From 6232b852e0b8b1c5678e8d1ff2e9d35a0fb5532c Mon Sep 17 00:00:00 2001
From: zsloan
Date: Mon, 4 Oct 2021 18:53:02 +0000
Subject: Fixed some issue with the way the Pair Scan tab appeared in
 show_trait_mapping_tools.html

---
 .../templates/show_trait_mapping_tools.html        | 108 +--------------------
 1 file changed, 2 insertions(+), 106 deletions(-)

diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html
index 80bc6509..3c6cd62a 100755
--- a/wqflask/wqflask/templates/show_trait_mapping_tools.html
+++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html
@@ -13,7 +13,7 @@
                 <li class="rqtl-geno-tab mapping-tab {% if dataset.group.mapping_id == '3' %}active{% endif %}">
                     <a href="#rqtl_geno" data-toggle="tab">R/qtl</a>
                 </li>
-                <li class="rqtl-pair-tab mapping-tab {% if dataset.group.mapping_id == '3' %}active{% endif %}">
+                <li class="rqtl-pair-tab mapping-tab">
                     <a href="#rqtl_pair" data-toggle="tab">Pair Scan</a>
                 </li>
                 {% elif mapping_method == "QTLReaper" %}
@@ -352,7 +352,7 @@
                         </div>
                     </div>
                 </div>
-                <div class="tab-pane {% if dataset.group.mapping_id == '3' %}active{% endif %}" id="rqtl_pair">
+                <div class="tab-pane" id="rqtl_pair">
                     <div class="form-horizontal section-form-div">
                         {% if genofiles and genofiles|length > 0 %}
                         <div class="mapping_method_fields form-group">
@@ -456,110 +456,6 @@
                         </div>
                     </div>
                 </div>
-                <div class="tab-pane {% if dataset.group.mapping_id == '3' %}active{% endif %}" id="rqtl_pair">
-                    <div class="form-horizontal section-form-div">
-                        {% if genofiles and genofiles|length > 0 %}
-                        <div class="mapping_method_fields form-group">
-                            <label for="genofiles" class="col-xs-3 control-label">Genotypes</label>
-                            <div class="col-xs-6 controls">
-                                <select id="genofile_rqtl_geno" class="form-control">
-                                    {% for item in genofiles %}
-                                    <option value="{{item['location']}}:{{item['title']}}">{{item['title']}}</option>
-                                    {% endfor %}
-                                </select>
-                            </div>
-                        </div>
-                        {% endif %}
-                        <div class="mapping_method_fields form-group">
-                            <label for="mapping_permutations" class="col-xs-3 control-label">Permutations</label>
-                            <div class="col-xs-4 controls">
-                                <input name="num_perm_rqtl_geno" value="200" type="text" class="form-control">
-                            </div>
-                        </div>
-                        {% if sample_groups[0].attributes|length > 0 %}
-                        <div class="mapping_method_fields form-group">
-                            <label class="col-xs-3 control-label">Stratified</label>
-                            <div class="col-xs-6 controls">
-                                <label class="radio-inline">
-                                    <input type="radio" name="perm_strata" value="True" checked=""> 
-                                    Yes
-                                </label>
-                                <label class="radio-inline">
-                                    <input type="radio" name="perm_strata" value="False" >
-                                    No
-                               </label>
-                            </div>
-                        </div>
-                        {% endif %}
-                        <div class="mapping_method_fields form-group">
-                            <label for="control_for" class="col-xs-3 control-label">Control&nbsp;for</label>
-                            <div class="col-xs-6 controls">
-                              <input name="control_rqtl_geno" value="{% if dataset.type == 'ProbeSet' and this_trait.locus_chr != '' %}{{ nearest_marker }}{% endif %}" type="text" class="form-control cofactor-input" />
-                              <label class="radio-inline">
-                                  <input type="radio" name="do_control_rqtl" value="true">
-                                  Yes
-                              </label>
-                              <label class="radio-inline">
-                                  <input type="radio" name="do_control_rqtl" value="false" checked="">
-                                  No
-                              </label>
-                            </div>
-                        </div>
-                        <div class="mapping_method_fields form-group">
-                            <label for="mapmodel_rqtl_geno" class="col-xs-3 control-label">Model</label>
-                            <div class="col-xs-4 controls">
-                              <select id="mapmodel_rqtl_geno" name="mapmodel_rqtl_geno" class="form-control">
-                                <option value="normal">Normal</option>
-                                {% if binary == "true" %}<option value="binary">Binary</option>{% endif %}
-                                <!--<option value="2part">2-part</option>-->
-                                <option value="np">Non-parametric</option>
-                              </select>
-                            </div>
-                        </div>
-                        <div class="mapping_method_fields form-group">
-                            <label for="mapmethod_rqtl_geno" class="col-xs-3 control-label">Method</label>
-                            <div class="col-xs-6 controls">
-                              <select id="mapmethod_rqtl_geno" name="mapmethod_rqtl_geno" class="form-control">
-                                <option value="hk" selected>Haley-Knott</option>
-                                <option value="ehk">Extended Haley-Knott</option>
-                                <option value="mr">Marker Regression</option>
-                                <option value="em">Expectation-Maximization</option>
-                                <option value="imp">Imputation</option>
-                              </select>
-                            </div>
-                        </div>
-                        <div id="missing_geno_div" class="mapping_method_fields form-group" style="display: none;">
-                            <label for="missing_genotypes" class="col-xs-3 control-label"></label>
-                            <div class="col-xs-6 controls">
-                              <select id="missing_genotype" name="missing_genotypes" class="form-control">
-                                <option value="mr">Remove Samples w/o Genotypes</option>
-                                <option value="mr-imp">Single Imputation</option>
-                                <option value="mr-argmax">Imputation w/ Viterbi Algorithm</option>
-                              </select>
-                            </div>
-                        </div>
-                        <div class="mapping_method_fields form-group">
-                          <label class="col-xs-3 control-label">Covariates<br><span class="covar-text">Select covariate(s) from a collection</span></label>
-                          <div class="col-xs-8 covar-options">
-                            {% if g.user_session.num_collections < 1 %}
-                            No collections available. Please add traits to a collection to use them as covariates.
-                            {% else %}
-                            <div class="select-covar-div">
-                              <button type="button" class="btn btn-default select-covar-button select_covariates">Select</button>
-                              <button type="button" class="btn btn-default select-covar-button remove_covariates">Remove</button>
-                            </div>
-                            <textarea rows="3" cols="50" readonly placeholder="No covariates selected" class="selected-covariates"></textarea>
-                            {% endif %}
-                          </div>
-                        </div>
-                        <div class="mapping_method_fields form-group">
-                            <label class="col-xs-3 control-label"></label>
-                            <div class="col-xs-6 controls">
-                              <button id="rqtl_pair_compute" class="btn submit_special btn-success" data-url="/marker_regression" title="Compute Pair Scan" value="Compute">Compute</button>
-                            </div>
-                        </div>
-                    </div>
-                </div>
                 {% endif %}
                 {% endfor %}
             </div>
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