Mercurial > repos > gbcs-embl-heidelberg > je_demultiplex
annotate macros.xml @ 3:8930b411a9d7 draft
planemo upload for repository https://git.embl.de/grp-gbcs/Je/tree/master/src/galaxy commit dd9e62bdb01d1252a90ce778103ce9b6b4a8cd52-dirty
| author | gbcs-embl-heidelberg |
|---|---|
| date | Wed, 21 Jun 2017 05:23:13 -0400 |
| parents | 88ebcd1ced0e |
| children | 6da7b7886cbf |
| rev | line source |
|---|---|
| 0 | 1 <macros> |
| 2 | |
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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
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3 <token name="@VERSION_STRING@">1.1</token> |
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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
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4 |
| 0 | 5 <token name="@single_or_paired_cmd@"> |
| 6 #if str( $library.type ) == "single": | |
| 7 F1=${library.input_1} | |
| 8 #elif str( $library.type ) == "paired": | |
| 9 F1=${library.input_1} | |
| 10 F2=${library.input_2} | |
| 11 SAME_HEADERS=${library.SAME_HEADERS} | |
| 12 #else | |
| 13 ## prepare paired-end collection | |
| 14 F1=${library.input_1.forward} | |
| 15 F2=${library.input_1.reverse} | |
| 16 SAME_HEADERS=${library.SAME_HEADERS} | |
| 17 #end if | |
| 18 </token> | |
| 19 | |
| 20 <xml name="paired_options"> | |
| 21 <when value="paired"> | |
|
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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
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22 <param name="input_1" format="fastq,gz" type="data" label="FASTQ file #1"/> |
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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
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23 <param name="input_2" format="fastq,gz" type="data" label="FASTQ file #2"/> |
| 0 | 24 <yield /> |
| 25 <param name="SAME_HEADERS" type="boolean" | |
| 26 label="Ensure headers of both reads of a pair are identical (SAME_HEADERS)" | |
| 27 help="Only applies if barcodes are added to the header (option ADD)" | |
| 28 truevalue="true" | |
| 29 falsevalue="false" checked="false"/> | |
| 30 </when> | |
| 31 <when value="paired_collection"> | |
|
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
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32 <param name="input_1" format="fastq,gz" type="data_collection" collection_type="paired" |
| 0 | 33 label="FASTQ Paired Dataset"/> |
| 34 <yield /> | |
| 35 <param name="SAME_HEADERS" type="boolean" | |
| 36 label="Ensure headers of both reads of a pair are identical (SAME_HEADERS)" | |
| 37 help="Only applies if barcodes are added to the header (option ADD)" | |
| 38 truevalue="true" | |
| 39 falsevalue="false" checked="false"/> | |
| 40 </when> | |
| 41 </xml> | |
| 42 | |
| 43 <token name="@single_or_paired_illu_cmd@"> | |
| 44 @single_or_paired_cmd@ | |
| 45 I1=$library.I1 | |
| 46 #if str( $library.type ) != "single": | |
| 47 #if str( $library.I2_CONDITIONAL.I2_AVAILABLE ) == "true": | |
| 48 I2=${library.I2_CONDITIONAL.I2} | |
| 49 BRED=${library.I2_CONDITIONAL.BRED_CONDITIONAL.BRED} | |
| 50 #if str( $library.I2_CONDITIONAL.BRED_CONDITIONAL.BRED ) == "true": | |
| 51 STRICT=${library.I2_CONDITIONAL.BRED_CONDITIONAL.STRICT} | |
| 52 #end if | |
| 53 #end if | |
| 54 #end if | |
| 55 </token> | |
| 56 | |
| 57 <xml name="single_or_paired_illu"> | |
| 58 <conditional name="library"> | |
| 59 <param name="type" type="select" label="Is this single or paired library"> | |
| 60 <option value="single">Single-end</option> | |
| 61 <option value="paired">Paired-end</option> | |
| 62 <option value="paired_collection">Paired-end Dataset Collection</option> | |
| 63 </param> | |
| 64 <when value="single"> | |
|
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
|
65 <param name="input_1" format="fastq,gz" type="data" label="FASTQ file"/> |
|
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
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66 <param name="I1" type="data" format="fastq,gz" label="First Index File"/> |
| 0 | 67 </when> |
| 68 <expand macro="paired_options"> | |
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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
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69 <param name="I1" type="data" format="fastq,gz" label="First Index File"/> |
| 0 | 70 <conditional name="I2_CONDITIONAL"> |
| 71 <param name="I2_AVAILABLE" type="select" label="Do you have a second index file?"> | |
| 72 <option value="true">Yes</option> | |
| 73 <option value="false" selected="true">No</option> | |
| 74 </param> | |
| 75 <when value="true"> | |
|
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
|
76 <param name="I2" type="data" format="fastq,gz" label="Second Index File"/> |
| 0 | 77 <expand macro="bred_conditional"/> |
| 78 </when> | |
| 79 <when value="false"/> | |
| 80 </conditional> | |
| 81 </expand> | |
| 82 </conditional> | |
| 83 </xml> | |
| 84 | |
| 85 <xml name="single_or_paired_general"> | |
| 86 <conditional name="library"> | |
| 87 <param name="type" type="select" label="Is this single or paired library"> | |
| 88 <option value="single">Single-end</option> | |
| 89 <option value="paired">Paired-end</option> | |
| 90 <option value="paired_collection">Paired-end Dataset Collection</option> | |
| 91 </param> | |
| 92 <when value="single"> | |
|
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
|
93 <param name="input_1" format="fastq,gz" type="data" label="FASTQ file"/> |
| 0 | 94 </when> |
| 95 <expand macro="paired_options"> | |
| 96 <yield /> | |
| 97 </expand> | |
| 98 </conditional> | |
| 99 </xml> | |
| 100 | |
| 101 <token name="@demultiplex_paired_end_cmd_options@"> | |
| 102 BPOS=$library.BPOS_CONDITIONAL.BPOS | |
| 103 #if str( $library.BPOS_CONDITIONAL.BPOS ) == "BOTH": | |
| 104 BM=${library.BPOS_CONDITIONAL.BM_CONDITIIONAL.BM} | |
| 105 #if str( $library.BPOS_CONDITIONAL.BM_CONDITIIONAL.BM ) == "BOTH": | |
| 106 BRED=${library.BPOS_CONDITIONAL.BM_CONDITIIONAL.BRED_CONDITIONAL.BRED} | |
| 107 #if str( $library.BPOS_CONDITIONAL.BM_CONDITIIONAL.BRED_CONDITIONAL.BRED ) == "true": | |
| 108 STRICT=${library.BPOS_CONDITIONAL.BM_CONDITIIONAL.BRED_CONDITIONAL.STRICT} | |
| 109 #end if | |
| 110 #end if | |
| 111 #end if | |
| 112 </token> | |
| 113 | |
| 114 <xml name="demultiplex_paired_end_options"> | |
| 115 <conditional name="BPOS_CONDITIONAL"> | |
| 116 <param name="BPOS" type="select" label="Barcode read position (BPOS)" help="where are the barcodes"> | |
| 117 <option value="READ_1" selected="true">READ_1 (beginning of read from the first fastq file)</option> | |
| 118 <option value="READ_2">READ_2 (beginning of read from the second fastq file)</option> | |
| 119 <option value="BOTH">BOTH (beginning of both reads)</option> | |
| 120 </param> | |
| 121 <when value="READ_1"/> | |
| 122 <when value="READ_2"/> | |
| 123 <when value="BOTH"> | |
| 124 <conditional name="BM_CONDITIIONAL"> | |
| 125 <param name="BM" type="select" label="Barcode for sample matching (BM)" | |
| 126 help="which barcode should be used for sample look up (BM option)." > | |
| 127 <option value="READ_1" selected="true"> | |
| 128 READ_1 (beginning of read from the first fastq file) | |
| 129 </option> | |
| 130 <option value="READ_2"> | |
| 131 READ_2 (beginning of read from the second fastq file) | |
| 132 </option> | |
| 133 <option value="BOTH"> | |
| 134 BOTH (beginning of both reads) | |
| 135 </option> | |
| 136 </param> | |
| 137 <when value="READ_1"/> | |
| 138 <when value="READ_2"/> | |
| 139 <when value="BOTH"> | |
| 140 <expand macro="bred_conditional"/> | |
| 141 </when> | |
| 142 </conditional> | |
| 143 </when> | |
| 144 </conditional> | |
| 145 </xml> | |
| 146 | |
| 147 <xml name="bred_conditional"> | |
| 148 <conditional name="BRED_CONDITIONAL"> | |
| 149 <param name="BRED" type="select" label="Redundant barcodes (BRED)" | |
| 150 help="are the barcodes REDUNDANT i.e. do they both resolve to the same sample."> | |
| 151 <option value="true" selected="true">Yes</option> | |
| 152 <option value="false">No</option> | |
| 153 </param> | |
| 154 <when value="true"> | |
| 155 <param name="STRICT" type="boolean" label="Strict (S)" | |
| 156 truevalue="true" | |
| 157 falsevalue="false" | |
| 158 checked="false" | |
| 159 /> | |
| 160 </when> | |
| 161 <when value="false"/> | |
| 162 </conditional> | |
| 163 </xml> | |
| 164 | |
| 165 <token name="@barcode_option_cmd@"> | |
| 166 #if str( $barcodes.barcode_list_type_con ) == "text": | |
| 167 BARCODE_FILE=${barcode_file_from_text} | |
| 168 #else if str( $barcodes.barcode_list_type_con ) == "file": | |
| 169 BARCODE_FILE=${barcodes.BARCODE_FILE} | |
| 170 #end if | |
| 171 </token> | |
| 172 | |
| 173 <xml name="barcode_option"> | |
| 174 <conditional name="barcodes"> | |
| 175 <param name="barcode_list_type_con" type="select" label="Barcode list input type"> | |
| 176 <option value="file" selected="true">Use a tab-delimited file from the history</option> | |
| 177 <option value="text">Paste the barcodes list in a text field within the form</option> | |
| 178 </param> | |
| 179 | |
| 180 <when value="file"> | |
| 181 <param name="BARCODE_FILE" type="data" format="tabular,txt" label="Barcode List" | |
| 182 help="Barcode list format: one sample per line. First column is sample name and second is the | |
| 183 barcode, separated by tab or space. A third and fourth column can be used to specify the resulting | |
| 184 file names. See help below."/> | |
| 185 </when> | |
| 186 | |
| 187 <when value="text"> | |
| 188 <param name="barcode_text" type="text" area="True" size="10x30" | |
| 189 value="sample_name\tbarcode\n" 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 <sanitizer> | |
| 194 <valid initial="string.printable"></valid> | |
| 195 <mapping initial="none"/> | |
| 196 </sanitizer> | |
| 197 </param> | |
| 198 </when> | |
| 199 </conditional> | |
| 200 </xml> | |
| 201 | |
| 202 <xml name="barcode_config_file"> | |
| 203 <configfile name="barcode_file_from_text">#set from_text_area = '' | |
| 204 #if str( $barcodes.barcode_list_type_con ) == "text": | |
| 205 #set from_text_area = $barcodes.barcode_text | |
| 206 #end if | |
| 207 ${from_text_area}</configfile> | |
| 208 </xml> | |
| 209 | |
| 210 <token name="@barcode_len_cmd@"> | |
| 211 #if str( $LEN ) != "": | |
| 212 BCLEN=$LEN | |
| 213 #end if | |
| 214 </token> | |
| 215 | |
| 216 <xml name="barcode_len_option"> | |
| 217 <param name="LEN" type="text" value="" label="Barcode Length (LEN)" | |
| 218 help="If 'Barcode read position'=BOTH and 'Redundant barcodes'=False, two distinct | |
| 219 lengths can be provided using the syntax LEN=X:Z where X and Z are 2 integers representing | |
| 220 the barcode length for read_1 and read_2 respectively. Default: empty"/> | |
| 221 </xml> | |
| 222 <xml name="clip_barcode"> | |
| 223 <param name="CLIP_BARCODE" type="boolean" label="Remove barcode sequence from read (C)" | |
| 224 truevalue="true" falsevalue="false" checked="true"/> | |
| 225 </xml> | |
| 226 | |
| 227 <token name="@demultiplexer_common_options_cmd@"> | |
| 228 ADD=${ADD} | |
| 229 MM=$MM | |
| 230 MMD=$MMD | |
| 231 Q=$MIN_BASE_QUALITY | |
| 232 QUALITY_FORMAT=$QUALITY_FORMAT | |
| 233 </token> | |
| 234 <xml name="demultiplexer_common_options"> | |
| 235 <param name="ADD" type="boolean" | |
| 236 label="Add matched barcode at the end of the read header (ADD)" | |
| 237 truevalue="true" | |
| 238 falsevalue="false" | |
| 239 checked="true" | |
| 240 /> | |
| 241 <param name="MM" type="text" value="1" label="Maximum Mismatches (MM)" | |
| 242 help="Maximum mismatches for a barcode to be considered a match." /> | |
| 243 | |
| 244 <param name="MMD" type="text" value="1" label="Minimum mismatch difference (MMD)" | |
| 245 help="Minimum difference between number of mismatches in the best and second best barcodes for a barcode | |
| 246 to be considered a match." /> | |
| 247 | |
| 248 <param name="MIN_BASE_QUALITY" type="text" value="10" label="Minimum base quality (Q)" | |
| 249 help="Any barcode bases falling below this quality will be | |
| 250 considered a mismatch even in the bases match." /> | |
| 251 | |
| 252 <param name="QUALITY_FORMAT" type="select" label="Fastq Quality Format (V)" | |
| 253 help="How are the quality values encoded in the fastq. Either 'Solexa' for | |
| 254 pre-pipeline 1.3 style scores (solexa scaling + 66), 'Illumina' for pipeline 1.3 and | |
| 255 above (phred scaling + 64) or 'Standard' for phred scaled scores with a character shift | |
| 256 of 33."> | |
| 257 <option value="Standard" selected="true"> | |
| 258 Fastq - Illumina Casava v1.8 with Sanger coding quality (phred scaling + 33) | |
| 259 </option> | |
| 260 <option value="Illumina"> | |
| 261 Fastq - Illumina v1.3 or above coding of quality (phred scaling + 64) | |
| 262 </option> | |
| 263 <option value="Solexa"> | |
| 264 Fastq - Solexa-style quality (solexa scaling + 66) | |
| 265 </option> | |
| 266 <option value="null"> | |
| 267 Detect automatically | |
| 268 </option> | |
| 269 </param> | |
| 270 </xml> | |
| 271 | |
| 272 <token name="@demultiplexer_common_output_options_cmd@"> | |
| 273 KEEP_UNASSIGNED_READ=$KEEP_UNASSIGNED_READ | |
| 274 STATS_ONLY=${adv_options.STATS_ONLY} | |
| 275 #if str( $adv_options.DIAG ) == "true": | |
| 276 BARCODE_DIAG_FILE=$BARCODE_DIAG_FILE | |
| 277 #end if | |
| 278 </token> | |
| 279 <xml name="demultiplexer_common_output_options"> | |
| 280 <param name="KEEP_UNASSIGNED_READ" type="boolean" label="Keep unassigned reads (KEEP_UNASSIGNED_READ)" | |
| 281 truealue="true" | |
| 282 falsevalue="false" | |
| 283 checked="true" | |
| 284 /> | |
| 285 <section name="adv_options" title="Advanced Options" expanded="False"> | |
| 286 <param name="DIAG" type="boolean" label="Output barcode match reporting file (DIAG)" | |
| 287 truevalue="true" falsevalue="false" checked="false" | |
| 288 help="This file will | |
| 289 contain a line per read pair with the barcode best matching the read subsequence or 'null' when no | |
| 290 match is found according to matching parameters. This file is useful for debugging or further | |
| 291 processing in case both ends are barcoded."/> | |
| 292 <param name="STATS_ONLY" type="boolean" label="Only produce metric and diagnostic reports (STATS_ONLY)" | |
| 293 truevalue="true" falsevalue="false" checked="false" | |
| 294 help="do not demultiplex." /> | |
| 295 </section> | |
| 296 </xml> | |
| 297 | |
| 298 <token name="@common_options_cmd@"> | |
| 299 XT=${XT} | |
| 300 ZT=${ZT} | |
| 301 #if str( $RCHAR ) != "": | |
| 302 RCHAR=${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
|
303 #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
|
304 RCHAR=null |
| 0 | 305 #end if |
| 306 GZ=${GZ} | |
| 307 OUTPUT_DIR=results | |
| 308 </token> | |
| 309 <xml name="common_options"> | |
| 310 <param name="XT" type="text" value="0" | |
| 311 label="Extra number of bases to be trimmed right after the barcode (XT)" /> | |
| 312 <param name="ZT" type="text" value="0" | |
| 313 label="Extra number of bases to be trimmed from the read end (ZT)" /> | |
| 314 | |
| 315 <param name="RCHAR" type="text" | |
| 316 label="Replace white space in the read name/header with speficied symbols (RCHAR)" | |
|
2
88ebcd1ced0e
planemo upload for repository https://git.embl.de/grp-gbcs/Je/tree/master/src/galaxy commit 62411561ae3bc65ea8762d27ec79a7d912503e5b
gbcs-embl-heidelberg
parents:
0
diff
changeset
|
317 help="Set to empty or null for no replacement." |
| 0 | 318 value=":"/> |
| 319 | |
| 320 <param name="GZ" type="boolean" hidden="true" label="Compress output (GZ)" | |
| 321 help="will result in fastq.gz files." | |
| 322 truevalue="true" | |
| 323 falsevalue="false" | |
| 324 checked="false"/> | |
| 325 </xml> | |
| 326 | |
| 327 <token name="@demultiplexer_common_outputs_cmd@"> | |
| 328 METRICS_FILE_NAME=$METRICS_FILE_NAME | |
| 329 </token> | |
| 330 <xml name="demultiplexer_common_outputs"> | |
| 331 <data name="METRICS_FILE_NAME" format="tabular" label="Je-Demultiplex result"> | |
| 332 <!--<discover_datasets pattern="(?P<name>.*)\.txt" ext="fastqsanger"--> | |
| 333 <discover_datasets pattern="(?P<name>.*)\.txt" directory="results" visible="true" ext="fastqsanger"/> | |
| 334 </data> | |
| 335 <data name="BARCODE_DIAG_FILE" format="tabular" label="Barcode statistics"> | |
| 336 <filter>(adv_options['DIAG'] == 'true')</filter> | |
| 337 </data> | |
| 338 </xml> | |
| 339 | |
| 340 </macros> |