From 0197d825542069f398cacda11a040865fb706a7b Mon Sep 17 00:00:00 2001
From: zsloan
Date: Tue, 17 Dec 2019 13:45:46 -0600
Subject: Changed some text for mapping options related to MAF

---
 wqflask/wqflask/templates/loading.html                  | 4 ++--
 wqflask/wqflask/templates/show_trait_mapping_tools.html | 6 +++---
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/wqflask/wqflask/templates/loading.html b/wqflask/wqflask/templates/loading.html
index 4c30664b..bc614e01 100644
--- a/wqflask/wqflask/templates/loading.html
+++ b/wqflask/wqflask/templates/loading.html
@@ -13,13 +13,13 @@
         <br>
         <i>n</i> = {{ start_vars.num_vals }}
         <br>
-        Method = {{ start_vars.method }}
+        Method = {% if start_vars.method == "gemma" %}GEMMA{% else %}{{ start_vars.method }}{% endif %}
         <br>
         {% if start_vars.transform != "" %}
         transform = {{ start_vars.transform }}
         <br>
         {% endif %}
-        MAF = {{ start_vars.maf }}
+        MAF >= {{ start_vars.maf }}
         {% else %}
         <h1>Loading&nbsp;{{ start_vars.tool_used }}&nbsp;Results...</h1>
         {% endif %}
diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html
index 3af9790e..009cc67d 100644
--- a/wqflask/wqflask/templates/show_trait_mapping_tools.html
+++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html
@@ -57,7 +57,7 @@
                         </div>
                         {% endif %}
                         <div class="mapping_method_fields form-group">
-                            <label for="maf_gemma" style="text-align: right;" class="col-xs-3 control-label">MAF</label>
+                            <label for="maf_gemma" style="text-align: right;" class="col-xs-3 control-label">MAF >=</label>
                             <div style="margin-left:20px;" class="col-xs-4 controls">
                                 <input name="maf_gemma" value="{{ maf }}" type="text" class="form-control" style="width: 80px;">
                             </div>
@@ -358,10 +358,10 @@
     <div class="col-xs-7">
         <dl style="width: 500px;">
              <dt style="padding-top: 20px;">GEMMA</dt>
-             <dd>Maps traits with correction for kinship among samples using a linear mixed model method, and also allows users to fit multiple covariates such as sex, age, treatment, and genetic markers (<a href="https://www.ncbi.nlm.nih.gov/pubmed/24531419">PMID: 2453419</a>, and <a href="https://github.com/genetics-statistics/GEMMA"> GitHub code</a>). GEMMA incorporates the Leave One Chromosome Out (LOCO) method to ensure that the correction for kinship does not remove useful genetic variance near each marker. Genotypes can be filtered to omit those markers with low minor allele frequencies (MAF of 0.05 is the default).</dd>
+             <dd>Maps traits with correction for kinship among samples using a linear mixed model method, and also allows users to fit multiple covariates such as sex, age, treatment, and genetic markers (<a href="https://www.ncbi.nlm.nih.gov/pubmed/24531419">PMID: 2453419</a>, and <a href="https://github.com/genetics-statistics/GEMMA"> GitHub code</a>). GEMMA incorporates the Leave One Chromosome Out (LOCO) method to ensure that the correction for kinship does not remove useful genetic variance near each marker. Markers can be filtered to include only those with minor allele frequencies (MAF) above a threshold. The default MAF is 0.05.</dd>
              {% if dataset.group.mapping_id == "1" %}
              <dt style="margin-top: 20px;">R/qtl</dt>
-             <dd>Major upgrade of R/qtl that supports most experimental populations including those with complex admixture and two or more parental lines as well as large omic data sets (<a href="https://www.ncbi.nlm.nih.gov/pubmed/30591514">PMID: 30591514</a>). Both R/qtl and R/qtl2 are available as a stand-alone R packages (<a href="https://kbroman.org/pages/software.html">R suite</a>).</dd>
+             <dd>Major upgrade of R/qtl that supports most experimental populations including those with complex admixture and two or more parental lines as well as large omic data sets (<a href="https://www.ncbi.nlm.nih.gov/pubmed/30591514">PMID: 30591514</a>). Both R/qtl and R/qtl2 are available as stand-alone R packages (<a href="https://kbroman.org/pages/software.html">R suite</a>).</dd>
              <dt style="margin-top: 20px;">Haley-Knott Regression</dt>
              <dd>Fast mapping linear mapping method (<a href="https://www.ncbi.nlm.nih.gov/pubmed/16718932">PMID 16718932</a>) works well with F2 intercrosses and backcrosses, but that is not recommended for complex or admixed populations (e.g., GWAS or heterogeneous stock studies) or for advanced intercrosses, recombinant inbred families, or diallel crosses. Interactive plots in GeneNetwork have relied on the fast HK mapping for two decades and we still use this method for mapping omics data sets and computing genome-wide permutation threshold (<a href="https://github.com/pjotrp/QTLReaper">QTL Reaper code</a>).</dd>
              {% endif %}
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