Namespace all modules under gn2.

We move all modules under a gn2 directory. This is important for
"correct" packaging and deployment as a Guix service.

1 files changed, 70 insertions, 0 deletions

diff --git a/gn2/wqflask/templates/ctl_setup.html b/gn2/wqflask/templates/ctl_setup.html
new file mode 100644
index 00000000..f5b0baf8
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+++ b/gn2/wqflask/templates/ctl_setup.html
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+{% extends "base.html" %}
+{% block title %}CTL analysis{% endblock %}
+{% block content %}
+<!-- Start of body -->
+<div class="container">
+    {% if request.form['trait_list'].split(",")|length < 2 %} <div class="alert alert-danger" role="alert">
+        <span class="glyphicon glyphicon-exclamation-sign" aria-hidden="true"></span>
+        <span class="sr-only">Error:</span>
+        <h2>Too few traits as input</h2>
+        Please make sure you select enough traits to perform CTL. Your collection needs to contain at least 2 different traits. You provided {{request.form['trait_list'].split(',')|length}} traits as input.
+</div>
+{% else %}
+<h1>CTL analysis</h1>
+CTL analysis is published as open source software, if you are using this method in your publications, please cite:<br><br>
+Arends D, Li Y, Brockmann GA, Jansen RC, Williams RW, Prins P<br>
+Correlation trait locus (CTL) mapping: Phenotype network inference subject to genotype.<br>
+The Journal of Open Source Software (2016)<br>
+Published in <a href="http://joss.theoj.org/papers/10.21105/joss.00087"><img src="http://joss.theoj.org/papers/10.21105/joss.00087/status.svg"></a>
+<br><br>
+<form class="col-md-8" action="/ctl_results" method="post" class="form-horizontal" id="ctl_form">
+    <input type="hidden" name="trait_list" id="trait_list" value="{{request.form['trait_list']}}">
+    <div class="form-group row">
+        <label for="Strategy" class="col-md-3 col-form-label col-form-label-sm">Strategy</label>
+        <div class="col-md-9">
+            <select class="form-control col-md-9" name="strategy" id="strategy">
+                <option value="Exact" selected="selected">Exact</option>
+                <option value="Full">Full</option>
+                <option value="Pairwise">Pairwise</option>
+            </select>
+        </div>
+    </div>
+    <div class="form-group row">
+        <label for="corType" class="col-md-3 col-form-label col-form-label-sm">Perform parametric analysis</label>
+        <div class="col-md-9">
+            <select class="form-control  col-md-9" name="parametric" id="parametric">
+                <option value="True" selected="selected">True</option>
+                <option value="False">False</option>
+            </select>
+        </div>
+    </div>
+    <div class="form-group row">
+        <label for="Permutations" class="col-md-3 col-form-label col-form-label-sm">Number of permutation <span style="color:red;">(Used when strategy is Full or Pairwise)</span></label>
+        <div class="col-md-9">
+            <select class="form-control" name="nperm" id="nperm">
+                <option value="100">100</option>
+                <option value="1000" selected="selected">1000</option>
+                <option value="10000">10000</option>
+            </select>
+        </div>
+    </div>
+    <div class="form-group row">
+        <label for="Significance" class="col-md-3 col-form-label col-form-label-sm"> Significance level</label>
+        <div class="col-md-9">
+            <select class="form-control" name="significance" id="significance">
+                <option value="0.1">0.1</option>
+                <option value="0.05" selected="selected">0.05</option>
+                <option value="0.001">0.001</option>
+            </select>
+        </div>
+    </div>
+    <div class="form-group">
+        <div class="text-center">
+            <input type="submit" class="btn btn-primary" value="Run CTL using these settings" />
+        </div>
+    </div>
+</form>
+{% endif %}
+</div>
+{% endblock %}
+