/tools/ngs_rna/tophat_color_wrapper.xml
XML | 611 lines | 536 code | 41 blank | 34 comment | 0 complexity | c7af5aea8dea08ea1c52104cb4d329d0 MD5 | raw file
1<tool id="tophat_color" name="Tophat for SOLiD" version="1.0.0"> 2 <description>Find splice junctions using RNA-seq data</description> 3 <requirements> 4 <requirement type="package">tophat</requirement> 5 </requirements> 6 <command interpreter="python"> 7 tophat_wrapper.py 8 ## Change this to accommodate the number of threads you have available. 9 --num-threads="4" 10 11 ## base- or color-space 12 --color-space 13 14 ## Provide outputs. 15 --junctions-output=$junctions 16 --hits-output=$accepted_hits 17 18 ## Handle reference file. 19 #if $refGenomeSource.genomeSource == "history": 20 --own-file=$refGenomeSource.ownFile 21 #else: 22 --indexes-path="${refGenomeSource.index.fields.path}" 23 #end if 24 25 ## Are reads single-end or paired? 26 --single-paired=$singlePaired.sPaired 27 28 ## First input file always required. 29 --input1=$input1 30 31 ## Set params based on whether reads are single-end or paired. 32 #if $singlePaired.sPaired == "single": 33 --settings=$singlePaired.sParams.sSettingsType 34 #if $singlePaired.sParams.sSettingsType == "full": 35 -a $singlePaired.sParams.anchor_length 36 -m $singlePaired.sParams.splice_mismatches 37 -i $singlePaired.sParams.min_intron_length 38 -I $singlePaired.sParams.max_intron_length 39 -F $singlePaired.sParams.junction_filter 40 -g $singlePaired.sParams.max_multihits 41 --min-segment-intron $singlePaired.sParams.min_segment_intron 42 --max-segment-intron $singlePaired.sParams.max_segment_intron 43 --initial-read-mismatches=$singlePaired.sParams.initial_read_mismatches 44 --seg-mismatches=$singlePaired.sParams.seg_mismatches 45 --seg-length=$singlePaired.sParams.seg_length 46 --library-type=$singlePaired.sParams.library_type 47 48 ## Indel search. 49 #if $singlePaired.sParams.indel_search.allow_indel_search == "Yes": 50 ## --allow-indels 51 --max-insertion-length $singlePaired.sParams.indel_search.max_insertion_length 52 --max-deletion-length $singlePaired.sParams.indel_search.max_deletion_length 53 #else: 54 --no-novel-indels 55 #end if 56 57 ## Supplying junctions parameters. 58 #if $singlePaired.sParams.own_junctions.use_junctions == "Yes": 59 #if $singlePaired.sParams.own_junctions.gene_model_ann.use_annotations == "Yes": 60 -G $singlePaired.sParams.own_junctions.gene_model_ann.gene_annotation_model 61 #end if 62 #if $singlePaired.sParams.own_junctions.raw_juncs.use_juncs == "Yes": 63 -j $singlePaired.sParams.own_junctions.raw_juncs.raw_juncs 64 #end if 65 ## TODO: No idea why a string cast is necessary, but it is: 66 #if str($singlePaired.sParams.own_junctions.no_novel_juncs) == "Yes": 67 --no-novel-juncs 68 #end if 69 #end if 70 71 #if $singlePaired.sParams.closure_search.use_search == "Yes": 72 --closure-search 73 --min-closure-exon $singlePaired.sParams.closure_search.min_closure_exon 74 --min-closure-intron $singlePaired.sParams.closure_search.min_closure_intron 75 --max-closure-intron $singlePaired.sParams.closure_search.max_closure_intron 76 #else: 77 --no-closure-search 78 #end if 79 #if $singlePaired.sParams.coverage_search.use_search == "Yes": 80 --coverage-search 81 --min-coverage-intron $singlePaired.sParams.coverage_search.min_coverage_intron 82 --max-coverage-intron $singlePaired.sParams.coverage_search.max_coverage_intron 83 #else: 84 --no-coverage-search 85 #end if 86 ## TODO: No idea why the type conversion is necessary, but it seems to be. 87 #if str($singlePaired.sParams.microexon_search) == "Yes": 88 --microexon-search 89 #end if 90 #end if 91 #else: 92 --input2=$singlePaired.input2 93 -r $singlePaired.mate_inner_distance 94 --settings=$singlePaired.pParams.pSettingsType 95 #if $singlePaired.pParams.pSettingsType == "full": 96 --mate-std-dev=$singlePaired.pParams.mate_std_dev 97 -a $singlePaired.pParams.anchor_length 98 -m $singlePaired.pParams.splice_mismatches 99 -i $singlePaired.pParams.min_intron_length 100 -I $singlePaired.pParams.max_intron_length 101 -F $singlePaired.pParams.junction_filter 102 -g $singlePaired.pParams.max_multihits 103 --min-segment-intron $singlePaired.pParams.min_segment_intron 104 --max-segment-intron $singlePaired.pParams.max_segment_intron 105 --initial-read-mismatches=$singlePaired.pParams.initial_read_mismatches 106 --seg-mismatches=$singlePaired.pParams.seg_mismatches 107 --seg-length=$singlePaired.pParams.seg_length 108 --library-type=$singlePaired.pParams.library_type 109 110 ## Indel search. 111 #if $singlePaired.pParams.indel_search.allow_indel_search == "Yes": 112 ## --allow-indels 113 --max-insertion-length $singlePaired.pParams.indel_search.max_insertion_length 114 --max-deletion-length $singlePaired.pParams.indel_search.max_deletion_length 115 #else: 116 --no-novel-indels 117 #end if 118 119 ## Supplying junctions parameters. 120 #if $singlePaired.pParams.own_junctions.use_junctions == "Yes": 121 #if $singlePaired.pParams.own_junctions.gene_model_ann.use_annotations == "Yes": 122 -G $singlePaired.pParams.own_junctions.gene_model_ann.gene_annotation_model 123 #end if 124 #if $singlePaired.pParams.own_junctions.raw_juncs.use_juncs == "Yes": 125 -j $singlePaired.pParams.own_junctions.raw_juncs.raw_juncs 126 #end if 127 ## TODO: No idea why type cast is necessary, but it is: 128 #if str($singlePaired.pParams.own_junctions.no_novel_juncs) == "Yes": 129 --no-novel-juncs 130 #end if 131 #end if 132 133 #if $singlePaired.pParams.closure_search.use_search == "Yes": 134 --closure-search 135 --min-closure-exon $singlePaired.pParams.closure_search.min_closure_exon 136 --min-closure-intron $singlePaired.pParams.closure_search.min_closure_intron 137 --max-closure-intron $singlePaired.pParams.closure_search.max_closure_intron 138 #else: 139 --no-closure-search 140 #end if 141 #if $singlePaired.pParams.coverage_search.use_search == "Yes": 142 --coverage-search 143 --min-coverage-intron $singlePaired.pParams.coverage_search.min_coverage_intron 144 --max-coverage-intron $singlePaired.pParams.coverage_search.max_coverage_intron 145 #else: 146 --no-coverage-search 147 #end if 148 ## TODO: No idea why the type conversion is necessary, but it seems to be. 149 #if str ($singlePaired.pParams.microexon_search) == "Yes": 150 --microexon-search 151 #end if 152 #end if 153 #end if 154 </command> 155 <inputs> 156 <param format="fastqcssanger" name="input1" type="data" label="RNA-Seq FASTQ file" help="Color-space: Must have Sanger-scaled quality values with ASCII offset 33" /> 157 <expand macro="refGenomeSourceConditional"> 158 <options from_data_table="tophat_indexes_color"> 159 <filter type="sort_by" column="2"/> 160 <validator type="no_options" message="No indexes are available for the selected input dataset"/> 161 </options> 162 </expand> 163 <conditional name="singlePaired"> 164 <param name="sPaired" type="select" label="Is this library mate-paired?"> 165 <option value="single">Single-end</option> 166 <option value="paired">Paired-end</option> 167 </param> 168 <when value="single"> 169 <conditional name="sParams"> 170 <param name="sSettingsType" type="select" label="TopHat settings to use" help="You can use the default settings or set custom values for any of Tophat's parameters."> 171 <option value="preSet">Default settings</option> 172 <option value="full">Full parameter list</option> 173 </param> 174 <when value="preSet" /> 175 <!-- Full/advanced params. --> 176 <when value="full"> 177 <param name="library_type" type="select" label="Library Type" help="TopHat will treat the reads as strand specific. Every read alignment will have an XS attribute tag. Consider supplying library type options below to select the correct RNA-seq protocol."> 178 <option value="fr-unstranded">FR Unstranded</option> 179 <option value="fr-firststrand">FR First Strand</option> 180 <option value="fr-secondstrand">FR Second Strand</option> 181 </param> 182 <param name="anchor_length" type="integer" value="8" label="Anchor length (at least 3)" help="Report junctions spanned by reads with at least this many bases on each side of the junction." /> 183 <param name="splice_mismatches" type="integer" value="0" label="Maximum number of mismatches that can appear in the anchor region of spliced alignment" /> 184 <param name="min_intron_length" type="integer" value="70" label="The minimum intron length" help="TopHat will ignore donor/acceptor pairs closer than this many bases apart." /> 185 <param name="max_intron_length" type="integer" value="500000" label="The maximum intron length" help="When searching for junctions ab initio, TopHat will ignore donor/acceptor pairs farther than this many bases apart, except when such a pair is supported by a split segment alignment of a long read." /> 186 <expand macro="indel_searchConditional" /> 187 <param name="junction_filter" type="float" value="0.15" label="Minimum isoform fraction: filter out junctions supported by too few alignments (number of reads divided by average depth of coverage)" help="0.0 to 1.0 (0 to turn off)" /> 188 <param name="max_multihits" type="integer" value="40" label="Maximum number of alignments to be allowed" /> 189 <param name="min_segment_intron" type="integer" value="50" label="Minimum intron length that may be found during split-segment (default) search" /> 190 <param name="max_segment_intron" type="integer" value="500000" label="Maximum intron length that may be found during split-segment (default) search" /> 191 <param name="initial_read_mismatches" type="integer" min="0" max="3" value="2" label="Number of mismatches allowed in the initial read mapping" /> 192 <param name="seg_mismatches" type="integer" min="0" max="3" value="2" label="Number of mismatches allowed in each segment alignment for reads mapped independently" /> 193 <param name="seg_length" type="integer" value="25" label="Minimum length of read segments" /> 194 195 <!-- Options for supplying own junctions. --> 196 <conditional name="own_junctions"> 197 <param name="use_junctions" type="select" label="Use Own Junctions"> 198 <option value="No">No</option> 199 <option value="Yes">Yes</option> 200 </param> 201 <when value="Yes"> 202 <conditional name="gene_model_ann"> 203 <param name="use_annotations" type="select" label="Use Gene Annotation Model"> 204 <option value="No">No</option> 205 <option value="Yes">Yes</option> 206 </param> 207 <when value="No" /> 208 <when value="Yes"> 209 <param format="gtf" name="gene_annotation_model" type="data" label="Gene Model Annotations" help="TopHat will use the exon records in this file to build a set of known splice junctions for each gene, and will attempt to align reads to these junctions even if they would not normally be covered by the initial mapping."/> 210 </when> 211 </conditional> 212 <expand macro="raw_juncsConditional" /> 213 <expand macro="no_novel_juncsParam" /> 214 </when> 215 <when value="No" /> 216 </conditional> <!-- /own_junctions --> 217 218 <!-- Closure search. --> 219 <conditional name="closure_search"> 220 <param name="use_search" type="select" label="Use Closure Search"> 221 <option value="No">No</option> 222 <option value="Yes">Yes</option> 223 </param> 224 <when value="Yes"> 225 <param name="min_closure_exon" type="integer" value="50" label="During closure search for paired end reads, exonic hops in the potential splice graph must be at least this long. The default is 50." /> 226 <param name="min_closure_intron" type="integer" value="50" label="Minimum intron length that may be found during closure search" /> 227 <param name="max_closure_intron" type="integer" value="5000" label="Maximum intron length that may be found during closure search" /> 228 </when> 229 <when value="No" /> 230 </conditional> 231 <!-- Coverage search. --> 232 <conditional name="coverage_search"> 233 <param name="use_search" type="select" label="Use Coverage Search"> 234 <option selected="true" value="Yes">Yes</option> 235 <option value="No">No</option> 236 </param> 237 <when value="Yes"> 238 <param name="min_coverage_intron" type="integer" value="50" label="Minimum intron length that may be found during coverage search" /> 239 <param name="max_coverage_intron" type="integer" value="20000" label="Maximum intron length that may be found during coverage search" /> 240 </when> 241 <when value="No" /> 242 </conditional> 243 <param name="microexon_search" type="select" label="Use Microexon Search" help="With this option, the pipeline will attempt to find alignments incident to microexons. Works only for reads 50bp or longer."> 244 <option value="No">No</option> 245 <option value="Yes">Yes</option> 246 </param> 247 </when> <!-- full --> 248 </conditional> <!-- sParams --> 249 </when> <!-- single --> 250 <when value="paired"> 251 <param format="fastqcssanger" name="input2" type="data" label="RNA-Seq FASTQ file" help="Color-space: Must have Sanger-scaled quality values with ASCII offset 33" /> 252 <param name="mate_inner_distance" type="integer" value="20" label="Mean Inner Distance between Mate Pairs" /> 253 <conditional name="pParams"> 254 <param name="pSettingsType" type="select" label="TopHat settings to use" help="Use the Full parameter list to change default settings."> 255 <option value="preSet">Default settings</option> 256 <option value="full">Full parameter list</option> 257 </param> 258 <when value="preSet" /> 259 <!-- Full/advanced params. --> 260 <when value="full"> 261 <param name="library_type" type="select" label="Library Type" help="TopHat will treat the reads as strand specific. Every read alignment will have an XS attribute tag. Consider supplying library type options below to select the correct RNA-seq protocol."> 262 <option value="fr-unstranded">FR Unstranded</option> 263 <option value="fr-firststrand">FR First Strand</option> 264 <option value="fr-secondstrand">FR Second Strand</option> 265 </param> 266 <param name="mate_std_dev" type="integer" value="20" label="Std. Dev for Distance between Mate Pairs" help="The standard deviation for the distribution on inner distances between mate pairs."/> 267 <param name="anchor_length" type="integer" value="8" label="Anchor length (at least 3)" help="Report junctions spanned by reads with at least this many bases on each side of the junction." /> 268 <param name="splice_mismatches" type="integer" value="0" label="Maximum number of mismatches that can appear in the anchor region of spliced alignment" /> 269 <param name="min_intron_length" type="integer" value="70" label="The minimum intron length" help="TopHat will ignore donor/acceptor pairs closer than this many bases apart." /> 270 <param name="max_intron_length" type="integer" value="500000" label="The maximum intron length" help="When searching for junctions ab initio, TopHat will ignore donor/acceptor pairs farther than this many bases apart, except when such a pair is supported by a split segment alignment of a long read." /> 271 <expand macro="indel_searchConditional" /> 272 <param name="junction_filter" type="float" value="0.15" label="Minimum isoform fraction: filter out junctions supported by too few alignments (number of reads divided by average depth of coverage)" help="0.0 to 1.0 (0 to turn off)" /> 273 <param name="max_multihits" type="integer" value="40" label="Maximum number of alignments to be allowed" /> 274 <param name="min_segment_intron" type="integer" value="50" label="Minimum intron length that may be found during split-segment (default) search" /> 275 <param name="max_segment_intron" type="integer" value="500000" label="Maximum intron length that may be found during split-segment (default) search" /> 276 <param name="initial_read_mismatches" type="integer" min="0" max="3" value="2" label="Number of mismatches allowed in the initial read mapping" /> 277 <param name="seg_mismatches" type="integer" min="0" max="3" value="2" label="Number of mismatches allowed in each segment alignment for reads mapped independently" /> 278 <param name="seg_length" type="integer" value="25" label="Minimum length of read segments" /> 279 <!-- Options for supplying own junctions. --> 280 <conditional name="own_junctions"> 281 <param name="use_junctions" type="select" label="Use Own Junctions"> 282 <option value="No">No</option> 283 <option value="Yes">Yes</option> 284 </param> 285 <when value="Yes"> 286 <conditional name="gene_model_ann"> 287 <param name="use_annotations" type="select" label="Use Gene Annotation Model"> 288 <option value="No">No</option> 289 <option value="Yes">Yes</option> 290 </param> 291 <when value="No" /> 292 <when value="Yes"> 293 <param format="gtf" name="gene_annotation_model" type="data" label="Gene Model Annotations" help="TopHat will use the exon records in this file to build a set of known splice junctions for each gene, and will attempt to align reads to these junctions even if they would not normally be covered by the initial mapping."/> 294 </when> 295 </conditional> 296 <conditional name="raw_juncs"> 297 <param name="use_juncs" type="select" label="Use Raw Junctions"> 298 <option value="No">No</option> 299 <option value="Yes">Yes</option> 300 </param> 301 <when value="No" /> 302 <when value="Yes"> 303 <param format="interval" name="raw_juncs" type="data" label="Raw Junctions" help="Supply TopHat with a list of raw junctions. Junctions are specified one per line, in a tab-delimited format. Records look like: [chrom] [left] [right] [+/-] left and right are zero-based coordinates, and specify the last character of the left sequenced to be spliced to the first character of the right sequence, inclusive."/> 304 </when> 305 </conditional> 306 <param name="no_novel_juncs" type="select" label="Only look for supplied junctions"> 307 <option value="No">No</option> 308 <option value="Yes">Yes</option> 309 </param> 310 </when> 311 <when value="No" /> 312 </conditional> <!-- /own_junctions --> 313 314 <!-- Closure search. --> 315 <conditional name="closure_search"> 316 <param name="use_search" type="select" label="Use Closure Search"> 317 <option value="No">No</option> 318 <option value="Yes">Yes</option> 319 </param> 320 <when value="Yes"> 321 <param name="min_closure_exon" type="integer" value="50" label="During closure search for paired end reads, exonic hops in the potential splice graph must be at least this long. The default is 50." /> 322 <param name="min_closure_intron" type="integer" value="50" label="Minimum intron length that may be found during closure search" /> 323 <param name="max_closure_intron" type="integer" value="5000" label="Maximum intron length that may be found during closure search" /> 324 </when> 325 <when value="No" /> 326 </conditional> 327 <!-- Coverage search. --> 328 <conditional name="coverage_search"> 329 <param name="use_search" type="select" label="Use Coverage Search"> 330 <option selected="true" value="Yes">Yes</option> 331 <option value="No">No</option> 332 </param> 333 <when value="Yes"> 334 <param name="min_coverage_intron" type="integer" value="50" label="Minimum intron length that may be found during coverage search" /> 335 <param name="max_coverage_intron" type="integer" value="20000" label="Maximum intron length that may be found during coverage search" /> 336 </when> 337 <when value="No" /> 338 </conditional> 339 <param name="microexon_search" type="select" label="Use Microexon Search" help="With this option, the pipeline will attempt to find alignments incident to microexons. Works only for reads 50bp or longer."> 340 <option value="No">No</option> 341 <option value="Yes">Yes</option> 342 </param> 343 </when> <!-- full --> 344 </conditional> <!-- pParams --> 345 </when> <!-- paired --> 346 </conditional> 347 </inputs> 348 349 <outputs> 350 <data format="bed" name="insertions" label="${tool.name} on ${on_string}: insertions" from_work_dir="tophat_out/insertions.bed"> 351 <filter> 352 ( 353 ( ( 'sParams' in singlePaired ) and ( 'indel_search' in singlePaired['sParams'] ) and 354 ( singlePaired['sParams']['indel_search']['allow_indel_search'] == 'Yes' ) ) or 355 ( ( 'pParams' in singlePaired ) and ( 'indel_search' in singlePaired['pParams'] ) and 356 ( singlePaired['pParams']['indel_search']['allow_indel_search'] == 'Yes' ) ) 357 ) 358 </filter> 359 <expand macro="dbKeyActions" /> 360 </data> 361 <data format="bed" name="deletions" label="${tool.name} on ${on_string}: deletions" from_work_dir="tophat_out/deletions.bed"> 362 <expand macro="dbKeyActions" /> 363 </data> 364 <data format="bed" name="junctions" label="${tool.name} on ${on_string}: splice junctions"> 365 <expand macro="dbKeyActions" /> 366 </data> 367 <data format="bam" name="accepted_hits" label="${tool.name} on ${on_string}: accepted_hits"> 368 <expand macro="dbKeyActions" /> 369 </data> 370 </outputs> 371 <macros> 372 <import>tophat_macros.xml</import> 373 <macro name="bedFilter"> 374 <filter> 375 ( 376 ( ( 'sParams' in singlePaired ) and ( 'indel_search' in singlePaired['sParams'] ) and 377 ( singlePaired['sParams']['indel_search']['allow_indel_search'] == 'Yes' ) ) or 378 ( ( 'pParams' in singlePaired ) and ( 'indel_search' in singlePaired['pParams'] ) and 379 ( singlePaired['pParams']['indel_search']['allow_indel_search'] == 'Yes' ) ) 380 ) 381 </filter> 382 </macro> 383 <macro name="dbKeyActions"> 384 <actions> 385 <conditional name="refGenomeSource.genomeSource"> 386 <when value="indexed"> 387 <action type="metadata" name="dbkey"> 388 <option type="from_data_table" name="tophat_indexes_color" column="1" offset="0"> 389 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/> 390 <filter type="param_value" ref="refGenomeSource.index" column="0"/> 391 </option> 392 </action> 393 </when> 394 <when value="history"> 395 <action type="metadata" name="dbkey"> 396 <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" /> 397 </action> 398 </when> 399 </conditional> 400 </actions> 401 </macro> 402 </macros> 403 <tests> 404 <!-- Test color-space single-end reads with user-supplied reference fasta and preset parameters --> 405 <test> 406 <!-- TopHat commands: 407 cp test-data/tophat_in5.fasta tophat_in5.fa 408 bowtie-build -C -f tophat_in5.fasta tophat_in5 409 tophat -p 1 -C tophat_in5 test-data/tophat_in4.fastqcssanger 410 Rename the files in tmp_dir appropriately 411 --> 412 <param name="input1" ftype="fastqcssanger" value="tophat_in4.fastqcssanger" /> 413 <param name="genomeSource" value="history" /> 414 <param name="ownFile" ftype="fasta" value="tophat_in5.fasta"/> 415 <param name="sPaired" value="single" /> 416 <param name="sSettingsType" value="preSet" /> 417 <output name="junctions" file="tophat_out5j.bed" /> 418 <output name="accepted_hits" file="tophat_out5h.bam" compare="sim_size" /> 419 </test> 420 <!-- Test color-space single-end reads with pre-built index and full parameters --> 421 <test> 422 <!-- Tophat commands: 423 tophat -p 1 -C -a 8 -m 0 -i 70 -I 500000 -F 0.15 -g 40 +allow-indels +coverage-search +min-coverage-intron 50 +max-coverage-intron 20000 +segment-mismatches 2 +segment-length 25 +closure-search +min-closure-exon 50 +min-closure-intron 50 +max-closure-intron 5000 +microexon-search partialMm9chrX_random_cs test-data/tophat_in4.fastqcssanger 424 Replace the + with double-dash 425 Rename the files in tmp_dir appropriately 426 --> 427 <param name="input1" ftype="fastqcssanger" value="tophat_in4.fastqcssanger"/> 428 <param name="genomeSource" value="indexed"/> 429 <param name="index" value="partialMm9chrX_random_cs" /> 430 <param name="sPaired" value="single"/> 431 <param name="sSettingsType" value="full"/> 432 <param name="library_type" value="FR Unstranded"/> 433 <param name="anchor_length" value="8"/> 434 <param name="splice_mismatches" value="0"/> 435 <param name="min_intron_length" value="70"/> 436 <param name="max_intron_length" value="500000"/> 437 <param name="junction_filter" value="0.15"/> 438 <param name="max_multihits" value="40"/> 439 <param name="min_segment_intron" value="50" /> 440 <param name="max_segment_intron" value="500000" /> 441 <param name="seg_mismatches" value="2"/> 442 <param name="seg_length" value="25"/> 443 <param name="allow_indel_search" value="Yes"/> 444 <param name="max_insertion_length" value="3"/> 445 <param name="max_deletion_length" value="3"/> 446 <param name="use_junctions" value="Yes" /> 447 <param name="use_annotations" value="No" /> 448 <param name="use_juncs" value="No" /> 449 <param name="no_novel_juncs" value="No" /> 450 <param name="use_search" value="Yes" /> 451 <param name="min_closure_exon" value="50" /> 452 <param name="min_closure_intron" value="50" /> 453 <param name="max_closure_intron" value="5000" /> 454 <param name="use_search" value="Yes" /> 455 <param name="min_coverage_intron" value="50" /> 456 <param name="max_coverage_intron" value="20000" /> 457 <param name="microexon_search" value="Yes" /> 458 <output name="insertions" file="tophat_out6i.bed" /> 459 <output name="deletions" file="tophat_out6d.bed" /> 460 <output name="junctions" file="tophat_out6j.bed" /> 461 <output name="accepted_hits" file="tophat_out6h.bam" compare="sim_size" /> 462 </test> 463 <!-- Test color-space paired-end reads with pre-built index and preset parameters --> 464 <test> 465 <!-- TopHat commands: 466 tophat -C -o tmp_dir -r 50 -p 1 partialMm9chrX_random_cs test-data/tophat_in6.fastqcssanger test-data/tophat_in7.fastqcssanger 467 Rename the files in tmp_dir appropriately 468 --> 469 <param name="input1" ftype="fastqcssanger" value="tophat_in6.fastqcssanger" /> 470 <param name="genomeSource" value="indexed" /> 471 <param name="index" value="partialMm9chrX_random_cs" /> 472 <param name="sPaired" value="paired" /> 473 <param name="input2" ftype="fastqcssanger" value="tophat_in7.fastqcssanger"/> 474 <param name="mate_inner_distance" value="50"/> 475 <param name="pSettingsType" value="preSet" /> 476 <output name="junctions" file="tophat_out7j.bed" /> 477 <output name="accepted_hits" file="tophat_out7h.bam" compare="sim_size" /> 478 </test> 479 <!-- Test color-space paired-end reads with user-supplied reference fasta and full parameters --> 480 <test> 481 <!-- TopHat commands: 482 cp test-data/tophat_in5.fasta tophat_in5.fa 483 bowtie-build -C -f tophat_in5.fa tophat_in5 484 tophat -C -o tmp_dir -r 20 -p 1 -a 8 -m 0 -i 70 -I 500000 -F 0.15 -g 40 +library-type fr-unstranded +allow-indels +closure-search +min-closure-exon 50 +min-closure-intron 50 +max-closure-intron 5000 +coverage-search +min-coverage-intron 50 +max-coverage-intron 15000 +mate-std-dev 20 +segment-mismatch 2 +segment-length 20 +min-segment-intron 50 +max-segment-intron 500000 tophat_in5 test-data/tophat_in6.fastqcssanger test-data/tophat_in7.fastqcssanger 485 Replace the + with double-dash 486 Rename the files in tmp_dir appropriately 487 --> 488 <param name="input1" ftype="fastqcssanger" value="tophat_in6.fastqcssanger"/> 489 <param name="genomeSource" value="history"/> 490 <param name="ownFile" ftype="fasta" value="tophat_in5.fasta"/> 491 <param name="sPaired" value="paired"/> 492 <param name="input2" ftype="fastqcssanger" value="tophat_in7.fastqcssanger"/> 493 <param name="mate_inner_distance" value="20"/> 494 <param name="pSettingsType" value="full"/> 495 <param name="library_type" value="FR Unstranded"/> 496 <param name="mate_std_dev" value="20"/> 497 <param name="anchor_length" value="8"/> 498 <param name="splice_mismatches" value="0"/> 499 <param name="min_intron_length" value="70"/> 500 <param name="max_intron_length" value="500000"/> 501 <param name="junction_filter" value="0.15"/> 502 <param name="max_multihits" value="40"/> 503 <param name="min_segment_intron" value="70" /> 504 <param name="max_segment_intron" value="400000" /> 505 <param name="seg_mismatches" value="2"/> 506 <param name="seg_length" value="20"/> 507 <param name="allow_indel_search" value="Yes"/> 508 <param name="max_insertion_length" value="3"/> 509 <param name="max_deletion_length" value="3"/> 510 <param name="use_junctions" value="No" /> 511 <param name="use_search" value="Yes" /> 512 <param name="min_closure_exon" value="50" /> 513 <param name="min_closure_intron" value="50" /> 514 <param name="max_closure_intron" value="5000" /> 515 <param name="use_search" value="Yes" /> 516 <param name="min_coverage_intron" value="50" /> 517 <param name="max_coverage_intron" value="20000" /> 518 <param name="microexon_search" value="No" /> 519 <output name="insertions" file="tophat_out8i.bed" /> 520 <output name="deletions" file="tophat_out8d.bed" /> 521 <output name="junctions" file="tophat_out8j.bed" /> 522 <output name="accepted_hits" file="tophat_out8h.bam" compare="sim_size" /> 523 </test> 524 </tests> 525 526 <help> 527**Tophat Overview** 528 529TopHat_ is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons. Please cite: Trapnell, C., Pachter, L. and Salzberg, S.L. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25, 1105-1111 (2009). 530 531.. _Tophat: http://tophat.cbcb.umd.edu/ 532 533------ 534 535**Know what you are doing** 536 537.. class:: warningmark 538 539There is no such thing (yet) as an automated gearshift in splice junction identification. It is all like stick-shift driving in San Francisco. In other words, running this tool with default parameters will probably not give you meaningful results. A way to deal with this is to **understand** the parameters by carefully reading the `documentation`__ and experimenting. Fortunately, Galaxy makes experimenting easy. 540 541.. __: http://tophat.cbcb.umd.edu/manual.html 542 543------ 544 545**Input formats** 546 547Tophat accepts files in Sanger FASTQ format. Use the FASTQ Groomer to prepare your files. 548 549------ 550 551**Outputs** 552 553Tophat produces two main output files: 554 555- junctions -- A UCSC BED_ track of junctions reported by TopHat. Each junction consists of two connected BED blocks, where each block is as long as the maximal overhang of any read spanning the junction. The score is the number of alignments spanning the junction. 556- accepted_hits -- A list of read alignments in BAM_ format. 557 558.. _BED: http://genome.ucsc.edu/FAQ/FAQformat.html#format1 559.. _BAM: http://samtools.sourceforge.net/ 560 561Two other possible outputs, depending on the options you choose, are insertions and deletions, both of which are in BED format. 562 563------- 564 565**Tophat settings** 566 567All of the options have a default value. You can change any of them. Some of the options in Tophat have been implemented here. 568 569------ 570 571**Tophat parameter list** 572 573This is a list of implemented Tophat options:: 574 575This is a list of implemented Tophat options:: 576 577 -r This is the expected (mean) inner distance between mate pairs. For, example, for paired end runs with fragments 578 selected at 300bp, where each end is 50bp, you should set -r to be 200. There is no default, and this parameter 579 is required for paired end runs. 580 --mate-std-dev INT The standard deviation for the distribution on inner distances between mate pairs. The default is 20bp. 581 -a/--min-anchor-length INT The "anchor length". TopHat will report junctions spanned by reads with at least this many bases on each side of the junction. Note that individual spliced 582 alignments may span a junction with fewer than this many bases on one side. However, every junction involved in spliced alignments is supported by at least one 583 read with this many bases on each side. This must be at least 3 and the default is 8. 584 -m/--splice-mismatches INT The maximum number of mismatches that may appear in the "anchor" region of a spliced alignment. The default is 0. 585 -i/--min-intron-length INT The minimum intron length. TopHat will ignore donor/acceptor pairs closer than this many bases apart. The default is 70. 586 -I/--max-intron-length INT The maximum intron length. When searching for junctions ab initio, TopHat will ignore donor/acceptor pairs farther than this many bases apart, except when such a pair is supported by a split segment alignment of a long read. The default is 500000. 587 -F/--min-isoform-fraction 0.0-1.0 TopHat filters out junctions supported by too few alignments. Suppose a junction spanning two exons, is supported by S reads. Let the average depth of coverage of 588 exon A be D, and assume that it is higher than B. If S / D is less than the minimum isoform fraction, the junction is not reported. A value of zero disables the 589 filter. The default is 0.15. 590 -g/--max-multihits INT Instructs TopHat to allow up to this many alignments to the reference for a given read, and suppresses all alignments for reads with more than this many 591 alignments. The default is 40. 592 -G/--GTF [GTF 2.2 file] Supply TopHat with a list of gene model annotations. TopHat will use the exon records in this file to build a set of known splice junctions for each gene, and will attempt to align reads to these junctions even if they would not normally be covered by the initial mapping. 593 -j/--raw-juncs [juncs file] Supply TopHat with a list of raw junctions. Junctions are specified one per line, in a tab-delimited format. Records look like: [chrom] [left] [right] [+/-], left and right are zero-based coordinates, and specify the last character of the left sequenced to be spliced to the first character of the right sequence, inclusive. 594 -no-novel-juncs Only look for junctions indicated in the supplied GFF file. (ignored without -G) 595 --no-closure-search Disables the mate pair closure-based search for junctions. Currently, has no effect - closure search is off by default. 596 --closure-search Enables the mate pair closure-based search for junctions. Closure-based search should only be used when the expected inner distance between mates is small (about or less than 50bp) 597 --no-coverage-search Disables the coverage based search for junctions. 598 --coverage-search Enables the coverage based search for junctions. Use when coverage search is disabled by default (such as for reads 75bp or longer), for maximum sensitivity. 599 --microexon-search With this option, the pipeline will attempt to find alignments incident to microexons. Works only for reads 50bp or longer. 600 --butterfly-search TopHat will use a slower but potentially more sensitive algorithm to find junctions in addition to its standard search. Consider using this if you expect that your experiment produced a lot of reads from pre-mRNA, that fall within the introns of your transcripts. 601 --segment-mismatches Read segments are mapped independently, allowing up to this many mismatches in each segment alignment. The default is 2. 602 --segment-length Each read is cut up into segments, each at least this long. These segments are mapped independently. The default is 25. 603 --min-closure-exon During closure search for paired end reads, exonic hops in the potential splice graph must be at least this long. The default is 50. 604 --min-closure-intron The minimum intron length that may be found during closure search. The default is 50. 605 --max-closure-intron The maximum intron length that may be found during closure search. The default is 5000. 606 --min-coverage-intron The minimum intron length that may be found during coverage search. The default is 50. 607 --max-coverage-intron The maximum intron length that may be found during coverage search. The default is 20000. 608 --min-segment-intron The minimum intron length that may be found during split-segment search. The default is 50. 609 --max-segment-intron The maximum intron length that may be found during split-segment search. The default is 500000. 610 </help> 611</tool>