61878cb225c4fafa3ba2d38af16330fbb57377ed angie Mon Jun 13 09:52:59 2016 -0700 Basic documentation of tableBrowser noGenome support in TB and DI. refs #4458 diff --git src/hg/hgTables/usage.c src/hg/hgTables/usage.c index a00e625..b4deb6d 100644 --- src/hg/hgTables/usage.c +++ src/hg/hgTables/usage.c @@ -1,164 +1,169 @@ /* usage - functions that display helpful usage info text go here. -jk)*/ /* Copyright (C) 2013 The Regents of the University of California * See README in this or parent directory 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 " <LI><B>Send output to GenomeSpace:</B> sends data to \n" " <A HREF=\"http://www.genomespace.org\">GenomeSpace</A> 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" "<A HREF=\"../goldenPath/help/hgTablesHelp.html\" TARGET=_blank>Table \n" "Browser User's Guide</A>.\n" " <UL>\n" " <LI><B>clade: </B>Specifies which clade the organism is in.</LI>\n" " \n" " <LI><B>genome: </B>Specifies which organism data to use.</LI>\n" " \n" " <LI><B>assembly: </B>Specifies which version of the organism's genome\n" " sequence to use.</LI>\n" " \n" " <LI><B>group: </B>Selects the type of tracks to be displayed in \n" " the <em>track</em> 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.</LI>\n" " \n" " <LI><B>database: </B> (with "All Tables" group option) Determines \n" " which database should be used for options in table menu.</LI>\n" " \n" " <LI><B>track: </B>Selects the annotation track data to work with. This \n" " list displays all tracks belonging to the group specified in the \n" -" <em>group</em> list. </LI>\n" +" <em>group</em> list. \n" +" Some tracks are not available when the region is set to <em>genome</em> \n" +" due to the data provider's restrictions on sharing. </LI>\n" " \n" " <LI><B>table: </B>Selects the SQL table data to use. This list shows \n" " all tables associated with the track specified in the <em>track</em> \n" -" list.</LI>\n" +" list. \n" +" Some tables may be unavailable due to the data provider's restrictions on sharing.</LI>\n" " \n" " <LI><B>describe table schema: </B>Displays schema information for the \n" " tables associated with the selected track.</LI>\n" " \n" " <LI><B>region: </B>Restricts the query to a\n" -" particular chromosome or region. Select <em>genome</em> to apply the \n" -" query to the entire genome or <em>ENCODE</em> to examine only the \n" +" particular chromosome or region.\n" +" Select <em>genome</em> 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 <em>ENCODE</em> to examine only the \n" " ENCODE Pilot regions.\n" " To limit the query to a specific position, type a \n" " chromosome name, e.g. <em>chrX</em>, 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 <a \n" " href=\"../FAQ/FAQformat.html#format1\">BED</a> file \n" " format.</LI>\n" " \n" " <LI><B>lookup:</B> 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" " <LI><B>identifiers</B> (selected tracks only)<B>: </B>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.</LI>\n" " \n" " <LI><B>filter: </B>Restricts the query to only those items that\n" " match certain criteria, e.g. genes with a single exon. Click the \n" " <em>Create</em> button to add a filter, the <em>Edit</em> button to \n" " modify an existing filter, or the <em>Clear</em> button to remove an \n" " existing filter.</LI>\n" " \n" " <LI><B>intersection </B> (selected tracks only)<B>: </B>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 <em>filter</em>\n" " option.</LI> \n" " <LI><B>output: </B>Specifies the output format (not all options are \n" " available for some tracks). Formats include:\n" " <UL>\n" " <LI><em><B>all fields from selected table</B></em> - 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" " <LI><em><B>selected fields from primary and related tables</B></em> - user-selected \n" " set of tab-separated fields \n" " from the selected table and (optionally) other related tables as well. \n" " <LI><em><B>sequence</B></em> - DNA (or protein sequence, in some cases) \n" " associated with the table.</LI>\n" " <LI><em><B>BED</B></em> - positions of data items in a standard\n" " UCSC Browser format.</LI>\n" " \n" " <LI><em><B>GTF</B></em> - positions of all data items in a standard\n" " gene prediction format. (Both BED and GTF formats can be\n" " used as the basis for custom tracks).</LI>\n" " \n" " <LI><em><B>CDS FASTA alignment from multiple alignment</B></em> \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.</LI>\n" " \n" " <LI><em><B>custom track</B></em> - customized Genome Browser annotation \n" " track based on the results of the query.</LI>\n" " \n" " <LI><em><B>hyperlinks to Genome Browser</B></em> - returns a page full of\n" " hyperlinks to the UCSC Genome Browser, one for each item in the table.</LI>\n" " \n" " <LI><em><B>data points</B></em> - the data points that make up a graph \n" " (aka wiggle) track.</LI>\n" " \n" " <LI><em><B>MAF</B></em> - multiple alignments in MAF format</LI>\n" " \n" " </UL>\n" " </LI>\n" " \n" " <LI><B>Send output to Galaxy:</B> displays results of query in \n" " <A HREF=\""GALAXY_URL_BASE"\">Galaxy</A>, a framework for \n" " interactive genome analysis.\n" " <LI><B>Send output to GREAT:</B> displays the functional enrichments of the \n" " query results in <A HREF=\"http://great.stanford.edu\">GREAT</A>, a tool for\n" " analysis of the biological function of cis-regulatory regions.\n" "%s" " <LI><B>file type returned: </B>When a filename is entered in the \n" " "output file" text box, specifies the format of the output file:\n" " <UL>\n" " <LI><em><B>plain text</B></em> - data is in ASCII format\n" " \n" " <LI><em><B>gzip compressed</B></em> - data is compressed in gzip format\n" " \n" " </UL>\n" " </LI>\n" " <LI><B>get output: </B>Submits a data query based on the specified \n" " parameters and returns the output.</LI>\n" " \n" " <LI><B>summary/statistics: </B>Displays statistics about the data \n" " specified by the parameters.</LI>\n" " \n" " </UL>\n" , getGenomeSpaceText() ); }