Mercurial > repos > gbcs-embl-heidelberg > je_demultiplex_illu
annotate je-demultiplex-illu.xml @ 8:d556679c88d6 draft
planemo upload for repository https://git.embl.de/grp-gbcs/Je/tree/master/src/galaxy commit bc2365188e0dd0f20925884276a27914bb714280
| author | gbcs-embl-heidelberg |
|---|---|
| date | Mon, 23 Apr 2018 05:47:54 -0400 |
| parents | 370d9764f670 |
| children | 9dad3d0b27bc |
| rev | line source |
|---|---|
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planemo upload for repository https://git.embl.de/grp-gbcs/Je/tree/master/src/galaxy commit dd9e62bdb01d1252a90ce778103ce9b6b4a8cd52-dirty
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1 <tool id="je_demultiplex_illu" name="Je-Demultiplex-Illu" version="@VERSION_STRING@"> |
| 0 | 2 <description>demultiplexes fastq files using Illumina Index file</description> |
| 3 <macros> | |
| 4 <import>macros.xml</import> | |
| 5 </macros> | |
|
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planemo upload for repository https://git.embl.de/grp-gbcs/Je/tree/master/src/galaxy commit 0eefd837333dae6fbecaf4f55b053268d844eff6
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6 <expand macro="requirements" /> |
| 0 | 7 <stdio> |
| 8 <exit_code range="1:" level="fatal" description="Tool exception" /> | |
| 9 </stdio> | |
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planemo upload for repository https://git.embl.de/grp-gbcs/Je/tree/master/src/galaxy commit 0eefd837333dae6fbecaf4f55b053268d844eff6
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parents:
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10 <expand macro="version_command" /> |
|
69c77f9fc064
planemo upload for repository https://git.embl.de/grp-gbcs/Je/tree/master/src/galaxy commit 0eefd837333dae6fbecaf4f55b053268d844eff6
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11 <command> |
| 0 | 12 <![CDATA[ |
| 13 je demultiplex-illu | |
| 14 | |
| 15 ## Fastq inputs | |
| 16 @single_or_paired_illu_cmd@ | |
| 17 | |
| 18 @barcode_option_cmd@ | |
| 19 | |
| 20 #if str($INTERNAL_BARCODES_CON.INTERNAL_BARCODES) == 'true': | |
| 21 BPOS=${INTERNAL_BARCODES_CON.BPOS} | |
| 22 C=${INTERNAL_BARCODES_CON.CLIP_BARCODE} | |
| 23 #if str( $INTERNAL_BARCODES_CON.LEN ) != "": | |
| 24 BCLEN=$INTERNAL_BARCODES_CON.LEN | |
| 25 #end if | |
| 26 #else: | |
| 27 BPOS=NONE | |
| 28 C=false | |
| 29 #end if | |
| 30 | |
| 31 @common_options_cmd@ | |
| 32 | |
| 33 @demultiplexer_common_output_options_cmd@ | |
| 34 @demultiplexer_common_outputs_cmd@ | |
| 35 ]]> | |
| 36 </command> | |
| 37 <configfiles> | |
| 38 <expand macro="barcode_config_file"/> | |
| 39 </configfiles> | |
| 40 <inputs> | |
| 41 <!-- single/paired - similar to macro 'single_or_paired_general' --> | |
| 42 <expand macro="single_or_paired_illu"> | |
| 43 <expand macro="demultiplex_illu_paired_end_options"/> | |
| 44 </expand> | |
| 45 <expand macro="barcode_option"/> | |
| 46 <conditional name="INTERNAL_BARCODES_CON"> | |
| 47 <param name="INTERNAL_BARCODES" type="select" | |
| 48 label="Do your reads contain Unique Molecular Identifiers(UMIs)"> | |
| 49 <option value="true">Yes</option> | |
| 50 <option value="false" selected="true">No</option> | |
| 51 </param> | |
| 52 <when value="true"> | |
| 53 <param name="BPOS" type="select" label="Barcode read position (BPOS)" help="where are the barcodes. | |
| 54 If not using paired-end it does not matter what you specify here."> | |
| 55 <option value="READ_1" selected="true">READ_1 (beginning of read from the first fastq file)</option> | |
| 56 <option value="READ_2">READ_2 (beginning of read from the second fastq file)</option> | |
| 57 <option value="BOTH">BOTH (beginning of both reads)</option> | |
| 58 </param> | |
| 59 <expand macro="barcode_len_option"/> | |
| 60 <expand macro="clip_barcode"/> | |
| 61 </when> | |
| 62 <when value="false"/> | |
| 63 </conditional> | |
| 64 | |
| 65 <expand macro="demultiplexer_common_options"/> | |
| 66 | |
| 67 <expand macro="common_options"/> | |
| 68 | |
| 69 <expand macro="demultiplexer_common_output_options"/> | |
| 70 | |
| 71 </inputs> | |
| 72 <outputs> | |
| 73 <expand macro="demultiplexer_common_outputs"/> | |
| 74 </outputs> | |
| 75 | |
| 76 <tests> | |
| 77 <test> | |
| 78 <!-- barcode at both ends, non-redundant --> | |
| 79 <param name="type" value="paired"/> | |
| 80 <param name="input_1" value="illu_file_1_sequence.txt" ftype="fastqsanger"/> | |
| 81 <param name="input_2" value="illu_file_2_sequence.txt" ftype="fastqsanger"/> | |
| 82 <param name="I1" value="illu_file_1_index.txt" ftype="fastqsanger"/> | |
| 83 <param name="I2_AVAILABLE" value="true"/> | |
| 84 <param name="I2" value="illu_file_2_index.txt" ftype="fastqsanger"/> | |
| 85 | |
| 86 <param name="INTERNAL_BARCODES" value="true"/> | |
| 87 <param name="barcode_list_type_con" value="file"/> | |
| 88 <param name="BARCODE_FILE" value="illu_dualindexing.txt" ftype="tabular"/> | |
| 89 <param name="LEN" value="8:8"/> | |
| 90 <param name="ZT" value="5:6"/> | |
| 91 <param name="BPOS" value="BOTH"/> | |
| 92 <param name="BM" value="BOTH"/> | |
| 93 <param name="BRED" value="false"/> | |
| 94 <param name="MM" value="3"/> | |
| 95 <param name="MMD" value="2"/> | |
| 96 <param name="Q" value="20"/> | |
|
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69c77f9fc064
planemo upload for repository https://git.embl.de/grp-gbcs/Je/tree/master/src/galaxy commit 0eefd837333dae6fbecaf4f55b053268d844eff6
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97 <param name="DIAG" value="false"/> |
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planemo upload for repository https://git.embl.de/grp-gbcs/Je/tree/master/src/galaxy commit e217faa15f73427979bb212036cb130a14c59750
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98 <output name="METRICS_FILE_NAME" file="illu_summary_PE.txt" ftype="tabular" lines_diff="4"/> |
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370d9764f670
planemo upload for repository https://git.embl.de/grp-gbcs/Je/tree/master/src/galaxy commit e217faa15f73427979bb212036cb130a14c59750
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99 <output name="DEMULTIPLEX_RESULTS" ftype="tabular"> |
| 0 | 100 <discovered_dataset designation="unassigned_1" file="illu_unassigned_1_PE.txt" /> |
| 101 <discovered_dataset designation="unassigned_2" file="illu_unassigned_2_PE.txt" /> | |
| 102 <discovered_dataset designation="emb681m5_GGACTCCTCTCTCTAT_2" file="emb681m5_GGACTCCTCTCTCTAT_2.txt"/> | |
| 103 <discovered_dataset designation="emb681m5_GGACTCCTCTCTCTAT_1" file="emb681m5_GGACTCCTCTCTCTAT_1.txt"/> | |
| 104 <discovered_dataset designation="emb681m4_TCCTGAGCCTCTCTAT_2" file="emb681m4_TCCTGAGCCTCTCTAT_2.txt"/> | |
| 105 <discovered_dataset designation="emb681m4_TCCTGAGCCTCTCTAT_1" file="emb681m4_TCCTGAGCCTCTCTAT_1.txt"/> | |
| 106 <discovered_dataset designation="emb681m1_TAAGGCGACTCTCTAT_2" file="emb681m1_TAAGGCGACTCTCTAT_2.txt"/> | |
| 107 <discovered_dataset designation="emb681m1_TAAGGCGACTCTCTAT_1" file="emb681m1_TAAGGCGACTCTCTAT_1.txt"/> | |
| 108 <discovered_dataset designation="emb6801m2_AGGCAGAATAGATCGC_2" file="emb6801m2_AGGCAGAATAGATCGC_2.txt"/> | |
| 109 <discovered_dataset designation="emb6801m2_AGGCAGAATAGATCGC_1" file="emb6801m2_AGGCAGAATAGATCGC_1.txt"/> | |
| 110 <discovered_dataset designation="emb6801m1_CGTACTAGTAGATCGC_2" file="emb6801m1_CGTACTAGTAGATCGC_2.txt"/> | |
| 111 <discovered_dataset designation="emb6801m1_CGTACTAGTAGATCGC_1" file="emb6801m1_CGTACTAGTAGATCGC_1.txt"/> | |
| 112 </output> | |
| 113 </test> | |
| 114 </tests> | |
| 115 | |
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69c77f9fc064
planemo upload for repository https://git.embl.de/grp-gbcs/Je/tree/master/src/galaxy commit 0eefd837333dae6fbecaf4f55b053268d844eff6
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116 <help> |
| 0 | 117 <![CDATA[ |
| 118 **What it does** | |
| 119 | |
| 120 Je demultiplex-illu: demultiplex fastq files using Illumina Index files, | |
| 121 with optional handling of Unique Molecular Identifiers for further use in 'markdupes' module | |
| 122 Input files are fastq files, and can be in gzip compressed format. | |
| 123 | |
| 124 Author: Charles Girardot (charles.girardot@embl.de). | |
| 125 | |
| 126 Wrapper by: Jelle Scholtalbers (jelle.scholtalbers@embl.de). | |
| 127 | |
|
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planemo upload for repository https://git.embl.de/grp-gbcs/Je/tree/master/src/galaxy commit e217faa15f73427979bb212036cb130a14c59750
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128 With contributions by: Mehmet Tekman (@mtekman) |
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370d9764f670
planemo upload for repository https://git.embl.de/grp-gbcs/Je/tree/master/src/galaxy commit e217faa15f73427979bb212036cb130a14c59750
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129 |
| 0 | 130 ------ |
| 131 | |
| 132 **Know what you are doing** | |
| 133 | |
| 134 .. class:: warningmark | |
| 135 | |
| 136 You will want to read the `documentation`__. | |
| 137 | |
| 138 .. __: http://gbcs.embl.de/portal/Je | |
| 139 | |
| 140 ------ | |
| 141 | |
| 142 **Parameter list** | |
| 143 | |
| 144 This is an exhaustive list of options:: | |
| 145 | |
| 146 FASTQ_FILE1=File | |
| 147 F1=File | |
| 148 | |
| 149 Input fastq file (optionally gzipped) for single end data, or first read in paired end | |
| 150 data. | |
| 151 | |
| 152 Required. | |
| 153 | |
| 154 FASTQ_FILE2=File | |
| 155 F2=File | |
| 156 | |
| 157 Input fastq file (optionally gzipped) for the second read of paired end data. | |
| 158 | |
| 159 Default value: null. | |
| 160 | |
| 161 INDEX_FILE1=File | |
| 162 I1=File | |
| 163 | |
| 164 Fastq file for index 1 (barcode) reads, optionally gzipped | |
| 165 | |
| 166 Required. | |
| 167 | |
| 168 INDEX_FILE2=File | |
| 169 I2=File | |
| 170 | |
| 171 Fastq file for index 2 (barcode) reads, optionally gzipped. | |
| 172 A INDEX_FILE1 MUST be provided when INDEX_FILE2 is given. This situation corresponds to | |
| 173 Illumina dual indexing. | |
| 174 | |
| 175 Default value: null. | |
| 176 | |
| 177 BARCODE_FILE=File | |
| 178 BF=File | |
| 179 | |
| 180 Barcode file describing sequence list and sample names. Tab-delimited file with 2 | |
| 181 columns, with the sample in col1 and the corresponding barcode in col2. | |
| 182 Simple barcode file format : 2 tab-delimited colums | |
| 183 If multiple barcode map to the same sample, either line can be duplicated e.g. | |
| 184 sample1 ATAT | |
| 185 sample1 GAGG | |
| 186 sample2 CCAA | |
| 187 sample2 TGTG | |
| 188 Or barcodes can be combined using the OR operator '|' i.e. the file above can be | |
| 189 re-written like | |
| 190 sample1 ATAT|GAGG | |
| 191 sample2 CCAA|TGTG | |
| 192 Finally, for the special situation of paired-end data in which barcodes differ at both | |
| 193 ends (ie BPOS=BOTH BRED=false BM=BOTH , see BRED option description), barcodes for read_1 | |
| 194 and read_2 can be distinguished using a ':' separator i.e. | |
| 195 sample1 ATAT:GAGG | |
| 196 sample2 CCAA:TGTG | |
| 197 This above syntax means that sample 1 is encoded with ATAT barcode at read_1 AND GAGG | |
| 198 barcode at read_2. Note that you can still combine barcodes using | e.g. | |
| 199 sample1 ATAT|GAGG:CCAA|TGTG | |
| 200 would mean that sample 1 is mapped by the combination of barcode: ATAT OR GAGG at read_1 | |
| 201 AND CCAA OR TGTG at read_2. | |
| 202 Extended barcode file format : 3 (single-end) or 4 (paired-end) tab-delimited colums | |
| 203 same as the simple barcode file format but the extra columns contains the file name(s) | |
| 204 to use to name output files. A unique extra column is expected for single-end while 2 | |
| 205 extra columns are expected for paired-end. In case, lines are duplicated (multiple | |
| 206 barcodesmapping the same sample), the same file name should be indicated in the third | |
| 207 (and fourth) column(s). | |
| 208 sample1 ATAT spl1_1.txt.gz spl1_2.txt.gz | |
| 209 sample1 GAGG spl1_1.txt.gz spl1_2.txt.gz | |
| 210 sample2 CCAA spl2_1.txt.gz spl2_2.txt.gz | |
| 211 Or | |
| 212 sample1 ATAT|GAGG:CCAA|TGTG spl1_1.txt.gz spl1_2.txt.gz | |
| 213 Ns in barcode sequence are allowed and are used to flag positions that should be ignored | |
| 214 in sample matching | |
| 215 i.e. they will be clipped off the read sequence (like in iCLIP protocol). | |
| 216 | |
| 217 Required. | |
| 218 | |
| 219 BARCODE_READ_POS=BarcodePosition | |
| 220 BPOS=BarcodePosition | |
| 221 | |
| 222 Indicates the location of additional barcodes present in the read(s). Setting this option | |
| 223 implies setting the LEN option. | |
| 224 Importantly, these additional barcodes must not encode sample identity information but | |
| 225 used for e.g. molecular barcoding (UMIs) or for any purpose other than sample identity encoding. | |
| 226 | |
| 227 Default value: BOTH. This option can be set to 'null' to clear the default value. | |
| 228 Possible values: {READ_1, READ_2, BOTH, NONE} | |
| 229 | |
| 230 BCLEN=String | |
| 231 LEN=String | |
| 232 | |
| 233 Length of the barcode sequences, optional. Taken from barcode file when not given. | |
| 234 In situations where BARCODE_READ_POS == BOTH AND REDUNDANT_BARCODES=false, two distinct | |
| 235 length can be provided using the syntax LEN=X:Z where X and Z are 2 integers representing | |
| 236 the barcode length for read_1 and read_2 respectively. | |
| 237 | |
| 238 Default value: null | |
| 239 | |
| 240 REDUNDANT_BARCODES=Boolean | |
| 241 BRED=Boolean | |
| 242 | |
| 243 This option only applies for paired-end data with *both* INDEX_FILE1 and INDEX_FILE2 | |
| 244 provided. | |
| 245 Indicates if both index barcodes encode redundant information i.e. if both barcodes are | |
| 246 supposed to be identical (or resolve to the same sample when a pool of barcodes is used | |
| 247 per sample). | |
| 248 When BRED=true, the STRICT option guides the sample lookup behavior When BRED=false, | |
| 249 barcodes are combined prior to sample lookup. | |
| 250 | |
| 251 Default value: true. This option can be set to 'null' to clear the default value. | |
| 252 Possible values: {true, false} | |
| 253 | |
| 254 STRICT=Boolean | |
| 255 S=Boolean | |
| 256 | |
| 257 For paired-end data and when two distinct barcodes/indices are used to encode samples, | |
| 258 this option tells if both barcodes should resolve to the same sample. | |
| 259 When true and if only one of the two reads has a barcode match, the read pair is | |
| 260 'unassigned'. | |
| 261 When false and if only one of the two reads has a barcode match, the read pair is | |
| 262 assigned to the | |
| 263 corresponding sample | |
| 264 When reads resolve to different samples, the read pair is always 'unassigned'. | |
| 265 | |
| 266 Default value: false. This option can be set to 'null' to clear the default value. | |
| 267 Possible values: {true, false} | |
| 268 | |
| 269 MAX_MISMATCHES=String | |
| 270 MM=String | |
| 271 | |
| 272 Maximum mismatches for a barcode to be considered a match. In situations where both | |
| 273 barcodes are used for sample matching i.e. BPOS=BOTH BM=BOTH (or 2 INDEX_FILE given), two | |
| 274 distinct | |
| 275 values can be given here using the syntax MM=X:Z where X and Z are 2 integers to use for | |
| 276 read_1 and read_2 respectively. | |
| 277 MM=null is like MM=0 | |
| 278 | |
| 279 Default value: 1. This option can be set to 'null' to clear the default value. | |
| 280 | |
| 281 MIN_MISMATCH_DELTA=String | |
| 282 MMD=String | |
| 283 | |
| 284 Minimum difference between the number of mismatches against the best and the second best | |
| 285 barcode. When MMD is not respected, the read remains unassigned. | |
| 286 When two distinct barcodes are used for sample matching (dual encoding), two distinct | |
| 287 values can be given using the syntax MMD=X:Z where X and Z are 2 integers to use for | |
| 288 first (e.g. from read_1 or index_1) | |
| 289 MMD=null is like MMD=0 | |
| 290 | |
| 291 Default value: 1. This option can be set to 'null' to clear the default value. | |
| 292 | |
| 293 MIN_BASE_QUALITY=String | |
| 294 Q=String | |
| 295 | |
| 296 Minimum base quality during barcode matching: bases which quality is less than this | |
| 297 cutoff are always considered as a mismatch.When two distinct barcodes are used for sample | |
| 298 matching (dual encoding), two distinct values can be given using the syntax Q=X:Z where X | |
| 299 and Z are 2 integers to use for first (e.g. from read_1 or index_1) and second barcode | |
| 300 (e.g. from read_2 or index_2) respectively. | |
| 301 Q=null is like Q=0. | |
| 302 | |
| 303 Default value: 10. This option can be set to 'null' to clear the default value. | |
| 304 | |
| 305 XTRIMLEN=String | |
| 306 XT=String | |
| 307 | |
| 308 Optional extra number of base to be trimmed right after the barcode (only used if | |
| 309 CLIP_BARCODE=true). | |
| 310 When running paired-end, two distinct values can be given using the syntax XT=X:Z where X | |
| 311 and Z are 2 integers to use for read_1 and read_2 respectively. Note that even when | |
| 312 BPOS=READ_1 or BPOS=READ_2, a X:Y synthax can be given to trim the read w/o barcode as to | |
| 313 end up with reads of the same length (note that this can also be operated using ZT). If a | |
| 314 unique value is given, e.g. XT=1, while running paired-end the following rule applies: | |
| 315 (1) BPOS=READ_1 or BPOS=READ_2, no trim is applied at the read w/o barcode | |
| 316 (2) BPOS=BOTH, the value is used for both reads. | |
| 317 | |
| 318 Note that XT=null is like XT=0. | |
| 319 Default value: 0. This option can be set to 'null' to clear the default value. | |
| 320 | |
| 321 ZTRIMLEN=String | |
| 322 ZT=String | |
| 323 | |
| 324 Optional extra number of bases to be trimmed from the read end i.e. 3' end. | |
| 325 When running paired-end, two distinct values can be given here using the syntax ZT=X:Z | |
| 326 where X and Z are 2 integers to use for read_1 and read_2 respectively. Note that even | |
| 327 when BPOS=READ_1 or BPOS=READ_2, a X:Y synthax can be given to trim the read w/o barcode | |
| 328 as to end up with reads of the same length (note that this can also be operated using | |
| 329 XT). Note that if a single value is passed, the value always applies to both reads in | |
| 330 paired-end mode without further consideration. | |
| 331 ZT=null is like ZT=0. | |
| 332 | |
| 333 Default value: 0. This option can be set to 'null' to clear the default value. | |
| 334 | |
| 335 CLIP_BARCODE=Boolean | |
| 336 C=Boolean | |
| 337 | |
| 338 Clip barcode sequence from read sequence, as well as XTRIMLEN (and ZTRIMLEN) bases if | |
| 339 applicable, before writing to output file. | |
| 340 If false, reads are written without modification to output file. | |
| 341 Apply to both barcodes when BPOS=BOTH. | |
| 342 | |
| 343 Default value: true. This option can be set to 'null' to clear the default value. | |
| 344 Possible values: {true, false} | |
| 345 | |
| 346 ADD_BARCODE_TO_HEADER=Boolean | |
| 347 ADD=Boolean | |
| 348 | |
| 349 Add matched barcode at the end of the read header. Applies to both index when INDEX_FILE2 | |
| 350 is also provided. | |
| 351 First the sample encoding barcodes from I1 (and I2 when relevant) are added to the read | |
| 352 headers like | |
| 353 @D3FCO8P1:178:C1WLBACXX:7:1101:1836:1965 2:N:0:I1_BARCODE:I2_BARCODE | |
| 354 Then, if BPOS!=NONE, the additional barcodes (UMIs) clipped from the read(s) are added | |
| 355 to their own header, like | |
| 356 @D3FCO8P1:178:C1WLBACXX:7:1101:1836:1965 2:N:0:I1_BARCODE:I2_BARCODE:CLIPPED_SEQ_FROMREAD | |
| 357 | |
| 358 Default value: true. This option can be set to 'null' to clear the default value. | |
| 359 Possible values: {true, false} | |
| 360 | |
| 361 ENSURE_IDENTICAL_HEADER_NAMES=Boolean | |
| 362 SAME_HEADERS=Boolean | |
| 363 | |
| 364 Makes sure that headers of both reads of a pair are identical, using the following read | |
| 365 header pattern (for both reads of a pair): | |
| 366 @D3FCO8P1:178:C1WLBACXX:7:1101:1836:1965 I1_BARCODE:I2_BARCODE(:CLIPPED_SEQ_FROMREAD1:CLIPPED_SEQ_FROMREAD2) | |
| 367 This option only makes sense in paired end mode and ADD=true. Some (if not all) mappers | |
| 368 will indeed complain when the read headers are not identical. When molecular barcodes are | |
| 369 present in reads and the RCHAR is used, you will end with (problematic) read headers like | |
| 370 this: | |
| 371 HISEQ:44:C6KC0ANXX:5:1101:1491:1994:1:N:0:TAGAACAC:TGGAGTAG | |
| 372 HISEQ:44:C6KC0ANXX:5:1101:1491:1994:3:N:0:TAGAACAC:CGTTGTAT | |
| 373 SAME_HEADERS=true will instead genetates the following identical header for both reads: | |
| 374 HISEQ:44:C6KC0ANXX:5:1101:1491:1994:TAGAACAC:TGGAGTAG:CGTTGTAT | |
| 375 Note that we also clipped the useless '1:N:0' and '3:N:0' has they will also result in | |
| 376 generating different headers | |
| 377 Important: this option will force RCHAR=: UNLESS you specify RCHAR=null ; in which | |
| 378 case a space will be preserved ie: | |
| 379 HISEQ:44:C6KC0ANXX:5:1101:1491:1994 TAGAACAC:TGGAGTAG:CGTTGTAT | |
| 380 | |
| 381 Default value: true. This option can be set to 'null' to clear the default value. | |
| 382 Possible values: {true, false} | |
| 383 | |
| 384 READ_NAME_REPLACE_CHAR=String | |
| 385 RCHAR=String | |
| 386 | |
| 387 Replace spaces in read name/header using provided character. This is particularly handy | |
| 388 when you need to retain ADDed barcode in read name/header during mapping (everything | |
| 389 after space in read name is usually clipped in BAM files). For example, with RCHAR=':': | |
| 390 '@D3FCO8P1:178:C1WLBACXX:7:1101:1836:1965 2:N:0:' | |
| 391 becomes | |
| 392 '@D3FCO8P1:178:C1WLBACXX:7:1101:1836:1965:2:N:0:BARCODE' | |
| 393 Default value: null. | |
| 394 | |
| 395 QUALITY_FORMAT=FastqQualityFormat | |
| 396 V=FastqQualityFormat | |
| 397 | |
| 398 A value describing how the quality values are encoded in the fastq. Either 'Solexa' for | |
| 399 pre-pipeline 1.3 style scores (solexa scaling + 66), 'Illumina' for pipeline 1.3 and | |
| 400 above (phred scaling + 64) or 'Standard' for phred scaled scores with a character shift | |
| 401 of 33. If this value is not specified (or 'null' is given), the quality format will be | |
| 402 detected. | |
| 403 | |
| 404 Default value: Standard. This option can be set to 'null' to clear the default value. | |
| 405 Possible values: {Solexa, Illumina, Standard} | |
| 406 | |
| 407 KEEP_UNASSIGNED_READ=Boolean | |
| 408 UN=Boolean | |
| 409 | |
| 410 Should un-assigned reads be saved in files or simply ignored. File names are | |
| 411 automatically created or can be given using UF1 & UF2 options. | |
| 412 | |
| 413 Default value: true. This option can be set to 'null' to clear the default value. | |
| 414 Possible values: {true, false} | |
| 415 | |
| 416 BARCODE_DIAG_FILE=String | |
| 417 DIAG=String | |
| 418 | |
| 419 Name for a barcode match reporting file (not generated by default).Either a name (in | |
| 420 which case the file will be created in the output dir) or full path. This file will | |
| 421 contain a line per read pair with the barcode best matching the read subsequence or | |
| 422 'null' when no match is found according to matching parameters ; and the final selected | |
| 423 sample. This file is useful for debugging or further processing in case both ends are | |
| 424 barcoded. | |
| 425 N.B: this file will have a size of about one of the fastq input files. | |
| 426 | |
| 427 Default value: null. | |
| 428 ]]> | |
|
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69c77f9fc064
planemo upload for repository https://git.embl.de/grp-gbcs/Je/tree/master/src/galaxy commit 0eefd837333dae6fbecaf4f55b053268d844eff6
gbcs-embl-heidelberg
parents:
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429 </help> |
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69c77f9fc064
planemo upload for repository https://git.embl.de/grp-gbcs/Je/tree/master/src/galaxy commit 0eefd837333dae6fbecaf4f55b053268d844eff6
gbcs-embl-heidelberg
parents:
3
diff
changeset
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430 <expand macro="citations"/> |
| 0 | 431 </tool> |