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-rw-r--r--qc_app/templates/index.html4
-rw-r--r--qc_app/templates/rqtl2/select-geno-dataset.html28
-rw-r--r--qc_app/templates/rqtl2/select-probeset-dataset.html35
-rw-r--r--qc_app/templates/rqtl2/select-probeset-study-id.html25
4 files changed, 84 insertions, 8 deletions
diff --git a/qc_app/templates/index.html b/qc_app/templates/index.html
index 358b521..00714f0 100644
--- a/qc_app/templates/index.html
+++ b/qc_app/templates/index.html
@@ -21,7 +21,7 @@
<button class="btn btn-main">upload R/qtl2 bundle</button></a>
</div>
-<h2>Expression Data</h2>
+<h2 class="heading">Expression Data</h2>
<div class="explainer">
<p>This application assumes that you are familiar with the basics of data
@@ -112,7 +112,7 @@
</form>
</div>
-<h2>samples/cases</h2>
+<h2 class="heading">samples/cases</h2>
<div class="explainer">
<p>For the expression data above, you need the samples/cases in your file to
diff --git a/qc_app/templates/rqtl2/select-geno-dataset.html b/qc_app/templates/rqtl2/select-geno-dataset.html
index 64f886e..1964a79 100644
--- a/qc_app/templates/rqtl2/select-geno-dataset.html
+++ b/qc_app/templates/rqtl2/select-geno-dataset.html
@@ -43,6 +43,10 @@
<option value="{{dset['Id']}}">{{dset["Name"]}} ({{dset["FullName"]}})</option>
{%endfor%}
</select>
+ <span class="form-col-2">
+ Select from the existing genotype datasets for species
+ {{species.SpeciesName}} ({{species.FullName}}).
+ </span>
</fieldset>
<fieldset>
@@ -76,6 +80,9 @@
id="txt:dataset-name"
name="dataset-name"
required="required" />
+ <span class="form-col-2">
+ Provide the new name for the genotype dataset, e.g. "BXDGeno"
+ </span>
</fieldset>
<fieldset>
@@ -84,21 +91,36 @@
id="txt:dataset-fullname"
name="dataset-fullname"
required="required" />
+
+ <span class="form-col-2">
+ Provide a longer name that better describes the genotype dataset, e.g.
+ "BXD Genotypes"
+ </span>
</fieldset>
<fieldset>
<label for="txt:dataset-shortname">Short Name</label>
<input type="text"
id="txt:dataset-shortname"
- name="dataset-shortname"
- required="required" />
+ name="dataset-shortname" />
+
+ <span class="form-col-2">
+ Provide a short name for the genotype dataset. This is optional. If not
+ provided, we'll default to the same value as the "Name" above.
+ </span>
</fieldset>
<fieldset>
<input type="checkbox"
id="chk:dataset-public"
- name="dataset-public" />
+ name="dataset-public"
+ checked="checked" />
<label for="chk:dataset-public">Public?</label>
+
+ <span class="form-col-2">
+ Specify whether the dataset will be available publicly. Check to make the
+ dataset publicly available and uncheck to limit who can access the dataset.
+ </span>
</fieldset>
<fieldset>
diff --git a/qc_app/templates/rqtl2/select-probeset-dataset.html b/qc_app/templates/rqtl2/select-probeset-dataset.html
index 3e160fd..ebd715e 100644
--- a/qc_app/templates/rqtl2/select-probeset-dataset.html
+++ b/qc_app/templates/rqtl2/select-probeset-dataset.html
@@ -45,6 +45,8 @@
</option>
{%endfor%}
</select>
+
+ <span class="form-col-2">Select from existing ProbeSet datasets.</span>
</fieldset>
<fieldset>
@@ -57,6 +59,10 @@
<p style="color:#FE3535; padding-left:20em; font-weight:bolder;">OR</p>
{%endif%}
+<div class="explainer">
+ <p>Create an entirely new ProbeSet dataset for your data.</p>
+</div>
+
<form method="POST"
action="{{url_for('upload.rqtl2.create_probeset_dataset',
species_id=species.SpeciesId, population_id=population.Id)}}"
@@ -86,6 +92,10 @@
</option>
{%endfor%}
</select>
+
+ <span class="form-col-2">
+ Select the averaging method used for your data.
+ </span>
</fieldset>
<fieldset>
@@ -93,6 +103,11 @@
<input type="text" id="txt:datasetname" name="datasetname"
required="required"
title="Name of the dataset, e.g 'BXDMicroArray_ProbeSet_June03'. (Required)" />
+
+ <span class="form-col-2">
+ Provide a name for the dataset e.g. "BXDMicroArray_ProbeSet_June03". This
+ is mandatory <strong>MUST</strong> be provided.
+ </span>
</fieldset>
<fieldset>
@@ -100,12 +115,23 @@
<input type="text" id="txt:datasetfullname" name="datasetfullname"
required="required"
title="A longer name for the dataset, e.g. 'UTHSC Brain mRNA U74Av2 (Jun03) MAS5'. (Required)" />
+
+ <span class="form-col-2">
+ Provide a longer, more descriptive name for the dataset e.g.
+ "UTHSC Brain mRNA U74Av2 (Jun03) MAS5". This is mandatory and
+ <strong>MUST</strong> be provided.
+ </span>
</fieldset>
<fieldset>
<label for="txt:datasetshortname">Short Name</label>
<input type="text" id="txt:datasetshortname" name="datasetshortname"
title="An abbreviated name for the dataset, e.g 'Br_U_0603_M'. (Optional)" />
+
+ <span class="form-col-2">
+ Provide a longer, more descriptive name for the dataset e.g. "Br_U_0603_M".
+ This is optional.
+ </span>
</fieldset>
<fieldset>
@@ -113,6 +139,11 @@
checked="checked"
title="Whether or not the dataset is accessible by the general public." />
<label for="chk:datasetpublic">Public?</label>
+
+ <span class="form-col-2">
+ Check to specify that the dataset will be publicly available. Uncheck to
+ limit access to the dataset.
+ </span>
</fieldset>
<fieldset>
@@ -126,6 +157,10 @@
<option value="linear">linear</option>
<option value="linear_positive">linear_positive</option>
</select>
+
+ <span class="form-col-2">
+ Select from a list of scaling methods.
+ </span>
</fieldset>
<fieldset>
diff --git a/qc_app/templates/rqtl2/select-probeset-study-id.html b/qc_app/templates/rqtl2/select-probeset-study-id.html
index 34aa54e..35fe655 100644
--- a/qc_app/templates/rqtl2/select-probeset-study-id.html
+++ b/qc_app/templates/rqtl2/select-probeset-study-id.html
@@ -9,7 +9,7 @@
<div class="explainer">
<p>The R/qtl2 bundle you uploaded contains (a) "<strong>pheno</strong>"
file(s). This data needs to be organised under a study.</p>
- <p>This page gives you the ability to do that.</p>
+ <p>In this page, you can either select from a existing dataset:</p>
</div>
{{flash_all_messages()}}
@@ -43,6 +43,7 @@
</option>
{%endfor%}
</select>
+ <span class="form-col-2">Select from existing ProbeSet studies.</span>
</fieldset>
<fieldset>
@@ -54,6 +55,10 @@
<p style="color:#FE3535; padding-left:20em; font-weight:bolder;">OR</p>
+<div class="explainer">
+ <p>Create a new ProbeSet dataset below:</p>
+</div>
+
<form method="POST"
action="{{url_for('upload.rqtl2.create_probeset_study',
species_id=species.SpeciesId, population_id=population.Id)}}"
@@ -80,6 +85,8 @@
</option>
{%endfor%}
</select>
+ <span class="form-col-2">Select from a list of known genomics platforms.
+ </span>
</fieldset>
<fieldset>
@@ -95,6 +102,9 @@
</option>
{%endfor%}
</select>
+ <span class="form-col-2">
+ Select the Tissue to which the data is concerned.
+ </span>
</fieldset>
<fieldset>
@@ -102,18 +112,27 @@
<input type="text" id="txt:studyname" name="studyname"
placeholder="Name of the study. (Required)"
required="required" />
+ <span class="form-col-2">Provide a name for the study.</span>
</fieldset>
<fieldset>
- <label for="txt:studyfullname">Study name</label>
+ <label for="txt:studyfullname">Full Study Name</label>
<input type="text" id="txt:studyfullname" name="studyfullname"
placeholder="Longer name of the study. (Optional)" />
+ <span class="form-col-2">
+ Provide a longer, more descriptive name for the study. This is optional
+ and you can leave it blank.
+ </span>
</fieldset>
<fieldset>
- <label for="txt:studyshortname">Study name</label>
+ <label for="txt:studyshortname">Short Study Name</label>
<input type="text" id="txt:studyshortname" name="studyshortname"
placeholder="Shorter name of the study. (Optional)" />
+ <span class="form-col-2">
+ Provide a shorter name for the study. This is optional and you can leave
+ it blank.
+ </span>
</fieldset>
<fieldset>