-
Notifications
You must be signed in to change notification settings - Fork 4
/
Copy pathfileformats.html
319 lines (295 loc) · 7.76 KB
/
fileformats.html
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
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
<!DOCTYPE html>
<html>
<head>
<title>Crux File Formats</title>
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<link rel="stylesheet" type="text/css" href="styles.css">
<!-- Google tag (gtag.js) -->
<script async src="https://www.googletagmanager.com/gtag/js?id=G-V7XKGGFPYX"></script>
<script>
window.dataLayer = window.dataLayer || [];
function gtag(){dataLayer.push(arguments);}
gtag('js', new Date());
gtag('config', 'G-V7XKGGFPYX');
</script>
<script src="http://ajax.googleapis.com/ajax/libs/jquery/1.8.3/jquery.min.js"></script>
<script type="text/javascript">
// Main Menu
$( document ).ready(function() {
var pull = $('.btn');
menu = $('nav ul');
menuHeight = menu.height();
$(pull).on('click', function(e) {
e.preventDefault();
menu.slideToggle();
});
$(window).resize(function(){
var w = $(window).width();
if(w > 320 && menu.is(':hidden')) {
menu.removeAttr('style');
}
});
});
</script>
</head>
<body>
<div class="page-wrap">
<nav>
<div class="btn">
</div>
<img src="images/crux-logo.png" id="logo"></a>
<ul id="navitems">
<li><a href="index.html">Home</a></li>
<li><a href="download.html">Download</a></li>
<li><a href="fileformats.html">File Formats</a></li>
<li><a href="http://groups.google.com/group/crux-users">Contact</a></li> <!--Link to google support board-->
</ul>
</nav>
<div id="content">
<!-- START CONTENT -->
<div id="content">
<h2>File formats</h2>
<table id="fileFormatsTable">
<tr>
<td> </td>
<td>bullseye</td>
<td>tide-index</td>
<td>tide-search</td>
<td>comet</td>
<td>percolator</td>
<td>spectral-counts</td>
</tr>
<tr>
<td>
<a href="file-formats/ms2-format.html">MS1</a>
</td>
<td>in</td>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
</tr>
<tr>
<td>
<a href="file-formats/ms2-format.html">MS2</a>
(<a href="example-files/demo.ms2">sample</a>) / CMS2
</td>
<td>in/out</td>
<td> </td>
<td>in</td>
<td>in</td>
<td>in</td>
<td>in</td>
</tr>
<tr>
<td>
<a href="http://www.matrixscience.com/help/data_file_help.html">MGF</a>
</td>
<td>in/out</td>
<td> </td>
<td>in</td>
<td> </td>
<td>in</td>
<td>in</td>
</tr>
<tr>
<td>
<a href="http://www.psidev.info/mzml_1_0_0">mzML</a>,
<a href="http://tools.proteomecenter.org/wiki/index.php?title=Formats:mzXML">mzXML</a>
</td>
<td>in</td>
<td> </td>
<td>in</td>
<td>in</td>
<td>in</td>
<td>in</td>
</tr>
<tr>
<td>
Thermo .raw files
(Windows only)
</td>
<td>in</td>
<td> </td>
<td>in</td>
<td>in</td>
<td> </td>
<td>in</td>
</tr>
<tr>
<td>
<a href="http://proteowizard.sourceforge.net/formats.shtml">Other
proprietary vendor formats</a> (Windows only)
</td>
<td> </td>
<td> </td>
<td>in</td>
<td> </td>
<td> </td>
<td>in</td>
</tr>
<tr>
<td>
<a href="file-formats/fasta-format.html">FASTA</a>
(<a href="file-formats/sample.fasta">sample</a>)
</td>
<td>in</td>
<td>in</td>
<td>in</td>
<td>in</td>
<td> </td>
<td> </td>
</tr>
<tr>
<td>
database index
</td>
<td> </td>
<td>out</td>
<td>in</td>
<td> </td>
<td> </td>
<td> </td>
</tr>
<tr>
<td>
<a href="file-formats/txt-format.html">Tab-delimited text</a>
(<a href="example-files/search.target.txt">sample</a>)
</td>
<td> </td>
<td> </td>
<td>out</td>
<td>out</td>
<td>in/out</td>
<td>in/out</td>
</tr>
<tr>
<td>
<a href="http://tools.proteomecenter.org/wiki/index.php?title=Formats:pepXML">
pepXML</a>
</td>
<td> </td>
<td> </td>
<td>out</td>
<td>out</td>
<td>in/out</td>
<td>in</td>
</tr>
<tr>
<td>
<a href="https://github.com/percolator/percolator/wiki/Interface">PIN</a>
</td>
<td> </td>
<td> </td>
<td>out</td>
<td> </td>
<td>in</td>
<td> </td>
</tr>
<tr>
<td>
<a href="https://github.com/percolator/percolator/wiki/Interface">POUT</a>
</td>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td>out</td>
<td> </td>
</tr>
<tr>
<td>
<a href="http://www.psidev.info/mzidentml">mzIdentML</a>
</td>
<td> </td>
<td> </td>
<td>out</td>
<td>out</td>
<td>out</td>
<td>in</td>
</tr>
<tr>
<td>
<a href="file-formats/sqt-format.html">SQT</a>
</td>
<td> </td>
<td> </td>
<td>out</td>
<td>out</td>
<td>in</td>
<td>in</td>
</tr>
<tr>
<td>
<a href="file-formats/features.html">Feature file</a>
</td>
<td> </td>
<td> </td>
<td> </td>
<td> </td>
<td>in/out</td>
<td> </td>
</tr>
<tr>
<td>
<a href="file-formats/parameter-file.html">Crux parameters</a>
(<a href="example-files/default.params">sample</a>)
</td>
<td>in/out</td>
<td>in/out</td>
<td>in/out</td>
<td>in/out</td>
<td>in/out</td>
<td>in/out</td>
</tr>
</table>
</div>
<!-- END CONTENT -->
</div>
</div>
<footer class="site-footer">
<div id="centerfooter">
<div class="footerimportantlinks">
<img src="images/linkicon.png" style="width:16px; height:16px"><h3>Important links</h3>
<ul>
<li><a href="faq.html">Crux FAQ</a></li>
<li><a href="glossary.html">Glossary of terminology</a></li>
<li><a href="http://scholar.google.com/citations?hl=en&user=Rw9S1HIAAAAJ">Google Scholar profile</a></li>
<li><a href="https://github.com/crux-toolkit/crux-toolkit">GitHub</a></li>
<li><a href="release-notes.html">Release Notes</a></li>
<li><a href="https://mailman1.u.washington.edu/mailman/listinfo/crux-users" title="Receive announcements of new versions">Join the mailing list</a></li>
<li><a href="http://www.apache.org/licenses/LICENSE-2.0">Apache license</a></li>
<li><a href="http://groups.google.com/group/crux-users">Support Board</a></li>
</ul>
</div>
<div class="footerimportantlinks tutoriallinks">
<img src="images/tutorialicon.png" style="height:16px"><h3>Tutorials</h3>
<ul>
<li><a href="tutorials/install.html">Installation</a></li>
<li><a href="tutorials/gettingstarted.html">Getting started with Crux</a></li>
<li><a href="tutorials/search.html">Running a simple search using Tide and Percolator</a></li>
<li><a href="tutorials/customizedsearch.html">Customization and search options</a></li>
<li><a href="tutorials/spectralcounts.html">Using spectral-counts</a></li>
</ul>
</div>
<div id="footertext">
<p>
The original version of Crux was written by Chris Park and Aaron Klammer
under the supervision
of <a href="http://www.gs.washington.edu/faculty/maccoss.htm">Prof. Michael
MacCoss</a>
and <a href="http://noble.gs.washington.edu/~noble">Prof. William
Stafford Noble</a> in the Department of Genome Sciences at the
University of Washington, Seattle. Website by <a href="http://www.yuvalboss.com/">Yuval Boss</a>.
<br />The complete list of contributors
can be found <a href="contributors.html">here</a>.
<br />
<br />
Maintenance and development of Crux is funded by the <a href="https://www.nih.gov/">National Institutes of Health</a> award P41 GM103533.
</p>
</div>
</div>
</footer>
</body>
</html>