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{%extends "base.html"%}
{%from "flash_messages.html" import flash_all_messages%}
{%block title%}Upload R/qtl2 Bundle{%endblock%}
{%block contents%}
<h2 class="heading">Phenotype(ProbeSet) Dataset</h2>
<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 dataset.</p>
<p>This page gives you the ability to do that.</p>
</div>
{{flash_all_messages()}}
{%if datasets | length > 0%}
<form method="POST"
action="{{url_for('upload.rqtl2.select_probeset_dataset',
species_id=species.SpeciesId, population_id=population.Id)}}"
id="frm:select-probeset-dataset">
<legend class="heading">Select from existing ProbeSet datasets</legend>
<input type="hidden" name="species_id" value="{{species.SpeciesId}}" />
<input type="hidden" name="population_id"
value="{{population.InbredSetId}}" />
<input type="hidden" name="rqtl2_bundle_file"
value="{{rqtl2_bundle_file}}" />
<input type="hidden" name="geno-dataset-id" value="{{geno_dataset.Id}}" />
<input type="hidden" name="probe-study-id" value="{{probe_study.Id}}" />
<fieldset>
<label for="select:probe-dataset">Dataset</label>
<select id="select:probe-dataset"
name="probe-dataset-id"
required="required"
{%if datasets | length == 0%}disabled="disabled"{%endif%}>
<option value="">Select a dataset</option>
{%for dataset in datasets%}
<option value={{dataset.Id}}>
{{dataset.Name}}
{%if dataset.FullName%}
-- ({{dataset.FullName}})
{%endif%}
</option>
{%endfor%}
</select>
<span class="form-col-2">Select from existing ProbeSet datasets.</span>
</fieldset>
<fieldset>
<input type="submit"
value="select dataset"
class="btn btn-main form-col-2" />
</fieldset>
</form>
<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)}}"
id="frm:create-probeset-dataset">
<legend class="heading">Create a new ProbeSet dataset</legend>
<input type="hidden" name="species_id" value="{{species.SpeciesId}}" />
<input type="hidden" name="population_id"
value="{{population.InbredSetId}}" />
<input type="hidden" name="rqtl2_bundle_file"
value="{{rqtl2_bundle_file}}" />
<input type="hidden" name="geno-dataset-id" value="{{geno_dataset.Id}}" />
<input type="hidden" name="probe-study-id" value="{{probe_study.Id}}" />
<fieldset>
<label for="select:average">averaging method</label>
<select id="select:average"
name="averageid"
required="required">
<option value="">Select averaging method</option>
{%for avgmethod in avgmethods%}
<option value="{{avgmethod.Id}}">
{{avgmethod.Name}}
{%if avgmethod.Normalization%}
({{avgmethod.Normalization}})
{%endif%}
</option>
{%endfor%}
</select>
<span class="form-col-2">
Select the averaging method used for your data.
</span>
</fieldset>
<fieldset>
<label for="txt:datasetname">Name</label>
<input type="text" id="txt:datasetname" name="datasetname"
required="required"
maxlength="40"
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>
<label for="txt:datasetfullname">Full Name</label>
<input type="text" id="txt:datasetfullname" name="datasetfullname"
required="required"
maxlength="100"
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"
maxlength="100"
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>
<input type="checkbox" id="chk:public" name="datasetpublic"
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>
<label for="select:datasetdatascale">Data Scale</label>
<select id="select:datasetdatascale"
name="datasetdatascale"
required="required">
<option value="log2" selected="selected">log2</option>
<option value="z_score">z_score</option>
<option value="log2_ratio">log2_ratio</option>
<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>
<input type="submit"
value="create dataset"
class="btn btn-main form-col-2" />
</fieldset>
</form>
{%endblock%}
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