<div class="container">
<script type="text/javascript">
function submitForm(s) {
s.value = "Compiling data, please wait ...";
return true;
}
</script>
[% # INCLUDE dumper.tt dump = request.path_info %]
[% # INCLUDE dumper.tt dump = dbs %]
[% # INCLUDE dumper.tt dump = params.err %]
[% IF params.err %]
<p class="alert alert-error">Error: [% params.err %]<p>
[% END %]
<!-- Browse and upload file form: -->
<form class="form-file-upload file-upload" enctype="multipart/form-data"
name="UploadForm" action="[% request.uri_base %]/vep"
onsubmit="return submitForm(this.submit);" method="post">
<fieldset>
<legend class="form-file-upload-heading">Select VEP data source</legend>
<div style="margin-left: 2em">
<ul>
<li>accepted file-types:
<ul>
<li>individual MySeq vcf file</li>
<li>zipped MySeq vcf file</li>
<li>zipped folder of MySeq vcf files</li>
<li>individual Roche 454 txt file</li>
</ul>
</li>
<li class="text-warning">all vcf filenames must contain request
number and 2-digit year in n(n)-yy format eg <b>1-13</b>,
H<b>123-14</b>, <b>1234-15</b>_rf, etc
</li>
</ul>
</div>
<!-- Start Bootstrap Template -->
<div class="fileupload fileupload-new" data-provides="fileupload">
<span class="fileupload-new thumbnail">
<img src="http://www.placehold.it/200x10" />
</span>
<span class="fileupload-preview fileupload-exists thumbnail"
style="max-width: 200px; max-height: 150px; line-height: 20px;">
</span>
<span class="btn btn-file">
<span class="fileupload-new">Select data file</span>
<span class="fileupload-exists">Change</span>
<input type="file" name="data_src"/>
</span>
<a href="data_src" class="btn fileupload-exists"
data-dismiss="fileupload">Remove</a>
<span class="text-error">[%- upload_error -%]</span>
</div>
<!-- End Bootstrap Template -->
<legend class="form-file-upload-heading">
Select options for current API version [% vars.api_version %]:
</legend>
<table>
<tr>
<td>
<div align="right"><strong>Transcript database</strong>:
Ensembl
<input type="radio" name="db" value="core"
[% IF vars.cache.core; 'checked';
ELSE; 'disabled=1'; END %] />
</div>
<div align="right">RefSeq
<input type="radio" name="db" value="refseq"
[% 'disabled=1' UNLESS vars.cache.refseq %] />
</div>
<div align="right">Merged
<input type="radio" name="db" value="merged"
[% 'disabled=1' UNLESS vars.cache.merged %] />
</div>
</td>
</tr>
<tr>
<td align="right"><strong>SIFT predictions:</strong>
<select name="sift" class="span2">
<option value="0">No</option>
<option value="p">Prediction only</option>
<option value="s">Score only</option>
<option value="b" selected>Prediction & Score</option>
</select>
</td>
</tr>
<tr>
<td align="right"><strong>PolyPhen predictions:</strong>
<select name="polyphen" class="span2">
<option value="0">No</option>
<option value="p">Prediction only</option>
<option value="s">Score only</option>
<option value="b" selected>Prediction & Score</option>
</select>
</td>
</tr>
<tr>
<td align="right"><strong>Get regulatory region consequences</strong>:
<input type="checkbox" name="regulatory" value="1" checked />
</td>
</tr>
<tr>
<td align="right"><strong>Check for existing co-located variants</strong>:
<input type="checkbox" name="check_existing" value="1" checked />
</td>
</tr>
<tr>
<td align="right"><strong>Results for variants in coding regions only</strong>:
<input type="checkbox" name="coding_only" value="1" checked />
</td>
</tr>
<tr>
<td align="right">
<strong>Report <a class="acronym" title="coding sequence">HGVSc</a>
& <a class="acronym" title="protein">HGVSp</a>
notations</strong>:
<input type="checkbox" name="hgvs" value="1" checked />
</td>
</tr>
</table>
<p class="text-info" style="padding: 1em">
Use experimental new theme ?
<input type="checkbox" name="theme" value="new" />
</p>
<div style="padding: 20px">
<input class="btn btn" value="Upload" type="submit" name="submit" />
</div>
<div>
<span class="text-error">[%- email_error -%]</span>
</div>
</fieldset>
</form>
<!-- <div id="progress"></div> -->
<div id="messages">
<p class="text-success">[%- success_message -%]</p>
<p class="text-info">[%- info_message -%]</p>
<p class="text-warning">[%- warning_message -%]</p>
<p class="text-error">[%- error_message -%]</p>
</div>
</div> <!-- /container -->