41e07184a720d35c7a981f2e019d961369bb637e
max
  Wed Feb 22 01:10:48 2023 -0800
adding back BED output for wiggle data, as Hiram found that one can do peak calling on a wiggle file by using the filter option and minimum value, refs #30585

diff --git src/hg/hgTables/mainPage.c src/hg/hgTables/mainPage.c
index a74c918..545bef2 100644
--- src/hg/hgTables/mainPage.c
+++ src/hg/hgTables/mainPage.c
@@ -384,31 +384,32 @@
 	hPrintf(" SELECTED");
     if (sameString(ot->name, outBed) || sameString(ot->name, outWigBed))
         hPrintf(" id=\"outBed\"");
     hPrintf(">%s</OPTION>\n", ot->label);
     }
 hPrintf("</SELECT>\n");
 hPrintf(" ");
 
 hPrintf("<DIV style='display:none; opacity:0.9; border: 1px solid #EEE; margin: 2px; padding: 4px' id='gffNote'>"
         "<b>Note:</b> Table Browser GTF files contain transcripts, but no gene identifiers or symbols.<br> "
         "If you are looking for fully formatted "
         "gene model files for use in genome analysis pipelines,<br>check the "
         "<a href='https://hgdownload.soe.ucsc.edu/goldenPath/%s/bigZips/genes'>bigZips/genes</a> "
         "directory on our download server.</DIV>", database);
 hPrintf("<DIV style='display:none; opacity:0.9; border: 1px solid #EEE; margin: 2px; padding: 4px' id='wigNote'>"
-        "<b>Signal data points format:</b> The Table Browser at the moment outputs signal track data points in wiggle text format. "
+        "<b>Signal data points format:</b> The Table Browser at the moment outputs signal track data points in "
+        "<a href='../goldenPath/help/wiggle.html' target=_blank>wiggle</a> text format. "
         "If you need the output in BED/bedGraph format, use our <a href=\"../goldenPath/help/bigWig.html#Extract\" "
         "target=_blank>bigWigToBedGraph</a> command line tool or contact us at genome@soe.ucsc.edu if that poses a problem.</div>");
 hPrintf(" ");
 
 // we should make an hgTables.js one day, this is ugly
 jsInline("function checkOutputNotes(event) {\n"
     "var outType=document.getElementById('outputTypeDropdown').value;\n"
     "if (outType==='gff')\n"
     "    document.getElementById('gffNote').style.display='';\n"
     "else if (outType==='wigData')\n"
     "    document.getElementById('wigNote').style.display='';\n"
     "else\n"
     "    $('.outputNote').hide();\n" // a lot shorter with Jquery than without
     "}\n"
     "$(document).ready(checkOutputNotes);\n"
@@ -502,31 +503,31 @@
 if (isBedGr)
     {
     if (! bedifiedOnly)
 	{
 	slAddTail(&otList, &otAllFields);
 	slAddTail(&otList, &otSelected);
 	}
     slAddTail(&otList, &otWigData);
     slAddTail(&otList, &otWigBed);
     slAddTail(&otList, &otCustomTrack);
     slAddTail(&otList, &otHyperlinks);
     }
 else if (isWig)
     {
     slAddTail(&otList, &otWigData);
-    // slAddTail(&otList, &otWigBed); removed in 2022 as output is not bedgraph and has no data points
+    slAddTail(&otList, &otWigBed);
     slAddTail(&otList, &otCustomTrack);
     // hyperlinks output works for db-wiggle but not for bigWig
     }
 else if (isHalSnake)
     {
     slAddTail(&otList, &otMaf);
     }
 else if (isMaf)
     {
     slAddTail(&otList, &otMaf);
     if (! bedifiedOnly)
 	slAddTail(&otList, &otAllFields);
     }
 else if (isChromGraphCt)
     {