diff options
Diffstat (limited to 'emacs.d/nxhtml/tests/in/josh-091115-cancer_summary.xsl')
| -rw-r--r-- | emacs.d/nxhtml/tests/in/josh-091115-cancer_summary.xsl | 490 |
1 files changed, 0 insertions, 490 deletions
diff --git a/emacs.d/nxhtml/tests/in/josh-091115-cancer_summary.xsl b/emacs.d/nxhtml/tests/in/josh-091115-cancer_summary.xsl deleted file mode 100644 index 043e9d2..0000000 --- a/emacs.d/nxhtml/tests/in/josh-091115-cancer_summary.xsl +++ /dev/null @@ -1,490 +0,0 @@ -<xsl:stylesheet xmlns:xsl="http://www.w3.org/1999/XSL/Transform" version="1.0" - xmlns:set="http://exslt.org/sets"> - - <xsl:output method="html"/> - <xsl:output encoding="utf-8"/> - <xsl:output doctype-system="http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"/> - <xsl:output doctype-public="-//W3C//DTD XHTML 1.0 Transitional//EN"/> - - <xsl:template match="/"> - - <html> - <head> - <title>Cancer Summary: <xsl:value-of select="//individual/@name"/> <xsl:value-of select="//individual/@gender"/> <xsl:value-of select="//individual/@id"/></title> - - <link rel="shortcut icon" href="/resources/report_resources/apipe_dashboard/images/gc_favicon.png" type="image/png" /> - - <link rel="stylesheet" href="/resources/report_resources/apipe_dashboard/css/master.css" type="text/css" media="screen" /> - <link rel="stylesheet" href="/resources/report_resources/apipe_dashboard/css/tablesorter.css" type="text/css" media="screen" /> - <script type="text/javascript" src="/resources/report_resources/jquery/jquery.js"></script> - <script type="text/javascript" src="/resources/report_resources/jquery/jquery.tablesorter.min.js"></script> - <script type="text/javascript"> - $(document).ready(function() { - $("#tier_1_snps").tablesorter({ - // sort on first column, ascending - // sortList: [[0,0]] - }); - - $("#tier_1_insertions").tablesorter({ - // sort on first column, ascending - //sortList: [[0,0]] - }); - - $("#tier_1_deletions").tablesorter({ - // sort on first column, ascending - //sortList: [[0,0]] - }); - }); - </script> - <link rel="stylesheet" href="/resources/report_resources/cancer_card/css/zoom2.css" type="text/css" media="screen"></link> - <script type="text/javascript" src="/resources/report_resources/cancer_card/js/dom-drag.js"></script> - - <script type="text/javascript" src="/resources/report_resources/cancer_card/js/HotSpot2.js"></script> - <script type="text/javascript"> - addEvent(window, 'load', function() { - HotSpotController.init("zoomImage",300, '<xsl:value-of select="//individual/circos-images/@large"/>','ZTbutton'); }); - - function addEvent(obj, evType, fn) { - if (obj.addEventListener) { - obj.addEventListener(evType, fn, false); - return true; - } else if (obj.attachEvent) { - var r = obj.attachEvent("on" + evType, fn); - return r; - } else { - return false; - } - } - </script> - - <script type="text/javascript"> - $(document).ready(function() { - $("input[type=checkbox]").click(function() { - alert("Clicked: " + this.value); - }); - }); - </script> - - <style type="text/css" media="screen"> - table.info_table_group td { - padding-right: 10px; - } - - div.content_padding { - padding: 0 10px 20px 10px; - } - - h3.group_header { - border-bottom: 2px solid #CCC; - } - div.circos_graph { - float: left; - width: 920px; - } - - form.status_selector { - margin: 0; - padding: 0; - float: right; - font-size: 85%; - font-weight: normal; - } - - form.status_selector table { - margin: 0; - padding: 0; - } - - form.status_selector table td.lbl { - padding-right: 10px; - padding-left: 5px; - } - - - form.status_selector table td.table_lbl { - font-weight: bold; - padding-right: 8px; - padding-left: 3px; - } - </style> - </head> - - <body> - <div class="container"> - <div class="background"> - <div class="page_header"> - <table cellpadding="0" cellspacing="0" border="0"> - <tr> - <td> - <img src="/resources/report_resources/apipe_dashboard/images/gc_header_logo2.png" width="44" height="45" align="absmiddle" /> - </td> - <td> - <h1><xsl:value-of select="//individual/@name"/> <xsl:value-of select="//individual/@gender"/> <xsl:value-of select="//individual/@id"/> Cancer Summary</h1> - </td> - </tr> - </table> - </div> - <div class="page_padding"> - <!-- <h2 class="page_title icon_instrument_data">Flow Cell <xsl:value-of select="//flow-cell/@id"/> Status</h2> --> - <table cellpadding="0" cellspacing="0" border="0" class="info_table_group"> - <tr> - <td> - <h3 class="group_header">Clinical Data</h3> - <table border="0" cellpadding="0" cellspacing="0"> - <tr> - <td> - <table border="0" cellpadding="0" cellspacing="0" class="info_table" width="100%"> - <colgroup> - <col/> - <col width="100%"/> - </colgroup> - <tr><td class="label">Name:</td><td class="value"><xsl:value-of select="//individual/@name"/></td></tr> - <tr> - <td class="label">Gender:</td> - <td class="value"> - <xsl:choose> - <xsl:when test="string(//individual/@gender)"> - <xsl:value-of select="//individual/@gender"/> - </xsl:when> - <xsl:otherwise> - Not Provided - </xsl:otherwise> - </xsl:choose> - </td> - </tr> - <tr><td class="label">ID:</td><td class="value"><xsl:value-of select="//individual/@id"/></td></tr> - - </table> - </td> - <td> - <table border="0" cellpadding="0" cellspacing="0" class="info_table" width="100%" style="float: left;"> - <colgroup> - <col/> - <col width="100%"/> - </colgroup> - - <tr><td class="label">Year Diagnosed:</td><td class="value"><xsl:value-of select="//clinical-data/@diagnosis-year"/></td></tr> - <tr><td class="label">Diagnosed at Age:</td><td class="value"><xsl:value-of select="//clinical-data/@diagnosis-age"/></td></tr> - <xsl:choose> - <xsl:when test="//clinical-data/@alive = '1'"> - <tr><td class="label">Survived:</td><td class="value">Yes</td></tr> - </xsl:when> - <xsl:otherwise> - <tr><td class="label">Survived:</td><td class="value">No</td></tr> - <tr><td class="label">Days Survived:</td><td class="value"><xsl:value-of select="//clinical-data/@days-survived"/></td></tr> - </xsl:otherwise> - </xsl:choose> - </table> - </td> - <td> - <table border="0" cellpadding="0" cellspacing="0" class="info_table" width="100%" style="float: left;"> - <colgroup> - <col/> - <col width="100%"/> - </colgroup> - - <tr><td class="label">Treatment:</td><td class="value"><xsl:value-of select="//clinical-data/@treatment"/></td></tr> - <tr><td class="label">Outcome:</td><td class="value"><xsl:value-of select="//clinical-data/@outcome"/></td></tr> - <tr><td class="label">AMP:</td><td class="value"><xsl:value-of select="//clinical-data/@amp"/></td></tr> - - </table> - </td> - </tr> - </table> - </td> - <td> - <h3 class="group_header">Sequencing Stats</h3> - <table border="0" cellpadding="0" cellspacing="0" class="info_table" width="100%"> - <colgroup> - <col/> - <col width="100%"/> - </colgroup> - <tr><td class="label">Normal Coverage:</td><td class="value"><xsl:value-of select="//samples/sample/models/model/@normal-haploid-coverage"/>X</td></tr> - <tr><td class="label">Tumor Coverage:</td><td class="value"><xsl:value-of select="//samples/sample/models/model/@tumor-haploid-coverage"/>X</td></tr> - </table> - </td> - </tr> - </table> - <hr style="margin-bottom: 0;"/> - <h2 class="report_section" style="margin-bottom: 0; margin-top: 0">Circos Graph   <a id="ZTbutton" href="javascript: void(0);" style="font-size: 85%; font-weight: normal;">[toggle zoom]</a></h2> - <p id="ZTthumbnail"> - <img> - <xsl:attribute name="id">zoomImage</xsl:attribute> - <xsl:attribute name="src"><xsl:value-of select="//individual/circos-images/@small"/></xsl:attribute> - <xsl:attribute name="width">920</xsl:attribute> - <xsl:attribute name="height">920</xsl:attribute> - </img> - </p> - <h2 class="report_section" style="margin-bottom: 0">Tier 1 SNPs -<!-- <form class="status_selector"> - <input type="hidden" name="table" value="tier_1_snps"/> - <table cellpadding="0" cellspacing="0"> - <tr> - <td class="table_lbl">Show:</td> - <xsl:for-each select="set:distinct(//variants/snps/snp/@validation-status)"> - <td class="cb"> - <input type="checkbox"><xsl:attribute name="value"><xsl:value-of select="."/></xsl:attribute></input> - </td> - <td class="lbl"> - <xsl:value-of select="."/> - </td> - </xsl:for-each> - </tr> - </table> - </form> ---> - - </h2> - <table id="tier_1_snps" class="list tablesorter" width="100%" cellspacing="0" cellpadding="0" border="0" style="margin-top: 0;"> - <xsl:choose> - <xsl:when test="count(//variants/snps/snp) > 0"> - - <thead> - <tr> - <th>validation status</th> - <th>chromosome</th> - <th class="last">start</th> - <th class="last">reference</th> - <th class="last">variant</th> - <th class="last">gene</th> - <th class="last">amino acid change</th> - <th class="last">trv type</th> - </tr> - </thead> - <tbody> - <xsl:for-each select="//variants/snps/snp"> - <xsl:sort select="@validation-status" data-type="text" order="ascending"/> - <xsl:sort select="@chromosome" data-type="number" order="ascending"/> - <tr> - <td class="validation_status"><xsl:value-of select="@validation-status"/></td> - <td><xsl:value-of select="@chromosome"/></td> - <td class="last"> - <xsl:variable name="start" select="@start"/><xsl:value-of select="format-number($start, '#,##0')"/> - </td> - <td class="last"><xsl:value-of select="@reference-allele"/></td> - <td class="last"><xsl:value-of select="@variant-allele"/></td> - <td class="last"><xsl:value-of select="@gene"/></td> - <td class="last"><xsl:value-of select="@amino-acid-change"/></td> - <td class="last"><xsl:value-of select="@trv-type"/></td> - </tr> - </xsl:for-each> - </tbody> - </xsl:when> - <xsl:otherwise> - <tr><td><span class="note">None found.</span></td></tr> - </xsl:otherwise> - </xsl:choose> - </table> - - <h2 class="report_section" style="margin-bottom: 0">Tier 1 Insertions</h2> - <table id="tier_1_insertions" class="list tablesorter" width="100%" cellspacing="0" cellpadding="0" border="0" style="margin-top: 0;"> - <xsl:choose> - <xsl:when test="count(//variants/insertions/insertion) > 0"> - <thead> - <tr> - <th>validation status</th> - <th>chromosome</th> - <th class="last">start</th> - <th class="last">stop</th> - <th class="last">variant</th> - <th class="last">gene</th> - <th class="last">amino acid change</th> - <th class="last">trv type</th> - </tr> - </thead> - <tbody> - <xsl:for-each select="//variants/insertions/insertion"> - <xsl:sort select="@validation-status" data-type="text" order="ascending"/> - <xsl:sort select="@chromosome" data-type="number" order="ascending"/> - <tr> - <td class="validation_status"><xsl:value-of select="@validation-status"/></td> - <td><xsl:value-of select="@chromosome"/></td> - <td class="last"> - <xsl:variable name="start" select="@start"/><xsl:value-of select="format-number($start, '#,##0')"/> - </td> - <td class="last"> - <xsl:variable name="stop" select="@stop"/><xsl:value-of select="format-number($stop, '#,##0')"/> - </td> - <td class="last"><xsl:value-of select="@variant-allele"/></td> - <td class="last"><xsl:value-of select="@gene"/></td> - <td class="last"><xsl:value-of select="@amino-acid-change"/></td> - <td class="last"><xsl:value-of select="@trv-type"/></td> - </tr> - </xsl:for-each> - </tbody> - </xsl:when> - <xsl:otherwise> - <tr><td><span class="note">None found.</span></td></tr> - </xsl:otherwise> - </xsl:choose> - </table> - - <h2 class="report_section" style="margin-bottom: 0">Tier 1 Deletions</h2> - <table id="tier_1_deletions" class="list tablesorter" width="100%" cellspacing="0" cellpadding="0" border="0" style="margin-top: 0;"> - <xsl:choose> - <xsl:when test="count(//variants/deletions/deletion) > 0"> - <thead> - <tr> - <th>validation status</th> - <th>chromosome</th> - <th class="last">start</th> - <th class="last">stop</th> - <th class="last">reference</th> - <th class="last">gene</th> - <th class="last">amino acid change</th> - <th class="last">trv type</th> - </tr> - </thead> - <tbody> - <xsl:for-each select="//variants/deletions/deletion"> - <xsl:sort select="@validation-status" data-type="text" order="ascending"/> - <xsl:sort select="@chromosome" data-type="number" order="ascending"/> - <tr> - <td class="validation_status"><xsl:value-of select="@validation-status"/></td> - <td><xsl:value-of select="@chromosome"/></td> - <td class="last"> - <xsl:variable name="start" select="@start"/><xsl:value-of select="format-number($start, '#,##0')"/> - </td> - <td class="last"> - <xsl:variable name="stop" select="@stop"/><xsl:value-of select="format-number($stop, '#,##0')"/> - </td> - <td class="last"><xsl:value-of select="@reference-allele"/></td> - <td class="last"><xsl:value-of select="@gene"/></td> - <td class="last"><xsl:value-of select="@amino-acid-change"/></td> - <td class="last"><xsl:value-of select="@trv-type"/></td> - </tr> - </xsl:for-each> - </tbody> - </xsl:when> - <xsl:otherwise> - <tr><td><span class="note">None found.</span></td></tr> - </xsl:otherwise> - </xsl:choose> - </table> - - <h2 class="report_section" style="margin-bottom: 0;">Structural Variations (translocations)</h2> - <table id="sv_translocations" class="list" width="100%" cellspacing="0" cellpadding="0" border="0" style="margin-top: 0;"> - <xsl:choose> - <xsl:when test="count(//structural-variants/translocations/translocation) > 0"> - <thead> - <tr> - <th>validation status</th> - <th class="last">chromosome</th> - <th class="last">position</th> - <th> </th> - <th class="last">chromosome</th> - <th class="last">position</th> - </tr> - </thead> - <tbody> - <xsl:for-each select="//structural-variants/translocations/translocation"> - <xsl:sort select="@validation-status" data-type="text" order="ascending"/> - <xsl:sort select="start/@chromosome" data-type="number" order="ascending"/> - <tr> - <td class="validation_status"><xsl:value-of select="@validation-status"/></td> - <td class="last"><xsl:value-of select="start/@chromosome"/></td> - <td class="last"> - <xsl:variable name="start_position" select="start/@position"/><xsl:value-of select="format-number($start_position, '#,##0')"/> - </td> - - <td class="last"><span style="font-size: 100%; font-weight: bold;">→</span></td> - - <td class="last"><xsl:value-of select="stop/@chromosome"/></td> - <td class="last"> - <xsl:variable name="stop_position" select="stop/@position"/><xsl:value-of select="format-number($stop_position, '#,##0')"/> - </td> - </tr> - </xsl:for-each> - </tbody> - </xsl:when> - <xsl:otherwise> - <tr><td><span class="note">None found.</span></td></tr> - </xsl:otherwise> - </xsl:choose> - </table> - - <h2 class="report_section" style="margin-bottom: 0;">Structural Variations (insertions)</h2> - <table id="sv_insertions" class="list" width="100%" cellspacing="0" cellpadding="0" border="0" style="margin-top: 0;"> - <tbody> - <xsl:choose> - <xsl:when test="count(//structural-variants/insertions/insertion) > 0"> - <thead> - <tr> - <th>validation status</th> - <th class="last">chromosome</th> - <th class="last">start</th> - <th class="last">stop</th> - <th class="last">size</th> - </tr> - </thead> - <xsl:for-each select="//structural-variants/insertions/insertion"> - <xsl:sort select="@validation-status" data-type="number" order="ascending"/> - <xsl:sort select="start/@chromosome" data-type="number" order="ascending"/> - <tr> - <td class="validation_status"><xsl:value-of select="@validation-status"/></td> - <td class="last"><xsl:value-of select="start/@chromosome"/></td> - <td class="last"> - <xsl:variable name="start_position" select="start/@position"/><xsl:value-of select="format-number($start_position, '#,##0')"/> - </td> - <td class="last"> - <xsl:variable name="stop_position" select="stop/@position"/><xsl:value-of select="format-number($stop_position, '#,##0')"/> - </td> - <xsl:variable name="size" select="@size"/><xsl:value-of select="format-number($size, '#,##0')"/> - - </tr> - </xsl:for-each> - </xsl:when> - <xsl:otherwise> - <tr><td><span class="note">None found.</span></td></tr> - </xsl:otherwise> - </xsl:choose> - </tbody> - </table> - - <h2 class="report_section" style="margin-bottom: 0;">Structural Variations (deletions)</h2> - <table id="sv_deletions" class="list" width="100%" cellspacing="0" cellpadding="0" border="0" style="margin-top: 0;"> - <xsl:choose> - <xsl:when test="count(//structural-variants/deletions/deletion) > 0"> - <thead> - <tr> - <th>validation status</th> - <th class="last">chromosome</th> - <th class="last">start</th> - <th class="last">stop</th> - <th class="last">size</th> - </tr> - </thead> - <tbody> - <xsl:for-each select="//structural-variants/deletions/deletion"> - <xsl:sort select="@validation-status" data-type="number" order="ascending"/> - <xsl:sort select="start/@chromosome" data-type="number" order="ascending"/> - <tr> - <td class="validation_status"><xsl:value-of select="@validation-status"/></td> - <td class="last"><xsl:value-of select="start/@chromosome"/></td> - <td class="last"> - <xsl:variable name="start_position" select="start/@position"/><xsl:value-of select="format-number($start_position, '#,##0')"/> - </td> - <td class="last"> - <xsl:variable name="stop_position" select="stop/@position"/><xsl:value-of select="format-number($stop_position, '#,##0')"/> - </td> - <td class="last"> - <xsl:variable name="size" select="@size"/><xsl:value-of select="format-number($size, '#,##0')"/> - </td> - </tr> - </xsl:for-each> - </tbody> - </xsl:when> - <xsl:otherwise> - <tr><td><span class="note">None found.</span></td></tr> - </xsl:otherwise> - </xsl:choose> - </table> - </div> - </div> - </div> - </body> - </html> - - </xsl:template> - -</xsl:stylesheet> |