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index.html
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index.html
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{% extends "tool_base.html" %}
{% load static %}
{% block head %}
<head>
<link rel="stylesheet" href="{% static "tcr_dist_style" %}">
<title>TCR Distance</title>
</head>
{% endblock %}
{% block content %}
<div id="header">
<div id="line"></div>
<h2 id="title-2">TCR Distance</h2>
</div>
<div id="content">
<form enctype="multipart/form-data" id="mainForm" name="mainForm" method="post" action="results/">
{% csrf_token %}
<p class="formitem">This tool converts certain cellranger output csv files into a distance matrix file using <a href="https://github.com/phbradley/tcr-dist">tcr-dist</a> which is compatible with the distance matrix visualizer. Additionally, clones files can be directly uploaded as long as they contain all of the following fields -> [cdr3a, cdr3b, va_genes, vb_genes, epitope, subject, clone_id]</p>
<p class="formitem">To use this tool, please upload the two files below which cellranger outputs, or a clones file, both in the <b>tsv</b> format.<br>You can configure how you recieve data, or if your file is forwarded to the visualizer in the <em>Output Options</em> section.</p>
<p>The max individual filesize is 50MB, if this is too small for you please contact the server administrator and it can likely be increased.</p>
<div id="procedureBox" class="formitem" style="float: left; margin: 4px;">
<h3 class="formitem">Input Options:</h3>
<label for="filef">Upload Filtered Contig Annotations : </label> <br>
<input class="formitem" name="filef" type="file" style="width: 18em;"> <!-- Uploads filtered contig annotatinos -->
<br>
<label for="filec">Upload Consensus Annotations : </label> <br>
<input class="formitem" name="filec" type="file" style="width: 18em;"> <!-- Uploads clonotype consensus annotations -->
<p> <em>or</em></p>
<label for="filef">Upload Clones File : </label> <br>
<input class="formitem" name="filecf" type="file" style="width: 18em;"> <!-- Uploads clones_file directly -->
<p syle="text-align: center;">-----------------------------------</p>
<div class="formitem">
<input class="customRadioButton" type="radio" name="organism" value="human"/> Human
<input class="customRadioButton" type="radio" name="organism" value="mouse"/> Mouse
</div>
</div>
<!-- All of the checkboxes go here -->
<div id="procedureBox" class="formitem" style="float: left; margin: 4px;">
<h3 class="formitem">Output Options:</h3>
<h4 class="formitem">After generating distance matrix:</h4>
<div class="formitem">
<input class="customCheckbox" type="checkbox" name="sendEmail" value="sendEmail" checked="checked">
<label for="sendEmail">: Send email to </label>
<input type="text" name="emailAddress" id="emailAddress" placeholder="[email protected]" style="width: 12em;">
<p>If filesize is too large (~18MB), defaults to downloading file.</p>
<input class="customCheckbox" type="checkbox" name="download" value="download" checked="checked">
<label for="download">: Download file</label>
<br>
<input class="customCheckbox" type="checkbox" name="visualizer" value="visualizer" disabled>
<label for="visualizer">: Forward file to visualizer</label>
<br>
</div>
</div>
<div class="formitem" style="float: left; width: 100%;">
<input id="formSubmit" type="submit" name="submitBtn" value="Calculate">
<input id="terminateBtn" type="button" name="terminateBtn" value="Terminate Search">
</div>
</form>
<div id="results" style="margin-left: 1em; float: left; width: 90%;"></div>
<p style="float: left; width: 100%;">------------------------------------------- </p>
<div id="info" style="white-space:pre-line; margin-left: 1em; float: left; width: 90%;">
</div>
</div>
<script src="https://ajax.googleapis.com/ajax/libs/jquery/3.5.1/jquery.min.js"></script>
<script src="{% static "tcr_dist.js" %}?v0.7"></script>
{% endblock %}