blob: 26f52ed2b042c230d7393d99370fbc2de0b7831d (
about) (
plain)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
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('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>
{{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('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>
{{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%}
|
