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Diffstat (limited to 'uploader/templates/populations/rqtl2/select-probeset-dataset.html')
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diff --git a/uploader/templates/populations/rqtl2/select-probeset-dataset.html b/uploader/templates/populations/rqtl2/select-probeset-dataset.html new file mode 100644 index 0000000..74f8f69 --- /dev/null +++ b/uploader/templates/populations/rqtl2/select-probeset-dataset.html @@ -0,0 +1,191 @@ +{%extends "base.html"%} +{%from "flash_messages.html" import flash_messages%} + +{%block title%}Upload R/qtl2 Bundle{%endblock%} + +{%block contents%} +<h2 class="heading">Phenotype(ProbeSet) Dataset</h2> + +<div class="row"> + <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> + +{%if datasets | length > 0%} +<div class="row"> + <form method="POST" + action="{{url_for('expression-data.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> + {{flash_messages("error-rqtl2")}} + + <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="tissueid" value="{{tissue.Id}}" /> + <input type="hidden" name="probe-study-id" value="{{probe_study.Id}}" /> + + <div class="form-group"> + <label class="form-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%} + class="form-control" + aria-describedby="help-probe-dataset"> + <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 id="help-probe-dataset" class="form-text text-muted"> + Select from existing ProbeSet datasets.</span> + </div> + + <button type="submit" class="btn btn-primary" />select dataset</button> +</form> +</div> + +<div class="row"> + <p style="color:#FE3535; padding-left:20em; font-weight:bolder;">OR</p> +</div> +{%endif%} + +<div class="row"> + <p>Create an entirely new ProbeSet dataset for your data.</p> +</div> + +<div class="row"> + <form method="POST" + action="{{url_for('expression-data.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> + {{flash_messages("error-rqtl2-create-probeset-dataset")}} + + <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="tissueid" value="{{tissue.Id}}" /> + <input type="hidden" name="probe-study-id" value="{{probe_study.Id}}" /> + + <div class="form-group"> + <label class="form-label" for="select:average">averaging method</label> + <select id="select:average" + name="averageid" + required="required" + class="form-control" + aria-describedby="help-average"> + <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 id="help-average" class="form-text text-muted"> + Select the averaging method used for your data. + </span> + </div> + + <div class="form-group"> + <label class="form-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)" + class="form-control" + aria-describedby="help-dataset-name" /> + + <span id="help-dataset-name" class="form-text text-muted"> + Provide a name for the dataset e.g. "BXDMicroArray_ProbeSet_June03". This + is mandatory <strong>MUST</strong> be provided. + </span> + </div> + + <div class="form-group"> + <label class="form-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)" + class="form-control" + aria-describedby="help-dataset-fullname" /> + + <span id="help-dataset-fullname" class="form-text text-muted"> + 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> + </div> + + <div class="form-group"> + <label class="form-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)" + class="form-control" + aria-describedby="help-dataset-shortname" /> + + <span id="help-dataset-shortname" class="form-text text-muted"> + Provide a longer, more descriptive name for the dataset e.g. "Br_U_0603_M". + This is optional. + </span> + </div> + + <div class="form-check"> + <input type="checkbox" id="chk:public" name="datasetpublic" + checked="checked" + title="Whether or not the dataset is accessible by the general public." + class="form-check-input" + aria-describedby="help-public" /> + <label class="form-check-label" for="chk:datasetpublic">Public?</label> + + <span id="help-public" class="form-text text-muted"> + Check to specify that the dataset will be publicly available. Uncheck to + limit access to the dataset. + </span> + </div> + + <div class="form-group"> + <label class="form-label" for="select:datasetdatascale">Data Scale</label> + <select id="select:datasetdatascale" + name="datasetdatascale" + required="required" + class="form-control" + aria-describedby="help-dataset-datascale"> + <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 id="help-dataset-datascale" class="form-text text-muted"> + Select from a list of scaling methods. + </span> + </div> + + <button type="submit" class="btn btn-primary">create dataset</button> + </form> +</div> + +{%endblock%} |