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commit/galaxy-central: dan: Add no_options validator to built-in reference genome selector in GATK tools.
by Bitbucket 30 Nov '11

30 Nov '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/c6f70cccce28/ changeset: c6f70cccce28 user: dan date: 2011-11-30 19:29:21 summary: Add no_options validator to built-in reference genome selector in GATK tools. affected #: 13 files diff -r 2ee4a6b8419b3da2b95e1600a92099fe547cd070 -r c6f70cccce287702f18c518175bec4a5e8ace23c tools/gatk/count_covariates.xml --- a/tools/gatk/count_covariates.xml +++ b/tools/gatk/count_covariates.xml @@ -146,6 +146,7 @@ <options from_data_table="gatk_picard_indexes"><filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/></options> + <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/></param></when><when value="history"> diff -r 2ee4a6b8419b3da2b95e1600a92099fe547cd070 -r c6f70cccce287702f18c518175bec4a5e8ace23c tools/gatk/depth_of_coverage.xml --- a/tools/gatk/depth_of_coverage.xml +++ b/tools/gatk/depth_of_coverage.xml @@ -194,6 +194,7 @@ <options from_data_table="gatk_picard_indexes"></options> + <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/></param></when><when value="history"> diff -r 2ee4a6b8419b3da2b95e1600a92099fe547cd070 -r c6f70cccce287702f18c518175bec4a5e8ace23c tools/gatk/indel_realigner.xml --- a/tools/gatk/indel_realigner.xml +++ b/tools/gatk/indel_realigner.xml @@ -124,6 +124,7 @@ <options from_data_table="gatk_picard_indexes"><filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/></options> + <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/></param></when><when value="history"> diff -r 2ee4a6b8419b3da2b95e1600a92099fe547cd070 -r c6f70cccce287702f18c518175bec4a5e8ace23c tools/gatk/realigner_target_creator.xml --- a/tools/gatk/realigner_target_creator.xml +++ b/tools/gatk/realigner_target_creator.xml @@ -112,6 +112,7 @@ <options from_data_table="gatk_picard_indexes"><filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/></options> + <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/></param></when><when value="history"> diff -r 2ee4a6b8419b3da2b95e1600a92099fe547cd070 -r c6f70cccce287702f18c518175bec4a5e8ace23c tools/gatk/table_recalibration.xml --- a/tools/gatk/table_recalibration.xml +++ b/tools/gatk/table_recalibration.xml @@ -129,6 +129,7 @@ <options from_data_table="gatk_picard_indexes"><filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/></options> + <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/></param></when><when value="history"> diff -r 2ee4a6b8419b3da2b95e1600a92099fe547cd070 -r c6f70cccce287702f18c518175bec4a5e8ace23c tools/gatk/unified_genotyper.xml --- a/tools/gatk/unified_genotyper.xml +++ b/tools/gatk/unified_genotyper.xml @@ -154,6 +154,7 @@ <options from_data_table="gatk_picard_indexes"></options> + <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/></param></when><when value="history"> diff -r 2ee4a6b8419b3da2b95e1600a92099fe547cd070 -r c6f70cccce287702f18c518175bec4a5e8ace23c tools/gatk/variant_annotator.xml --- a/tools/gatk/variant_annotator.xml +++ b/tools/gatk/variant_annotator.xml @@ -157,6 +157,7 @@ <options from_data_table="gatk_picard_indexes"><filter type="data_meta" key="dbkey" ref="input_variant" column="dbkey"/></options> + <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/></param></when><when value="history"> diff -r 2ee4a6b8419b3da2b95e1600a92099fe547cd070 -r c6f70cccce287702f18c518175bec4a5e8ace23c tools/gatk/variant_apply_recalibration.xml --- a/tools/gatk/variant_apply_recalibration.xml +++ b/tools/gatk/variant_apply_recalibration.xml @@ -109,6 +109,7 @@ <options from_data_table="gatk_picard_indexes"></options> + <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/></param></when><when value="history"> diff -r 2ee4a6b8419b3da2b95e1600a92099fe547cd070 -r c6f70cccce287702f18c518175bec4a5e8ace23c tools/gatk/variant_combine.xml --- a/tools/gatk/variant_combine.xml +++ b/tools/gatk/variant_combine.xml @@ -121,6 +121,7 @@ <options from_data_table="gatk_picard_indexes"></options> + <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/></param></when><when value="history"> diff -r 2ee4a6b8419b3da2b95e1600a92099fe547cd070 -r c6f70cccce287702f18c518175bec4a5e8ace23c tools/gatk/variant_eval.xml --- a/tools/gatk/variant_eval.xml +++ b/tools/gatk/variant_eval.xml @@ -160,6 +160,7 @@ <options from_data_table="gatk_picard_indexes"></options> + <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/></param></when><when value="history"> diff -r 2ee4a6b8419b3da2b95e1600a92099fe547cd070 -r c6f70cccce287702f18c518175bec4a5e8ace23c tools/gatk/variant_filtration.xml --- a/tools/gatk/variant_filtration.xml +++ b/tools/gatk/variant_filtration.xml @@ -110,6 +110,7 @@ <options from_data_table="gatk_picard_indexes"><filter type="data_meta" key="dbkey" ref="input_variant" column="dbkey"/></options> + <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/></param></when><when value="history"> diff -r 2ee4a6b8419b3da2b95e1600a92099fe547cd070 -r c6f70cccce287702f18c518175bec4a5e8ace23c tools/gatk/variant_recalibrator.xml --- a/tools/gatk/variant_recalibrator.xml +++ b/tools/gatk/variant_recalibrator.xml @@ -156,6 +156,7 @@ <options from_data_table="gatk_picard_indexes"></options> + <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/></param></when><when value="history"> diff -r 2ee4a6b8419b3da2b95e1600a92099fe547cd070 -r c6f70cccce287702f18c518175bec4a5e8ace23c tools/gatk/variants_validate.xml --- a/tools/gatk/variants_validate.xml +++ b/tools/gatk/variants_validate.xml @@ -96,6 +96,7 @@ <options from_data_table="gatk_picard_indexes"><filter type="data_meta" key="dbkey" ref="input_variant" column="dbkey"/></options> + <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/></param></when><when value="history"> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jgoecks: Provide chromInfo correctly during conversions of datasets with custom build dbkeys.
by Bitbucket 30 Nov '11

30 Nov '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/2ee4a6b8419b/ changeset: 2ee4a6b8419b user: jgoecks date: 2011-11-30 19:06:12 summary: Provide chromInfo correctly during conversions of datasets with custom build dbkeys. affected #: 1 file diff -r 665853dfd9e12e137f26777d1a2d2167df4b4275 -r 2ee4a6b8419b3da2b95e1600a92099fe547cd070 lib/galaxy/tools/actions/__init__.py --- a/lib/galaxy/tools/actions/__init__.py +++ b/lib/galaxy/tools/actions/__init__.py @@ -191,7 +191,16 @@ db_datasets[ "chromInfo" ] = db_dataset incoming[ "chromInfo" ] = db_dataset.file_name else: - incoming[ "chromInfo" ] = os.path.join( trans.app.config.tool_data_path, 'shared','ucsc','chrom', "%s.len" % input_dbkey ) + # For custom builds, chrom info resides in converted dataset; for built-in builds, chrom info resides in tool-data/shared. + if trans.user and ( input_dbkey in trans.user.preferences[ 'dbkeys' ] ): + # Custom build. + custom_build_dict = from_json_string( trans.user.preferences[ 'dbkeys' ] )[ input_dbkey ] + build_fasta_dataset = trans.app.model.HistoryDatasetAssociation.get( custom_build_dict[ 'fasta' ] ) + chrom_info = build_fasta_dataset.get_converted_dataset( trans, 'len' ).file_name + else: + # Default to built-in build. + chrom_info = os.path.join( trans.app.config.tool_data_path, 'shared','ucsc','chrom', "%s.len" % input_dbkey ) + incoming[ "chromInfo" ] = chrom_info inp_data.update( db_datasets ) # Determine output dataset permission/roles list 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: richard_burhans: python version of "phyloP interspecies conservation scores" tool
by Bitbucket 30 Nov '11

30 Nov '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/665853dfd9e1/ changeset: 665853dfd9e1 user: richard_burhans date: 2011-11-30 18:05:59 summary: python version of "phyloP interspecies conservation scores" tool affected #: 3 files diff -r 36998f5a7ddb12ee93068b8001a09b84a47944f4 -r 665853dfd9e12e137f26777d1a2d2167df4b4275 tool-data/add_scores.loc.sample --- a/tool-data/add_scores.loc.sample +++ b/tool-data/add_scores.loc.sample @@ -1,21 +1,20 @@ -#This is a sample file distributed with Galaxy that enables tools to use a -#directory of gzipped genome files for use with add_scores. You will need to -#supply these files and then create a add_scores.loc file similar to this one -#(store it in this directory) that points to the directories in which those -#files are stored. The add_scores.loc file has this format (white space -#characters are TAB characters): +#This is a sample file distributed with Galaxy that lists the BigWig files +#available for use with the add_scores (phyloP interspecies conservation +#scores) tool. You will need to supply these BigWig files and then create +#an add_scores.loc file similar to this one (store it in this directory) +#that lists their locations. The add_scores.loc file has the following +#format (white space characters are TAB characters): # -#<build><file_path> +#<build><BigWig_file_path> # #So, for example, if your add_scores.loc began like this: # -#hg18 /galaxy/data/hg18/misc/phyloP +#hg18 /galaxy/data/hg18/misc/phyloP44way.primate.bw # -#then your /galaxy/data/hg18/misc/phyloP directory would need to contain -#the following gzipped files, among others: +#then your /galaxy/data/hg18/misc/ directory would need to contain a +#BigWig file named phyloP44way.primate.bw, among others: # -#-rw-r--r-- 1 g2data g2data 161981190 2010-03-19 12:48 chr10.phyloP44way.primate.wigFix.gz -#-rw-r--r-- 1 g2data g2data 54091 2010-03-19 12:56 chr10_random.phyloP44way.primate.wigFix.gz -#-rw-r--r-- 1 g2data g2data 158621990 2010-03-19 12:46 chr11.phyloP44way.primate.wigFix.gz +#-rw-r--r-- 1 g2data g2data 6057387572 Nov 23 10:11 phyloP44way.primate.bw # -#hg18 /galaxy/data/hg18/misc/phyloP +#hg18 /galaxy/data/hg18/misc/phyloP44way.primate.bw +#hg19 /galaxy/data/hg19/misc/phyloP46way.primate.bw diff -r 36998f5a7ddb12ee93068b8001a09b84a47944f4 -r 665853dfd9e12e137f26777d1a2d2167df4b4275 tools/evolution/add_scores.py --- /dev/null +++ b/tools/evolution/add_scores.py @@ -0,0 +1,120 @@ +#!/usr/bin/env python + +import sys +from galaxy import eggs +import pkg_resources +pkg_resources.require( "bx-python" ) +pkg_resources.require( "numpy" ) +from bx.bbi.bigwig_file import BigWigFile +import os + +################################################################################ + +def die( message ): + print >> sys.stderr, message + sys.exit(1) + +def open_or_die( filename, mode='r', message=None ): + if message is None: + message = 'Error opening {0}'.format( filename ) + try: + fh = open( filename, mode ) + except IOError, err: + die( '{0}: {1}'.format( message, err.strerror ) ) + return fh + +################################################################################ + +class LocationFile( object ): + def __init__( self, filename, comment_chars=None, delimiter='\t', key_column=0 ): + self.filename = filename + if comment_chars is None: + self.comment_chars = ( '#' ) + else: + self.comment_chars = tuple( comment_chars ) + self.delimiter = delimiter + self.key_column = key_column + self._map = {} + self._populate_map() + + def _populate_map( self ): + try: + with open( self.filename ) as fh: + line_number = 0 + for line in fh: + line_number += 1 + line = line.rstrip( '\r\n' ) + if not line.startswith( self.comment_chars ): + elems = line.split( self.delimiter ) + if len( elems ) <= self.key_column: + die( 'Location file {0} line {1}: less than {2} columns'.format( self.filename, line_number, self.key_column + 1 ) ) + else: + key = elems.pop( self.key_column ) + if key in self._map: + if self._map[key] != elems: + die( 'Location file {0} line {1}: duplicate key "{2}"'.format( self.filename, line_number, key ) ) + else: + self._map[key] = elems + except IOError, err: + die( 'Error opening location file {0}: {1}'.format( self.filename, err.strerror ) ) + + def get_values( self, key ): + if key in self._map: + rval = self._map[key] + if len( rval ) == 1: + return rval[0] + else: + return rval + else: + die( 'key "{0}" not found in location file {1}'.format( key, self.filename ) ) + +################################################################################ + +def main(): + input_filename, output_filename, loc_filename, loc_key, chrom_col, start_col = sys.argv[1:] + + # open input, output, and bigwig files + location_file = LocationFile( loc_filename ) + bigwig_filename = location_file.get_values( loc_key ) + bwfh = open_or_die( bigwig_filename, message='Error opening BigWig file {0}'.format( bigwig_filename ) ) + bw = BigWigFile( file=bwfh ) + ifh = open_or_die( input_filename, message='Error opening input file {0}'.format( input_filename ) ) + ofh = open_or_die( output_filename, mode='w', message='Error opening output file {0}'.format( output_filename ) ) + + # make column numbers 0-based + chrom_col = int( chrom_col ) - 1 + start_col = int( start_col ) - 1 + min_cols = max( chrom_col, start_col ) + + # add score column to imput file + line_number = 0 + for line in ifh: + line_number += 1 + line = line.rstrip( '\r\n' ) + elems = line.split( '\t' ) + if len( elems ) > min_cols: + chrom = elems[chrom_col].strip() + # base-0 position in chrom + start = int( elems[start_col] ) + score_list = bw.get( chrom, start, start + 1 ) + score_list_len = len( score_list ) + if score_list_len == 1: + beg, end, score = score_list[0] + score_val = '{0:1.3f}'.format( score ) + elif score_list_len == 0: + score_val = 'NA' + else: + die( '{0} line {1}: chrom={2}, start={3}, score_list_len = {4}'.format( input_filename, line_number, chrom, start, score_list_len ) ) + print >> ofh, '\t'.join( [line, score_val] ) + else: + print >> ofh, line + + bwfh.close() + ifh.close() + ofh.close() + +################################################################################ + +if __name__ == "__main__": + main() + diff -r 36998f5a7ddb12ee93068b8001a09b84a47944f4 -r 665853dfd9e12e137f26777d1a2d2167df4b4275 tools/evolution/add_scores.xml --- a/tools/evolution/add_scores.xml +++ b/tools/evolution/add_scores.xml @@ -1,8 +1,8 @@ <tool id="hgv_add_scores" name="phyloP" version="1.0.0"><description>interspecies conservation scores</description> - <command> - add_scores $input1 ${input1.metadata.dbkey} ${input1.metadata.chromCol} ${input1.metadata.startCol} ${GALAXY_DATA_INDEX_DIR}/add_scores.loc $out_file1 + <command interpreter="python"> + add_scores.py "$input1" "$out_file1" "${GALAXY_DATA_INDEX_DIR}/add_scores.loc" "${input1.metadata.dbkey}" "${input1.metadata.chromCol}" "${input1.metadata.startCol}" </command><inputs> @@ -34,7 +34,7 @@ <help> .. class:: warningmark -This currently works only for build hg18. +This currently works only for builds hg18 and hg19. ----- Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: dan: Fix for frames inside of frames issue introduced in 5db0da0007fc. Seen when require_login=True.
by Bitbucket 30 Nov '11

30 Nov '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/36998f5a7ddb/ changeset: 36998f5a7ddb user: dan date: 2011-11-30 16:20:15 summary: Fix for frames inside of frames issue introduced in 5db0da0007fc. Seen when require_login=True. affected #: 1 file diff -r 834de698004e1306b4424d0a8dbd3e7c1938ee9c -r 36998f5a7ddb12ee93068b8001a09b84a47944f4 lib/galaxy/web/framework/__init__.py --- a/lib/galaxy/web/framework/__init__.py +++ b/lib/galaxy/web/framework/__init__.py @@ -407,6 +407,7 @@ def _ensure_logged_in_user( self, environ, session_cookie ): # The value of session_cookie can be one of # 'galaxysession' or 'galaxycommunitysession' + # Currently this method does nothing unless session_cookie is 'galaxysession' if session_cookie == 'galaxysession': # TODO: re-engineer to eliminate the use of allowed_paths # as maintenance overhead is far too high. @@ -436,8 +437,8 @@ host = None if host in UCSC_SERVERS: return - if self.request.path not in allowed_paths: - self.response.send_redirect( url_for( controller='root', action='index' ) ) + if self.request.path not in allowed_paths: + self.response.send_redirect( url_for( controller='root', action='index' ) ) def __create_new_session( self, prev_galaxy_session=None, user_for_new_session=None ): """ Create a new GalaxySession for this request, possibly with a connection 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: greg: Revert 2 changes made in 5db0da0007fc in an attempt to correct the broken behavior of rendering Galaxy correctly when using apache proxying, possibly in adition to requiring users to login.
by Bitbucket 30 Nov '11

30 Nov '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/834de698004e/ changeset: 834de698004e user: greg date: 2011-11-30 15:16:37 summary: Revert 2 changes made in 5db0da0007fc in an attempt to correct the broken behavior of rendering Galaxy correctly when using apache proxying, possibly in adition to requiring users to login. affected #: 2 files diff -r de03f821784bcbe04a7514ad3d8e43fb1b635e4b -r 834de698004e1306b4424d0a8dbd3e7c1938ee9c lib/galaxy/web/controllers/user.py --- a/lib/galaxy/web/controllers/user.py +++ b/lib/galaxy/web/controllers/user.py @@ -358,7 +358,7 @@ else: refresh_frames = [ 'masthead', 'history' ] message, status, user, success = self.__validate_login( trans, webapp, **kwd ) - if success and referer and not referer.startswith( url_for( trans.request.base + url_for( controller='user', action='logout' ) ) ): + if success and referer and not referer.startswith( trans.request.base + url_for( controller='user', action='logout' ) ): redirect_url = referer elif success: redirect_url = url_for( '/' ) diff -r de03f821784bcbe04a7514ad3d8e43fb1b635e4b -r 834de698004e1306b4424d0a8dbd3e7c1938ee9c templates/webapps/galaxy/base_panels.mako --- a/templates/webapps/galaxy/base_panels.mako +++ b/templates/webapps/galaxy/base_panels.mako @@ -142,7 +142,11 @@ menu_options.append( [ _('Preferences'), h.url_for( controller='/user', action='index', cntrller='user', webapp='galaxy' ), "galaxy_main" ] ) if app.config.get_bool( 'enable_tracks', False ): menu_options.append( [ 'Custom Builds', h.url_for( controller='/user', action='dbkeys' ), "galaxy_main" ] ) - menu_options.append( [ 'Logout', h.url_for( controller='/user', action='logout', webapp='galaxy' ), "_top" ] ) + if app.config.require_login: + logout_url = h.url_for( controller='/root', action='index', m_c='user', m_a='logout', webapp='galaxy' ) + else: + logout_url = h.url_for( controller='/user', action='logout', webapp='galaxy' ) + menu_options.append( [ 'Logout', logout_url, "_top" ] ) menu_options.append( None ) menu_options.append( [ _('Saved Histories'), h.url_for( controller='/history', action='list' ), "galaxy_main" ] ) menu_options.append( [ _('Saved Datasets'), h.url_for( controller='/dataset', action='list' ), "galaxy_main" ] ) 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: dannon: Fix for browsing libraries, json2 wasn't being loaded, needed in IE for jstorage to work.
by Bitbucket 30 Nov '11

30 Nov '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/de03f821784b/ changeset: de03f821784b user: dannon date: 2011-11-30 13:29:32 summary: Fix for browsing libraries, json2 wasn't being loaded, needed in IE for jstorage to work. affected #: 1 file diff -r b751663f3f64ea794951f57b2ff4686debd1b455 -r de03f821784bcbe04a7514ad3d8e43fb1b635e4b templates/library/common/browse_library.mako --- a/templates/library/common/browse_library.mako +++ b/templates/library/common/browse_library.mako @@ -48,6 +48,7 @@ <%def name="javascripts()"> ${parent.javascripts()} + ${h.js("json2")} ${h.js("jstorage")} ${common_javascripts()} ${self.grid_javascripts()} 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: Minor fix for 04e8ed0cd930.
by Bitbucket 29 Nov '11

29 Nov '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/b751663f3f64/ changeset: b751663f3f64 user: dan date: 2011-11-29 23:35:14 summary: Minor fix for 04e8ed0cd930. affected #: 1 file diff -r 04e8ed0cd930023fea4d7d942e1a12694c4526e6 -r b751663f3f64ea794951f57b2ff4686debd1b455 tools/sr_mapping/PerM.xml --- a/tools/sr_mapping/PerM.xml +++ b/tools/sr_mapping/PerM.xml @@ -13,7 +13,7 @@ #if $s.space == "color" "${s.sourceOfRef.index.fields.path}" #elif $s.space == "base" - "${s.sourceOfRef.index.fields.path" + "${s.sourceOfRef.index.fields.path}" #end if #end if #if $s.mate.singleOrPairs == "single": 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: Replace old filter() on tool_data_tables by param value hack with param.fields.path for several tools.
by Bitbucket 29 Nov '11

29 Nov '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/04e8ed0cd930/ changeset: 04e8ed0cd930 user: dan date: 2011-11-29 23:30:14 summary: Replace old filter() on tool_data_tables by param value hack with param.fields.path for several tools. affected #: 13 files diff -r 0532712a2708855e77d1a6a9a1099121983458a4 -r 04e8ed0cd930023fea4d7d942e1a12694c4526e6 tools/metag_tools/megablast_wrapper.xml --- a/tools/metag_tools/megablast_wrapper.xml +++ b/tools/metag_tools/megablast_wrapper.xml @@ -2,7 +2,7 @@ <description> compare short reads against htgs, nt, and wgs databases</description><command interpreter="python"> megablast_wrapper.py - --db_build="${ filter( lambda x: str( x[0] ) == str( $source_select ), $__app__.tool_data_tables[ 'blastdb' ].get_fields() )[0][-1] }" + --db_build="${source_select.fields.path}" --input=$input_query --word_size=$word_size --identity_cutoff=$iden_cutoff diff -r 0532712a2708855e77d1a6a9a1099121983458a4 -r 04e8ed0cd930023fea4d7d942e1a12694c4526e6 tools/ngs_rna/tophat_color_wrapper.xml --- a/tools/ngs_rna/tophat_color_wrapper.xml +++ b/tools/ngs_rna/tophat_color_wrapper.xml @@ -19,7 +19,7 @@ #if $refGenomeSource.genomeSource == "history": --own-file=$refGenomeSource.ownFile #else: - --indexes-path="${ filter( lambda x: str( x[0] ) == str( $refGenomeSource.index ), $__app__.tool_data_tables[ 'tophat_indexes_color' ].get_fields() )[0][-1] }" + --indexes-path="${refGenomeSource.index.fields.path}" #end if ## Are reads single-end or paired? diff -r 0532712a2708855e77d1a6a9a1099121983458a4 -r 04e8ed0cd930023fea4d7d942e1a12694c4526e6 tools/ngs_rna/tophat_wrapper.xml --- a/tools/ngs_rna/tophat_wrapper.xml +++ b/tools/ngs_rna/tophat_wrapper.xml @@ -17,7 +17,7 @@ #if $refGenomeSource.genomeSource == "history": --own-file=$refGenomeSource.ownFile #else: - --indexes-path="${ filter( lambda x: str( x[0] ) == str( $refGenomeSource.index ), $__app__.tool_data_tables[ 'tophat_indexes' ].get_fields() )[0][-1] }" + --indexes-path="${refGenomeSource.index.fields.path}" #end if ## Are reads single-end or paired? diff -r 0532712a2708855e77d1a6a9a1099121983458a4 -r 04e8ed0cd930023fea4d7d942e1a12694c4526e6 tools/ngs_simulation/ngs_simulation.xml --- a/tools/ngs_simulation/ngs_simulation.xml +++ b/tools/ngs_simulation/ngs_simulation.xml @@ -4,7 +4,7 @@ <command interpreter="python"> ngs_simulation.py #if $in_type.input_type == "built-in" - --input="${ filter( lambda x: str( x[0] ) == str( $in_type.genome ), $__app__.tool_data_tables[ 'ngs_sim_fasta' ].get_fields() )[0][-1] }" + --input="${in_type.genome.fields.path}" --genome=$in_type.genome #else --input=$in_type.input1 diff -r 0532712a2708855e77d1a6a9a1099121983458a4 -r 04e8ed0cd930023fea4d7d942e1a12694c4526e6 tools/picard/rgPicardASMetrics.xml --- a/tools/picard/rgPicardASMetrics.xml +++ b/tools/picard/rgPicardASMetrics.xml @@ -6,7 +6,7 @@ #if $genomeSource.refGenomeSource == "history": --ref-file "$genomeSource.ownFile" #else - --ref "${ filter( lambda x: str( x[0] ) == str( $genomeSource.index ), $__app__.tool_data_tables[ 'all_fasta' ].get_fields() )[0][-1] }" + --ref "${genomeSource.index.fields.path}" #end if </command><requirements><requirement type="package">picard</requirement></requirements> diff -r 0532712a2708855e77d1a6a9a1099121983458a4 -r 04e8ed0cd930023fea4d7d942e1a12694c4526e6 tools/sr_mapping/PerM.xml --- a/tools/sr_mapping/PerM.xml +++ b/tools/sr_mapping/PerM.xml @@ -11,9 +11,9 @@ $s.sourceOfRef.ref #else #if $s.space == "color" - "${ filter( lambda x: str( x[0] ) == str( $s.sourceOfRef.index ), $__app__.tool_data_tables[ 'perm_color_indexes' ].get_fields() )[0][-1] }" + "${s.sourceOfRef.index.fields.path}" #elif $s.space == "base" - "${ filter( lambda x: str( x[0] ) == str( $s.sourceOfRef.index ), $__app__.tool_data_tables[ 'perm_base_indexes' ].get_fields() )[0][-1] }" + "${s.sourceOfRef.index.fields.path" #end if #end if #if $s.mate.singleOrPairs == "single": diff -r 0532712a2708855e77d1a6a9a1099121983458a4 -r 04e8ed0cd930023fea4d7d942e1a12694c4526e6 tools/sr_mapping/bowtie_color_wrapper.xml --- a/tools/sr_mapping/bowtie_color_wrapper.xml +++ b/tools/sr_mapping/bowtie_color_wrapper.xml @@ -58,7 +58,7 @@ #end if #else ##use pre-built index - --ref="${ filter( lambda x: str( x[0] ) == str( $refGenomeSource.index ), $__app__.tool_data_tables[ 'bowtie_indexes_color' ].get_fields() )[0][-1] }" + --ref="${refGenomeSource.index.fields.path}" #end if --paired=$singlePaired.sPaired #if $singlePaired.sPaired == "single": diff -r 0532712a2708855e77d1a6a9a1099121983458a4 -r 04e8ed0cd930023fea4d7d942e1a12694c4526e6 tools/sr_mapping/bowtie_wrapper.xml --- a/tools/sr_mapping/bowtie_wrapper.xml +++ b/tools/sr_mapping/bowtie_wrapper.xml @@ -61,8 +61,7 @@ #end if #else ##use pre-built index - ##--ref="${ filter( lambda x: str( x[0] ) == str( $refGenomeSource.index ), $__app__.tool_data_tables[ 'bowtie_indexes' ].get_fields() )[0][-1] }" - --ref="${ refGenomeSource.index.fields.path }" + --ref="${refGenomeSource.index.fields.path}" #end if --paired=$singlePaired.sPaired #if $singlePaired.sPaired == "single": diff -r 0532712a2708855e77d1a6a9a1099121983458a4 -r 04e8ed0cd930023fea4d7d942e1a12694c4526e6 tools/sr_mapping/bwa_color_wrapper.xml --- a/tools/sr_mapping/bwa_color_wrapper.xml +++ b/tools/sr_mapping/bwa_color_wrapper.xml @@ -14,7 +14,7 @@ --dbkey=$dbkey #else: ##use precomputed indexes - --ref="${ filter( lambda x: str( x[0] ) == str( $genomeSource.indices ), $__app__.tool_data_tables[ 'bwa_indexes_color' ].get_fields() )[0][-1] }" + --ref="${genomeSource.indices.fields.path}" --do_not_build_index #end if diff -r 0532712a2708855e77d1a6a9a1099121983458a4 -r 04e8ed0cd930023fea4d7d942e1a12694c4526e6 tools/sr_mapping/bwa_wrapper.xml --- a/tools/sr_mapping/bwa_wrapper.xml +++ b/tools/sr_mapping/bwa_wrapper.xml @@ -17,7 +17,7 @@ --dbkey=$dbkey #else: ##use precomputed indexes - --ref="${ filter( lambda x: str( x[0] ) == str( $genomeSource.indices ), $__app__.tool_data_tables[ 'bwa_indexes' ].get_fields() )[0][-1] }" + --ref="${genomeSource.indices.fields.path}" --do_not_build_index #end if diff -r 0532712a2708855e77d1a6a9a1099121983458a4 -r 04e8ed0cd930023fea4d7d942e1a12694c4526e6 tools/sr_mapping/lastz_paired_reads_wrapper.xml --- a/tools/sr_mapping/lastz_paired_reads_wrapper.xml +++ b/tools/sr_mapping/lastz_paired_reads_wrapper.xml @@ -12,7 +12,7 @@ --input1=$source.input1 --ref_sequences=$input1.metadata.sequences #else: - --input1="${ filter( lambda x: str( x[0] ) == str( $source.input1_2bit ), $__app__.tool_data_tables[ 'lastz_seqs' ].get_fields() )[0][-1] }" + --input1="${source.input1_2bit.fields.path}" #end if --output=$output1 --lastz_seqs_file_dir=${GALAXY_DATA_INDEX_DIR} diff -r 0532712a2708855e77d1a6a9a1099121983458a4 -r 04e8ed0cd930023fea4d7d942e1a12694c4526e6 tools/sr_mapping/lastz_wrapper.xml --- a/tools/sr_mapping/lastz_wrapper.xml +++ b/tools/sr_mapping/lastz_wrapper.xml @@ -12,7 +12,7 @@ --input1=$source.input1 --ref_sequences=$input1.metadata.sequences #else: - --input1="${ filter( lambda x: str( x[0] ) == str( $source.input1_2bit ), $__app__.tool_data_tables[ 'lastz_seqs' ].get_fields() )[0][-1] }" + --input1="${source.input1_2bit.fields.path}" --ref_sequences="None" #end if #if $params.source_select=="pre_set": diff -r 0532712a2708855e77d1a6a9a1099121983458a4 -r 04e8ed0cd930023fea4d7d942e1a12694c4526e6 tools/sr_mapping/mosaik.xml --- a/tools/sr_mapping/mosaik.xml +++ b/tools/sr_mapping/mosaik.xml @@ -13,7 +13,7 @@ #end if MosaikBuild -fr #if $genomeSource.refGenomeSource == 'indexed': - ${ filter( lambda x: str( x[0] ) == str( $genomeSource.indexReference ), $__app__.tool_data_tables[ 'mosaik_indexes' ].get_fields() )[0][-1] } + ${genomeSource.indexReference.fields.path} #else: $genomeSource.historyReference #end if Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: dan: Fix tab to 4 spaces in tool_conf.xml.sample.
by Bitbucket 29 Nov '11

29 Nov '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/0532712a2708/ changeset: 0532712a2708 user: dan date: 2011-11-29 23:07:06 summary: Fix tab to 4 spaces in tool_conf.xml.sample. affected #: 1 file diff -r 9ee4e2e41fd60c75c2b87d55648c538438809430 -r 0532712a2708855e77d1a6a9a1099121983458a4 tool_conf.xml.sample --- a/tool_conf.xml.sample +++ b/tool_conf.xml.sample @@ -469,7 +469,7 @@ <tool file="human_genome_variation/lps.xml" /><tool file="human_genome_variation/hilbertvis.xml" /><tool file="human_genome_variation/freebayes.xml" /> - <tool file="human_genome_variation/master2pg.xml" /> + <tool file="human_genome_variation/master2pg.xml" /></section><section name="Genome Diversity" id="gd"><tool file="genome_diversity/extract_primers.xml" /> 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: Updates for GATK tools.
by Bitbucket 29 Nov '11

29 Nov '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/9ee4e2e41fd6/ changeset: 9ee4e2e41fd6 user: dan date: 2011-11-29 22:45:37 summary: Updates for GATK tools. affected #: 2 files diff -r 347cd30ff32ffcb7d3796304774bc5bfa675feb0 -r 9ee4e2e41fd60c75c2b87d55648c538438809430 tools/gatk/unified_genotyper.xml --- a/tools/gatk/unified_genotyper.xml +++ b/tools/gatk/unified_genotyper.xml @@ -1,4 +1,4 @@ -<tool id="gatk_unified_genotyper" name="Unified Genotyper" version="0.0.4"> +<tool id="gatk_unified_genotyper" name="Unified Genotyper" version="0.0.5"><description>SNP and indel caller</description><requirements><requirement type="package" version="1.3">gatk</requirement> @@ -122,7 +122,18 @@ --group "${group}" #end for #end if + #if str( $analysis_param_type.exclude_annotations ) != "None": + #for $annotation in str( $analysis_param_type.exclude_annotations ).split( ','): + --excludeAnnotation "${annotation}" + #end for + #end if ' +## #if str( $analysis_param_type.snpEff_rod_bind_type.snpEff_rod_bind_type_selector ) == 'set_snpEff': +## -p '--annotation "SnpEff"' +## -d "--snpEffFile:${analysis_param_type.snpEff_rod_bind_type.snpEff_rod_name},%(file_type)s" "${analysis_param_type.snpEff_rod_bind_type.snpEff_input_rod}" "${analysis_param_type.snpEff_rod_bind_type.snpEff_input_rod.ext}" "input_snpEff_${analysis_param_type.snpEff_rod_bind_type.snpEff_rod_name}" +## #else: +## -p '--excludeAnnotation "SnpEff"' +## #end if #end if </command><inputs> @@ -354,42 +365,91 @@ <param name="indelHaplotypeSize" type="integer" value="80" label="Indel haplotype size" /><param name="doContextDependentGapPenalties" type="boolean" truevalue="--doContextDependentGapPenalties" falsevalue="" label="Vary gap penalties by context" /><param name="annotation" type="select" multiple="True" display="checkboxes" label="Annotation Types"> - <option value="ChromosomeCounts"/> - <option value="IndelType"/> - <option value="SpanningDeletions"/> - <option value="HardyWeinberg"/> - <option value="NBaseCount"/> - <option value="MappingQualityZero"/> - <option value="AlleleBalance"/> - <option value="BaseCounts"/> - <option value="LowMQ"/> - <option value="InbreedingCoeff"/> - <option value="RMSMappingQuality"/> - <option value="HaplotypeScore"/> - <option value="TechnologyComposition"/> - <option value="SampleList"/> - <option value="FisherStrand"/> - <option value="HomopolymerRun"/> - <option value="DepthOfCoverage"/> - <option value="SnpEff"/> - <option value="MappingQualityZeroFraction"/> - <option value="GCContent"/> - <option value="MappingQualityRankSumTest"/> - <option value="ReadPosRankSumTest"/> - <option value="BaseQualityRankSumTest"/> - <option value="QualByDepth"/> - <option value="SBByDepth"/> - <option value="ReadDepthAndAllelicFractionBySample"/> - <option value="AlleleBalanceBySample"/> - <option value="DepthPerAlleleBySample"/> - <option value="MappingQualityZeroBySample"/> + <option value="AlleleBalance" /> + <option value="AlleleBalanceBySample" /> + <option value="BaseCounts" /> + <option value="BaseQualityRankSumTest" /> + <option value="ChromosomeCounts" /> + <option value="DepthOfCoverage" /> + <option value="DepthPerAlleleBySample" /> + <option value="FisherStrand" /> + <option value="GCContent" /> + <option value="HaplotypeScore" /> + <option value="HardyWeinberg" /> + <option value="HomopolymerRun" /> + <option value="InbreedingCoeff" /> + <option value="IndelType" /> + <option value="LowMQ" /> + <option value="MVLikelihoodRatio" /> + <option value="MappingQualityRankSumTest" /> + <option value="MappingQualityZero" /> + <option value="MappingQualityZeroBySample" /> + <option value="MappingQualityZeroFraction" /> + <option value="NBaseCount" /> + <option value="QualByDepth" /> + <option value="RMSMappingQuality" /> + <option value="ReadDepthAndAllelicFractionBySample" /> + <option value="ReadPosRankSumTest" /> + <option value="SampleList" /> +  + <option value="SpanningDeletions" /> + <option value="TechnologyComposition" /></param> +<param name="group" type="select" multiple="True" display="checkboxes" label="Annotation Interfaces/Groups"> - <option value="Standard">Standard</option> - <option value="Experimental">Experimental</option> - <option value="WorkInProgress">WorkInProgress</option> -  + <option value="RodRequiringAnnotation">RodRequiringAnnotation</option> + <option value="Standard">Standard</option> + <option value="Experimental">Experimental</option> + <option value="WorkInProgress">WorkInProgress</option> + <option value="RankSumTest">RankSumTest</option> + </param> +  + <param name="exclude_annotations" type="select" multiple="True" display="checkboxes" label="Annotations to exclude" > +  + <option value="AlleleBalance" /> + <option value="AlleleBalanceBySample" /> + <option value="BaseCounts" /> + <option value="BaseQualityRankSumTest" /> + <option value="ChromosomeCounts" /> + <option value="DepthOfCoverage" /> + <option value="DepthPerAlleleBySample" /> + <option value="FisherStrand" /> + <option value="GCContent" /> + <option value="HaplotypeScore" /> + <option value="HardyWeinberg" /> + <option value="HomopolymerRun" /> + <option value="InbreedingCoeff" /> + <option value="IndelType" /> + <option value="LowMQ" /> + <option value="MVLikelihoodRatio" /> + <option value="MappingQualityRankSumTest" /> + <option value="MappingQualityZero" /> + <option value="MappingQualityZeroBySample" /> + <option value="MappingQualityZeroFraction" /> + <option value="NBaseCount" /> + <option value="QualByDepth" /> + <option value="RMSMappingQuality" /> + <option value="ReadDepthAndAllelicFractionBySample" /> + <option value="ReadPosRankSumTest" /> + <option value="SampleList" /> +  + <option value="SpanningDeletions" /> + <option value="TechnologyComposition" /> + </param></when></conditional></inputs> diff -r 347cd30ff32ffcb7d3796304774bc5bfa675feb0 -r 9ee4e2e41fd60c75c2b87d55648c538438809430 tools/gatk/variant_annotator.xml --- a/tools/gatk/variant_annotator.xml +++ b/tools/gatk/variant_annotator.xml @@ -1,4 +1,4 @@ -<tool id="gatk_variant_annotator" name="Variant Annotator" version="0.0.3"> +<tool id="gatk_variant_annotator" name="Variant Annotator" version="0.0.4"><description></description><requirements><requirement type="package" version="1.3">gatk</requirement> @@ -13,6 +13,7 @@ -d "--variant" "${reference_source.input_variant}" "${reference_source.input_variant.ext}" "input_variant" -p 'java -jar "${GALAXY_DATA_INDEX_DIR}/shared/jars/gatk/GenomeAnalysisTK.jar" + ##--list -T "VariantAnnotator" ##--num_threads 4 ##hard coded, for now -et "NO_ET" ##ET no phone home @@ -30,6 +31,11 @@ #end for #end if #end if + #if str( $exclude_annotations ) != "None": + #for $annotation in str( $exclude_annotations ).split( ',' ): + --excludeAnnotation "${annotation}" + #end for + #end if ## #for $additional_annotation in $additional_annotations: ## --annotation "${additional_annotation.additional_annotation_type.additional_annotation_type_selector}" ## #for $name, $param in $additional_annotation.additional_annotation_type.iteritems(): @@ -55,7 +61,10 @@ #end for #if str( $snpEff_rod_bind_type.snpEff_rod_bind_type_selector ) == 'set_snpEff': - -d "--snpEff:${snpEff_rod_bind_type.snpEff_rod_name},%(file_type)s" "${snpEff_rod_bind_type.snpEff_input_rod}" "${snpEff_rod_bind_type.snpEff_input_rod.ext}" "input_snpEff_${snpEff_rod_bind_type.snpEff_rod_name}" + -p '--annotation "SnpEff"' + -d "--snpEffFile:${snpEff_rod_bind_type.snpEff_rod_name},%(file_type)s" "${snpEff_rod_bind_type.snpEff_input_rod}" "${snpEff_rod_bind_type.snpEff_input_rod.ext}" "input_snpEff_${snpEff_rod_bind_type.snpEff_rod_name}" + #else: + -p '--excludeAnnotation "SnpEff"' #end if #for $expression in $expressions: @@ -124,6 +133,10 @@ --group "${group}" #end for #end if + #if str( $family_string ) != "": + --family_string "${family_string}" + #end if + --MendelViolationGenotypeQualityThreshold "${mendel_violation_genotype_quality_threshold}" ' </command><inputs> @@ -166,35 +179,35 @@ <when value="choose"><param name="annotations" type="select" multiple="True" display="checkboxes" label="Annotations to apply" > - <option value="ChromosomeCounts"/> - <option value="IndelType"/> - <option value="SpanningDeletions"/> - <option value="HardyWeinberg"/> - <option value="NBaseCount"/> - <option value="MappingQualityZero"/> - <option value="AlleleBalance"/> - <option value="BaseCounts"/> - <option value="LowMQ"/> - <option value="InbreedingCoeff"/> - <option value="RMSMappingQuality"/> - <option value="HaplotypeScore"/> - <option value="TechnologyComposition"/> - <option value="SampleList"/> - <option value="FisherStrand"/> - <option value="HomopolymerRun"/> - <option value="DepthOfCoverage"/> - <option value="SnpEff"/> - <option value="MappingQualityZeroFraction"/> - <option value="GCContent"/> - <option value="MappingQualityRankSumTest"/> - <option value="ReadPosRankSumTest"/> - <option value="BaseQualityRankSumTest"/> - <option value="QualByDepth"/> - <option value="SBByDepth"/> - <option value="ReadDepthAndAllelicFractionBySample"/> - <option value="AlleleBalanceBySample"/> - <option value="DepthPerAlleleBySample"/> - <option value="MappingQualityZeroBySample"/> + <option value="AlleleBalance" /> + <option value="AlleleBalanceBySample" /> + <option value="BaseCounts" /> + <option value="BaseQualityRankSumTest" /> + <option value="ChromosomeCounts" /> + <option value="DepthOfCoverage" /> + <option value="DepthPerAlleleBySample" /> + <option value="FisherStrand" /> + <option value="GCContent" /> + <option value="HaplotypeScore" /> + <option value="HardyWeinberg" /> + <option value="HomopolymerRun" /> + <option value="InbreedingCoeff" /> + <option value="IndelType" /> + <option value="LowMQ" /> + <option value="MVLikelihoodRatio" /> + <option value="MappingQualityRankSumTest" /> + <option value="MappingQualityZero" /> + <option value="MappingQualityZeroBySample" /> + <option value="MappingQualityZeroFraction" /> + <option value="NBaseCount" /> + <option value="QualByDepth" /> + <option value="RMSMappingQuality" /> + <option value="ReadDepthAndAllelicFractionBySample" /> + <option value="ReadPosRankSumTest" /> + <option value="SampleList" /> + <option value="SnpEff" /> + <option value="SpanningDeletions" /> + <option value="TechnologyComposition" /></param></when></conditional> @@ -371,7 +384,41 @@ <option value="WorkInProgress">WorkInProgress</option><option value="RankSumTest">RankSumTest</option></param> - + <param name="family_string" type="text" value="" label="Family String"/> + <param name="mendel_violation_genotype_quality_threshold" type="float" value="0.0" label="genotype quality treshold in order to annotate mendelian violation ratio."/> + <param name="exclude_annotations" type="select" multiple="True" display="checkboxes" label="Annotations to exclude" > +  + <option value="AlleleBalance" /> + <option value="AlleleBalanceBySample" /> + <option value="BaseCounts" /> + <option value="BaseQualityRankSumTest" /> + <option value="ChromosomeCounts" /> + <option value="DepthOfCoverage" /> + <option value="DepthPerAlleleBySample" /> + <option value="FisherStrand" /> + <option value="GCContent" /> + <option value="HaplotypeScore" /> + <option value="HardyWeinberg" /> + <option value="HomopolymerRun" /> + <option value="InbreedingCoeff" /> + <option value="IndelType" /> + <option value="LowMQ" /> + <option value="MVLikelihoodRatio" /> + <option value="MappingQualityRankSumTest" /> + <option value="MappingQualityZero" /> + <option value="MappingQualityZeroBySample" /> + <option value="MappingQualityZeroFraction" /> + <option value="NBaseCount" /> + <option value="QualByDepth" /> + <option value="RMSMappingQuality" /> + <option value="ReadDepthAndAllelicFractionBySample" /> + <option value="ReadPosRankSumTest" /> + <option value="SampleList" /> + <option value="SnpEff" /> + <option value="SpanningDeletions" /> + <option value="TechnologyComposition" /> + </param> + </inputs><outputs><data format="vcf" name="output_vcf" label="${tool.name} on ${on_string} (Variant File)" /> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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