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<!DOCTYPE html>
<html lang="en">
<head>
<title>Experiment Metadata</title>
<!-- JS -->
<script src="//cdnjs.cloudflare.com/ajax/libs/jquery/2.1.4/jquery.min.js"></script>
<script src="//cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.5/js/bootstrap.min.js"></script>
<script src="//cdnjs.cloudflare.com/ajax/libs/d3/3.5.9/d3.min.js"></script>
<script src="//cdnjs.cloudflare.com/ajax/libs/underscore.js/1.8.3/underscore-min.js"></script>
<script src="lib/select2.js"></script>
<script src="//cdnjs.cloudflare.com/ajax/libs/bootstrap-datepicker/1.5.0/js/bootstrap-datepicker.min.js"></script>
<script src="//cdnjs.cloudflare.com/ajax/libs/FileSaver.js/2014-11-29/FileSaver.min.js"></script>
<script src="lib/filereader.js"></script>
<script src="lib/csv.min.js"></script>
<script src="lib/bootstrap-number-input.js"></script>
<script src="lib/jszip.min.js"></script>
<script src="main.js"></script>
<!-- CSS -->
<link href="//cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.5/css/bootstrap.min.css" rel="stylesheet" />
<link href="//cdnjs.cloudflare.com/ajax/libs/select2/4.0.0/css/select2.min.css" rel="stylesheet" />
<link href="//cdnjs.cloudflare.com/ajax/libs/bootstrap-datepicker/1.5.0/css/bootstrap-datepicker.min.css" rel="stylesheet" />
<link href="style.css" rel="stylesheet" />
<!-- Bootstrap Toggle -->
<link href="https://gitcdn.github.io/bootstrap-toggle/2.2.2/css/bootstrap-toggle.min.css" rel="stylesheet">
<script src="https://gitcdn.github.io/bootstrap-toggle/2.2.2/js/bootstrap-toggle.min.js"></script>
<meta charset="utf-8">
<meta name="viewport" content="width=device-width, initial-scale=1.0, maximum-scale=1.0, user-scalable=no"/>
<meta name="google" content="notranslate">
<meta http-equiv="Content-Language" content="en">
</head>
<body>
<div class="container">
<h1>
Experimental Metadata
<small>[<a href="http://github.com/SBRG/experiment_metadata">GitHub</a>]</small>
</h1>
<p class="lead">
Use this tool to generate a CSV file with all the relevant metadata for
an experiment.
</p>
<hr/>
<p>
Toggle between <i>Generic</i> or <i>ALE</i> metadata workflows
</p>
<input id="switch" type="checkbox" checked data-toggle="toggle" data-on="Generic" data-off="ALE"
data-offstyle="success">
<script>
$(function () {
$('#switch').change(function () {
if ($(this).prop('checked')) {
create_form('Generic');
} else {
create_form('ALE');
}
})
})
</script>
<hr/>
<div id="generic_instructions">
<p>
<i>Using this tool at SBRG:</i>
<ol>
<li>
<strong>Create a new folder</strong> on Nucleoid with the form
<code>data/raw_data/{User}/{Project Name}/{Folder Name}/</code>.
</li>
<ul>
<li>
Each data type collected on a given day gets a unique folder.
</li>
<li>
The Project Name can be anything you want, but try to make it
short, unique, and descriptive.
</li>
<li>
The Folder Name looks like <code>{YYYY}-{MM}-{DD}_{data type}</code>.
</li>
<li>
To make things easier, after you fill out this form, the Folder
Name is provided at the bottom of the page.
</li>
<li>
If there are duplicates, then add <code>_1</code>,
<code>_2</code>, … to the end.
</li>
<li>
Example: <code>data/raw_data/z1king/Y-ome/2015-11-19_Tn-Seq_1/</code>
</li>
</ul>
<li>
<strong>Copy</strong> raw data files (e.g. <code>*.fastq.gz</code>
from the MiSeq) to the new folder.
</li>
<li>
<strong>Fill out this form</strong>, save the CSV file, and put it
in your folder.
</li>
</ol>
</p>
<hr/>
</div>
<div class="panel panel-default">
<div class="panel-heading">
<strong>(Optional)</strong> Load an existing CSV file as a starting point for the new
metadata file.
</div>
<div class="panel-body">
<div id="file-upload">Drag and drop a CSV file.</div>
</div>
</div>
<div class="panel panel-default">
<div class="panel-heading">
Enter your metadata.
</div>
<div id="center-column" class="panel-body">
</div>
</div>
<div class="panel panel-default" id="csv_drag_and_drop">
<div class="panel-heading">
<strong>(Optional: ALE Specific)</strong> CSV with ALE sample names (row: ALE#, Flask#, Isolate#, Technical Replicate#).
<button id="download_example" type="submit" class="btn btn-default">
Download Example
</button>
</div>
<div class="panel-body">
<div id="name-file-upload">Drag and drop a CSV file.</div>
</div>
</div>
<div class="row">
<div class="col-sm-8">
<div class="panel panel-default">
<div class="panel-heading">
Save the metadata CSV file with your dataset.
</div>
<div class="panel-body match-height">
<button id="submit" type="submit" class="btn btn-default">
Download CSV
</button>
<span id="required-to-submit" class="alert alert-danger" style="display: none">
Some required attributes are missing.
</span>
</div>
</div>
</div>
<div class="col-sm-4" id="folder-name-panel">
<div class="panel panel-default">
<div class="panel-heading">Folder name</div>
<div class="panel-body match-height">
<input id="folder-name" class="form-control" onclick="select();" readonly></input>
</div>
</div>
</div>
</div>
</div>
</body>
</html>