source: branches/uk_ac_ebi_Tab2MageImporter/html/hybridizations.html @ 550

Last change on this file since 550 was 550, checked in by mbayer, 13 years ago

have restructured the code completely that writes the hybs section

File size: 9.5 KB
Line 
1<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
2<html>
3<head>
4<meta http-equiv="Content-Type" content="text/html; charset=ISO-8859-1">
5<title>Tab2MAGE Importer -- Hybridizations</title>
6
7<link rel="stylesheet" type="text/css" href="../jsp/uk/ac/ebi/nugo/plugins/styles.css" />
8
9<script type="text/javascript">
10    function hideTwoChannelQuestions()
11    {
12      var dyeSwapRow = document.getElementById('dyeSwapRow');
13      var refSampleRow = document.getElementById('refSampleRow');
14      var poolingRow = document.getElementById('poolingRow');
15
16            //items are currently displayed, so hide them
17          dyeSwapRow.style.display = "none";
18          refSampleRow.style.display = "none";
19          poolingRow.style.display = "none";
20    }
21   
22    function showTwoChannelQuestions()
23    {
24      var dyeSwapRow = document.getElementById('dyeSwapRow');
25      var refSampleRow = document.getElementById('refSampleRow');
26      var poolingRow = document.getElementById('poolingRow');
27
28           //items are currently hidden, so display them
29          dyeSwapRow.style.display = "table-row";
30          refSampleRow.style.display = "table-row";
31          poolingRow.style.display = "table-row";
32    }
33   
34    function checkRefSampleLogic()
35    {
36        if(document.getElementById("dyeSwapYes").checked && document.getElementById("refSampleYes").checked)
37        {
38          alert('Reference Sample and Dye Swap cannot both be set to "yes"');
39        }
40    }
41
42   
43    </script>
44
45</head>
46
47<body>
48
49
50
51
52
53<form name="hybridizations"action="<%= request.getContextPath()%>/plugins/uk/ac/ebi/nugo/plugins/userchoice2.jsp?ID=<%=ID%>" method="post">
54<input type="hidden" name="ID" value="<%=ID%>"> 
55<input type="hidden" name="cmd" value="SetParameters"> 
56<input type="hidden"name="requestId" value="<%=requestId%>"> 
57
58<input type="hidden" name="file_id" value="">
59<input type="hidden" name="zipFile" value="/home/michab/potato_small.zip"  id="zipFile">
60
61<h2>Tab2MAGE Import Wizard -- Your Hybridizations</h2>
62
63<p>
64<!--  table with the input form -->
65<table cellpadding="15">
66
67  <!-- platform -->
68  <tr >
69    <td class="boldText">Microarray platform:</td>
70    <td class="input">
71    <select name="platform">
72    <option onclick="hideTwoChannelQuestions();" selected="selected" >Affymetrix</option>
73    <option onclick="showTwoChannelQuestions();">Agilent</option>
74    <option onclick="showTwoChannelQuestions();">AIDA</option>
75    <option onclick="showTwoChannelQuestions();">BZScan</option>
76    <option onclick="showTwoChannelQuestions();">ChipSkipper</option>
77    <option onclick="showTwoChannelQuestions();">GenePix</option>
78    <option onclick="showTwoChannelQuestions();">GeneTAC</option>
79    <option onclick="showTwoChannelQuestions();">Illumina</option>
80    <option onclick="showTwoChannelQuestions();">Imagene</option>
81    <option onclick="showTwoChannelQuestions();">QuantArray Biotin</option>
82    <option onclick="showTwoChannelQuestions();">QuantArray Cy</option>
83    <option onclick="showTwoChannelQuestions();">Spotfinder</option>
84    <option onclick="showTwoChannelQuestions();"><i>Custom</i></option>
85    </select></td>
86    <td>The manufacturer of the microarray chip used.</td>
87  </tr>
88
89  <!-- organism -->
90  <tr>
91    <td class="boldText">Experimental organism:</td>
92    <td class="input"><input type="text" size="50" name="organism" value="Hordeum vulgare"/></td>
93    <td>The full scientific name of the experimental organism used.</td>
94  </tr>
95
96  <!-- num array designs -->
97  <tr>
98    <td class="boldText">Number of different arrays designs used:</td>
99    <td class="input"><input type="text" size="3" name="numDesigns" value="1"/></td>
100    <td>If more than one array design was used in parallel, please specify the number here.
101    We assume that all samples are applied once to each array design</td>
102  </tr>
103
104
105  <!-- num treatment grps -->
106  <tr>
107    <td class="boldText">Number of treatment groups:</td>
108    <td class="input"><input type="text" size="3" name="numTreatmentGroups" value="2"/></td>
109    <td>The number of discrete combinations of factor values, i.e. the product of the number of factor levels(values) from all factors. <p>
110    Example: an experiment with 2 factors and 3 factor values in each will have 6 treatment groups (2 X 3).
111    </td>
112  </tr>
113
114  <!-- exp factors -->
115  <tr>
116    <td class="boldText">Experimental factors:
117    </td>
118    <td class="input"><textarea rows="7" cols="32" name="expFactors">Strain(mutant,wildtype)</textarea></td>
119    <td>Please list all experimental factors and value ranges using the following format (one per
120    line):<br>
121    <i>Factor 1(value1,value2,...valueN)<br></i>
122    <p>Example: <i><br>
123    Compound(aspirin,ibuprofen) <br>
124    Dose(control,low,medium,high)</i></td>
125  </tr>
126
127  <!-- num subjects -->
128  <tr>
129    <td class="boldText">Number of subjects per group:</td>
130    <td class="input"><input type="text" size="3" name="numReplicates" value="2"/></td>
131    <td>This is the number of biological replicates in each treatment group.</td>
132  </tr>
133 
134  <!-- subject labels -->
135  <tr>
136    <td class="boldText">Subject (replicate) labels:</td>
137    <td class="input"><textarea rows="8" cols="32" name="subjectNames"></textarea></td>
138    <td>Please provide a list of labels(names) for the experimental subjects, one per line,
139     in no particular order (copy and paste from Excel works).</td>
140  </tr> 
141 
142  <!-- tissues -->
143  <tr>
144    <td class="boldText">Target tissues:</td>
145    <td class="input"><textarea rows="4" cols="32" name="tissues">stem</textarea></td>
146    <td>List all target tissues one per line, in no particular order (copy and paste from Excel works).</td>
147  </tr>
148
149
150  <!-- dye swap -->
151  <tr id="dyeSwapRow"  style="display:none">
152    <td class="boldText">Dye-swap</td>
153    <td class="input">
154    <table class="noBorder" cellpadding="4">
155      <tr>
156        <td class="noBorder"><input type="radio" name="dyeSwap" id="dyeSwapYes" value="yes" onchange="checkRefSampleLogic();"/></td>
157        <td class="noBorder">yes</td>
158      </tr>
159
160      <tr>
161        <td class="noBorder"><input type="radio" name="dyeSwap" id="dyeSwapNo" value="no" checked="checked"  onchange="checkRefSampleLogic();"/></td>
162        <td class="noBorder">no</td>
163      </tr>
164    </table>     
165    </td>
166    <td>If you used a dye-swap design please indicate this here.</td>
167  </tr>
168
169  <!-- ref sample -->
170  <tr id="refSampleRow"  style="display:none">
171    <td class="boldText">Reference sample</td>
172    <td class="input"> 
173    <table class="noBorder" cellpadding="4">
174      <tr>
175        <td class="noBorder"><input type="radio" name="refSample" id="refSampleYes" value="yes"  onchange="checkRefSampleLogic();"/></td>
176        <td class="noBorder">yes</td>
177      </tr>
178
179      <tr>
180        <td class="noBorder"><input type="radio"name="refSample" id="refSampleNo" value="no"  checked="checked"  onchange="checkRefSampleLogic();"/></td>
181        <td class="noBorder">no</td>
182      </tr>
183    </table>       
184    </td>
185    <td>If you used a reference sample please indicate this here.</td>
186  </tr>
187 
188  <!-- pooling -->
189  <tr id="poolingRow"  style="display:none">
190    <td class="boldText">Sample pooling:</td>
191    <td class="input">
192    <table class="noBorder" cellpadding="4">
193      <tr>
194        <td class="noBorder"><input type="radio" name="pooling" value="yes"></td>
195        <td class="noBorder">yes</td>
196      </tr>
197      <tr>
198        <td class="noBorder"><input type="radio" name="pooling" value="no" checked="checked"></td>
199        <td class="noBorder">no</td>
200      </tr>
201    </table>   
202    </td>
203    <td>If the samples were pooled please indicate this here.</td>
204  </tr>
205
206
207  <!-- file upload -->
208  <tr>
209    <td class="boldText">Zip file:</td>
210
211    <td class="input">
212    <table class="noBorder" border="0" cellspacing="0" cellpadding="5">
213      <tr class="noBorder" >
214     
215        <td style="vertical-align: middle;border-style: none;"><input type="text" name="path" size="35" value=""></td>
216       
217        <td  style="vertical-align: middle;border-style: none;">
218        <div class="buttons"
219          onmouseover="this.className='buttons_hover';"
220          onmouseout="this.className='buttons';"
221          onclick="browseOnClick()">
222        <div class="buttons_inner">
223
224        <table class="noBorder" cellspacing="0" cellpadding="0">
225          <tr class="noBorder">
226            <td style="border-style: none;">&nbsp;&nbsp;<img src="/base/images/browse.png" border="0"></td>
227            <td style="border-style: none;">Browse&hellip;</td>
228          </tr>
229        </table>
230
231        </div>
232        </div>
233        </td>
234       
235      </tr>
236    </table>
237    </td>
238
239    <td>Please select the zip file on your local disk that contains the data files for import.
240   All files must be of the same data format (e.g. Genepix or Affymetrix etc.).</td>
241  </tr>
242
243</table>
244
245<p>
246
247  <table align="center" class="noBorder" cellspacing="5"  cellpadding="5">
248  <tr class="noBorder">
249    <td id="next" width="50%" style="border-style: none;"><div class="buttons" onmouseover="this.className='buttons_hover';" onmouseout="this.className='buttons';" onclick="submit()"><div class="buttons_inner"><table  class="noBorder" cellspacing="0" cellpadding="0"><tr  class="noBorder"><td style="border-style: none;"><img src="/base/images/gonext.gif" border="0"></td><td style="border-style: none;">Next</td></tr></table></div></div></td>
250    <td id="close" width="50%" style="border-style: none;"><div class="buttons" onmouseover="this.className='buttons_hover';" onmouseout="this.className='buttons';" onclick="window.close()"><div class="buttons_inner"><table  class="noBorder" cellspacing="0" cellpadding="0"><tr  class="noBorder"><td style="border-style: none;"><img src="/base/images/cancel.gif" border="0"></td><td style="border-style: none;">Cancel</td></tr></table></div></div></td>  </tr>
251  </table>
252
253
254</form>
255
256</body>
257</html>
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