|
0
|
1 <macros>
|
|
|
2
|
|
|
3 <token name="@single_or_paired_cmd@">
|
|
|
4 #if str( $library.type ) == "single":
|
|
|
5 F1=${library.input_1}
|
|
|
6 #elif str( $library.type ) == "paired":
|
|
|
7 F1=${library.input_1}
|
|
|
8 F2=${library.input_2}
|
|
|
9 SAME_HEADERS=${library.SAME_HEADERS}
|
|
|
10 #else
|
|
|
11 ## prepare paired-end collection
|
|
|
12 F1=${library.input_1.forward}
|
|
|
13 F2=${library.input_1.reverse}
|
|
|
14 SAME_HEADERS=${library.SAME_HEADERS}
|
|
|
15 #end if
|
|
|
16 </token>
|
|
|
17
|
|
|
18 <xml name="paired_options">
|
|
|
19 <when value="paired">
|
|
|
20 <param name="input_1" format="fastq" type="data" label="FASTQ file #1"/>
|
|
|
21 <param name="input_2" format="fastq" type="data" label="FASTQ file #2"/>
|
|
|
22 <yield />
|
|
|
23 <param name="SAME_HEADERS" type="boolean"
|
|
|
24 label="Ensure headers of both reads of a pair are identical (SAME_HEADERS)"
|
|
|
25 help="Only applies if barcodes are added to the header (option ADD)"
|
|
|
26 truevalue="true"
|
|
|
27 falsevalue="false" checked="false"/>
|
|
|
28 </when>
|
|
|
29 <when value="paired_collection">
|
|
|
30 <param name="input_1" format="fastq" type="data_collection" collection_type="paired"
|
|
|
31 label="FASTQ Paired Dataset"/>
|
|
|
32 <yield />
|
|
|
33 <param name="SAME_HEADERS" type="boolean"
|
|
|
34 label="Ensure headers of both reads of a pair are identical (SAME_HEADERS)"
|
|
|
35 help="Only applies if barcodes are added to the header (option ADD)"
|
|
|
36 truevalue="true"
|
|
|
37 falsevalue="false" checked="false"/>
|
|
|
38 </when>
|
|
|
39 </xml>
|
|
|
40
|
|
|
41 <token name="@single_or_paired_illu_cmd@">
|
|
|
42 @single_or_paired_cmd@
|
|
|
43 I1=$library.I1
|
|
|
44 #if str( $library.type ) != "single":
|
|
|
45 #if str( $library.I2_CONDITIONAL.I2_AVAILABLE ) == "true":
|
|
|
46 I2=${library.I2_CONDITIONAL.I2}
|
|
|
47 BRED=${library.I2_CONDITIONAL.BRED_CONDITIONAL.BRED}
|
|
|
48 #if str( $library.I2_CONDITIONAL.BRED_CONDITIONAL.BRED ) == "true":
|
|
|
49 STRICT=${library.I2_CONDITIONAL.BRED_CONDITIONAL.STRICT}
|
|
|
50 #end if
|
|
|
51 #end if
|
|
|
52 #end if
|
|
|
53 </token>
|
|
|
54
|
|
|
55 <xml name="single_or_paired_illu">
|
|
|
56 <conditional name="library">
|
|
|
57 <param name="type" type="select" label="Is this single or paired library">
|
|
|
58 <option value="single">Single-end</option>
|
|
|
59 <option value="paired">Paired-end</option>
|
|
|
60 <option value="paired_collection">Paired-end Dataset Collection</option>
|
|
|
61 </param>
|
|
|
62 <when value="single">
|
|
|
63 <param name="input_1" format="fastq" type="data" label="FASTQ file"/>
|
|
|
64 <param name="I1" type="data" format="fastq" label="First Index File"/>
|
|
|
65 </when>
|
|
|
66 <expand macro="paired_options">
|
|
|
67 <param name="I1" type="data" format="fastq" label="First Index File"/>
|
|
|
68 <conditional name="I2_CONDITIONAL">
|
|
|
69 <param name="I2_AVAILABLE" type="select" label="Do you have a second index file?">
|
|
|
70 <option value="true">Yes</option>
|
|
|
71 <option value="false" selected="true">No</option>
|
|
|
72 </param>
|
|
|
73 <when value="true">
|
|
|
74 <param name="I2" type="data" format="fastq" label="Second Index File"/>
|
|
|
75 <expand macro="bred_conditional"/>
|
|
|
76 </when>
|
|
|
77 <when value="false"/>
|
|
|
78 </conditional>
|
|
|
79 </expand>
|
|
|
80 </conditional>
|
|
|
81 </xml>
|
|
|
82
|
|
|
83 <xml name="single_or_paired_general">
|
|
|
84 <conditional name="library">
|
|
|
85 <param name="type" type="select" label="Is this single or paired library">
|
|
|
86 <option value="single">Single-end</option>
|
|
|
87 <option value="paired">Paired-end</option>
|
|
|
88 <option value="paired_collection">Paired-end Dataset Collection</option>
|
|
|
89 </param>
|
|
|
90 <when value="single">
|
|
|
91 <param name="input_1" format="fastq" type="data" label="FASTQ file"/>
|
|
|
92 </when>
|
|
|
93 <expand macro="paired_options">
|
|
|
94 <yield />
|
|
|
95 </expand>
|
|
|
96 </conditional>
|
|
|
97 </xml>
|
|
|
98
|
|
|
99 <token name="@demultiplex_paired_end_cmd_options@">
|
|
|
100 BPOS=$library.BPOS_CONDITIONAL.BPOS
|
|
|
101 #if str( $library.BPOS_CONDITIONAL.BPOS ) == "BOTH":
|
|
|
102 BM=${library.BPOS_CONDITIONAL.BM_CONDITIIONAL.BM}
|
|
|
103 #if str( $library.BPOS_CONDITIONAL.BM_CONDITIIONAL.BM ) == "BOTH":
|
|
|
104 BRED=${library.BPOS_CONDITIONAL.BM_CONDITIIONAL.BRED_CONDITIONAL.BRED}
|
|
|
105 #if str( $library.BPOS_CONDITIONAL.BM_CONDITIIONAL.BRED_CONDITIONAL.BRED ) == "true":
|
|
|
106 STRICT=${library.BPOS_CONDITIONAL.BM_CONDITIIONAL.BRED_CONDITIONAL.STRICT}
|
|
|
107 #end if
|
|
|
108 #end if
|
|
|
109 #end if
|
|
|
110 </token>
|
|
|
111
|
|
|
112 <xml name="demultiplex_paired_end_options">
|
|
|
113 <conditional name="BPOS_CONDITIONAL">
|
|
|
114 <param name="BPOS" type="select" label="Barcode read position (BPOS)" help="where are the barcodes">
|
|
|
115 <option value="READ_1" selected="true">READ_1 (beginning of read from the first fastq file)</option>
|
|
|
116 <option value="READ_2">READ_2 (beginning of read from the second fastq file)</option>
|
|
|
117 <option value="BOTH">BOTH (beginning of both reads)</option>
|
|
|
118 </param>
|
|
|
119 <when value="READ_1"/>
|
|
|
120 <when value="READ_2"/>
|
|
|
121 <when value="BOTH">
|
|
|
122 <conditional name="BM_CONDITIIONAL">
|
|
|
123 <param name="BM" type="select" label="Barcode for sample matching (BM)"
|
|
|
124 help="which barcode should be used for sample look up (BM option)." >
|
|
|
125 <option value="READ_1" selected="true">
|
|
|
126 READ_1 (beginning of read from the first fastq file)
|
|
|
127 </option>
|
|
|
128 <option value="READ_2">
|
|
|
129 READ_2 (beginning of read from the second fastq file)
|
|
|
130 </option>
|
|
|
131 <option value="BOTH">
|
|
|
132 BOTH (beginning of both reads)
|
|
|
133 </option>
|
|
|
134 </param>
|
|
|
135 <when value="READ_1"/>
|
|
|
136 <when value="READ_2"/>
|
|
|
137 <when value="BOTH">
|
|
|
138 <expand macro="bred_conditional"/>
|
|
|
139 </when>
|
|
|
140 </conditional>
|
|
|
141 </when>
|
|
|
142 </conditional>
|
|
|
143 </xml>
|
|
|
144
|
|
|
145 <xml name="bred_conditional">
|
|
|
146 <conditional name="BRED_CONDITIONAL">
|
|
|
147 <param name="BRED" type="select" label="Redundant barcodes (BRED)"
|
|
|
148 help="are the barcodes REDUNDANT i.e. do they both resolve to the same sample.">
|
|
|
149 <option value="true" selected="true">Yes</option>
|
|
|
150 <option value="false">No</option>
|
|
|
151 </param>
|
|
|
152 <when value="true">
|
|
|
153 <param name="STRICT" type="boolean" label="Strict (S)"
|
|
|
154 truevalue="true"
|
|
|
155 falsevalue="false"
|
|
|
156 checked="false"
|
|
|
157 />
|
|
|
158 </when>
|
|
|
159 <when value="false"/>
|
|
|
160 </conditional>
|
|
|
161 </xml>
|
|
|
162
|
|
|
163 <token name="@barcode_option_cmd@">
|
|
|
164 #if str( $barcodes.barcode_list_type_con ) == "text":
|
|
|
165 BARCODE_FILE=${barcode_file_from_text}
|
|
|
166 #else if str( $barcodes.barcode_list_type_con ) == "file":
|
|
|
167 BARCODE_FILE=${barcodes.BARCODE_FILE}
|
|
|
168 #end if
|
|
|
169 </token>
|
|
|
170
|
|
|
171 <xml name="barcode_option">
|
|
|
172 <conditional name="barcodes">
|
|
|
173 <param name="barcode_list_type_con" type="select" label="Barcode list input type">
|
|
|
174 <option value="file" selected="true">Use a tab-delimited file from the history</option>
|
|
|
175 <option value="text">Paste the barcodes list in a text field within the form</option>
|
|
|
176 </param>
|
|
|
177
|
|
|
178 <when value="file">
|
|
|
179 <param name="BARCODE_FILE" type="data" format="tabular,txt" label="Barcode List"
|
|
|
180 help="Barcode list format: one sample per line. First column is sample name and second is the
|
|
|
181 barcode, separated by tab or space. A third and fourth column can be used to specify the resulting
|
|
|
182 file names. See help below."/>
|
|
|
183 </when>
|
|
|
184
|
|
|
185 <when value="text">
|
|
|
186 <param name="barcode_text" type="text" area="True" size="10x30"
|
|
|
187 value="sample_name\tbarcode\n" label="Barcode List"
|
|
|
188 help="Barcode list format: one sample per line. First column is sample name and second is the
|
|
|
189 barcode, separated by tab or space. A third and fourth column can be used to specify the resulting
|
|
|
190 file names. See help below.">
|
|
|
191 <sanitizer>
|
|
|
192 <valid initial="string.printable"></valid>
|
|
|
193 <mapping initial="none"/>
|
|
|
194 </sanitizer>
|
|
|
195 </param>
|
|
|
196 </when>
|
|
|
197 </conditional>
|
|
|
198 </xml>
|
|
|
199
|
|
|
200 <xml name="barcode_config_file">
|
|
|
201 <configfile name="barcode_file_from_text">#set from_text_area = ''
|
|
|
202 #if str( $barcodes.barcode_list_type_con ) == "text":
|
|
|
203 #set from_text_area = $barcodes.barcode_text
|
|
|
204 #end if
|
|
|
205 ${from_text_area}</configfile>
|
|
|
206 </xml>
|
|
|
207
|
|
|
208 <token name="@barcode_len_cmd@">
|
|
|
209 #if str( $LEN ) != "":
|
|
|
210 BCLEN=$LEN
|
|
|
211 #end if
|
|
|
212 </token>
|
|
|
213
|
|
|
214 <xml name="barcode_len_option">
|
|
|
215 <param name="LEN" type="text" value="" label="Barcode Length (LEN)"
|
|
|
216 help="If 'Barcode read position'=BOTH and 'Redundant barcodes'=False, two distinct
|
|
|
217 lengths can be provided using the syntax LEN=X:Z where X and Z are 2 integers representing
|
|
|
218 the barcode length for read_1 and read_2 respectively. Default: empty"/>
|
|
|
219 </xml>
|
|
|
220 <xml name="clip_barcode">
|
|
|
221 <param name="CLIP_BARCODE" type="boolean" label="Remove barcode sequence from read (C)"
|
|
|
222 truevalue="true" falsevalue="false" checked="true"/>
|
|
|
223 </xml>
|
|
|
224
|
|
|
225 <token name="@demultiplexer_common_options_cmd@">
|
|
|
226 ADD=${ADD}
|
|
|
227 MM=$MM
|
|
|
228 MMD=$MMD
|
|
|
229 Q=$MIN_BASE_QUALITY
|
|
|
230 QUALITY_FORMAT=$QUALITY_FORMAT
|
|
|
231 </token>
|
|
|
232 <xml name="demultiplexer_common_options">
|
|
|
233 <param name="ADD" type="boolean"
|
|
|
234 label="Add matched barcode at the end of the read header (ADD)"
|
|
|
235 truevalue="true"
|
|
|
236 falsevalue="false"
|
|
|
237 checked="true"
|
|
|
238 />
|
|
|
239 <param name="MM" type="text" value="1" label="Maximum Mismatches (MM)"
|
|
|
240 help="Maximum mismatches for a barcode to be considered a match." />
|
|
|
241
|
|
|
242 <param name="MMD" type="text" value="1" label="Minimum mismatch difference (MMD)"
|
|
|
243 help="Minimum difference between number of mismatches in the best and second best barcodes for a barcode
|
|
|
244 to be considered a match." />
|
|
|
245
|
|
|
246 <param name="MIN_BASE_QUALITY" type="text" value="10" label="Minimum base quality (Q)"
|
|
|
247 help="Any barcode bases falling below this quality will be
|
|
|
248 considered a mismatch even in the bases match." />
|
|
|
249
|
|
|
250 <param name="QUALITY_FORMAT" type="select" label="Fastq Quality Format (V)"
|
|
|
251 help="How are the quality values encoded in the fastq. Either 'Solexa' for
|
|
|
252 pre-pipeline 1.3 style scores (solexa scaling + 66), 'Illumina' for pipeline 1.3 and
|
|
|
253 above (phred scaling + 64) or 'Standard' for phred scaled scores with a character shift
|
|
|
254 of 33.">
|
|
|
255 <option value="Standard" selected="true">
|
|
|
256 Fastq - Illumina Casava v1.8 with Sanger coding quality (phred scaling + 33)
|
|
|
257 </option>
|
|
|
258 <option value="Illumina">
|
|
|
259 Fastq - Illumina v1.3 or above coding of quality (phred scaling + 64)
|
|
|
260 </option>
|
|
|
261 <option value="Solexa">
|
|
|
262 Fastq - Solexa-style quality (solexa scaling + 66)
|
|
|
263 </option>
|
|
|
264 <option value="null">
|
|
|
265 Detect automatically
|
|
|
266 </option>
|
|
|
267 </param>
|
|
|
268 </xml>
|
|
|
269
|
|
|
270 <token name="@demultiplexer_common_output_options_cmd@">
|
|
|
271 KEEP_UNASSIGNED_READ=$KEEP_UNASSIGNED_READ
|
|
|
272 STATS_ONLY=${adv_options.STATS_ONLY}
|
|
|
273 #if str( $adv_options.DIAG ) == "true":
|
|
|
274 BARCODE_DIAG_FILE=$BARCODE_DIAG_FILE
|
|
|
275 #end if
|
|
|
276 </token>
|
|
|
277 <xml name="demultiplexer_common_output_options">
|
|
|
278 <param name="KEEP_UNASSIGNED_READ" type="boolean" label="Keep unassigned reads (KEEP_UNASSIGNED_READ)"
|
|
|
279 truealue="true"
|
|
|
280 falsevalue="false"
|
|
|
281 checked="true"
|
|
|
282 />
|
|
|
283 <section name="adv_options" title="Advanced Options" expanded="False">
|
|
|
284 <param name="DIAG" type="boolean" label="Output barcode match reporting file (DIAG)"
|
|
|
285 truevalue="true" falsevalue="false" checked="false"
|
|
|
286 help="This file will
|
|
|
287 contain a line per read pair with the barcode best matching the read subsequence or 'null' when no
|
|
|
288 match is found according to matching parameters. This file is useful for debugging or further
|
|
|
289 processing in case both ends are barcoded."/>
|
|
|
290 <param name="STATS_ONLY" type="boolean" label="Only produce metric and diagnostic reports (STATS_ONLY)"
|
|
|
291 truevalue="true" falsevalue="false" checked="false"
|
|
|
292 help="do not demultiplex." />
|
|
|
293 </section>
|
|
|
294 </xml>
|
|
|
295
|
|
|
296 <token name="@common_options_cmd@">
|
|
|
297 XT=${XT}
|
|
|
298 ZT=${ZT}
|
|
|
299 #if str( $RCHAR ) != "":
|
|
|
300 RCHAR=${RCHAR}
|
|
|
301 #end if
|
|
|
302 GZ=${GZ}
|
|
|
303 OUTPUT_DIR=results
|
|
|
304 </token>
|
|
|
305 <xml name="common_options">
|
|
|
306 <param name="XT" type="text" value="0"
|
|
|
307 label="Extra number of bases to be trimmed right after the barcode (XT)" />
|
|
|
308 <param name="ZT" type="text" value="0"
|
|
|
309 label="Extra number of bases to be trimmed from the read end (ZT)" />
|
|
|
310
|
|
|
311 <param name="RCHAR" type="text"
|
|
|
312 label="Replace white space in the read name/header with speficied symbols (RCHAR)"
|
|
|
313 help="Set to empty for no replacement"
|
|
|
314 value=":"/>
|
|
|
315
|
|
|
316 <param name="GZ" type="boolean" hidden="true" label="Compress output (GZ)"
|
|
|
317 help="will result in fastq.gz files."
|
|
|
318 truevalue="true"
|
|
|
319 falsevalue="false"
|
|
|
320 checked="false"/>
|
|
|
321 </xml>
|
|
|
322
|
|
|
323 <token name="@demultiplexer_common_outputs_cmd@">
|
|
|
324 METRICS_FILE_NAME=$METRICS_FILE_NAME
|
|
|
325 </token>
|
|
|
326 <xml name="demultiplexer_common_outputs">
|
|
|
327 <data name="METRICS_FILE_NAME" format="tabular" label="Je-Demultiplex result">
|
|
|
328 <!--<discover_datasets pattern="(?P<name>.*)\.txt" ext="fastqsanger"-->
|
|
|
329 <discover_datasets pattern="(?P<name>.*)\.txt" directory="results" visible="true" ext="fastqsanger"/>
|
|
|
330 </data>
|
|
|
331 <data name="BARCODE_DIAG_FILE" format="tabular" label="Barcode statistics">
|
|
|
332 <filter>(adv_options['DIAG'] == 'true')</filter>
|
|
|
333 </data>
|
|
|
334 </xml>
|
|
|
335
|
|
|
336 </macros>
|
