c0af5f216f8ff00466f0d222cede7f491fd17d81 galt Fri Jan 20 23:09:35 2023 -0800 More fixes for stuff found by htmlCheck, refs #7914 diff --git src/hg/hgTables/usage.c src/hg/hgTables/usage.c index 461ea28..a0eb2a0 100644 --- src/hg/hgTables/usage.c +++ src/hg/hgTables/usage.c @@ -1,173 +1,173 @@ /* usage - functions that display helpful usage info text go here. -jk)*/ /* Copyright (C) 2013 The Regents of the University of California * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */ #include "common.h" #include "jksql.h" #include "hgTables.h" static char *getGenomeSpaceText() /* Return GenomeSpace help text if it is enabled */ { if (isGenomeSpaceEnabled()) { return "

Send output to GenomeSpace: sends data to \n" " GenomeSpace Data Manager for use with\n" -" diverse computational tools.\n"; +" diverse computational tools.

\n"; } else { return ""; } } void printMainHelp() /* Put up main page help info. */ { hPrintf( "This section provides brief line-by-line descriptions of the Table \n" "Browser controls. For more information on using this program, see the \n" "Table \n" "Browser User's Guide.\n" "

clade: Specifies which clade the organism is in.
genome: Specifies which organism data to use.
assembly: Specifies which version of the organism's genome\n" " sequence to use.
group: Selects the type of tracks to be displayed in \n" " the track list. The options correspond to the track groupings\n" " shown in the Genome Browser. Select 'All Tracks' for an alphabetical list\n" " of all available tracks in all groups. Select 'All Tables' to see all tables\n" " including those not associated with a track.
database: (with "All Tables" group option) Determines \n" " which database should be used for options in table menu.
track: Selects the annotation track data to work with. This \n" " list displays all tracks belonging to the group specified in the \n" " group list. \n" " Some tracks are not available when the region is set to genome \n" " due to the data provider's restrictions on sharing.
table: Selects the SQL table data to use. This list shows \n" " all tables associated with the track specified in the track \n" " list. \n" " Some tables may be unavailable due to the data provider's restrictions on sharing.
describe table schema: Displays schema information for the \n" " tables associated with the selected track.
region: Restricts the query to a\n" " particular chromosome or region.\n" " Select genome to apply the query to the entire genome \n" " (not available for certain tracks with restrictions on data sharing).\n" " In some Human assemblies, you may select ENCODE to examine only the \n" " ENCODE Pilot regions.\n" " To limit the query to a specific position, type a \n" " chromosome name, e.g. chrX, or a chromosome coordinate \n" " range, such as chrX:100000-200000, or a gene name or other id in \n" " the text box.\n" " You can select multiple genomic regions by clicking the "define regions" \n" " button and entering up to 1,000 regions in a 3- or 4-field BED file \n" " format.
lookup: Press this button after typing in a gene name or \n" -" other id in the position text box to look up the chromosome position\n" +" other id in the position text box to look up the chromosome position
identifiers (selected tracks only): Restricts the \n" " output to table data that match a list of identifiers, for\n" " instance RefSeq accessions for the RefSeq track. If no identifiers \n" " are entered, all table data within the specified region will be \n" " displayed.
filter: Restricts the query to only those items that\n" " match certain criteria, e.g. genes with a single exon. Click the \n" " Create button to add a filter, the Edit button to \n" " modify an existing filter, or the Clear button to remove an \n" " existing filter.
intersection (selected tracks only): Combines the output \n" " of two queries into a \n" " single set of data based on specific join criteria. For example, this \n" " can be used to find all SNPs that intersect with RefSeq coding \n" " regions. The intersection can be configured to retain the \n" " existing alignment structure of the table with a specified amount of \n" " overlap, or discard the structure in favor of a simple list of position\n" " ranges using a base-pair intersection or union of the two data sets. \n" " The button functionalities are similar to those of the filter\n" " option.
output: Specifies the output format (not all options are \n" " available for some tracks). Formats include:\n" "
- all fields from selected table - data from the selected table\n" " displayed in a tab-separated format suitable \n" " for import into spreadsheets and relational databases. The ASCII \n" -" format may be read in any web browser or text editor.\n" +" format may be read in any web browser or text editor.
- selected fields from primary and related tables - user-selected \n" " set of tab-separated fields \n" -" from the selected table and (optionally) other related tables as well. \n" +" from the selected table and (optionally) other related tables as well.
- sequence - DNA (or protein sequence, in some cases) \n" " associated with the table.
- BED - positions of data items in a standard UCSC Browser \n" " format with the name \n" " column containing exon information separated by underscores.
- GTF - positions of all data items in a\n" " limited gene transfer format \n" " (both BED and GTF formats can be used as the basis for custom tracks).
- CDS FASTA alignment from multiple alignment \n" " - FASTA alignments of the CDS regions of a gene prediction track \n" " using any of the multiple alignment tracks for the current database. \n" " Output sequence can be in either nucleotide-space or translated to \n" " protein-space. Available only for genePred tracks.
- custom track - customized Genome Browser annotation \n" " track based on the results of the query.
- hyperlinks to Genome Browser - returns a page full of\n" " hyperlinks to the UCSC Genome Browser, one for each item in the table.
- data points - the data points that make up a graph \n" " (aka wiggle) track.
- MAF - multiple alignments in MAF format
\n" " Note that all start-end coordinate ranges are returned in UCSC's internal zero-based/half-open format, see our " " FAQ, with the exception of the formats GTF, data points (aka \"wiggle\") " " and hyperlinks, which are one-based/closed." "
Send output to Galaxy: displays results of query in \n" " Galaxy, a framework for \n" -" interactive genome analysis.\n" +" interactive genome analysis.
Send output to GREAT: displays the functional enrichments of the \n" " query results in GREAT, a tool for\n" -" analysis of the biological function of cis-regulatory regions.\n" +" analysis of the biological function of cis-regulatory regions.
file type returned: When a filename is entered in the \n" " "output file" text box, specifies the format of the output file:\n" "
- plain text - data is in ASCII format\n" +"
- plain text - data is in ASCII format
- gzip compressed - data is compressed in gzip format\n" +"
- gzip compressed - data is compressed in gzip format
\n" "
get output: Submits a data query based on the specified \n" " parameters and returns the output.
summary/statistics: Displays statistics about the data \n" " specified by the parameters.

\n" , getGenomeSpaceText() ); }