From e8f96b1a4b506fed6b62ffa6b0ea2b530f4550f3 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Wed, 5 Oct 2016 19:00:17 +0000
Subject: CTL now displays proper error if fewer than 4 traits are selected.
 Also, WGCNA previously incorrectly gave an error when fewer than 5 traits
 were selected instead of fewer than 4 (because it said '<= 4').

I also improved the formatting for the html for both CTl and WGCNA Analysis.
---
 wqflask/wqflask/templates/ctl_setup.html   | 109 +++++++++++++++--------------
 wqflask/wqflask/templates/wgcna_setup.html |  85 +++++++++++-----------
 2 files changed, 98 insertions(+), 96 deletions(-)

diff --git a/wqflask/wqflask/templates/ctl_setup.html b/wqflask/wqflask/templates/ctl_setup.html
index 9c0d7bea..592e4b36 100644
--- a/wqflask/wqflask/templates/ctl_setup.html
+++ b/wqflask/wqflask/templates/ctl_setup.html
@@ -1,65 +1,70 @@
 {% extends "base.html" %}
-{% block title %}WCGNA analysis{% endblock %}
+{% block title %}CTL analysis{% endblock %}
 
 {% block content %} <!-- Start of body -->
 <div class="container">
+  {% if request.form['trait_list'].split(",")|length < 4 %}
+  <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 phenotypes as input</h2>
+    Please make sure you select enough phenotypes / genes to perform CTL. Your collection needs to contain at least 4 different traits. You provided {{request.form['trait_list'].split(',')|length}} traits as input.
+  </div>
+  {% else %}
   <h1>CTL analysis parameters</h1>
   {{(request.form['trait_list'].split(',')|length -1)}} phenotypes as input
 
-<form action="/ctl_results" method="post" class="form-horizontal">
-	<input type="hidden" name="trait_list" id="trait_list" value= "{{request.form['trait_list']}}">
+  <form action="/ctl_results" method="post" class="form-horizontal">
+    <input type="hidden" name="trait_list" id="trait_list" value= "{{request.form['trait_list']}}">
+    <div class="dropdown">
+      <label for="Strategy">Strategy</label>
+      <div class="col-sm-10">
+        <select  name="strategy" id="strategy">
+          <option value="Exact">Exact</option>
+          <option value="Full">Full</option>
+          <option value="Pairwise">Pairwise</option>
+        </select>
+      </div>
+    </div>
 
-	<div class="dropdown">
-		<label for="Strategy">Strategy</label>
-		<div class="col-sm-10">
-		<select  name="strategy" id="strategy">
-			<option value="Exact">Exact</option>
-			<option value="Full">Full</option>
-			<option value="Pairwise">Pairwise</option>
-		</select>
-		</div>
-	</div>
+    <div class="dropdown">
+      <label for="Permutations">Number of permutation (Used when strategy is Full or Pairwise)</label>
+      <div class="col-sm-10">
+        <select  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="dropdown">
-		<label for="Permutations">Number of permutation (Used when strategy is Full or Pairwise)</label>
-		<div class="col-sm-10">
-		<select  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="dropdown">
-		<label for="Coefficient">Type of correlation coefficient</label>
-		<div class="col-sm-10">
-		<select  name="parametric" id="parametric">
-			<option value="False">Spearman</option>
-			<option value="True">Pearson</option>
-		</select>
-		</div>
-	</div>
-
-
-	<div class="dropdown">
-		<label for="Significance">Significance level</label>
-		<div class="col-sm-10">
-		<select  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>
-  <br>
-	<div class="form-group">
-		<div class="col-sm-10">
-			<input type="submit" class="btn btn-primary" value="Run CTL using these settings" />
-		</div>
-	</div>
+    <div class="dropdown">
+      <label for="Coefficient">Type of correlation coefficient</label>
+      <div class="col-sm-10">
+        <select  name="parametric" id="parametric">
+          <option value="False">Spearman</option>
+          <option value="True">Pearson</option>
+        </select>
+      </div>
+    </div>
 
+    <div class="dropdown">
+      <label for="Significance">Significance level</label>
+      <div class="col-sm-10">
+        <select  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>
+    <br>
+    <div class="form-group">
+      <div class="col-sm-10">
+        <input type="submit" class="btn btn-primary" value="Run CTL using these settings" />
+      </div>
+    </div>
 </form>
-
+{% endif %}
 </div>
 {% endblock %}
diff --git a/wqflask/wqflask/templates/wgcna_setup.html b/wqflask/wqflask/templates/wgcna_setup.html
index b4a5730d..c5461497 100644
--- a/wqflask/wqflask/templates/wgcna_setup.html
+++ b/wqflask/wqflask/templates/wgcna_setup.html
@@ -4,49 +4,46 @@
 {% block content %} <!-- Start of body -->
 <h1> WGCNA analysis parameters</h1>
 <div class="container">
-		{% if request.form['trait_list'].split(",")|length <= 4 %}
-
-		<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 phenotypes as input
-				</h2>
-				Please make sure you select enough phenotypes / genes to perform WGCNA, your collection needs to contain at least 4 different phenotypes. You provided {{request.form['trait_list'].split(',')|length}} phenotypes as input
-		</div>
-    {% else %}
- 		<form action="/wgcna_results" method="post" class="form-horizontal">
-				<input type="hidden" name="trait_list" id="trait_list" value= "{{request.form['trait_list']}}">
-				<div class="form-group">
-					<label for="SoftThresholds"> Soft threshold: </label>
-					<div class="col-sm-10">
-						<input type="text" class="form-inline" name="SoftThresholds" id="SoftThresholds" value="1,2,3,4,5,6,7,8,9">
-					</div>
-				</div>
-				<div class="form-group">
-					<label for="MinModuleSize"> Minimum module size: </label>
-					<div class="col-sm-10">
-						<input type="text" class="form-inline" name="MinModuleSize" id="MinModuleSize" value="30">
-					</div>
-				</div>
-				<div class="form-group">
-					<label for="TOMtype"> TOMtype: </label>
-					<div class="col-sm-10">
-						<input type="text" class="form-inline" name="TOMtype" id="TOMtype" value="unsigned">
-					</div>
-				</div>
-				<div class="form-group">
-					<label for="mergeCutHeight"> mergeCutHeight: </label>
-					<div class="col-sm-10">
-						<input type="text" class="form-inline" name="mergeCutHeight" id="mergeCutHeight" value="0.25">
-					</div>
-				</div>
-				<div class="form-group">
-					<div class="col-sm-10">
-						<input type="submit" class="btn btn-primary" value="Run WGCNA using these settings" />
-					</div>
-				</div>
-		</form>
-		{% endif %}
+  {% if request.form['trait_list'].split(",")|length < 4 %}
+  <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 phenotypes as input</h2>
+    Please make sure you select enough phenotypes / genes to perform WGCNA. Your collection needs to contain at least 4 different phenotypes. You provided {{request.form['trait_list'].split(',')|length}} phenotypes as input.
+  </div>
+  {% else %}
+  <form action="/wgcna_results" method="post" class="form-horizontal">
+    <input type="hidden" name="trait_list" id="trait_list" value= "{{request.form['trait_list']}}">
+    <div class="form-group">
+      <label for="SoftThresholds"> Soft threshold: </label>
+      <div class="col-sm-10">
+        <input type="text" class="form-inline" name="SoftThresholds" id="SoftThresholds" value="1,2,3,4,5,6,7,8,9">
+      </div>
+    </div>
+    <div class="form-group">
+      <label for="MinModuleSize"> Minimum module size: </label>
+      <div class="col-sm-10">
+        <input type="text" class="form-inline" name="MinModuleSize" id="MinModuleSize" value="30">
+      </div>
+    </div>
+    <div class="form-group">
+      <label for="TOMtype"> TOMtype: </label>
+      <div class="col-sm-10">
+        <input type="text" class="form-inline" name="TOMtype" id="TOMtype" value="unsigned">
+      </div>
+    </div>
+    <div class="form-group">
+      <label for="mergeCutHeight"> mergeCutHeight: </label>
+      <div class="col-sm-10">
+        <input type="text" class="form-inline" name="mergeCutHeight" id="mergeCutHeight" value="0.25">
+      </div>
+    </div>
+    <div class="form-group">
+      <div class="col-sm-10">
+        <input type="submit" class="btn btn-primary" value="Run WGCNA using these settings" />
+      </div>
+    </div>
+  </form>
+  {% endif %}
 </div>
 {% endblock %}
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