Mercurial > repos > gbcs-embl-heidelberg > je_demultiplex
annotate macros.xml @ 8:47c0d9f76232 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 05:47:17 -0400 |
| parents | 8f16495dc5f2 |
| children | e7e1aa83d5b1 |
| rev | line source |
|---|---|
| 0 | 1 <macros> |
| 2 | |
|
7
8f16495dc5f2
planemo upload for repository https://git.embl.de/grp-gbcs/Je/tree/master/src/galaxy commit e217faa15f73427979bb212036cb130a14c59750
gbcs-embl-heidelberg
parents:
6
diff
changeset
|
3 <token name="@VERSION_STRING@">1.2.1</token> |
|
5
222819c87d90
planemo upload for repository https://git.embl.de/grp-gbcs/Je/tree/master/src/galaxy commit 0eefd837333dae6fbecaf4f55b053268d844eff6
gbcs-embl-heidelberg
parents:
4
diff
changeset
|
4 <xml name="requirements"> |
|
222819c87d90
planemo upload for repository https://git.embl.de/grp-gbcs/Je/tree/master/src/galaxy commit 0eefd837333dae6fbecaf4f55b053268d844eff6
gbcs-embl-heidelberg
parents:
4
diff
changeset
|
5 <requirements> |
|
222819c87d90
planemo upload for repository https://git.embl.de/grp-gbcs/Je/tree/master/src/galaxy commit 0eefd837333dae6fbecaf4f55b053268d844eff6
gbcs-embl-heidelberg
parents:
4
diff
changeset
|
6 <requirement type="package" version="1.2">je-suite</requirement> |
|
222819c87d90
planemo upload for repository https://git.embl.de/grp-gbcs/Je/tree/master/src/galaxy commit 0eefd837333dae6fbecaf4f55b053268d844eff6
gbcs-embl-heidelberg
parents:
4
diff
changeset
|
7 </requirements> |
|
222819c87d90
planemo upload for repository https://git.embl.de/grp-gbcs/Je/tree/master/src/galaxy commit 0eefd837333dae6fbecaf4f55b053268d844eff6
gbcs-embl-heidelberg
parents:
4
diff
changeset
|
8 </xml> |
|
222819c87d90
planemo upload for repository https://git.embl.de/grp-gbcs/Je/tree/master/src/galaxy commit 0eefd837333dae6fbecaf4f55b053268d844eff6
gbcs-embl-heidelberg
parents:
4
diff
changeset
|
9 <xml name="version_command"> |
|
222819c87d90
planemo upload for repository https://git.embl.de/grp-gbcs/Je/tree/master/src/galaxy commit 0eefd837333dae6fbecaf4f55b053268d844eff6
gbcs-embl-heidelberg
parents:
4
diff
changeset
|
10 <version_command>je version 2>&1 | tail -n 1</version_command> |
|
222819c87d90
planemo upload for repository https://git.embl.de/grp-gbcs/Je/tree/master/src/galaxy commit 0eefd837333dae6fbecaf4f55b053268d844eff6
gbcs-embl-heidelberg
parents:
4
diff
changeset
|
11 </xml> |
|
3
8930b411a9d7
planemo upload for repository https://git.embl.de/grp-gbcs/Je/tree/master/src/galaxy commit dd9e62bdb01d1252a90ce778103ce9b6b4a8cd52-dirty
gbcs-embl-heidelberg
parents:
2
diff
changeset
|
12 |
| 0 | 13 <token name="@single_or_paired_cmd@"> |
| 14 #if str( $library.type ) == "single": | |
| 15 F1=${library.input_1} | |
| 16 #elif str( $library.type ) == "paired": | |
| 17 F1=${library.input_1} | |
| 18 F2=${library.input_2} | |
| 19 SAME_HEADERS=${library.SAME_HEADERS} | |
| 20 #else | |
| 21 ## prepare paired-end collection | |
| 22 F1=${library.input_1.forward} | |
| 23 F2=${library.input_1.reverse} | |
| 24 SAME_HEADERS=${library.SAME_HEADERS} | |
| 25 #end if | |
| 26 </token> | |
| 27 | |
| 28 <xml name="paired_options"> | |
| 29 <when value="paired"> | |
|
6
dacd089d81ae
planemo upload for repository https://git.embl.de/grp-gbcs/Je/tree/master/src/galaxy commit 25e8fd2946fda4b9d280f2178841b2231bc3a3d0
gbcs-embl-heidelberg
parents:
5
diff
changeset
|
30 <param name="input_1" format="fastq,fastq.gz,fastqsanger,fastqsanger.gz" type="data" label="FASTQ file #1"/> |
|
dacd089d81ae
planemo upload for repository https://git.embl.de/grp-gbcs/Je/tree/master/src/galaxy commit 25e8fd2946fda4b9d280f2178841b2231bc3a3d0
gbcs-embl-heidelberg
parents:
5
diff
changeset
|
31 <param name="input_2" format="fastq,fastq.gz,fastqsanger,fastqsanger.gz" type="data" label="FASTQ file #2"/> |
| 0 | 32 <yield /> |
| 33 <param name="SAME_HEADERS" type="boolean" | |
| 34 label="Ensure headers of both reads of a pair are identical (SAME_HEADERS)" | |
| 35 help="Only applies if barcodes are added to the header (option ADD)" | |
| 36 truevalue="true" | |
| 37 falsevalue="false" checked="false"/> | |
| 38 </when> | |
| 39 <when value="paired_collection"> | |
|
6
dacd089d81ae
planemo upload for repository https://git.embl.de/grp-gbcs/Je/tree/master/src/galaxy commit 25e8fd2946fda4b9d280f2178841b2231bc3a3d0
gbcs-embl-heidelberg
parents:
5
diff
changeset
|
40 <param name="input_1" format="fastq,fastq.gz,fastqsanger,fastqsanger.gz" type="data_collection" collection_type="paired" |
| 0 | 41 label="FASTQ Paired Dataset"/> |
| 42 <yield /> | |
| 43 <param name="SAME_HEADERS" type="boolean" | |
| 44 label="Ensure headers of both reads of a pair are identical (SAME_HEADERS)" | |
| 45 help="Only applies if barcodes are added to the header (option ADD)" | |
| 46 truevalue="true" | |
| 47 falsevalue="false" checked="false"/> | |
| 48 </when> | |
| 49 </xml> | |
| 50 | |
| 51 <token name="@single_or_paired_illu_cmd@"> | |
| 52 @single_or_paired_cmd@ | |
| 53 I1=$library.I1 | |
| 54 #if str( $library.type ) != "single": | |
| 55 #if str( $library.I2_CONDITIONAL.I2_AVAILABLE ) == "true": | |
| 56 I2=${library.I2_CONDITIONAL.I2} | |
| 57 BRED=${library.I2_CONDITIONAL.BRED_CONDITIONAL.BRED} | |
| 58 #if str( $library.I2_CONDITIONAL.BRED_CONDITIONAL.BRED ) == "true": | |
| 59 STRICT=${library.I2_CONDITIONAL.BRED_CONDITIONAL.STRICT} | |
| 60 #end if | |
| 61 #end if | |
| 62 #end if | |
| 63 </token> | |
| 64 | |
| 65 <xml name="single_or_paired_illu"> | |
| 66 <conditional name="library"> | |
| 67 <param name="type" type="select" label="Is this single or paired library"> | |
| 68 <option value="single">Single-end</option> | |
| 69 <option value="paired">Paired-end</option> | |
| 70 <option value="paired_collection">Paired-end Dataset Collection</option> | |
| 71 </param> | |
| 72 <when value="single"> | |
|
6
dacd089d81ae
planemo upload for repository https://git.embl.de/grp-gbcs/Je/tree/master/src/galaxy commit 25e8fd2946fda4b9d280f2178841b2231bc3a3d0
gbcs-embl-heidelberg
parents:
5
diff
changeset
|
73 <param name="input_1" format="fastq,fastq.gz,fastqsanger,fastqsanger.gz" type="data" label="FASTQ file"/> |
|
dacd089d81ae
planemo upload for repository https://git.embl.de/grp-gbcs/Je/tree/master/src/galaxy commit 25e8fd2946fda4b9d280f2178841b2231bc3a3d0
gbcs-embl-heidelberg
parents:
5
diff
changeset
|
74 <param name="I1" type="data" format="fastq,fastq.gz,fastqsanger,fastqsanger.gz" label="First Index File"/> |
| 0 | 75 </when> |
| 76 <expand macro="paired_options"> | |
|
6
dacd089d81ae
planemo upload for repository https://git.embl.de/grp-gbcs/Je/tree/master/src/galaxy commit 25e8fd2946fda4b9d280f2178841b2231bc3a3d0
gbcs-embl-heidelberg
parents:
5
diff
changeset
|
77 <param name="I1" type="data" format="fastq,fastq.gz,fastqsanger,fastqsanger.gz" label="First Index File"/> |
| 0 | 78 <conditional name="I2_CONDITIONAL"> |
| 79 <param name="I2_AVAILABLE" type="select" label="Do you have a second index file?"> | |
| 80 <option value="true">Yes</option> | |
| 81 <option value="false" selected="true">No</option> | |
| 82 </param> | |
| 83 <when value="true"> | |
|
6
dacd089d81ae
planemo upload for repository https://git.embl.de/grp-gbcs/Je/tree/master/src/galaxy commit 25e8fd2946fda4b9d280f2178841b2231bc3a3d0
gbcs-embl-heidelberg
parents:
5
diff
changeset
|
84 <param name="I2" type="data" format="fastq,fastq.gz,fastqsanger,fastqsanger.gz" label="Second Index File"/> |
| 0 | 85 <expand macro="bred_conditional"/> |
| 86 </when> | |
| 87 <when value="false"/> | |
| 88 </conditional> | |
| 89 </expand> | |
| 90 </conditional> | |
| 91 </xml> | |
| 92 | |
| 93 <xml name="single_or_paired_general"> | |
| 94 <conditional name="library"> | |
| 95 <param name="type" type="select" label="Is this single or paired library"> | |
| 96 <option value="single">Single-end</option> | |
| 97 <option value="paired">Paired-end</option> | |
| 98 <option value="paired_collection">Paired-end Dataset Collection</option> | |
| 99 </param> | |
| 100 <when value="single"> | |
|
6
dacd089d81ae
planemo upload for repository https://git.embl.de/grp-gbcs/Je/tree/master/src/galaxy commit 25e8fd2946fda4b9d280f2178841b2231bc3a3d0
gbcs-embl-heidelberg
parents:
5
diff
changeset
|
101 <param name="input_1" format="fastq,fastq.gz,fastqsanger,fastqsanger.gz" type="data" label="FASTQ file"/> |
| 0 | 102 </when> |
| 103 <expand macro="paired_options"> | |
| 104 <yield /> | |
| 105 </expand> | |
| 106 </conditional> | |
| 107 </xml> | |
| 108 | |
| 109 <token name="@demultiplex_paired_end_cmd_options@"> | |
| 110 BPOS=$library.BPOS_CONDITIONAL.BPOS | |
| 111 #if str( $library.BPOS_CONDITIONAL.BPOS ) == "BOTH": | |
| 112 BM=${library.BPOS_CONDITIONAL.BM_CONDITIIONAL.BM} | |
| 113 #if str( $library.BPOS_CONDITIONAL.BM_CONDITIIONAL.BM ) == "BOTH": | |
| 114 BRED=${library.BPOS_CONDITIONAL.BM_CONDITIIONAL.BRED_CONDITIONAL.BRED} | |
| 115 #if str( $library.BPOS_CONDITIONAL.BM_CONDITIIONAL.BRED_CONDITIONAL.BRED ) == "true": | |
| 116 STRICT=${library.BPOS_CONDITIONAL.BM_CONDITIIONAL.BRED_CONDITIONAL.STRICT} | |
| 117 #end if | |
| 118 #end if | |
| 119 #end if | |
| 120 </token> | |
| 121 | |
| 122 <xml name="demultiplex_paired_end_options"> | |
| 123 <conditional name="BPOS_CONDITIONAL"> | |
| 124 <param name="BPOS" type="select" label="Barcode read position (BPOS)" help="where are the barcodes"> | |
| 125 <option value="READ_1" selected="true">READ_1 (beginning of read from the first fastq file)</option> | |
| 126 <option value="READ_2">READ_2 (beginning of read from the second fastq file)</option> | |
| 127 <option value="BOTH">BOTH (beginning of both reads)</option> | |
| 128 </param> | |
| 129 <when value="READ_1"/> | |
| 130 <when value="READ_2"/> | |
| 131 <when value="BOTH"> | |
| 132 <conditional name="BM_CONDITIIONAL"> | |
| 133 <param name="BM" type="select" label="Barcode for sample matching (BM)" | |
| 134 help="which barcode should be used for sample look up (BM option)." > | |
| 135 <option value="READ_1" selected="true"> | |
| 136 READ_1 (beginning of read from the first fastq file) | |
| 137 </option> | |
| 138 <option value="READ_2"> | |
| 139 READ_2 (beginning of read from the second fastq file) | |
| 140 </option> | |
| 141 <option value="BOTH"> | |
| 142 BOTH (beginning of both reads) | |
| 143 </option> | |
| 144 </param> | |
| 145 <when value="READ_1"/> | |
| 146 <when value="READ_2"/> | |
| 147 <when value="BOTH"> | |
| 148 <expand macro="bred_conditional"/> | |
| 149 </when> | |
| 150 </conditional> | |
| 151 </when> | |
| 152 </conditional> | |
| 153 </xml> | |
| 154 | |
| 155 <xml name="bred_conditional"> | |
| 156 <conditional name="BRED_CONDITIONAL"> | |
| 157 <param name="BRED" type="select" label="Redundant barcodes (BRED)" | |
| 158 help="are the barcodes REDUNDANT i.e. do they both resolve to the same sample."> | |
| 159 <option value="true" selected="true">Yes</option> | |
| 160 <option value="false">No</option> | |
| 161 </param> | |
| 162 <when value="true"> | |
| 163 <param name="STRICT" type="boolean" label="Strict (S)" | |
| 164 truevalue="true" | |
| 165 falsevalue="false" | |
| 166 checked="false" | |
| 167 /> | |
| 168 </when> | |
| 169 <when value="false"/> | |
| 170 </conditional> | |
| 171 </xml> | |
| 172 | |
| 173 <token name="@barcode_option_cmd@"> | |
| 174 #if str( $barcodes.barcode_list_type_con ) == "text": | |
| 175 BARCODE_FILE=${barcode_file_from_text} | |
| 176 #else if str( $barcodes.barcode_list_type_con ) == "file": | |
| 177 BARCODE_FILE=${barcodes.BARCODE_FILE} | |
| 178 #end if | |
| 179 </token> | |
| 180 | |
| 181 <xml name="barcode_option"> | |
| 182 <conditional name="barcodes"> | |
| 183 <param name="barcode_list_type_con" type="select" label="Barcode list input type"> | |
| 184 <option value="file" selected="true">Use a tab-delimited file from the history</option> | |
| 185 <option value="text">Paste the barcodes list in a text field within the form</option> | |
| 186 </param> | |
| 187 | |
| 188 <when value="file"> | |
| 189 <param name="BARCODE_FILE" type="data" format="tabular,txt" label="Barcode List" | |
| 190 help="Barcode list format: one sample per line. First column is sample name and second is the | |
| 191 barcode, separated by tab or space. A third and fourth column can be used to specify the resulting | |
| 192 file names. See help below."/> | |
| 193 </when> | |
| 194 | |
| 195 <when value="text"> | |
| 196 <param name="barcode_text" type="text" area="True" size="10x30" | |
| 197 value="sample_name\tbarcode\n" label="Barcode List" | |
| 198 help="Barcode list format: one sample per line. First column is sample name and second is the | |
| 199 barcode, separated by tab or space. A third and fourth column can be used to specify the resulting | |
| 200 file names. See help below."> | |
| 201 <sanitizer> | |
| 202 <valid initial="string.printable"></valid> | |
| 203 <mapping initial="none"/> | |
| 204 </sanitizer> | |
| 205 </param> | |
| 206 </when> | |
| 207 </conditional> | |
| 208 </xml> | |
| 209 | |
| 210 <xml name="barcode_config_file"> | |
| 211 <configfile name="barcode_file_from_text">#set from_text_area = '' | |
| 212 #if str( $barcodes.barcode_list_type_con ) == "text": | |
| 213 #set from_text_area = $barcodes.barcode_text | |
| 214 #end if | |
| 215 ${from_text_area}</configfile> | |
| 216 </xml> | |
| 217 | |
| 218 <token name="@barcode_len_cmd@"> | |
| 219 #if str( $LEN ) != "": | |
| 220 BCLEN=$LEN | |
| 221 #end if | |
| 222 </token> | |
| 223 | |
| 224 <xml name="barcode_len_option"> | |
| 225 <param name="LEN" type="text" value="" label="Barcode Length (LEN)" | |
| 226 help="If 'Barcode read position'=BOTH and 'Redundant barcodes'=False, two distinct | |
| 227 lengths can be provided using the syntax LEN=X:Z where X and Z are 2 integers representing | |
| 228 the barcode length for read_1 and read_2 respectively. Default: empty"/> | |
| 229 </xml> | |
| 230 <xml name="clip_barcode"> | |
| 231 <param name="CLIP_BARCODE" type="boolean" label="Remove barcode sequence from read (C)" | |
| 232 truevalue="true" falsevalue="false" checked="true"/> | |
| 233 </xml> | |
| 234 | |
| 235 <token name="@demultiplexer_common_options_cmd@"> | |
| 236 ADD=${ADD} | |
| 237 MM=$MM | |
| 238 MMD=$MMD | |
| 239 Q=$MIN_BASE_QUALITY | |
| 240 QUALITY_FORMAT=$QUALITY_FORMAT | |
| 241 </token> | |
| 242 <xml name="demultiplexer_common_options"> | |
| 243 <param name="ADD" type="boolean" | |
| 244 label="Add matched barcode at the end of the read header (ADD)" | |
| 245 truevalue="true" | |
| 246 falsevalue="false" | |
| 247 checked="true" | |
| 248 /> | |
| 249 <param name="MM" type="text" value="1" label="Maximum Mismatches (MM)" | |
| 250 help="Maximum mismatches for a barcode to be considered a match." /> | |
| 251 | |
| 252 <param name="MMD" type="text" value="1" label="Minimum mismatch difference (MMD)" | |
| 253 help="Minimum difference between number of mismatches in the best and second best barcodes for a barcode | |
| 254 to be considered a match." /> | |
| 255 | |
| 256 <param name="MIN_BASE_QUALITY" type="text" value="10" label="Minimum base quality (Q)" | |
| 257 help="Any barcode bases falling below this quality will be | |
| 258 considered a mismatch even in the bases match." /> | |
| 259 | |
| 260 <param name="QUALITY_FORMAT" type="select" label="Fastq Quality Format (V)" | |
| 261 help="How are the quality values encoded in the fastq. Either 'Solexa' for | |
| 262 pre-pipeline 1.3 style scores (solexa scaling + 66), 'Illumina' for pipeline 1.3 and | |
| 263 above (phred scaling + 64) or 'Standard' for phred scaled scores with a character shift | |
| 264 of 33."> | |
| 265 <option value="Standard" selected="true"> | |
| 266 Fastq - Illumina Casava v1.8 with Sanger coding quality (phred scaling + 33) | |
| 267 </option> | |
| 268 <option value="Illumina"> | |
| 269 Fastq - Illumina v1.3 or above coding of quality (phred scaling + 64) | |
| 270 </option> | |
| 271 <option value="Solexa"> | |
| 272 Fastq - Solexa-style quality (solexa scaling + 66) | |
| 273 </option> | |
| 274 <option value="null"> | |
| 275 Detect automatically | |
| 276 </option> | |
| 277 </param> | |
| 278 </xml> | |
| 279 | |
| 280 <token name="@demultiplexer_common_output_options_cmd@"> | |
|
7
8f16495dc5f2
planemo upload for repository https://git.embl.de/grp-gbcs/Je/tree/master/src/galaxy commit e217faa15f73427979bb212036cb130a14c59750
gbcs-embl-heidelberg
parents:
6
diff
changeset
|
281 KEEP_UNASSIGNED_READ=${KEEP_UNASSIGNED_READ} |
|
8f16495dc5f2
planemo upload for repository https://git.embl.de/grp-gbcs/Je/tree/master/src/galaxy commit e217faa15f73427979bb212036cb130a14c59750
gbcs-embl-heidelberg
parents:
6
diff
changeset
|
282 STATS_ONLY=${STATS_ONLY} |
|
8f16495dc5f2
planemo upload for repository https://git.embl.de/grp-gbcs/Je/tree/master/src/galaxy commit e217faa15f73427979bb212036cb130a14c59750
gbcs-embl-heidelberg
parents:
6
diff
changeset
|
283 #if str( $DIAG ) == "true": |
| 0 | 284 BARCODE_DIAG_FILE=$BARCODE_DIAG_FILE |
| 285 #end if | |
| 286 </token> | |
| 287 <xml name="demultiplexer_common_output_options"> | |
|
7
8f16495dc5f2
planemo upload for repository https://git.embl.de/grp-gbcs/Je/tree/master/src/galaxy commit e217faa15f73427979bb212036cb130a14c59750
gbcs-embl-heidelberg
parents:
6
diff
changeset
|
288 <!--<section name="output_options" title="Output Options" expanded="True">--> |
|
8f16495dc5f2
planemo upload for repository https://git.embl.de/grp-gbcs/Je/tree/master/src/galaxy commit e217faa15f73427979bb212036cb130a14c59750
gbcs-embl-heidelberg
parents:
6
diff
changeset
|
289 <param name="COLLECT_OUTPUTS" type="boolean" |
|
8f16495dc5f2
planemo upload for repository https://git.embl.de/grp-gbcs/Je/tree/master/src/galaxy commit e217faa15f73427979bb212036cb130a14c59750
gbcs-embl-heidelberg
parents:
6
diff
changeset
|
290 truevalue="true" falsevalue="false" checked="false" |
|
8f16495dc5f2
planemo upload for repository https://git.embl.de/grp-gbcs/Je/tree/master/src/galaxy commit e217faa15f73427979bb212036cb130a14c59750
gbcs-embl-heidelberg
parents:
6
diff
changeset
|
291 label="Output forward and reverse reads in dataset collections" /> |
|
8f16495dc5f2
planemo upload for repository https://git.embl.de/grp-gbcs/Je/tree/master/src/galaxy commit e217faa15f73427979bb212036cb130a14c59750
gbcs-embl-heidelberg
parents:
6
diff
changeset
|
292 <param name="KEEP_UNASSIGNED_READ" type="boolean" label="Keep unassigned reads (KEEP_UNASSIGNED_READ)" |
|
8f16495dc5f2
planemo upload for repository https://git.embl.de/grp-gbcs/Je/tree/master/src/galaxy commit e217faa15f73427979bb212036cb130a14c59750
gbcs-embl-heidelberg
parents:
6
diff
changeset
|
293 truevalue="true" falsevalue="false" checked="true"/> |
| 0 | 294 <param name="DIAG" type="boolean" label="Output barcode match reporting file (DIAG)" |
| 295 truevalue="true" falsevalue="false" checked="false" | |
| 296 help="This file will | |
| 297 contain a line per read pair with the barcode best matching the read subsequence or 'null' when no | |
| 298 match is found according to matching parameters. This file is useful for debugging or further | |
| 299 processing in case both ends are barcoded."/> | |
| 300 <param name="STATS_ONLY" type="boolean" label="Only produce metric and diagnostic reports (STATS_ONLY)" | |
| 301 truevalue="true" falsevalue="false" checked="false" | |
| 302 help="do not demultiplex." /> | |
|
7
8f16495dc5f2
planemo upload for repository https://git.embl.de/grp-gbcs/Je/tree/master/src/galaxy commit e217faa15f73427979bb212036cb130a14c59750
gbcs-embl-heidelberg
parents:
6
diff
changeset
|
303 <!--</section>--> |
| 0 | 304 </xml> |
| 305 | |
| 306 <token name="@common_options_cmd@"> | |
| 307 XT=${XT} | |
| 308 ZT=${ZT} | |
| 309 #if str( $RCHAR ) != "": | |
| 310 RCHAR=${RCHAR} | |
|
2
88ebcd1ced0e
planemo upload for repository https://git.embl.de/grp-gbcs/Je/tree/master/src/galaxy commit 62411561ae3bc65ea8762d27ec79a7d912503e5b
gbcs-embl-heidelberg
parents:
0
diff
changeset
|
311 #else: |
|
88ebcd1ced0e
planemo upload for repository https://git.embl.de/grp-gbcs/Je/tree/master/src/galaxy commit 62411561ae3bc65ea8762d27ec79a7d912503e5b
gbcs-embl-heidelberg
parents:
0
diff
changeset
|
312 RCHAR=null |
| 0 | 313 #end if |
| 314 GZ=${GZ} | |
| 315 OUTPUT_DIR=results | |
| 316 </token> | |
| 317 <xml name="common_options"> | |
| 318 <param name="XT" type="text" value="0" | |
| 319 label="Extra number of bases to be trimmed right after the barcode (XT)" /> | |
| 320 <param name="ZT" type="text" value="0" | |
| 321 label="Extra number of bases to be trimmed from the read end (ZT)" /> | |
| 322 | |
| 323 <param name="RCHAR" type="text" | |
| 324 label="Replace white space in the read name/header with speficied symbols (RCHAR)" | |
|
2
88ebcd1ced0e
planemo upload for repository https://git.embl.de/grp-gbcs/Je/tree/master/src/galaxy commit 62411561ae3bc65ea8762d27ec79a7d912503e5b
gbcs-embl-heidelberg
parents:
0
diff
changeset
|
325 help="Set to empty or null for no replacement." |
| 0 | 326 value=":"/> |
| 327 | |
|
5
222819c87d90
planemo upload for repository https://git.embl.de/grp-gbcs/Je/tree/master/src/galaxy commit 0eefd837333dae6fbecaf4f55b053268d844eff6
gbcs-embl-heidelberg
parents:
4
diff
changeset
|
328 <param name="GZ" type="hidden" label="Compress output (GZ)" |
| 0 | 329 help="will result in fastq.gz files." |
|
5
222819c87d90
planemo upload for repository https://git.embl.de/grp-gbcs/Je/tree/master/src/galaxy commit 0eefd837333dae6fbecaf4f55b053268d844eff6
gbcs-embl-heidelberg
parents:
4
diff
changeset
|
330 value="false"/> |
| 0 | 331 </xml> |
| 332 | |
| 333 <token name="@demultiplexer_common_outputs_cmd@"> | |
| 334 METRICS_FILE_NAME=$METRICS_FILE_NAME | |
| 335 </token> | |
|
7
8f16495dc5f2
planemo upload for repository https://git.embl.de/grp-gbcs/Je/tree/master/src/galaxy commit e217faa15f73427979bb212036cb130a14c59750
gbcs-embl-heidelberg
parents:
6
diff
changeset
|
336 |
| 0 | 337 <xml name="demultiplexer_common_outputs"> |
|
7
8f16495dc5f2
planemo upload for repository https://git.embl.de/grp-gbcs/Je/tree/master/src/galaxy commit e217faa15f73427979bb212036cb130a14c59750
gbcs-embl-heidelberg
parents:
6
diff
changeset
|
338 <data name="DEMULTIPLEX_RESULTS" format="tabular" label="Je-Demultiplex result placeholder" hidden="true"> |
|
8f16495dc5f2
planemo upload for repository https://git.embl.de/grp-gbcs/Je/tree/master/src/galaxy commit e217faa15f73427979bb212036cb130a14c59750
gbcs-embl-heidelberg
parents:
6
diff
changeset
|
339 <filter>COLLECT_OUTPUTS == False and STATS_ONLY == False</filter> |
| 0 | 340 <discover_datasets pattern="(?P<name>.*)\.txt" directory="results" visible="true" ext="fastqsanger"/> |
| 341 </data> | |
|
7
8f16495dc5f2
planemo upload for repository https://git.embl.de/grp-gbcs/Je/tree/master/src/galaxy commit e217faa15f73427979bb212036cb130a14c59750
gbcs-embl-heidelberg
parents:
6
diff
changeset
|
342 <data name="METRICS_FILE_NAME" format="tabular" label="Je-Demultiplex Metrics"/> |
| 0 | 343 <data name="BARCODE_DIAG_FILE" format="tabular" label="Barcode statistics"> |
|
7
8f16495dc5f2
planemo upload for repository https://git.embl.de/grp-gbcs/Je/tree/master/src/galaxy commit e217faa15f73427979bb212036cb130a14c59750
gbcs-embl-heidelberg
parents:
6
diff
changeset
|
344 <filter>DIAG</filter> |
| 0 | 345 </data> |
|
7
8f16495dc5f2
planemo upload for repository https://git.embl.de/grp-gbcs/Je/tree/master/src/galaxy commit e217faa15f73427979bb212036cb130a14c59750
gbcs-embl-heidelberg
parents:
6
diff
changeset
|
346 <collection name="COLLECTION_1" type="list" label="${tool.name} on ${on_string} : Reads_1" > |
|
8f16495dc5f2
planemo upload for repository https://git.embl.de/grp-gbcs/Je/tree/master/src/galaxy commit e217faa15f73427979bb212036cb130a14c59750
gbcs-embl-heidelberg
parents:
6
diff
changeset
|
347 <filter>COLLECT_OUTPUTS and STATS_ONLY == False</filter> |
|
8
47c0d9f76232
planemo upload for repository https://git.embl.de/grp-gbcs/Je/tree/master/src/galaxy commit bc2365188e0dd0f20925884276a27914bb714280
gbcs-embl-heidelberg
parents:
7
diff
changeset
|
348 <discover_datasets pattern="(?P<designation>.+_1\..+)" ext="fastqsanger" directory="results" visible="false" /> |
|
7
8f16495dc5f2
planemo upload for repository https://git.embl.de/grp-gbcs/Je/tree/master/src/galaxy commit e217faa15f73427979bb212036cb130a14c59750
gbcs-embl-heidelberg
parents:
6
diff
changeset
|
349 </collection> |
|
8f16495dc5f2
planemo upload for repository https://git.embl.de/grp-gbcs/Je/tree/master/src/galaxy commit e217faa15f73427979bb212036cb130a14c59750
gbcs-embl-heidelberg
parents:
6
diff
changeset
|
350 <collection name="COLLECTION_2" type="list" label="${tool.name} on ${on_string} : Reads_2" > |
|
8f16495dc5f2
planemo upload for repository https://git.embl.de/grp-gbcs/Je/tree/master/src/galaxy commit e217faa15f73427979bb212036cb130a14c59750
gbcs-embl-heidelberg
parents:
6
diff
changeset
|
351 <filter>COLLECT_OUTPUTS and STATS_ONLY == False</filter> |
|
8
47c0d9f76232
planemo upload for repository https://git.embl.de/grp-gbcs/Je/tree/master/src/galaxy commit bc2365188e0dd0f20925884276a27914bb714280
gbcs-embl-heidelberg
parents:
7
diff
changeset
|
352 <discover_datasets pattern="(?P<designation>.+_2\..+)" ext="fastqsanger" directory="results" visible="false" /> |
|
7
8f16495dc5f2
planemo upload for repository https://git.embl.de/grp-gbcs/Je/tree/master/src/galaxy commit e217faa15f73427979bb212036cb130a14c59750
gbcs-embl-heidelberg
parents:
6
diff
changeset
|
353 </collection> |
| 0 | 354 </xml> |
|
5
222819c87d90
planemo upload for repository https://git.embl.de/grp-gbcs/Je/tree/master/src/galaxy commit 0eefd837333dae6fbecaf4f55b053268d844eff6
gbcs-embl-heidelberg
parents:
4
diff
changeset
|
355 <xml name="citations"> |
|
222819c87d90
planemo upload for repository https://git.embl.de/grp-gbcs/Je/tree/master/src/galaxy commit 0eefd837333dae6fbecaf4f55b053268d844eff6
gbcs-embl-heidelberg
parents:
4
diff
changeset
|
356 <citations> |
|
222819c87d90
planemo upload for repository https://git.embl.de/grp-gbcs/Je/tree/master/src/galaxy commit 0eefd837333dae6fbecaf4f55b053268d844eff6
gbcs-embl-heidelberg
parents:
4
diff
changeset
|
357 <citation type="doi">10.1186/s12859-016-1284-2</citation> |
|
222819c87d90
planemo upload for repository https://git.embl.de/grp-gbcs/Je/tree/master/src/galaxy commit 0eefd837333dae6fbecaf4f55b053268d844eff6
gbcs-embl-heidelberg
parents:
4
diff
changeset
|
358 </citations> |
|
222819c87d90
planemo upload for repository https://git.embl.de/grp-gbcs/Je/tree/master/src/galaxy commit 0eefd837333dae6fbecaf4f55b053268d844eff6
gbcs-embl-heidelberg
parents:
4
diff
changeset
|
359 </xml> |
| 0 | 360 </macros> |