From ebb515b9091237f5f3217517b3675675cbf56eb4 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Mon, 5 Oct 2020 16:14:03 -0500
Subject: Added square root to the transform functions that are only active if
 there are no negative values

* wqflask/wqflask/templates/show_trait_transform_and_filter.html - made sqrt option contingent on no negative values
---
 .../templates/show_trait_transform_and_filter.html | 145 ++++++++++-----------
 1 file changed, 70 insertions(+), 75 deletions(-)

diff --git a/wqflask/wqflask/templates/show_trait_transform_and_filter.html b/wqflask/wqflask/templates/show_trait_transform_and_filter.html
index b4118b04..9fb560a0 100644
--- a/wqflask/wqflask/templates/show_trait_transform_and_filter.html
+++ b/wqflask/wqflask/templates/show_trait_transform_and_filter.html
@@ -1,83 +1,78 @@
 <div>
-    <div class="form-horizontal">
-            <p>Edit or delete values in the Trait Data boxes, and use the
-                <strong>Reset</strong> option as
-                needed.
-            </p>
+  <div class="form-horizontal">
+          <p>Edit or delete values in the Trait Data boxes, and use the
+              <strong>Reset</strong> option as
+              needed.
+          </p>
 
-            <div id="blockMenuSpan" class="input-append" style="margin-bottom: 10px;">
-                <label for="remove_samples_field">Block samples by index:</label>
-                <input type="text" id="remove_samples_field" placeholder="Example: 3, 5-10, 12">
-                <select id="block_group" size="1">
-                  <option value="primary">
-                    {{ sample_group_types['samples_primary'] }}
-                  </option>
-                  <option value="other">
-                    {{ sample_group_types['samples_other'] }}
-                  </option>
-                </select>
-                <input type="button" id="block_by_index" class="btn btn-danger" value="Block">
-            </div>
-            <div id="remove_samples_invalid" class="alert alert-error" style="display:none;">
-                  Please check that your input is formatted correctly, e.g. <strong>3, 5-10, 12</strong>
-            </div>
-            {% if sample_groups[0].attributes %}
-            <div class="input-append" style="margin-top:10px; margin-bottom:10px;">
-                <label for="exclude_menu">Block samples by group:</label>
-                <select id="exclude_menu" size=1>
-                  {% for attribute in sample_groups[0].attributes %}
-                  <option value="{{ sample_groups[0].attributes[attribute].name.replace(' ', '_') }}">
-                      {{ sample_groups[0].attributes[attribute].name }}</option>
-                  {% endfor %}
-                </select>
-                <select id="attribute_values" size=1>
-                </select>
-                <input type="button" id="exclude_group" class="btn" value="Block">
-            </div>
-            {% endif %}
-            <div>
-              <input type="button" id="hide_no_value" class="btn btn-default" value="Hide No Value">
-              <input type="button" id="block_outliers" class="btn btn-default" value="Block Outliers">
-              <input type="button" class="btn btn-success reset" value="Reset">
-              <span class="input-append">
-                <input type="button" class="btn btn-default export" value="Export">
-                <select class="select optional span2 export_format">
-                  <option value="excel">Excel</option>
-                  <option value="csv">CSV</option>
-                </select>
-              </span>
-              <br>
-              <div style="margin-top:10px;">
-              <input type="button" id="normalize" class="btn btn-success" value="Normalize">
-              <select id="norm_method" class="select optional span2">
-                {% if negative_vals_exist == "false" %}
-                <option value="log2">Log2</option>
-                <option value="log10">Log10</option>
-                {% endif %}
-                <option value="zscore">Z-score</option>
-                <option value="qnorm">Quantile</option>
-                <option value="sqrt">Square Root</option>
-                <option value="invert">Invert +/-</option>
+          <div id="blockMenuSpan" class="input-append" style="margin-bottom: 10px;">
+              <label for="remove_samples_field">Block samples by index:</label>
+              <input type="text" id="remove_samples_field" placeholder="Example: 3, 5-10, 12">
+              <select id="block_group" size="1">
+                <option value="primary">
+                  {{ sample_group_types['samples_primary'] }}
+                </option>
+                <option value="other">
+                  {{ sample_group_types['samples_other'] }}
+                </option>
+              </select>
+              <input type="button" id="block_by_index" class="btn btn-danger" value="Block">
+          </div>
+          <div id="remove_samples_invalid" class="alert alert-error" style="display:none;">
+                Please check that your input is formatted correctly, e.g. <strong>3, 5-10, 12</strong>
+          </div>
+          {% if sample_groups[0].attributes %}
+          <div class="input-append" style="margin-top:10px; margin-bottom:10px;">
+              <label for="exclude_menu">Block samples by group:</label>
+              <select id="exclude_menu" size=1>
+                {% for attribute in sample_groups[0].attributes %}
+                <option value="{{ sample_groups[0].attributes[attribute].name.replace(' ', '_') }}">
+                    {{ sample_groups[0].attributes[attribute].name }}</option>
+                {% endfor %}
+              </select>
+              <select id="attribute_values" size=1>
+              </select>
+              <input type="button" id="exclude_group" class="btn" value="Block">
+          </div>
+          {% endif %}
+          <div>
+            <input type="button" id="hide_no_value" class="btn btn-default" value="Hide No Value">
+            <input type="button" id="block_outliers" class="btn btn-default" value="Block Outliers">
+            <input type="button" class="btn btn-success reset" value="Reset">
+            <span class="input-append">
+              <input type="button" class="btn btn-default export" value="Export">
+              <select class="select optional span2 export_format">
+                <option value="excel">Excel</option>
+                <option value="csv">CSV</option>
               </select>
-              </div>
-              <!--
-              {% if sample_groups[0].sample_qnorm is not none %}
-              <input type="button" id="qnorm" class="btn btn-default" value="Quantile Normalize">
+            </span>
+            <br>
+            <div style="margin-top:10px;">
+            <input type="button" id="normalize" class="btn btn-success" value="Normalize">
+            <select id="norm_method" class="select optional span2">
+              {% if negative_vals_exist == "false" %}
+              <option value="log2">Log2</option>
+              <option value="log10">Log10</option>
+              <option value="sqrt">Square Root</option>
               {% endif %}
-              -->
+              <option value="zscore">Z-score</option>
+              <option value="qnorm">Quantile</option>
+              <option value="invert">Invert +/-</option>
+            </select>
             </div>
-        <br>
+          </div>
+      <br>
 
-        <div>
-            <p>Outliers highlighted in
-                    <strong style="background-color:orange;">orange</strong>
-                    can be hidden using
-                    the <strong>Hide Outliers</strong> button.
-            </p>
+      <div>
+          <p>Outliers highlighted in
+                  <strong style="background-color:orange;">orange</strong>
+                  can be hidden using
+                  the <strong>Hide Outliers</strong> button.
+          </p>
 
-            <p>Samples with no value (x) can be hidden by clicking
-                    <strong>Hide No Value</strong> button.
-            </p>
-        </div>
-    </div>
+          <p>Samples with no value (x) can be hidden by clicking
+                  <strong>Hide No Value</strong> button.
+          </p>
+      </div>
+  </div>
 </div>
\ No newline at end of file
-- 
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