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[hg] galaxy 1501: Upgrade bx-python to r448.
by Nate Coraor 12 Sep '08

12 Sep '08

details: http://www.bx.psu.edu/hg/galaxy/rev/362a1c02da3d changeset: 1501:362a1c02da3d user: Nate Coraor <nate(a)bx.psu.edu> date: Thu Sep 11 12:22:32 2008 -0400 description: Upgrade bx-python to r448. 1 file(s) affected in this change: eggs.ini diffs (18 lines): diff -r 30f4ab3cc266 -r 362a1c02da3d eggs.ini --- a/eggs.ini Wed Sep 10 09:58:29 2008 -0400 +++ b/eggs.ini Thu Sep 11 12:22:32 2008 -0400 @@ -55,12 +55,12 @@ MySQL_python = _5.0.51a_static python_lzo = _static flup = .dev_r2311 -bx_python = _dev_r427 +bx_python = _dev_r448 nose = .dev_r101 ; source location, necessary for scrambling [source] -bx_python = http://dist.g2.bx.psu.edu/bx-python_dist-r427.tar.bz2 +bx_python = http://dist.g2.bx.psu.edu/bx-python_dist-r448.tar.bz2 Cheetah = http://umn.dl.sourceforge.net/sourceforge/cheetahtemplate/Cheetah-1.0.tar.gz DRMAA_python = http://gridengine.sunsource.net/files/documents/7/36/DRMAA-python-0.2.tar.gz MySQL_python = http://superb-west.dl.sourceforge.net/sourceforge/mysql-python/MySQL-python… http://mysql.mirrors.pair.com/Downloads/MySQL-5.0/mysql-5.0.51a.tar.gz

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[hg] galaxy 1500: Allow complete logging configuration to be spe...
by Nate Coraor 12 Sep '08

12 Sep '08

details: http://www.bx.psu.edu/hg/galaxy/rev/30f4ab3cc266 changeset: 1500:30f4ab3cc266 user: James Taylor <james(a)jamestaylor.org> date: Wed Sep 10 09:58:29 2008 -0400 description: Allow complete logging configuration to be specified in the ini file, in which case this is used instead of the "log_level" and "log_format" keys under the app configuration. PasteScript actually handles this, so we just do nothing related to logging config if the ini file contains a "[loggers]" section. For example, you could add this to the end of your universe_wsgi.ini to include SQLAlchemy debugging and include the thread name with every log message. # Logger overrides [loggers] keys = root, sqlalchemy.engine, sqlalchemy.orm.unitofwork, paste.httpserver.ThreadPool [logger_root] level = DEBUG handlers = console [logger_sqlalchemy.engine] level = INFO handlers = console qualname = sqlalchemy.engine [logger_sqlalchemy.orm.unitofwork] level = DEBUG handlers = console qualname = sqlalchemy.orm.unitofwork [logger_paste.httpserver.ThreadPool] level = INFO handlers = console qualname = paste.httpserver.ThreadPool [handlers] keys = console [handler_console] class = StreamHandler args = (sys.stderr,) level = NOTSET formatter = generic [formatters] keys = generic [formatter_generic] format = %(threadName)s %(name)s %(levelname)s %(asctime)s %(message)s 1 file(s) affected in this change: lib/galaxy/config.py diffs (28 lines): diff -r f9d00dbefdec -r 30f4ab3cc266 lib/galaxy/config.py --- a/lib/galaxy/config.py Mon Sep 08 16:00:49 2008 -0400 +++ b/lib/galaxy/config.py Wed Sep 10 09:58:29 2008 -0400 @@ -64,9 +64,10 @@ self.bugs_email = kwargs.get( 'bugs_email', None ) self.blog_url = kwargs.get( 'blog_url', None ) self.screencasts_url = kwargs.get( 'screencasts_url', None ) - #Parse global_conf + # Parse global_conf and save the parser global_conf = kwargs.get( 'global_conf', None ) global_conf_parser = ConfigParser.ConfigParser() + self.global_conf_parser = global_conf_parser if global_conf and "__file__" in global_conf: global_conf_parser.read(global_conf['__file__']) #Store per-tool runner config @@ -118,6 +119,12 @@ Allow some basic logging configuration to be read from the cherrpy config. """ + # PasteScript will have already configured the logger if the appropriate + # sections were found in the config file, so we do nothing if the + # config has a loggers section, otherwise we do some simple setup + # using the 'log_*' values from the config. + if config.global_conf_parser.has_section( "loggers" ): + return format = config.get( "log_format", "%(name)s %(levelname)s %(asctime)s %(message)s" ) level = logging._levelNames[ config.get( "log_level", "DEBUG" ) ] destination = config.get( "log_destination", "stdout" )

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[hg] galaxy 1497: Fix for scatterplot.py: Handling an uncaught e...
by Nate Coraor 12 Sep '08

12 Sep '08

details: http://www.bx.psu.edu/hg/galaxy/rev/a17b2cd3d9a4 changeset: 1497:a17b2cd3d9a4 user: guru date: Mon Sep 08 14:36:37 2008 -0400 description: Fix for scatterplot.py: Handling an uncaught exception. 1 file(s) affected in this change: tools/plotting/scatterplot.py diffs (15 lines): diff -r 2a361ee9ce3e -r a17b2cd3d9a4 tools/plotting/scatterplot.py --- a/tools/plotting/scatterplot.py Mon Sep 08 11:15:58 2008 -0400 +++ b/tools/plotting/scatterplot.py Mon Sep 08 14:36:37 2008 -0400 @@ -44,7 +44,10 @@ skipped_lines += 1 if not first_invalid_line: first_invalid_line = i + 1 - invalid_value = fields[column] + try: + invalid_value = fields[column] + except: + invalid_value = '' invalid_column = column + 1 break else:

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[hg] galaxy 1496: The interval to BED converter will now use the...
by Nate Coraor 12 Sep '08

12 Sep '08

details: http://www.bx.psu.edu/hg/galaxy/rev/2a361ee9ce3e changeset: 1496:2a361ee9ce3e user: Dan Blankenberg <dan(a)bx.psu.edu> date: Mon Sep 08 11:15:58 2008 -0400 description: The interval to BED converter will now use the name field specified via metadata, if available. 2 file(s) affected in this change: lib/galaxy/datatypes/converters/interval_to_bed_converter.py lib/galaxy/datatypes/converters/interval_to_bed_converter.xml diffs (48 lines): diff -r 49fe600b9499 -r 2a361ee9ce3e lib/galaxy/datatypes/converters/interval_to_bed_converter.py --- a/lib/galaxy/datatypes/converters/interval_to_bed_converter.py Mon Sep 08 09:47:37 2008 -0400 +++ b/lib/galaxy/datatypes/converters/interval_to_bed_converter.py Mon Sep 08 11:15:58 2008 -0400 @@ -31,18 +31,28 @@ strandCol = int( sys.argv[6] ) - 1 except: strandCol = -1 + try: + nameCol = int( sys.argv[7] ) - 1 + except: + nameCol = -1 skipped_lines = 0 first_skipped_line = 0 - count = 0 out = open( output_name,'w' ) - for region in bx.intervals.io.NiceReaderWrapper( open( input_name, 'r' ), chrom_col=chromCol, start_col=startCol, end_col=endCol, strand_col=strandCol, fix_strand=True, return_header=False, return_comments=False ): + for count, region in enumerate( bx.intervals.io.NiceReaderWrapper( open( input_name, 'r' ), chrom_col=chromCol, start_col=startCol, end_col=endCol, strand_col=strandCol, fix_strand=True, return_header=False, return_comments=False ) ): try: - out.write( region.chrom + "\t" + str( region.start ) + "\t" + str( region.end ) + "\tregion_" + str( count ) + "\t" + "0\t" + region.strand + "\n" ) + if nameCol >= 0: + name = region.fields[nameCol] + else: + raise IndexError + except: + name = "region_%i" % count + try: + + out.write( "%s\t%i\t%i\t%s\t%i\t%s\n" % ( region.chrom, region.start, region.end, name, 0, region.strand ) ) except: skipped_lines += 1 if not first_skipped_line: first_skipped_line = count + 1 - count += 1 out.close() info_msg = "%i regions converted to BED." % ( count - skipped_lines ) if skipped_lines > 0: diff -r 49fe600b9499 -r 2a361ee9ce3e lib/galaxy/datatypes/converters/interval_to_bed_converter.xml --- a/lib/galaxy/datatypes/converters/interval_to_bed_converter.xml Mon Sep 08 09:47:37 2008 -0400 +++ b/lib/galaxy/datatypes/converters/interval_to_bed_converter.xml Mon Sep 08 11:15:58 2008 -0400 @@ -1,7 +1,7 @@ <tool id="CONVERTER_interval_to_bed_0" name="Convert Genomic Intervals To BED">   - <command interpreter="python">interval_to_bed_converter.py $output1 $input1 ${input1.metadata.chromCol} ${input1.metadata.startCol} ${input1.metadata.endCol} ${input1.metadata.strandCol}</command> + <command interpreter="python">interval_to_bed_converter.py $output1 $input1 ${input1.metadata.chromCol} ${input1.metadata.startCol} ${input1.metadata.endCol} ${input1.metadata.strandCol} ${input1.metadata.nameCol}</command> <inputs> <page> <param format="interval" name="input1" type="data" label="Choose intervals"/>

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[hg] galaxy 1498: Fix for grouping.py: New line character append...
by Nate Coraor 12 Sep '08

12 Sep '08

details: http://www.bx.psu.edu/hg/galaxy/rev/ad69f789d1cd changeset: 1498:ad69f789d1cd user: guru date: Mon Sep 08 14:54:40 2008 -0400 description: Fix for grouping.py: New line character appended when grouping by the last column will now be trimmed. 1 file(s) affected in this change: tools/stats/grouping.py diffs (11 lines): diff -r a17b2cd3d9a4 -r ad69f789d1cd tools/stats/grouping.py --- a/tools/stats/grouping.py Mon Sep 08 14:36:37 2008 -0400 +++ b/tools/stats/grouping.py Mon Sep 08 14:54:40 2008 -0400 @@ -90,6 +90,7 @@ for ii, line in enumerate( file( tmpfile.name )): if line and not line.startswith( '#' ): + line = line.strip() try: fields = line.split("\t") item = fields[group_col]

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[hg] galaxy 1499: Update GMAJ tool to allow the specifying of an...
by Nate Coraor 12 Sep '08

12 Sep '08

details: http://www.bx.psu.edu/hg/galaxy/rev/f9d00dbefdec changeset: 1499:f9d00dbefdec user: Dan Blankenberg <dan(a)bx.psu.edu> date: Mon Sep 08 16:00:49 2008 -0400 description: Update GMAJ tool to allow the specifying of annotations in two styles. 1 file(s) affected in this change: tools/visualization/GMAJ.xml diffs (144 lines): diff -r ad69f789d1cd -r f9d00dbefdec tools/visualization/GMAJ.xml --- a/tools/visualization/GMAJ.xml Mon Sep 08 14:54:40 2008 -0400 +++ b/tools/visualization/GMAJ.xml Mon Sep 08 16:00:49 2008 -0400 @@ -1,21 +1,40 @@ -<tool id="gmaj_1" name="GMAJ" Version="2.0.0"> +<tool id="gmaj_1" name="GMAJ" Version="2.0.1"> <description>Multiple Alignment Viewer</description> <command interpreter="python">GMAJ.py $out_file1 $maf_input $gmaj_file $filenames_file</command> <inputs> <param name="maf_input" type="data" format="maf" label="Alignment File" optional="False"/> <param name="refseq" label="Reference Sequence" value="" type="text" help="Leave empty to allow interactive selection."/> <repeat name="annotations" title="Annotations"> - <param name="species" type="select" label="Species of Annotation" multiple="False"> - <options> - <filter type="data_meta" ref="maf_input" key="species" /> - </options> - </param> - <param name="exons_file" type="data" format="bed,gff" label="Exons File" optional="True"/> - <param name="highlights_file" type="data" format="bed,gff" label="Highlights File" optional="True"/> - <param name="underlays_file" type="data" format="bed,gff" label="Underlays File" optional="True"/> - <param name="repeats_file" type="data" format="bed,gff" label="Repeats File" optional="True"/> - <param name="links_file" type="data" format="bed,gff" label="Links File" optional="True"/> - <param name="offset" label="Offset" value="0" type="integer"/> + <conditional name="annotation_style"> + <param name="style" type="select" label="Annotation Style" help="If your data is not in a style similar to what is available from Galaxy (and the UCSC table browser), choose 'Basic'."> + <option value="galaxy" selected="true">Galaxy</option> + <option value="basic">Basic</option> + </param> + <when value="galaxy"> + <param name="species" type="select" label="Species of Annotation" multiple="False"> + <options> + <filter type="data_meta" ref="maf_input" key="species" /> + </options> + </param> + <param name="exons_file" type="data" format="bed,gff" label="Exons File" optional="True"/> + <param name="highlights_file" type="data" format="bed,gff" label="Highlights File" optional="True"/> + <param name="underlays_file" type="data" format="bed,gff" label="Underlays File" optional="True"/> + <param name="repeats_file" type="data" format="bed,gff" label="Repeats File" optional="True"/> + <param name="links_file" type="data" format="bed,gff" label="Links File" optional="True"/> + <param name="offset" label="Offset" value="0" type="integer"/> + </when> + <when value="basic"> + <param name="seq_name" label="Full Sequence Name" value="" type="text"> + <validator type="empty_field" message="You must supply the sequence name"/> + </param> + <param name="exons_file" type="data" format="bed,gff" label="Exons File" optional="True"/> + <param name="highlights_file" type="data" format="bed,gff" label="Highlights File" optional="True"/> + <param name="underlays_file" type="data" format="bed,gff" label="Underlays File" optional="True"/> + <param name="repeats_file" type="data" format="bed,gff" label="Repeats File" optional="True"/> + <param name="links_file" type="data" format="bed,gff" label="Links File" optional="True"/> + <param name="offset" label="Offset" value="0" type="integer"/> + </when> + </conditional> </repeat> <param name="nowarn" type="drill_down" display="checkbox" hierarchy="recurse" multiple="true" label="Choose Warnings to Suppress" separator=" " help="These do not affect behavior, only suppress warning messages."> <options> @@ -81,52 +100,59 @@ #end if #set $seq_count = 0 -#for $spec_count, $annotation in $enumerate( $annotations ): -#if $maf_input.metadata.species_chromosomes and $annotation['species'].value in $maf_input.metadata.species_chromosomes and $maf_input.metadata.species_chromosomes[$annotation['species'].value]: -#set $seq_names = [ "%s.%s" % ( $annotation['species'].value, $chrom ) for $chrom in $maf_input.metadata.species_chromosomes[$annotation['species'].value]] -#else -#set $seq_names = [$annotation['species'].value] +#for $annotation_count, $annotation in $enumerate( $annotations ): +#if $annotation.annotation_style.style == "galaxy": +#if $maf_input.metadata.species_chromosomes and $annotation.annotation_style['species'].value in $maf_input.metadata.species_chromosomes and $maf_input.metadata.species_chromosomes[$annotation.annotation_style['species'].value]: +#set $seq_names = [ "%s.%s" % ( $annotation.annotation_style['species'].value, $chrom ) for $chrom in $maf_input.metadata.species_chromosomes[$annotation.annotation_style['species'].value]] +#set $aliases = [ " %s" % $chrom for $chrom in $maf_input.metadata.species_chromosomes[$annotation.annotation_style['species'].value]] +#else: +#set $seq_names = [$annotation.annotation_style['species']] +#set $aliases = [""] #end if -#for $seq_name in $seq_names: +#else: +#set $seq_names = [$annotation.annotation_style['seq_name']] +#set $aliases = [""] +#end if +#for $seq_name, $alias in $zip( $seq_names, $aliases ): seq ${seq_count}: seqname = $seq_name -#if $annotation['exons_file'].dataset: -exons = ${spec_count}.exons.${annotation['exons_file'].extension} +#if $annotation.annotation_style['exons_file'].dataset: +exons = ${annotation_count}.exons.${annotation.annotation_style['exons_file'].extension}$alias #end if -#if $annotation['repeats_file'].dataset: -repeats = ${spec_count}.repeats.${annotation['repeats_file'].extension} +#if $annotation.annotation_style['repeats_file'].dataset: +repeats = ${annotation_count}.repeats.${annotation.annotation_style['repeats_file'].extension}$alias #end if -#if $annotation['links_file'].dataset: -links = ${spec_count}.links.${annotation['links_file'].extension} +#if $annotation.annotation_style['links_file'].dataset: +links = ${annotation_count}.links.${annotation.annotation_style['links_file'].extension}$alias #end if -#if $annotation['underlays_file'].dataset: -underlays = ${spec_count}.underlays.${annotation['underlays_file'].extension} +#if $annotation.annotation_style['underlays_file'].dataset: +underlays = ${annotation_count}.underlays.${annotation.annotation_style['underlays_file'].extension}$alias #end if -#if $annotation['highlights_file'].dataset: -highlights = ${spec_count}.highlights.${annotation['highlights_file'].extension} +#if $annotation.annotation_style['highlights_file'].dataset: +highlights = ${annotation_count}.highlights.${annotation.annotation_style['highlights_file'].extension}$alias #end if -offset = $annotation['offset'] +offset = $annotation.annotation_style['offset'] #set $seq_count = $seq_count + 1 #end for #end for </configfile> <configfile name="filenames_file"> -#for $spec_count, $annotation in $enumerate( $annotations ): -#if $annotation['exons_file'].dataset: -$annotation['exons_file'] = ${spec_count}.exons.${annotation['exons_file'].extension} +#for $annotation_count, $annotation in $enumerate( $annotations ): +#if $annotation.annotation_style['exons_file'].dataset: +$annotation.annotation_style['exons_file'] = ${annotation_count}.exons.${annotation.annotation_style['exons_file'].extension} #end if -#if $annotation['repeats_file'].dataset: -$annotation['repeats_file'] = ${spec_count}.repeats.${annotation['repeats_file'].extension} +#if $annotation.annotation_style['repeats_file'].dataset: +$annotation.annotation_style['repeats_file'] = ${annotation_count}.repeats.${annotation.annotation_style['repeats_file'].extension} #end if -#if $annotation['links_file'].dataset: -$annotation['links_file'] = ${spec_count}.links.${annotation['links_file'].extension} +#if $annotation.annotation_style['links_file'].dataset: +$annotation.annotation_style['links_file'] = ${annotation_count}.links.${annotation.annotation_style['links_file'].extension} #end if -#if $annotation['underlays_file'].dataset: -$annotation['underlays_file'] = ${spec_count}.underlays.${annotation['underlays_file'].extension} +#if $annotation.annotation_style['underlays_file'].dataset: +$annotation.annotation_style['underlays_file'] = ${annotation_count}.underlays.${annotation.annotation_style['underlays_file'].extension} #end if -#if $annotation['highlights_file'].dataset: -$annotation['highlights_file'] = ${spec_count}.highlights.${annotation['highlights_file'].extension} +#if $annotation.annotation_style['highlights_file'].dataset: +$annotation.annotation_style['highlights_file'] = ${annotation_count}.highlights.${annotation.annotation_style['highlights_file'].extension} #end if #end for </configfile>

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Main is at rev 1495:49fe600b9499
by Greg Von Kuster 08 Sep '08

08 Sep '08

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[hg] galaxy 1491: Fix for GMAJ tool when species chromosomes are...
by greg＠scofield.bx.psu.edu 08 Sep '08

08 Sep '08

details: http://www.bx.psu.edu/hg/galaxy/rev/9b8d06eea5b7 changeset: 1491:9b8d06eea5b7 user: Dan Blankenberg <dan(a)bx.psu.edu> date: Wed Sep 03 12:06:33 2008 -0400 description: Fix for GMAJ tool when species chromosomes are not specified. Error appears in paster.log as 'TypeError: iterable argument required' 1 file(s) affected in this change: tools/visualization/GMAJ.xml diffs (12 lines): diff -r cefbb71490a2 -r 9b8d06eea5b7 tools/visualization/GMAJ.xml --- a/tools/visualization/GMAJ.xml Sun Aug 31 21:14:06 2008 -0400 +++ b/tools/visualization/GMAJ.xml Wed Sep 03 12:06:33 2008 -0400 @@ -82,7 +82,7 @@ #set $seq_count = 0 #for $spec_count, $annotation in $enumerate( $annotations ): -#if $annotation['species'].value in $maf_input.metadata.species_chromosomes and $maf_input.metadata.species_chromosomes[$annotation['species'].value]: +#if $maf_input.metadata.species_chromosomes and $annotation['species'].value in $maf_input.metadata.species_chromosomes and $maf_input.metadata.species_chromosomes[$annotation['species'].value]: #set $seq_names = [ "%s.%s" % ( $annotation['species'].value, $chrom ) for $chrom in $maf_input.metadata.species_chromosomes[$annotation['species'].value]] #else #set $seq_names = [$annotation['species'].value]

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[hg] galaxy 1492: Fix for save link of history items.
by greg＠scofield.bx.psu.edu 08 Sep '08

08 Sep '08

details: http://www.bx.psu.edu/hg/galaxy/rev/d7e7804572fd changeset: 1492:d7e7804572fd user: Dan Blankenberg <dan(a)bx.psu.edu> date: Thu Sep 04 12:19:32 2008 -0400 description: Fix for save link of history items. 1 file(s) affected in this change: templates/root/history_common.mako diffs (12 lines): diff -r 9b8d06eea5b7 -r d7e7804572fd templates/root/history_common.mako --- a/templates/root/history_common.mako Wed Sep 03 12:06:33 2008 -0400 +++ b/templates/root/history_common.mako Thu Sep 04 12:19:32 2008 -0400 @@ -57,7 +57,7 @@ <div class="info">Info: ${data.display_info()} </div> <div> %if data.has_data: - <a href="${h.url_for( action='display', id=data.id, tofile='yes', toext='data.ext' )}" target="_blank">save</a> + <a href="${h.url_for( action='display', id=data.id, tofile='yes', toext=data.ext )}" target="_blank">save</a> %for display_app in data.datatype.get_display_types(): <% display_links = data.datatype.get_display_links( data, display_app, app, request.base ) %> %if len( display_links ) > 0:

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[hg] galaxy 1494: Fix functional test for count tool and correct...
by greg＠scofield.bx.psu.edu 08 Sep '08

08 Sep '08

details: http://www.bx.psu.edu/hg/galaxy/rev/d427760f8fec changeset: 1494:d427760f8fec user: Greg Von Kuster <greg(a)bx.psu.edu> date: Mon Sep 08 09:16:32 2008 -0400 description: Fix functional test for count tool and correct spelling errors in template. 1 file(s) affected in this change: tools/filters/uniq.xml diffs (33 lines): diff -r e85d660c46ee -r d427760f8fec tools/filters/uniq.xml --- a/tools/filters/uniq.xml Fri Sep 05 16:36:51 2008 -0400 +++ b/tools/filters/uniq.xml Mon Sep 08 09:16:32 2008 -0400 @@ -1,9 +1,9 @@ <tool id="Count1" name="Count"> - <description>occurences of each record</description> + <description>occurrences of each record</description> <command interpreter="python">uniq.py -i $input -o $out_file1 -c "$column" -d $delim</command> <inputs> <param name="input" type="data" format="tabular" label="from query" help="Query missing? See TIP below"/> - <param name="column" type="data_column" data_ref="input" multiple="True" numerical="False" label="Count occurencies of values in column(s)" help="Multi-select list - hold the appropriate key while clicking to select multiple columns" /> + <param name="column" type="data_column" data_ref="input" multiple="True" numerical="False" label="Count occurrences of values in column(s)" help="Multi-select list - hold the appropriate key while clicking to select multiple columns" /> <param name="delim" type="select" label="Delimited by"> <option value="T">Tab</option> <option value="Sp">Whitespace</option> @@ -21,7 +21,7 @@ <test> <param name="input" value="1.bed"/> <output name="out_file1" file="uniq_out.dat"/> - <param name="column" value="c1"/> + <param name="column" value="1"/> <param name="delim" value="T"/> </test> </tests> @@ -35,7 +35,7 @@ **Syntax** -This tool counts occurences of unique values in selected column(s). +This tool counts occurrences of unique values in selected column(s). - If multiple columns are selected, counting is performed on each unique group of all values in the selected columns. - The first column of the resulting query will be the count of unique values in the selected column(s) and will be followed by each value.

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