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-rwxr-xr-x[-rw-r--r--]wqflask/wqflask/templates/show_trait_mapping_tools.html189
1 files changed, 10 insertions, 179 deletions
diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html
index 60219cf5..03590c2c 100644..100755
--- a/wqflask/wqflask/templates/show_trait_mapping_tools.html
+++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html
@@ -1,11 +1,6 @@
<div>
-<<<<<<< HEAD
- {% if (use_pylmm_rqtl and dataset.group.species != "human") or use_plink_gemma %}
- <div class="col-xs-4">
-=======
{% if dataset.group.mapping_names|length > 0 %}
<div class="col-xs-5">
->>>>>>> cbc4e86... Changed appearance of mapping and correlation options on trait page
<div class="tabbable"> <!-- Only required for left/right tabs -->
<ul class="nav nav-pills">
@@ -43,16 +38,11 @@
{# if use_pylmm_rqtl and not use_plink_gemma and dataset.group.species != "human" #}
{% if dataset.group.mapping_id == "1" %}
<div class="tab-pane active" id="gemma">
- <div style="padding-top: 10px;" class="form-horizontal">
+ <div style="padding-top: 20px;" class="form-horizontal">
{% if genofiles and genofiles|length>0 %}
<div class="mapping_method_fields form-group">
-<<<<<<< HEAD
- <label for="genofiles" class="col-xs-3 control-label">Genotypes</label>
- <div style="margin-left: 20px;" class="col-xs-8 controls">
-=======
<label for="genofiles" style="text-align: right;" class="col-xs-3 control-label">Genotypes</label>
<div style="margin-left:20px;" class="col-xs-4 controls">
->>>>>>> cbc4e86... Changed appearance of mapping and correlation options on trait page
<select id="genofile_gemma" class="form-control">
{% for item in genofiles %}
<option value="{{item['location']}}:{{item['title']}}">{{item['title']}}</option>
@@ -62,24 +52,14 @@
</div>
{% endif %}
<div class="mapping_method_fields form-group">
-<<<<<<< HEAD
- <label for="maf_gemma" class="col-xs-5 control-label">Minor allele threshold</label>
- <div style="margin-left: 20px;" class="col-xs-3 controls">
-=======
<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">
->>>>>>> cbc4e86... Changed appearance of mapping and correlation options on trait page
<input name="maf_gemma" value="0.01" type="text" class="form-control">
</div>
</div>
<div class="mapping_method_fields form-group">
-<<<<<<< HEAD
- <label class="col-xs-4 control-label">Use LOCO</label>
- <div style="margin-left: 20px;" class="col-xs-4 controls">
-=======
<label style="text-align: right;" class="col-xs-3 control-label">Use LOCO</label>
<div style="margin-left:20px;" class="col-xs-6 controls">
->>>>>>> cbc4e86... Changed appearance of mapping and correlation options on trait page
<label class="radio-inline">
<input type="radio" name="use_loco" value="True" checked="">
Yes
@@ -90,16 +70,9 @@
</label>
</div>
</div>
+ <!--
</div>
<div style="padding-top: 5px; padding-bottom: 5px; padding-left: 20px;" class="form-horizontal">
-<<<<<<< HEAD
- <div class="mapping_method_fields form-group">
- <button type="button" id="select_covariates" class="btn btn-default">
- Select Covariates
- </button>
- <button type="button" id="remove_covariates" class="btn btn-default">
- Remove Covariates
-=======
-->
<div class="mapping_method_fields form-group">
<label style="text-align: right;" class="col-xs-3 control-label">Covariates</label>
@@ -122,30 +95,29 @@
<div style="margin-left:20px;" class="col-xs-6">
<button id="gemma_bimbam_compute" class="btn submit_special btn-success" data-url="/marker_regression" title="Compute Marker Regression">
Compute
->>>>>>> cbc4e86... Changed appearance of mapping and correlation options on trait page
</button>
+ </div>
</div>
</div>
-
+<!--
<div class="form-group">
<div class="col-xs-4 controls">
+ <label class="col-xs-2 control-label"></label>
+ <div class="col-xs-4">
<button id="gemma_bimbam_compute" class="btn submit_special btn-success" data-url="/marker_regression" title="Compute Marker Regression">
Compute
</button>
+ </div>
</div>
</div>
+-->
</div>
<div class="tab-pane" id="interval_mapping">
<div style="margin-top: 20px" class="form-horizontal">
{% if genofiles and genofiles|length>0 %}
<div class="mapping_method_fields form-group">
-<<<<<<< HEAD
- <label for="genofiles" class="col-xs-3 control-label">Genotypes</label>
- <div style="margin-left: 20px;" class="col-xs-8 controls">
-=======
<label style="text-align: right;" for="genofiles" class="col-xs-3 control-label">Genotypes</label>
<div style="margin-left:20px;" class="col-xs-4 controls">
->>>>>>> cbc4e86... Changed appearance of mapping and correlation options on trait page
<select id="genofile_reaper" class="form-control">
{% for item in genofiles %}
<option value="{{item['location']}}:{{item['title']}}">{{item['title']}}</option>
@@ -155,35 +127,20 @@
</div>
{% endif %}
<div class="mapping_method_fields form-group">
-<<<<<<< HEAD
- <label for="mapping_permutations" class="col-xs-3 control-label">Permutations</label>
- <div style="margin-left: 20px;" class="col-xs-4 controls">
-=======
<label style="text-align: right;" for="mapping_permutations" class="col-xs-3 control-label">Permutations</label>
<div style="margin-left:20px;" class="col-xs-4 controls">
->>>>>>> cbc4e86... Changed appearance of mapping and correlation options on trait page
<input name="num_perm_reaper" value="2000" type="text" class="form-control">
</div>
</div>
<div class="mapping_method_fields form-group">
-<<<<<<< HEAD
- <label for="mapping_bootstraps" class="col-xs-3 control-label">Bootstraps</label>
- <div style="margin-left: 20px;" class="col-xs-4 controls">
-=======
<label style="text-align: right;" for="mapping_bootstraps" class="col-xs-3 control-label">Bootstraps</label>
<div style="margin-left:20px;" class="col-xs-4 controls">
->>>>>>> cbc4e86... Changed appearance of mapping and correlation options on trait page
<input name="num_bootstrap" value="2000" type="text" class="form-control">
</div>
</div>
<div class="mapping_method_fields form-group">
-<<<<<<< HEAD
- <label for="control_for" class="col-xs-3 control-label">Control&nbsp;for</label>
- <div style="margin-left: 20px;" class="col-xs-4 controls">
-=======
<label style="text-align: right;" for="control_for" class="col-xs-3 control-label">Control&nbsp;for</label>
<div style="margin-left:20px;" class="col-xs-6 controls">
->>>>>>> cbc4e86... Changed appearance of mapping and correlation options on trait page
{% if dataset.type == 'ProbeSet' and this_trait.locus_chr != "" %}
<input name="control_reaper" value="{{ nearest_marker }}" type="text" style="width: 160px;" class="form-control" />
{% else %}
@@ -227,13 +184,8 @@
<div class="mapping_method_fields form-group">
-<<<<<<< HEAD
- <label style="text-align:left;" class="col-xs-3 control-label">Marker<br>Regression</label>
- <div style="margin-left: 20px;" class="col-xs-4 controls">
-=======
<label style="text-align: right;" class="col-xs-3 control-label">Marker<br>Regression</label>
<div style="margin-left:20px;" class="col-xs-6 controls">
->>>>>>> cbc4e86... Changed appearance of mapping and correlation options on trait page
<label class="radio-inline">
<input type="radio" name="manhattan_plot_reaper" value="True">
Yes
@@ -244,20 +196,12 @@
</label>
</div>
</div>
-<<<<<<< HEAD
- <div class="form-group">
- <div style="padding-left:15px;" class="controls">
- <button id="interval_mapping_compute" class="btn submit_special btn-success" data-url="/marker_regression" title="Compute Interval Mapping">
- <i class="icon-ok-circle icon-white"></i> Compute
- </button>
-=======
<div class="mapping_method_fields form-group">
<label class="col-xs-3 control-label"></label>
<div style="margin-left:20px;" class="col-xs-6">
<button id="interval_mapping_compute" class="btn submit_special btn-success" data-url="/marker_regression" title="Compute Interval Mapping">
Compute
</button>
->>>>>>> cbc4e86... Changed appearance of mapping and correlation options on trait page
</div>
</div>
<!--<div id="alert_placeholder"></div>-->
@@ -268,13 +212,8 @@
<div style="margin-top: 20px" class="form-horizontal">
{% if genofiles and genofiles|length>0 %}
<div class="mapping_method_fields form-group">
-<<<<<<< HEAD
- <label for="genofiles" class="col-xs-3 control-label">Genotypes</label>
- <div style="margin-left: 20px;" class="col-xs-8 controls">
-=======
<label style="text-align:right;" for="genofiles" class="col-xs-3 control-label">Genotypes</label>
<div style="margin-left:20px;" class="col-xs-4 controls">
->>>>>>> cbc4e86... Changed appearance of mapping and correlation options on trait page
<select id="genofile_rqtl_geno" class="form-control">
{% for item in genofiles %}
<option value="{{item['location']}}:{{item['title']}}">{{item['title']}}</option>
@@ -284,28 +223,14 @@
</div>
{% endif %}
<div class="mapping_method_fields form-group">
-<<<<<<< HEAD
- <label for="mapping_permutations" class="col-xs-3 control-label">Permutations</label>
- <div style="margin-left: 20px;" class="col-xs-4 controls">
- <input name="num_perm_rqtl_geno" value="" type="text" class="form-control">
-=======
<label style="text-align:right;" for="mapping_permutations" class="col-xs-3 control-label">Permutations</label>
<div style="margin-left:20px;" class="col-xs-4 controls">
<input name="num_perm_rqtl_geno" value="2000" type="text" class="form-control">
->>>>>>> cbc4e86... Changed appearance of mapping and correlation options on trait page
</div>
</div>
- <div id="permutations_alert" class="alert alert-error alert-warning" style="display:none;">
- Please be aware that permutations can take a very long time (~20 minutes for 500 permutations)
- </div>
<div class="mapping_method_fields form-group">
-<<<<<<< HEAD
- <label for="control_for" class="col-xs-3 control-label">Control&nbsp;for</label>
- <div style="margin-left: 20px;" class="col-xs-4 controls">
-=======
<label style="text-align:right;" for="control_for" class="col-xs-3 control-label">Control&nbsp;for</label>
<div style="margin-left:20px;" class="col-xs-6 controls">
->>>>>>> cbc4e86... Changed appearance of mapping and correlation options on trait page
{% if dataset.type == 'ProbeSet' and this_trait.locus_chr != "" %}
<input name="control_rqtl_geno" value="{{ nearest_marker }}" type="text" style="width: 160px;" class="form-control" />
{% else %}
@@ -323,13 +248,8 @@
</div>
<div class="mapping_method_fields form-group">
-<<<<<<< HEAD
- <label for="mapmethod_rqtl_geno" style="text-align:left;" class="col-xs-3 control-label">Method</label>
- <div class="col-xs-4 controls">
-=======
<label style="text-align:right;" for="mapmethod_rqtl_geno" class="col-xs-3 control-label">Method</label>
<div style="margin-left:20px;" class="col-xs-4 controls">
->>>>>>> cbc4e86... Changed appearance of mapping and correlation options on trait page
<select name="mapmethod_rqtl_geno" class="form-control">
<option value="em">em</option>
<option value="imp">imp</option>
@@ -343,13 +263,8 @@
</div>
<div class="mapping_method_fields form-group">
-<<<<<<< HEAD
- <label for="mapmodel_rqtl_geno" style="text-align:left;" class="col-xs-3 control-label">Model</label>
- <div class="col-xs-4 controls">
-=======
<label style="text-align:right;" for="mapmodel_rqtl_geno" class="col-xs-3 control-label">Model</label>
<div style="margin-left:20px;" class="col-xs-4 controls">
->>>>>>> cbc4e86... Changed appearance of mapping and correlation options on trait page
<select name="mapmodel_rqtl_geno" class="form-control">
<option value="normal">normal</option>
<!--<option value="binary">binary</option>
@@ -374,13 +289,8 @@
</div>
-->
<div class="mapping_method_fields form-group">
-<<<<<<< HEAD
- <label style="text-align:left;" class="col-xs-12 control-label">Manhattan Plot</label>
- <div class="col-xs-12 controls">
-=======
<label style="text-align:right;" class="col-xs-3 control-label">Marker<br>Regression</label>
<div style="margin-left:20px;" class="col-xs-6 controls">
->>>>>>> cbc4e86... Changed appearance of mapping and correlation options on trait page
<label class="radio-inline">
<input type="radio" name="manhattan_plot_rqtl" value="True">
Yes
@@ -392,20 +302,12 @@
</div>
</div>
-<<<<<<< HEAD
- <div class="form-group">
- <div style="padding-left:15px;" class="controls">
- <button id="rqtl_geno_compute" class="btn submit_special btn-success" data-url="/marker_regression" title="Compute Marker Regression">
- <i class="icon-ok-circle icon-white"></i> Compute
- </button>
-=======
<div class="mapping_method_fields form-group">
<label class="col-xs-3 control-label"></label>
<div style="margin-left:20px;" class="col-xs-6">
<button id="rqtl_geno_compute" class="btn submit_special btn-success" data-url="/marker_regression" title="Compute Interval Mapping">
Compute
</button>
->>>>>>> cbc4e86... Changed appearance of mapping and correlation options on trait page
</div>
</div>
</div>
@@ -414,13 +316,8 @@
<div style="margin-top: 20px" class="form-horizontal">
{% if genofiles and genofiles|length>0 %}
<div class="mapping_method_fields form-group">
-<<<<<<< HEAD
- <label for="genofiles" class="col-xs-3 control-label">Genotypes</label>
- <div style="margin-left: 20px;" class="col-xs-8 controls">
-=======
<label style="text-align:right;" class="col-xs-3 control-label">Genotypes</label>
<div style="margin-left: 20px;" class="col-xs-4 controls">
->>>>>>> cbc4e86... Changed appearance of mapping and correlation options on trait page
<select id="genofile_pylmm" class="form-control">
{% for item in genofiles %}
<option value="{{item['location']}}:{{item['title']}}">{{item['title']}}</option>
@@ -429,52 +326,12 @@
</div>
</div>
{% endif %}
-<!--
<div class="mapping_method_fields form-group">
-<<<<<<< HEAD
- <label for="control_for" class="col-xs-3 control-label">Control&nbsp;for</label>
- <div style="margin-left: 20px;" class="col-xs-4 controls">
- {% if dataset.type == 'ProbeSet' and this_trait.locus_chr != "" %}
- <input name="control_pylmm" value="{{ nearest_marker }}" type="text" />
- {% else %}
- <input name="control_pylmm" value="" type="text" />
- {% endif %}
- <label class="radio-inline">
- <input type="radio" name="do_control_pylmm" value="true">
- Yes
- </label>
- <label class="radio-inline">
- <input type="radio" name="do_control_pylmm" value="false" checked="">
- No
- </label>
- </div>
- </div>
- <div class="mapping_method_fields form-group">
- <label style="text-align:left;" class="col-xs-12 control-label">Manhattan Plot</label>
- <div class="col-xs-12 controls">
- <label class="radio-inline">
- <input type="radio" name="manhattan_plot_pylmm" value="True">
- Yes
- </label>
- <label class="radio-inline">
- <input type="radio" name="manhattan_plot_pylmm" value="False" checked="">
- No
- </label>
- </div>
- </div>
--->
- <div class="form-group">
- <div style="padding-left:15px;" class="controls">
- <button id="pylmm_compute" class="btn submit_special btn-success" title="Compute Marker Regression">
- <i class="icon-ok-circle icon-white"></i> Compute
- </button>
-=======
<label class="col-xs-3 control-label"></label>
<div style="margin-left:20px;" class="col-xs-6">
<button id="pylmm_compute" class="btn submit_special btn-success" data-url="/marker_regression" title="Compute Interval Mapping">
Compute
</button>
->>>>>>> cbc4e86... Changed appearance of mapping and correlation options on trait page
</div>
</div>
</div>
@@ -486,13 +343,8 @@
<div style="padding-top: 10px;" class="form-horizontal">
{% if genofiles and genofiles|length>0 %}
<div class="mapping_method_fields form-group">
-<<<<<<< HEAD
- <label for="genofiles" class="col-xs-3 control-label">Genotypes</label>
- <div style="margin-left: 20px;" class="col-xs-8 controls">
-=======
<label style="text-align:right;" class="col-xs-3 control-label">Genotypes</label>
<div style="margin-left: 20px;" class="col-xs-4 controls">
->>>>>>> cbc4e86... Changed appearance of mapping and correlation options on trait page
<select id="genofile_gemma" class="form-control">
{% for item in genofiles %}
<option value="{{item['location']}}:{{item['title']}}">{{item['title']}}</option>
@@ -502,33 +354,12 @@
</div>
{% endif %}
<div class="mapping_method_fields form-group">
-<<<<<<< HEAD
- <label for="maf_gemma" class="col-xs-5 control-label">Minor allele threshold</label>
- <div style="margin-left: 20px;" class="col-xs-3 controls">
-=======
<label style="text-align:right;" class="col-xs-3 control-label">MAF</label>
<div style="margin-left: 20px;" class="col-xs-4 controls">
->>>>>>> cbc4e86... Changed appearance of mapping and correlation options on trait page
<input name="maf_gemma" value="0.01" type="text" class="form-control">
</div>
</div>
- </div>
-
- <div style="padding-top: 5px; padding-bottom: 5px; padding-left: 20px;" class="form-horizontal">
<div class="mapping_method_fields form-group">
-<<<<<<< HEAD
- <button type="button" id="select_covariates" class="btn btn-default">
- Select Covariates
- </button>
- <button type="button" id="remove_covariates" class="btn btn-default">
- Remove Covariates
- </button>
- </div>
- </div>
-
- <div class="form-group">
- <div class="col-xs-4 controls">
-=======
<label style="text-align: right;" class="col-xs-3 control-label">Covariates</label>
<div style="margin-left:20px;" class="col-xs-7">
{% if g.user_session.user_ob and (g.user_session.user_ob.display_num_collections() == "") %}
@@ -547,10 +378,10 @@
<div class="mapping_method_fields form-group">
<label class="col-xs-3 control-label"></label>
<div style="margin-left:20px;" class="col-xs-6">
->>>>>>> cbc4e86... Changed appearance of mapping and correlation options on trait page
<button id="gemma_compute" class="btn submit_special btn-success" data-url="/marker_regression" title="Compute Marker Regression">
Compute
</button>
+ </div>
</div>
</div>
</div>
@@ -579,7 +410,7 @@
</div>
</div>
</div>
- <div class="col-xs-6">
+ <div class="col-xs-5">
{% if dataset.group.mapping_id == "1" %}
<dl>
<dt>GEMMA</dt>