source: extensions/net.sf.basedb.reggie/trunk/resources/analysis/vcall_build.jsp @ 5766

Last change on this file since 5766 was 5766, checked in by Nicklas Nordborg, 3 years ago

References #1208: Implement wizard for building database of variant frequencies in SCAN-B samples

Implemented export step for creating a file with patient and VCF file information. This file is intended to be used by the statistics script.

File size: 4.3 KB
Line 
1<%@ page
2  pageEncoding="UTF-8"
3  session="false"
4  import="net.sf.basedb.core.User"
5  import="net.sf.basedb.core.DbControl"
6  import="net.sf.basedb.core.SessionControl"
7  import="net.sf.basedb.core.Application"
8  import="net.sf.basedb.clients.web.Base" 
9  import="net.sf.basedb.clients.web.util.HTML" 
10  import="net.sf.basedb.clients.web.extensions.ExtensionsControl"
11%>
12<%@ taglib prefix="base" uri="/WEB-INF/base.tld" %>
13<%@ taglib prefix="p" uri="/WEB-INF/path.tld" %>
14<%
15final SessionControl sc = Base.getExistingSessionControl(request, "net.sf.basedb.reggie", true);
16final String ID = sc.getId();
17final float scale = Base.getScale(sc);
18final String home = ExtensionsControl.getHomeUrl("net.sf.basedb.reggie");
19DbControl dc = null;
20try
21{
22  dc = sc.newDbControl();
23  final User user = User.getById(dc, sc.getLoggedInUserId());
24%>
25<base:page type="default" >
26<base:head 
27  scripts="~../reggie-2.js,~vcall_build.js" 
28  styles="path.css,~../css/reggie-2.css"
29/>
30<base:body>
31
32  <p:path><p:pathelement 
33    title="Reggie" href="<%="../index.jsp?ID="+ID%>" 
34    /><p:pathelement title="Build SCAN-B variant database" 
35    /></p:path>
36
37  <div class="content">
38  <form name="reggie" id="wizard" class="wizard">
39
40  <div class="step" id="step-1">
41    <div class="step-no">1</div>
42    <div class="step-title">Select list with alignments</div>
43    <div class="step-content">
44   
45      <table class="step-form">
46      <tr class="align-top">
47        <td class="prompt">Item list</td>
48        <td class="input">
49       
50          <table style="width: 100%;">
51          <tr>
52          <td>
53            <select class="required" name="itemList" id="itemList"></select>
54          </td>
55          <td style="padding-left: 4px; width: 7em;">
56            <base:button title="Select&hellip;" id="btnSelectList" />
57          </td>
58          </tr>
59          </table>
60
61        </td>
62        <td class="status" id="itemList.status"></td>
63        <td class="help"><span id="itemList.message" class="message"></span>
64          Select a list containing the alignments that should be used to
65          build the database. All alignments in the list need to have a raw
66          variant calling file already. They also need to be linked all the
67          way up to a patient item. This is needed since the script calculates
68          per-patient frequencies of variants.
69        </td>
70      </tr>
71      </table>
72    </div>
73  </div>
74 
75 
76  <div class="step" id="step-2">
77    <div class="step-no">2</div>
78    <div class="step-title">Parameters</div>
79    <div class="step-content">
80
81      <table class="step-form">
82      <tbody>
83        <tr class="section-header">
84          <td colspan="4">Open Grid Scheduler</td>
85        </tr>
86        <tr>
87          <td class="subprompt">Cluster</td>
88          <td class="input">
89            <select name="clusters" id="clusters" class="required"></select></td>
90          <td class="status" id="clusters.status"></td>
91          <td class="help">
92            <span id="clusters.message" class="message"></span>
93            Select the cluster to use for running the software.
94          </td>
95        </tr>
96        <tr id="job-priority" style="display: none;">
97          <td class="subprompt">Job priority</td>
98          <td class="input">
99            <select name="priority" id="priority"></select>
100          </td>
101          <td class="status" id="priority.status"></td>
102          <td class="help">
103            <span id="priority.message" class="message"></span>
104            Select the priority of the job.
105          </td>
106        </tr>
107        <tr>
108          <td class="subprompt">Debug</td>
109          <td class="input"><input type="checkbox" name="debug"></td>
110          <td class="status" id="debug.status"></td>
111          <td class="help">
112            <span id="debug.message" class="message"></span>
113            When running in debug mode temporary files are not removed from the
114            cluster node.
115          </td>
116        </tr>
117      </tbody>
118      </table>
119    </div>
120  </div>
121   
122    <div id="wizard-status"></div>
123    <div id="wizard-progress"></div>
124 
125    <table class="navigation" id="navigation">
126    <tr>
127      <td><base:button id="gocancel" title="Cancel" /></td>
128      <td><base:button id="gonext" title="Next" image="<%=home+"/images/gonext.png"%>" /></td>
129      <td><base:button id="goregister" title="Register" image="<%=home+"/images/import.png"%>"  /></td>
130      <td><base:button id="gorestart" title="Restart" image="<%=home+"/images/goback.png"%>" /></td>
131      <td id="gonext-message" class="message"></td>
132    </tr>
133    </table>
134 
135  </form>
136  </div>
137 
138</base:body>
139</base:page>
140<%
141}
142finally
143{
144  if (dc != null) dc.close();
145}
146%>
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