/* 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";
}
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"
" \n"
" - clade: Specifies which clade the organism is in.
\n"
" \n"
" - genome: Specifies which organism data to use.
\n"
" \n"
" - assembly: Specifies which version of the organism's genome\n"
" sequence to use.
\n"
" \n"
" - 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.
\n"
" \n"
" - database: (with "All Tables" group option) Determines \n"
" which database should be used for options in table menu.
\n"
" \n"
" - 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.
\n"
" \n"
" - 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.
\n"
" \n"
" - data format description: Displays format information for the \n"
" tables or files associated with the selected track.
\n"
" \n"
" - 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.
\n"
" \n"
" - 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"
" \n"
" - 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.
\n"
" \n"
" - 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.
\n"
" \n"
" - 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.
\n"
" - output: Specifies the output format (not all options are \n"
" available for some tracks). Formats include:\n"
"
\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"
" - 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"
" - sequence - DNA (or protein sequence, in some cases) \n"
" associated with the table.
\n"
" - BED - positions of data items in a standard UCSC Browser \n"
" format with the name \n"
" column containing exon information separated by underscores.
\n"
" \n"
" - 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).
\n"
" \n"
" - 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.
\n"
" \n"
" - custom track - customized Genome Browser annotation \n"
" track based on the results of the query.
\n"
" \n"
" - hyperlinks to Genome Browser - returns a page full of\n"
" hyperlinks to the UCSC Genome Browser, one for each item in the table.
\n"
" \n"
" - data points - the data points that make up a graph \n"
" (aka wiggle) track.
\n"
" \n"
" - MAF - multiple alignments in MAF format
\n"
" \n"
"
\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."
" \n"
" \n"
" - Send output to Galaxy: displays results of query in \n"
" Galaxy, a framework for \n"
" interactive genome analysis.
\n"
" - 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"
"%s"
" - file type returned: When a filename is entered in the \n"
" "output file" text box, specifies the format of the output file:\n"
"
\n"
" - plain text - data is in ASCII format
\n"
" \n"
" - gzip compressed - data is compressed in gzip format
\n"
" \n"
"
\n"
" \n"
" - get output: Submits a data query based on the specified \n"
" parameters and returns the output.
\n"
" \n"
" - summary/statistics: Displays statistics about the data \n"
" specified by the parameters.
\n"
" \n"
"
\n"
, getGenomeSpaceText()
);
}