnings; - -# condenses all consecutive characters of one type -# convert_characters.pl [input] [character] [output] - -die "Check arguments" unless @ARGV == 3; - -my $inputfile = $ARGV[0]; -my $character = $ARGV[1]; -my $outputfile = $ARGV[2]; - - -my $convert_from; -my $convert_to; - - -if ($character eq "s") -{ - $convert_from = '\s'; -} -elsif ($character eq "T") -{ - $convert_from = '\t'; -} -elsif ($character eq "Sp") -{ - $convert_from = " "; -} -elsif ($character eq "Dt") -{ - $convert_from = '\.'; -} -elsif ($character eq "C") -{ - $convert_from = ","; -} -elsif ($character eq "D") -{ - $convert_from = "-"; -} -elsif ($character eq "U") -{ - $convert_from = "_"; -} -elsif ($character eq "P") -{ - $convert_from = '\|'; -} -else -{ - die "Invalid value specified for convert from\n"; -} - - -if ($character eq "T") -{ - $convert_to = "\t"; -} -elsif ($character eq "Sp") -{ - $convert_to = " "; -} -elsif ($character eq "Dt") -{ - $convert_to = "\."; -} -elsif ($character eq "C") -{ - $convert_to = ","; -} -elsif ($character eq "D") -{ - $convert_to = "-"; -} -elsif ($character eq "U") -{ - $convert_to = "_"; -} -elsif ($character eq "P") -{ - $convert_to = "|"; -} -else -{ - die "Invalid value specified for Convert to\n"; -} - -my $fhIn; -open ($fhIn, "< $inputfile") or die "Cannot open source file"; - -my $fhOut; -open ($fhOut, "> $outputfile"); - -while (<$fhIn>) -{ - my $thisLine = $_; - chomp $thisLine; - $thisLine =~ s/${convert_from}+/$convert_to/g; - print $fhOut $thisLine,"\n"; -} -close ($fhIn) or die "Cannot close source file"; -close ($fhOut) or die "Cannot close output file"; diff -r 63fc9cbe381d2719134f87c019911565e3a934a1 -r c68762fcb5a521007d89cb01455a0ad409011528 tools/filters/condense_characters.xml --- a/tools/filters/condense_characters.xml +++ /dev/null @@ -1,48 +0,0 @@ -<tool id="Condense characters1" name="Condense"> - <description>consecutive characters</description> - <command interpreter="perl">condense_characters.pl $input $character $out_file1</command> - <inputs> - - <param name="character" type="select" label="Condense all consecutive"> - <option value="T">Tabs</option> - <option value="Sp">Spaces</option> - <option value="Dt">Dots</option> - <option value="C">Commas</option> - <option value="D">Dashes</option> - <option value="U">Underscores</option> - <option value="P">Pipes</option> - </param> - <param format="txt" name="input" type="data" label="in this Query"/> - </inputs> - <outputs> - <data format="input" name="out_file1" metadata_source="input" /> - </outputs> - <tests> - <test> - <param name="character" value="T"/> - <param name="input" value="1.bed"/> - <output name="out_file1" file="eq-condense.dat"/> - </test> - </tests> - <help> - -**What it does** - -This tool condenses all consecutive characters of a specified type. - ------ - -**Example** - -- Input file:: - - geneX,,,10,,,,,20 - geneY,,5,,,,,12,15,9, - -- Condense all consecutive commas. The above file will be converted into:: - - geneX,10,20 - geneY,5,12,15,9 - -</help> -</tool> diff -r 63fc9cbe381d2719134f87c019911565e3a934a1 -r c68762fcb5a521007d89cb01455a0ad409011528 tools/filters/convert_characters.py --- a/tools/filters/convert_characters.py +++ /dev/null @@ -1,42 +0,0 @@ -#!/usr/bin/env python -#By, Guruprasad Ananda. - -from galaxy import eggs -import sys, re - -def stop_err(msg): - sys.stderr.write(msg) - sys.exit() - -def main(): - if len(sys.argv) != 4: - stop_err("usage: convert_characters infile from_char outfile") - - try: - fin = open(sys.argv[1],'r') - except: - stop_err("Input file cannot be opened for reading.") - - from_char = sys.argv[2] - - try: - fout = open(sys.argv[3],'w') - except: - stop_err("Output file cannot be opened for writing.") - - char_dict = {'T':'\t','s':'\s','Dt':'\.','C':',','D':'-','U':'_','P':'\|','Co':':'} - from_ch = char_dict[from_char] + '+' #making an RE to match 1 or more occurences. - skipped = 0 - - for line in fin: - line = line.strip() - try: - fout.write("%s\n" %(re.sub(from_ch,'\t',line))) - except: - skipped += 1 - - if skipped: - print "Skipped %d lines as invalid." %skipped - -if __name__ == "__main__": - main() \ No newline at end of file diff -r 63fc9cbe381d2719134f87c019911565e3a934a1 -r c68762fcb5a521007d89cb01455a0ad409011528 tools/filters/convert_characters.xml --- a/tools/filters/convert_characters.xml +++ /dev/null @@ -1,58 +0,0 @@ -<tool id="Convert characters1" name="Convert"> - <description>delimiters to TAB</description> - <command interpreter="python">convert_characters.py $input $convert_from $out_file1</command> - <inputs> - <param name="convert_from" type="select" label="Convert all"> - <option value="s">Whitespaces</option> - <option value="T">Tabs</option> -  - <option value="Dt">Dots</option> - <option value="C">Commas</option> - <option value="D">Dashes</option> - <option value="U">Underscores</option> - <option value="P">Pipes</option> - <option value="Co">Colons</option> - </param> - <param format="txt" name="input" type="data" label="in Query"/> - </inputs> - <outputs> - <data format="tabular" name="out_file1" /> - </outputs> - <tests> - <test> - <param name="convert_from" value="s"/> - <param name="input" value="1.bed"/> - <output name="out_file1" file="eq-convert.dat"/> - </test> - <test> - <param name="convert_from" value="s"/> - <param name="input" value="a.txt"/> - <output name="out_file1" file="a.tab"/> - </test> - </tests> - <help> - -**What it does** - -Converts all delimiters of a specified type into TABs. Consecutive characters are condensed. For example, if columns are separated by 5 spaces they will converted into 1 tab. - ------ - -**Example** - -- Input file:: - - chrX||151283558|151283724|NM_000808_exon_8_0_chrX_151283559_r|0|- - chrX|151370273|151370486|NM_000808_exon_9_0_chrX_151370274_r|0|- - chrX|151559494|151559583|NM_018558_exon_1_0_chrX_151559495_f|0|+ - chrX|151564643|151564711|NM_018558_exon_2_0_chrX_151564644_f||||0|+ - -- Converting all pipe delimiters of the above file to TABs will get:: - - chrX 151283558 151283724 NM_000808_exon_8_0_chrX_151283559_r 0 - - chrX 151370273 151370486 NM_000808_exon_9_0_chrX_151370274_r 0 - - chrX 151559494 151559583 NM_018558_exon_1_0_chrX_151559495_f 0 + - chrX 151564643 151564711 NM_018558_exon_2_0_chrX_151564644_f 0 + - -</help> -</tool> diff -r 63fc9cbe381d2719134f87c019911565e3a934a1 -r c68762fcb5a521007d89cb01455a0ad409011528 tools/filters/cutWrapper.pl --- a/tools/filters/cutWrapper.pl +++ /dev/null @@ -1,77 +0,0 @@ -#!/usr/bin/perl -w - -use strict; -use warnings; - -my @columns = (); -my $del = ""; -my @in = (); -my @out = (); -my $command = ""; -my $field = 0; - -# a wrapper for cut for use in galaxy -# cutWrapper.pl [filename] [columns] [delim] [output] - -die "Check arguments\n" unless @ARGV == 4; - -$ARGV[1] =~ s/\s+//g; -foreach ( split /,/, $ARGV[1] ) { - if (m/^c\d{1,}$/i) { - push (@columns, $_); - $columns[@columns-1] =~s/c//ig; - } -} - -die "No columns specified, columns are not preceded with 'c', or commas are not used to separate column numbers: $ARGV[1]\n" if @columns == 0; - -my $column_delimiters_href = { - 'T' => q{\t}, - 'C' => ",", - 'D' => "-", - 'U' => "_", - 'P' => q{\|}, - 'Dt' => q{\.}, - 'Sp' => q{\s+} -}; - -$del = $column_delimiters_href->{$ARGV[2]}; - -open (OUT, ">$ARGV[3]") or die "Cannot create $ARGV[2]:$!\n"; -open (IN, "<$ARGV[0]") or die "Cannot open $ARGV[0]:$!\n"; - -while (my $line=<IN>) { - if ($line =~ /^#/) { - #Ignore comment lines - } else { - chop($line); - @in = split(/$del/, $line); - foreach $field (@columns) { - if (defined($in[$field-1])) { - push(@out, $in[$field-1]); - } else { - push(@out, "."); - } - } - print OUT join("\t",@out), "\n"; - @out = (); - } -} - -#while (<IN>) { -# chop; -# @in = split /$del/; -# foreach $field (@columns) { -# if (defined($in[$field-1])) { -# push(@out, $in[$field-1]); -# } else { -# push(@out, "."); -# } -# } -# print OUT join("\t",@out), "\n"; -# @out = (); -#} -close IN; - -close OUT; - diff -r 63fc9cbe381d2719134f87c019911565e3a934a1 -r c68762fcb5a521007d89cb01455a0ad409011528 tools/filters/cutWrapper.xml --- a/tools/filters/cutWrapper.xml +++ /dev/null @@ -1,202 +0,0 @@ -<tool id="Cut1" name="Cut" version="1.0.1"> - <description>columns from a table</description> - <command interpreter="perl">cutWrapper.pl $input "$columnList" $delimiter $out_file1</command> - <inputs> - <param name="columnList" size="10" type="text" value="c1,c2" label="Cut columns"/> - <param name="delimiter" type="select" label="Delimited by"> - <option value="T">Tab</option> - <option value="Sp">Whitespace</option> - <option value="Dt">Dot</option> - <option value="C">Comma</option> - <option value="D">Dash</option> - <option value="U">Underscore</option> - <option value="P">Pipe</option> - </param> - <param format="txt" name="input" type="data" label="From"/> - </inputs> - <outputs> - <data format="tabular" name="out_file1" > - <actions> - <conditional name="delimiter"> - <when value="T"> - <conditional name="input"> - <when datatype_isinstance="interval"> - <action type="format" default="tabular"> - <option type="from_param" name="columnList" column="0" offset="0"> - - <filter type="insert_column" column="0" value="interval"/> - - <filter type="insert_column" ref="columnList" /> - - <filter type="insert_column" ref="columnList" /> - - <filter type="multiple_splitter" column="1" separator=","/> - <filter type="column_strip" column="1"/> - <filter type="string_function" column="1" name="lower" /> - <filter type="param_value" column="1" value="^c\d{1,}$" compare="re_search" keep="True"/> - <filter type="column_strip" column="1" strip="c"/> - <filter type="boolean" column="1" cast="int" /> - - <filter type="multiple_splitter" column="2" separator=","/> - <filter type="column_strip" column="2"/> - <filter type="string_function" column="2" name="lower" /> - <filter type="param_value" column="2" value="^c\d{1,}$" compare="re_search" keep="True"/> - <filter type="column_strip" column="2" strip="c"/> - <filter type="boolean" column="2" cast="int" /> - - <filter type="multiple_splitter" column="3" separator=","/> - <filter type="column_strip" column="3"/> - <filter type="string_function" column="3" name="lower" /> - <filter type="param_value" column="3" value="^c\d{1,}$" compare="re_search" keep="True"/> - <filter type="column_strip" column="3" strip="c"/> - <filter type="boolean" column="3" cast="int" /> - - <filter type="metadata_value" ref="input" name="chromCol" column="1" /> - <filter type="metadata_value" ref="input" name="startCol" column="2" /> - <filter type="metadata_value" ref="input" name="endCol" column="3" /> - - </option> - </action> - - <conditional name="out_file1"> - <when datatype_isinstance="interval"> - <action type="metadata" name="chromCol"> - <option type="from_param" name="columnList" column="0" offset="0"> - <filter type="multiple_splitter" column="0" separator=","/> - <filter type="column_strip" column="0"/> - <filter type="string_function" column="0" name="lower" /> - <filter type="param_value" column="0" value="^c\d{1,}$" compare="re_search" keep="True"/> - <filter type="column_strip" column="0" strip="c"/> - <filter type="insert_column" value="1" iterate="True" column="0"/> - <filter type="boolean" column="1" cast="int" /> - <filter type="metadata_value" ref="input" name="chromCol" column="1" /> - </option> - </action> - - <action type="metadata" name="startCol"> - <option type="from_param" name="columnList" column="0" offset="0"> - <filter type="multiple_splitter" column="0" separator=","/> - <filter type="column_strip" column="0"/> - <filter type="string_function" column="0" name="lower" /> - <filter type="param_value" column="0" value="^c\d{1,}$" compare="re_search" keep="True"/> - <filter type="column_strip" column="0" strip="c"/> - <filter type="insert_column" value="1" iterate="True" column="0"/> - <filter type="boolean" column="1" cast="int" /> - <filter type="metadata_value" ref="input" name="startCol" column="1" /> - </option> - </action> - - <action type="metadata" name="endCol"> - <option type="from_param" name="columnList" column="0" offset="0"> - <filter type="multiple_splitter" column="0" separator=","/> - <filter type="column_strip" column="0"/> - <filter type="string_function" column="0" name="lower" /> - <filter type="param_value" column="0" value="^c\d{1,}$" compare="re_search" keep="True"/> - <filter type="column_strip" column="0" strip="c"/> - <filter type="insert_column" value="1" iterate="True" column="0"/> - <filter type="boolean" column="1" cast="int" /> - <filter type="metadata_value" ref="input" name="endCol" column="1" /> - </option> - </action> - - <action type="metadata" name="nameCol" default="0"> - <option type="from_param" name="columnList" column="0" offset="0"> - <filter type="multiple_splitter" column="0" separator=","/> - <filter type="column_strip" column="0"/> - <filter type="string_function" column="0" name="lower" /> - <filter type="param_value" column="0" value="^c\d{1,}$" compare="re_search" keep="True"/> - <filter type="column_strip" column="0" strip="c"/> - <filter type="insert_column" value="1" iterate="True" column="0"/> - <filter type="boolean" column="1" cast="int" /> - <filter type="metadata_value" ref="input" name="nameCol" column="1" /> - </option> - </action> - - <action type="metadata" name="strandCol" default="0"> - <option type="from_param" name="columnList" column="0" offset="0"> - <filter type="multiple_splitter" column="0" separator=","/> - <filter type="column_strip" column="0"/> - <filter type="string_function" column="0" name="lower" /> - <filter type="param_value" column="0" value="^c\d{1,}$" compare="re_search" keep="True"/> - <filter type="column_strip" column="0" strip="c"/> - <filter type="insert_column" value="1" iterate="True" column="0"/> - <filter type="boolean" column="1" cast="int" /> - <filter type="metadata_value" ref="input" name="strandCol" column="1" /> - </option> - </action> - </when> - </conditional> - - </when> - </conditional> - </when> - </conditional> - </actions> - </data> - </outputs> - <tests> - <test> - <param name="columnList" value="c1,c4,c2,c3"/> - <param name="delimiter" value="T"/> - <param name="input" value="1.bed"/> - <output name="out_file1" file="eq-cut.dat"/> - </test> - </tests> - <help> - -.. class:: warningmark - -**WARNING: This tool breaks column assignments.** To re-establish column assignments run the tools and click on the pencil icon in the latest history item. - -.. class:: infomark - -The output of this tool is always in tabular format (e.g., if your original delimiters are commas, they will be replaced with tabs). For example: - - Cutting columns 1 and 3 from:: - - apple,is,good - windows,is,bad - - will give:: - - apple good - windows bad - ------ - -**What it does** - -This tool selects (cuts out) specified columns from the dataset. - -- Columns are specified as **c1**, **c2**, and so on. Column count begins with **1** -- Columns can be specified in any order (e.g., **c2,c1,c6**) -- If you specify more columns than actually present - empty spaces will be filled with dots - ------ - -**Example** - -Input dataset (six columns: c1, c2, c3, c4, c5, and c6):: - - chr1 10 1000 gene1 0 + - chr2 100 1500 gene2 0 + - -**cut** on columns "**c1,c4,c6**" will return:: - - chr1 gene1 + - chr2 gene2 + - -**cut** on columns "**c6,c5,c4,c1**" will return:: - - + 0 gene1 chr1 - + 0 gene2 chr2 - - -**cut** on columns "**c8,c7,c4**" will return:: - - . . gene1 - . . gene2 - - -</help> -</tool> diff -r 63fc9cbe381d2719134f87c019911565e3a934a1 -r c68762fcb5a521007d89cb01455a0ad409011528 tools/filters/fixedValueColumn.pl --- a/tools/filters/fixedValueColumn.pl +++ /dev/null @@ -1,34 +0,0 @@ -#! /usr/bin/perl -w - -use strict; -use warnings; - -# fixedValueColumn.pl $input $out_file1 "expression" "iterate [yes|no]" - -my ($input, $out_file1, $expression, $iterate) = @ARGV; -my $i = 0; -my $numeric = 0; - -die "Check arguments\n" unless @ARGV == 4; - -open (DATA, "<$input") or die "Cannot open $input:$!\n"; -open (OUT, ">$out_file1") or die "Cannot create $out_file1:$!\n"; - -if ($expression =~ m/^\d+$/) { - $numeric = 1; - $i = $expression; -} - -while (<DATA>) { - chop; - if ($iterate eq "no") { - print OUT "$_\t$expression\n"; - } else { - print OUT "$_\t$i\n" if $numeric == 1; - print OUT "$_\t$expression-$i\n" if $numeric == 0; - ++$i; - } -} - -close DATA; -close OUT; diff -r 63fc9cbe381d2719134f87c019911565e3a934a1 -r c68762fcb5a521007d89cb01455a0ad409011528 tools/filters/fixedValueColumn.xml --- a/tools/filters/fixedValueColumn.xml +++ /dev/null @@ -1,61 +0,0 @@ -<tool id="addValue" name="Add column"> - <description>to an existing dataset</description> - <command interpreter="perl">fixedValueColumn.pl $input $out_file1 "$exp" $iterate</command> - <inputs> - <param name="exp" size="20" type="text" value="1" label="Add this value"/> - <param format="tabular" name="input" type="data" label="to Dataset" help="Dataset missing? See TIP below" /> - <param name="iterate" type="select" label="Iterate?"> - <option value="no">NO</option> - <option value="yes">YES</option> - </param> - </inputs> - <outputs> - <data format="input" name="out_file1" metadata_source="input"/> - </outputs> - <tests> - <test> - <param name="exp" value="1"/> - <param name="input" value="1.bed"/> - <param name="iterate" value="no"/> - <output name="out_file1" file="eq-addvalue.dat"/> - </test> - </tests> - <help> - -.. class:: infomark - -**TIP:** If your data is not TAB delimited, use *Text Manipulation->Convert* - ------ - -**What it does** - -You can enter any value and it will be added as a new column to your dataset - ------ - -**Example** - -If you original data looks like this:: - - chr1 10 100 geneA - chr2 200 300 geneB - chr2 400 500 geneC - -Typing **+** in the text box will generate:: - - chr1 10 100 geneA + - chr2 200 300 geneB + - chr2 400 500 geneC + - - -You can also add line numbers by selecting **Iterate: YES**. In this case if you enter **1** in the text box you will get:: - - chr1 10 100 geneA 1 - chr2 200 300 geneB 2 - chr2 400 500 geneC 3 - - - -</help> -</tool> diff -r 63fc9cbe381d2719134f87c019911565e3a934a1 -r c68762fcb5a521007d89cb01455a0ad409011528 tools/filters/headWrapper.pl --- a/tools/filters/headWrapper.pl +++ /dev/null @@ -1,19 +0,0 @@ -#! /usr/bin/perl -w - -use strict; -use warnings; - -# a wrapper for head for use in galaxy -# headWrapper.pl [filename] [# lines to show] [output] - -die "Check arguments" unless @ARGV == 3; -die "Line number must be an integer\n" unless $ARGV[1]=~ m/^\d+$/; - -open (OUT, ">$ARGV[2]") or die "Cannot create $ARGV[2]:$!\n"; -open (HEAD, "head -n $ARGV[1] $ARGV[0]|") or die "Cannot run head:$!\n"; -while (<HEAD>) { - print OUT; -} -close OUT; -close HEAD; - diff -r 63fc9cbe381d2719134f87c019911565e3a934a1 -r c68762fcb5a521007d89cb01455a0ad409011528 tools/filters/headWrapper.xml --- a/tools/filters/headWrapper.xml +++ /dev/null @@ -1,42 +0,0 @@ -<tool id="Show beginning1" name="Select first"> - <description>lines from a dataset</description> - <command interpreter="perl">headWrapper.pl $input $lineNum $out_file1</command> - <inputs> - <param name="lineNum" size="5" type="integer" value="10" label="Select first" help="lines"/> - <param format="txt" name="input" type="data" label="from"/> - </inputs> - <outputs> - <data format="input" name="out_file1" metadata_source="input"/> - </outputs> - <tests> - <test> - <param name="lineNum" value="10"/> - <param name="input" value="1.bed"/> - <output name="out_file1" file="eq-showbeginning.dat"/> - </test> - </tests> - <help> - -**What it does** - -This tool outputs specified number of lines from the **beginning** of a dataset - ------ - -**Example** - -Selecting 2 lines from this:: - - chr7 56632 56652 D17003_CTCF_R6 310 + - chr7 56736 56756 D17003_CTCF_R7 354 + - chr7 56761 56781 D17003_CTCF_R4 220 + - chr7 56772 56792 D17003_CTCF_R7 372 + - chr7 56775 56795 D17003_CTCF_R4 207 + - -will produce:: - - chr7 56632 56652 D17003_CTCF_R6 310 + - chr7 56736 56756 D17003_CTCF_R7 354 + - - </help> -</tool> diff -r 63fc9cbe381d2719134f87c019911565e3a934a1 -r c68762fcb5a521007d89cb01455a0ad409011528 tools/filters/mergeCols.py --- a/tools/filters/mergeCols.py +++ /dev/null @@ -1,37 +0,0 @@ -import sys, re - -def stop_err( msg ): - sys.stderr.write( msg ) - sys.exit() - -def __main__(): - try: - infile = open ( sys.argv[1], 'r') - outfile = open ( sys.argv[2], 'w') - except: - stop_err( 'Cannot open or create a file\n' ) - - if len( sys.argv ) < 4: - stop_err( 'No columns to merge' ) - else: - cols = sys.argv[3:] - - skipped_lines = 0 - - for line in infile: - line = line.rstrip( '\r\n' ) - if line and not line.startswith( '#' ): - fields = line.split( '\t' ) - line += '\t' - for col in cols: - try: - line += fields[ int( col ) -1 ] - except: - skipped_lines += 1 - - print >>outfile, line - - if skipped_lines > 0: - print 'Skipped %d invalid lines' % skipped_lines - -if __name__ == "__main__" : __main__() \ No newline at end of file diff -r 63fc9cbe381d2719134f87c019911565e3a934a1 -r c68762fcb5a521007d89cb01455a0ad409011528 tools/filters/mergeCols.xml --- a/tools/filters/mergeCols.xml +++ /dev/null @@ -1,63 +0,0 @@ -<tool id="mergeCols1" name="Merge Columns" version="1.0.1"> - <description>together</description> - <command interpreter="python"> - mergeCols.py - $input1 - $out_file1 - $col1 - $col2 - #for $col in $columns - ${col.datacol} - #end for - </command> - <inputs> - <param format="tabular" name="input1" type="data" label="Select data" help="Dataset missing? See TIP below."/> - <param name="col1" label="Merge column" type="data_column" data_ref="input1" /> - <param name="col2" label="with column" type="data_column" data_ref="input1" help="Need to add more columns? Use controls below."/> - <repeat name="columns" title="Columns"> - <param name="datacol" label="Add column" type="data_column" data_ref="input1" /> - </repeat> - </inputs> - <outputs> - <data format="tabular" name="out_file1" /> - </outputs> - <tests> - <test> - <param name="input1" value="1.bed"/> - <param name="col1" value="4" /> - <param name="col2" value="1" /> - <param name="datacol" value="6" /> - <output name="out_file1" file="mergeCols.dat"/> - </test> - </tests> -<help> - -.. class:: infomark - -**TIP:** If your data is not TAB delimited, use *Text Manipulation->Convert* - ------ - -**What it does** - -This tool merges columns together. Any number of valid columns can be merged in any order. - ------ - -**Example** - -Input dataset (five columns: c1, c2, c3, c4, and c5):: - - 1 10 1000 gene1 chr - 2 100 1500 gene2 chr - -merging columns "**c5,c1**" will return:: - - 1 10 1000 gene1 chr chr1 - 2 100 1500 gene2 chr chr2 - -.. class:: warningmark - -Note that all original columns are preserved and the result of merge is added as the rightmost column. - </help> -</tool> diff -r 63fc9cbe381d2719134f87c019911565e3a934a1 -r c68762fcb5a521007d89cb01455a0ad409011528 tools/filters/remove_beginning.pl --- a/tools/filters/remove_beginning.pl +++ /dev/null @@ -1,33 +0,0 @@ -#! /usr/bin/perl -w - -use strict; -use warnings; - -# Removes the specified number of lines from the beginning of the file. -# remove_beginning.pl [input] [num_lines] [output] - -die "Check arguments" unless @ARGV == 3; - -my $inputfile = $ARGV[0]; -my $num_lines = $ARGV[1]; -my $outputfile = $ARGV[2]; - -my $curCount=0; - -my $fhIn; -open ($fhIn, "< $inputfile") or die "Cannot open source file"; - -my $fhOut; -open ($fhOut, "> $outputfile"); - -while (<$fhIn>) -{ - $curCount++; - if ($curCount<=$num_lines) - { - next; - } - print $fhOut $_; -} -close ($fhIn) or die "Cannot close source file"; -close ($fhOut) or die "Cannot close output file"; diff -r 63fc9cbe381d2719134f87c019911565e3a934a1 -r c68762fcb5a521007d89cb01455a0ad409011528 tools/filters/remove_beginning.xml --- a/tools/filters/remove_beginning.xml +++ /dev/null @@ -1,42 +0,0 @@ -<tool id="Remove beginning1" name="Remove beginning"> - <description>of a file</description> - <command interpreter="perl">remove_beginning.pl $input $num_lines $out_file1</command> - <inputs> - <param name="num_lines" size="5" type="integer" value="1" label="Remove first" help="lines"/> - <param format="txt" name="input" type="data" label="from"/> - </inputs> - <outputs> - <data format="input" name="out_file1" metadata_source="input"/> - </outputs> - <tests> - <test> - <param name="num_lines" value="5"/> - <param name="input" value="1.bed"/> - <output name="out_file1" file="eq-removebeginning.dat"/> - </test> - </tests> - <help> - -**What it does** - -This tool removes a specified number of lines from the beginning of a dataset. - ------ - -**Example** - -Input File:: - - chr7 56632 56652 D17003_CTCF_R6 310 + - chr7 56736 56756 D17003_CTCF_R7 354 + - chr7 56761 56781 D17003_CTCF_R4 220 + - chr7 56772 56792 D17003_CTCF_R7 372 + - chr7 56775 56795 D17003_CTCF_R4 207 + - -After removing the first 3 lines the dataset will look like this:: - - chr7 56772 56792 D17003_CTCF_R7 372 + - chr7 56775 56795 D17003_CTCF_R4 207 + - -</help> -</tool> diff -r 63fc9cbe381d2719134f87c019911565e3a934a1 -r c68762fcb5a521007d89cb01455a0ad409011528 tools/filters/tailWrapper.pl --- a/tools/filters/tailWrapper.pl +++ /dev/null @@ -1,19 +0,0 @@ -#! /usr/bin/perl -w - -use strict; -use warnings; - -# a wrapper for tail for use in galaxy -# lessWrapper.pl [filename] [# lines to show] [output] - -die "Check arguments" unless @ARGV == 3; -die "Line number should be an integer\n" unless $ARGV[1]=~ m/^\d+$/; - -open (OUT, ">$ARGV[2]") or die "Cannot create $ARGV[2]:$!\n"; -open (TAIL, "tail -n $ARGV[1] $ARGV[0]|") or die "Cannot run tail:$!\n"; -while (<TAIL>) { - print OUT; -} -close OUT; -close TAIL; - diff -r 63fc9cbe381d2719134f87c019911565e3a934a1 -r c68762fcb5a521007d89cb01455a0ad409011528 tools/filters/tailWrapper.xml --- a/tools/filters/tailWrapper.xml +++ /dev/null @@ -1,42 +0,0 @@ -<tool id="Show tail1" name="Select last"> - <description>lines from a dataset</description> - <command interpreter="perl">tailWrapper.pl $input $lineNum $out_file1</command> - <inputs> - <param name="lineNum" size="5" type="integer" value="10" label="Select last" help="lines"/> - <param format="txt" name="input" type="data" label="from"/> - </inputs> - <outputs> - <data format="input" name="out_file1" metadata_source="input"/> - </outputs> - <tests> - <test> - <param name="lineNum" value="10"/> - <param name="input" value="1.bed"/> - <output name="out_file1" file="eq-showtail.dat"/> - </test> - </tests> - <help> - -**What it does** - -This tool outputs specified number of lines from the **end** of a dataset - ------ - -**Example** - -- Input File:: - - chr7 57134 57154 D17003_CTCF_R7 356 - - chr7 57247 57267 D17003_CTCF_R4 207 + - chr7 57314 57334 D17003_CTCF_R5 269 + - chr7 57341 57361 D17003_CTCF_R7 375 + - chr7 57457 57477 D17003_CTCF_R3 188 + - -- Show last two lines of above file. The result is:: - - chr7 57341 57361 D17003_CTCF_R7 375 + - chr7 57457 57477 D17003_CTCF_R3 188 + - - </help> -</tool> diff -r 63fc9cbe381d2719134f87c019911565e3a934a1 -r c68762fcb5a521007d89cb01455a0ad409011528 tools/filters/trimmer.py --- a/tools/filters/trimmer.py +++ /dev/null @@ -1,106 +0,0 @@ -#!/usr/bin/env python - -import sys -import optparse - -def stop_err( msg ): - sys.stderr.write( msg ) - sys.exit() - -def main(): - usage = """%prog [options] - -options (listed below) default to 'None' if omitted - """ - parser = optparse.OptionParser(usage=usage) - - parser.add_option( - '-a','--ascii', - dest='ascii', - action='store_true', - default = False, - help='Use ascii codes to defined ignored beginnings instead of raw characters') - - parser.add_option( - '-q','--fastq', - dest='fastq', - action='store_true', - default = False, - help='The input data in fastq format. It selected the script skips every even line since they contain sequence ids') - - parser.add_option( - '-i','--ignore', - dest='ignore', - help='A comma separated list on ignored beginnings (e.g., ">,@"), or its ascii codes (e.g., "60,42") if option -a is enabled') - - parser.add_option( - '-s','--start', - dest='start', - default = '0', - help='Trim from beginning to here (1-based)') - - parser.add_option( - '-e','--end', - dest='end', - default = '0', - help='Trim from here to the ned (1-based)') - - parser.add_option( - '-f','--file', - dest='input_txt', - default = False, - help='Name of file to be chopped. STDIN is default') - - parser.add_option( - '-c','--column', - dest='col', - default = '0', - help='Column to chop. If 0 = chop the whole line') - - - options, args = parser.parse_args() - invalid_starts = [] - - if options.input_txt: - infile = open ( options.input_txt, 'r') - else: - infile = sys.stdin - - if options.ignore and options.ignore != "None": - invalid_starts = options.ignore.split(',') - - if options.ascii and options.ignore and options.ignore != "None": - for i, item in enumerate( invalid_starts ): - invalid_starts[i] = chr( int( item ) ) - - col = int( options.col ) - - for i, line in enumerate( infile ): - line = line.rstrip( '\r\n' ) - if line: - - if options.fastq and i % 2 == 0: - print line - continue - - - if line[0] not in invalid_starts: - if col == 0: - if int( options.end ) > 0: - line = line[ int( options.start )-1 : int( options.end ) ] - else: - line = line[ int( options.start )-1 : ] - else: - fields = line.split( '\t' ) - if col-1 > len( fields ): - stop_err('Column %d does not exist. Check input parameters\n' % col) - - if int( options.end ) > 0: - fields[col - 1] = fields[col - 1][ int( options.start )-1 : int( options.end ) ] - else: - fields[col - 1] = fields[col - 1][ int( options.start )-1 : ] - line = '\t'.join(fields) - print line - -if __name__ == "__main__": main() - diff -r 63fc9cbe381d2719134f87c019911565e3a934a1 -r c68762fcb5a521007d89cb01455a0ad409011528 tools/filters/trimmer.xml --- a/tools/filters/trimmer.xml +++ /dev/null @@ -1,120 +0,0 @@ -<tool id="trimmer" name="Trim" version="0.0.1"> - <description>leading or trailing characters</description> - <command interpreter="python"> - trimmer.py -a -f $input1 -c $col -s $start -e $end -i $ignore $fastq > $out_file1 - </command> - <inputs> - <param format="tabular,txt" name="input1" type="data" label="this dataset"/> - <param name="col" type="integer" value="0" label="Trim this column only" help="0 = process entire line" /> - <param name="start" type="integer" size="10" value="1" label="Trim from the beginning to this position" help="1 = do not trim the beginning"/> - <param name="end" type="integer" size="10" value="0" label="Remove everything from this position to the end" help="0 = do not trim the end"/> - <param name="fastq" type="select" label="Is input dataset in fastq format?" help="If set to YES, the tool will not trim evenly numbered lines (0, 2, 4, etc...)"> - <option selected="true" value="">No</option> - <option value="-q">Yes</option> - </param> - <param name="ignore" type="select" display="checkboxes" multiple="True" label="Ignore lines beginning with these characters" help="lines beginning with these are not trimmed"> - <option value="62">></option> - <option value="64">@</option> - <option value="43">+</option> - <option value="60"><</option> - <option value="42">*</option> - <option value="45">-</option> - <option value="61">=</option> - <option value="124">|</option> - <option value="63">?</option> - <option value="36">$</option> - <option value="46">.</option> - <option value="58">:</option> - <option value="38">&</option> - <option value="37">%</option> - <option value="94">^</option> - <option value="35">#</option> - </param> - </inputs> - <outputs> - <data name="out_file1" format="input" metadata_source="input1"/> - </outputs> - <tests> - <test> - <param name="input1" value="trimmer_tab_delimited.dat"/> - <param name="col" value="0"/> - <param name="start" value="1"/> - <param name="end" value="13"/> - <param name="ignore" value="62"/> - <param name="fastq" value="No"/> - <output name="out_file1" file="trimmer_a_f_c0_s1_e13_i62.dat"/> - </test> - <test> - <param name="input1" value="trimmer_tab_delimited.dat"/> - <param name="col" value="2"/> - <param name="start" value="1"/> - <param name="end" value="2"/> - <param name="ignore" value="62"/> - <param name="fastq" value="No"/> - <output name="out_file1" file="trimmer_a_f_c2_s1_e2_i62.dat"/> - </test> - - </tests> - - <help> - - -**What it does** - -Trims specified number of characters from a dataset or its field (if dataset is tab-delimited). - ------ - -**Example 1** - -Trimming this dataset:: - - 1234567890 - abcdefghijk - -by setting **Trim from the beginning to this position** to *2* and **Remove everything from this position to the end** to *6* will produce:: - - 23456 - bcdef - ------ - -**Example 2** - -Trimming column 2 of this dataset:: - - abcde 12345 fghij 67890 - fghij 67890 abcde 12345 - -by setting **Trim content of this column only** to *2*, **Trim from the beginning to this position** to *2*, and **Remove everything from this position to the end** to *4* will produce:: - - abcde 234 fghij 67890 - fghij 789 abcde 12345 - ------ - -**Trimming FASTQ datasets** - -This tool can be used to trim sequences and quality strings in fastq datasets. This is done by selected *Yes* from the **Is input dataset in fastq format?** dropdown. If set to *Yes*, the tool will skip all even numbered lines (see warning below). For example, trimming last 5 bases of this dataset:: - - @081017-and-081020:1:1:1715:1759 - GGACTCAGATAGTAATCCACGCTCCTTTAAAATATC - + - II#IIIIIII$5+.(9IIIIIII$%*$G$A31I&&B - -cab done by setting **Remove everything from this position to the end** to 31:: - - @081017-and-081020:1:1:1715:1759 - GGACTCAGATAGTAATCCACGCTCCTTTAAA - + - II#IIIIIII$5+.(9IIIIIII$%*$G$A3 - -**Note** that headers are skipped. - -.. class:: warningmark - -**WARNING:** This tool will only work on properly formatted fastq datasets where (1) each read and quality string occupy one line and (2) '@' (read header) and "+" (quality header) lines are evenly numbered like in the above example. - - - </help> -</tool> https://bitbucket.org/galaxy/galaxy-central/changeset/2f45da781f92/ changeset: 2f45da781f92 user: inithello date: 2012-12-07 22:08:58 summary: Remove migrated tools from Galaxy main tool configuration. affected #: 1 file diff -r c68762fcb5a521007d89cb01455a0ad409011528 -r 2f45da781f926f667dd90ad23d23fd123716a535 tool_conf.xml.main --- a/tool_conf.xml.main +++ b/tool_conf.xml.main @@ -33,21 +33,11 @@ <tool file="extract/liftOver_wrapper.xml" /></section><section name="Text Manipulation" id="textutil"> - <tool file="filters/fixedValueColumn.xml" /><tool file="stats/column_maker.xml" /><tool file="filters/catWrapper.xml" /> - <tool file="filters/condense_characters.xml" /> - <tool file="filters/convert_characters.xml" /> - <tool file="filters/mergeCols.xml" /><tool file="filters/CreateInterval.xml" /> - <tool file="filters/cutWrapper.xml" /> - <tool file="filters/changeCase.xml" /><tool file="filters/pasteWrapper.xml" /> - <tool file="filters/remove_beginning.xml" /><tool file="filters/randomlines.xml" /> - <tool file="filters/headWrapper.xml" /> - <tool file="filters/tailWrapper.xml" /> - <tool file="filters/trimmer.xml" /><tool file="filters/wc_gnu.xml" /><tool file="filters/secure_hash_message_digest.xml" /></section> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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