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comparison libs/sratoolkit.2.8.0-centos_linux64/schema/sra/generic-fastq.vschema @ 3:38ad1130d077 draft

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planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
author charles_s_test
date Mon, 27 Nov 2017 11:21:07 -0500
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2:0d65b71ff8df 3:38ad1130d077
1 /*===========================================================================
2 *
3 * PUBLIC DOMAIN NOTICE
4 * National Center for Biotechnology Information
5 *
6 * This software/database is a "United States Government Work" under the
7 * terms of the United States Copyright Act. It was written as part of
8 * the author's official duties as a United States Government employee and
9 * thus cannot be copyrighted. This software/database is freely available
10 * to the public for use. The National Library of Medicine and the U.S.
11 * Government have not placed any restriction on its use or reproduction.
12 *
13 * Although all reasonable efforts have been taken to ensure the accuracy
14 * and reliability of the software and data, the NLM and the U.S.
15 * Government do not and cannot warrant the performance or results that
16 * may be obtained by using this software or data. The NLM and the U.S.
17 * Government disclaim all warranties, express or implied, including
18 * warranties of performance, merchantability or fitness for any particular
19 * purpose.
20 *
21 * Please cite the author in any work or product based on this material.
22 *
23 * ===========================================================================
24 *
25 */
26
27 /*==========================================================================
28 * NCBI Generic Fastq Sequence Read Archive schema
29 */
30 version 1;
31
32 include 'insdc/sra.vschema';
33 include 'ncbi/sra.vschema';
34 include 'ncbi/clip.vschema';
35 include 'ncbi/spotname.vschema';
36
37 /* tokenize_spot_name - currently ascii only capability */
38
39 extern function NCBI:SRA:spot_name_token
40 NCBI:SRA:GenericFastq:tokenize_spot_name #1 ( ascii name );
41
42 /*--------------------------------------------------------------------------
43 * NCBI:SRA:GenericFastq:sequence
44 * Generic Fastq SRA Platform
45 */
46 table NCBI:SRA:GenericFastq:sequence #1
47 = NCBI:SRA:tbl:sra #2.1.3
48 , NCBI:tbl:base_space #2.0.3
49 , NCBI:tbl:phred_quality #2.0.4
50 , NCBI:SRA:tbl:clip #1.0.2
51 {
52 ascii platform_name
53 = < ascii > echo < "UNDEFINED" > ();
54
55 INSDC:SRA:platform_id out_platform
56 = < INSDC:SRA:platform_id > echo < SRA_PLATFORM_UNDEFINED > ();
57
58 /* ascii only spot name tokenizer */
59
60 NCBI:SRA:spot_name_token out_spot_name_tok
61 = NCBI:SRA:GenericFastq:tokenize_spot_name ( _out_name );
62
63 NCBI:SRA:spot_name_token in_spot_name_tok
64 = NCBI:SRA:GenericFastq:tokenize_spot_name ( NAME );
65
66 /* clips */
67
68 physical column < INSDC:coord:one > izip_encoding
69 .CLIP_ADAPTER_LEFT = CLIP_ADAPTER_LEFT;
70 physical column < INSDC:coord:one > izip_encoding
71 .CLIP_ADAPTER_RIGHT = CLIP_ADAPTER_RIGHT;
72 physical column < INSDC:coord:one > izip_encoding
73 .CLIP_QUALITY_LEFT = CLIP_QUALITY_LEFT;
74 physical column < INSDC:coord:one > izip_encoding
75 .CLIP_QUALITY_RIGHT = CLIP_QUALITY_RIGHT;
76 }
77
78 database NCBI:SRA:GenericFastq:db #1
79 {
80 table NCBI:SRA:GenericFastq:sequence #1.0 SEQUENCE;
81 };
82
83 /*--------------------------------------------------------------------------
84 * NCBI:SRA:GenericFastq:sequence_no_name
85 * Generic Fastq SRA Platform (without name)
86 */
87 table NCBI:SRA:GenericFastq:sequence_no_name #1
88 = NCBI:SRA:tbl:sra #2.1.3
89 , NCBI:tbl:base_space #2.0.3
90 , NCBI:tbl:phred_quality #2.0.4
91 , NCBI:SRA:tbl:clip #1.0.2
92 {
93 ascii platform_name
94 = < ascii > echo < "UNDEFINED" > ();
95
96 INSDC:SRA:platform_id out_platform
97 = < INSDC:SRA:platform_id > echo < SRA_PLATFORM_UNDEFINED > ();
98
99 /* clips */
100
101 physical column < INSDC:coord:one > izip_encoding
102 .CLIP_ADAPTER_LEFT = CLIP_ADAPTER_LEFT;
103 physical column < INSDC:coord:one > izip_encoding
104 .CLIP_ADAPTER_RIGHT = CLIP_ADAPTER_RIGHT;
105 physical column < INSDC:coord:one > izip_encoding
106 .CLIP_QUALITY_LEFT = CLIP_QUALITY_LEFT;
107 physical column < INSDC:coord:one > izip_encoding
108 .CLIP_QUALITY_RIGHT = CLIP_QUALITY_RIGHT;
109 }
110
111 database NCBI:SRA:GenericFastqNoNames:db #1
112 {
113 table NCBI:SRA:GenericFastq:sequence_no_name #1.0 SEQUENCE;
114 };
115
116 /*--------------------------------------------------------------------------
117 * NCBI:SRA:GenericFastq:sequence_log_odds
118 * Generic Fastq SRA Platform (for log_odds)
119 */
120 table NCBI:SRA:GenericFastq:sequence_log_odds #1
121 = NCBI:SRA:tbl:sra #2.1.3
122 , NCBI:tbl:base_space #2.0.3
123 , NCBI:tbl:log_odds_quality #2.1.0
124 , NCBI:SRA:tbl:clip #1.0.2
125 {
126 ascii platform_name
127 = < ascii > echo < "UNDEFINED" > ();
128
129 INSDC:SRA:platform_id out_platform
130 = < INSDC:SRA:platform_id > echo < SRA_PLATFORM_UNDEFINED > ();
131
132 /* ascii only spot name tokenizer */
133
134 NCBI:SRA:spot_name_token out_spot_name_tok
135 = NCBI:SRA:GenericFastq:tokenize_spot_name ( _out_name );
136
137 NCBI:SRA:spot_name_token in_spot_name_tok
138 = NCBI:SRA:GenericFastq:tokenize_spot_name ( NAME );
139
140 /* clips */
141
142 physical column < INSDC:coord:one > izip_encoding
143 .CLIP_ADAPTER_LEFT = CLIP_ADAPTER_LEFT;
144 physical column < INSDC:coord:one > izip_encoding
145 .CLIP_ADAPTER_RIGHT = CLIP_ADAPTER_RIGHT;
146 physical column < INSDC:coord:one > izip_encoding
147 .CLIP_QUALITY_LEFT = CLIP_QUALITY_LEFT;
148 physical column < INSDC:coord:one > izip_encoding
149 .CLIP_QUALITY_RIGHT = CLIP_QUALITY_RIGHT;
150 }
151
152 database NCBI:SRA:GenericFastqLogOdds:db #1
153 {
154 table NCBI:SRA:GenericFastq:sequence_log_odds #1.0 SEQUENCE;
155 };
156
157 /*--------------------------------------------------------------------------
158 * NCBI:SRA:GenericFastq:sequence_nanopore
159 * Oxford Nanopore SRA Platform
160 */
161 table NCBI:SRA:GenericFastq:sequence_nanopore #1
162 = NCBI:SRA:tbl:sra #2.1.3
163 , NCBI:tbl:base_space #2.0.3
164 , NCBI:tbl:phred_quality #2.0.4
165 {
166 ascii platform_name
167 = < ascii > echo < "OXFORD_NANOPORE" > ();
168
169 INSDC:SRA:platform_id out_platform
170 = < INSDC:SRA:platform_id > echo < SRA_PLATFORM_OXFORD_NANOPORE > ();
171
172 /* ascii only spot name tokenizer */
173
174 NCBI:SRA:spot_name_token out_spot_name_tok
175 = NCBI:SRA:GenericFastq:tokenize_spot_name ( _out_name );
176
177 NCBI:SRA:spot_name_token in_spot_name_tok
178 = NCBI:SRA:GenericFastq:tokenize_spot_name ( NAME );
179
180 /* channel and read number columns */
181
182 extern column < U32 > izip_encoding #1 CHANNEL;
183 extern column < U32 > izip_encoding #1 READ_NUMBER;
184 }
185
186 /*--------------------------------------------------------------------------
187 * NCBI:SRA:GenericFastq:consensus_nanopore
188 * Oxford Nanopore SRA Platform
189 */
190 table NCBI:SRA:GenericFastq:consensus_nanopore #1
191 = NCBI:SRA:tbl:sra #2.1.3
192 , NCBI:tbl:base_space #2.0.3
193 , NCBI:tbl:phred_quality #2.0.4
194 {
195 ascii platform_name
196 = < ascii > echo < "OXFORD_NANOPORE" > ();
197
198 INSDC:SRA:platform_id out_platform
199 = < INSDC:SRA:platform_id > echo < SRA_PLATFORM_OXFORD_NANOPORE > ();
200
201 /* ascii only spot name tokenizer */
202
203 NCBI:SRA:spot_name_token out_spot_name_tok
204 = NCBI:SRA:GenericFastq:tokenize_spot_name ( _out_name );
205
206 NCBI:SRA:spot_name_token in_spot_name_tok
207 = NCBI:SRA:GenericFastq:tokenize_spot_name ( NAME );
208
209 /* channel and read number columns */
210
211 extern column < U32 > izip_encoding #1 CHANNEL;
212 extern column < U32 > izip_encoding #1 READ_NUMBER;
213 }
214
215 database NCBI:SRA:GenericFastqNanopore:db #1
216 {
217 table NCBI:SRA:GenericFastq:sequence_nanopore #1.0 SEQUENCE;
218 table NCBI:SRA:GenericFastq:consensus_nanopore #1.0 CONSENSUS;
219 };
220
221 database NCBI:SRA:GenericFastqNanoporeConsensusOnly:db #1
222 {
223 table NCBI:SRA:GenericFastq:consensus_nanopore #1.0 CONSENSUS;
224 };
225
226 /*--------------------------------------------------------------------------
227 * NCBI:SRA:GenericFastq:absolid
228 * Generic fastq for AB Solid platform
229 */
230 table NCBI:SRA:GenericFastq:absolid #1
231 = NCBI:SRA:tbl:sra #2.1.3
232 , NCBI:tbl:color_space #2.1.0
233 , NCBI:tbl:phred_quality #2.0.4
234 , NCBI:SRA:tbl:clip #1.0.2
235 {
236 ascii platform_name
237 = < ascii > echo < "UNDEFINED" > ();
238
239 INSDC:SRA:platform_id out_platform
240 = < INSDC:SRA:platform_id > echo < SRA_PLATFORM_UNDEFINED > ();
241
242 /* ascii only spot name tokenizer */
243
244 NCBI:SRA:spot_name_token out_spot_name_tok
245 = NCBI:SRA:GenericFastq:tokenize_spot_name ( _out_name );
246
247 NCBI:SRA:spot_name_token in_spot_name_tok
248 = NCBI:SRA:GenericFastq:tokenize_spot_name ( NAME );
249
250 /* clips */
251
252 physical column < INSDC:coord:one > izip_encoding
253 .CLIP_ADAPTER_LEFT = CLIP_ADAPTER_LEFT;
254 physical column < INSDC:coord:one > izip_encoding
255 .CLIP_ADAPTER_RIGHT = CLIP_ADAPTER_RIGHT;
256 physical column < INSDC:coord:one > izip_encoding
257 .CLIP_QUALITY_LEFT = CLIP_QUALITY_LEFT;
258 physical column < INSDC:coord:one > izip_encoding
259 .CLIP_QUALITY_RIGHT = CLIP_QUALITY_RIGHT;
260 }
261
262 database NCBI:SRA:GenericFastqAbsolid:db #1
263 {
264 table NCBI:SRA:GenericFastq:absolid #1.0 SEQUENCE;
265 };