/tools/sr_mapping/bowtie_color_wrapper.xml
XML | 714 lines | 646 code | 34 blank | 34 comment | 0 complexity | a6683c6b4d0b4568e6d7d8c8db89d47d MD5 | raw file
1<tool id="bowtie_color_wrapper" name="Map with Bowtie for SOLiD" version="1.1.2"> 2 <requirements><requirement type='package'>bowtie</requirement></requirements> 3 <description></description> 4 <command interpreter="python"> 5 bowtie_wrapper.py 6 ## Hackish setting of number of threads 7 --threads="4" 8 ## Outputs 9 --output=$output 10 #if str( $singlePaired.sPaired ) == "single" 11 #if $output_unmapped_reads_l 12 --output_unmapped_reads=$output_unmapped_reads_l 13 #end if 14 #if $output_suppressed_reads_l 15 --output_suppressed_reads=$output_suppressed_reads_l 16 #end if 17 #else 18 #if $output_unmapped_reads_l and $output_unmapped_reads_r 19 --output_unmapped_reads_l=$output_unmapped_reads_l 20 --output_unmapped_reads_r=$output_unmapped_reads_r 21 #end if 22 #if $output_suppressed_reads_l and $output_suppressed_reads_l 23 --output_suppressed_reads_l=$output_suppressed_reads_l 24 --output_suppressed_reads_r=$output_suppressed_reads_r 25 #end if 26 #end if 27 ## Inputs 28 --dataType="solid" 29 --suppressHeader=$suppressHeader 30 --genomeSource=$refGenomeSource.genomeSource 31 #if $refGenomeSource.genomeSource == "history": 32 ##index already exists 33 #if $refGenomeSource.ownFile.extension.startswith( 'bowtie_' ): 34 ##user previously built 35 --ref="${refGenomeSource.ownFile.extra_files_path}/${refGenomeSource.ownFile.metadata.base_name}" 36 --do_not_build_index 37 #else: 38 ##build index on the fly 39 --ref=$refGenomeSource.ownFile 40 --indexSettings=$refGenomeSource.indexParams.indexSettings 41 #if $refGenomeSource.indexParams.indexSettings == "indexFull": 42 --iautoB=$refGenomeSource.indexParams.autoBehavior.autoB 43 #if $refGenomeSource.indexParams.autoBehavior.autoB == "set": 44 --ipacked=$refGenomeSource.indexParams.autoBehavior.packed 45 --ibmax=$refGenomeSource.indexParams.autoBehavior.bmax 46 --ibmaxdivn=$refGenomeSource.indexParams.autoBehavior.bmaxdivn 47 --idcv=$refGenomeSource.indexParams.autoBehavior.dcv 48 #end if 49 --inodc=$refGenomeSource.indexParams.nodc 50 --inoref=$refGenomeSource.indexParams.noref 51 --ioffrate=$refGenomeSource.indexParams.offrate 52 --iftab=$refGenomeSource.indexParams.ftab 53 --intoa=$refGenomeSource.indexParams.ntoa 54 --iendian=$refGenomeSource.indexParams.endian 55 --iseed=$refGenomeSource.indexParams.seed 56 --icutoff=$refGenomeSource.indexParams.cutoff 57 #end if 58 #end if 59 #else 60 ##use pre-built index 61 --ref="${ filter( lambda x: str( x[0] ) == str( $refGenomeSource.index ), $__app__.tool_data_tables[ 'bowtie_indexes_color' ].get_fields() )[0][-1] }" 62 #end if 63 --paired=$singlePaired.sPaired 64 #if $singlePaired.sPaired == "single": 65 --input1=$singlePaired.sInput1 66 --params=$singlePaired.sParams.sSettingsType 67 #if $singlePaired.sParams.sSettingsType == "full": 68 --skip=$singlePaired.sParams.sSkip 69 --alignLimit=$singlePaired.sParams.sAlignLimit 70 --trimH=$singlePaired.sParams.sTrimH 71 --trimL=$singlePaired.sParams.sTrimL 72 --mismatchSeed=$singlePaired.sParams.sMismatchSeed 73 --mismatchQual=$singlePaired.sParams.sMismatchQual 74 --seedLen=$singlePaired.sParams.sSeedLen 75 --rounding=$singlePaired.sParams.sRounding 76 --maqSoapAlign=$singlePaired.sParams.sMaqSoapAlign 77 --tryHard=$singlePaired.sParams.sTryHard 78 --valAlign=$singlePaired.sParams.sValAlign 79 --allValAligns=$singlePaired.sParams.sAllValAligns 80 --suppressAlign=$singlePaired.sParams.sSuppressAlign 81 --best=$singlePaired.sParams.sBestOption.sBest 82 #if $singlePaired.sParams.sBestOption.sBest == "doBest": 83 --maxBacktracks=$singlePaired.sParams.sBestOption.sdMaxBacktracks 84 --strata=$singlePaired.sParams.sBestOption.sdStrata 85 #else: 86 --maxBacktracks=$singlePaired.sParams.sBestOption.snMaxBacktracks 87 #end if 88 --offrate=$singlePaired.sParams.sOffrate 89 --seed=$singlePaired.sParams.sSeed 90 --snpphred=$singlePaired.sParams.sSnpphred 91 --snpfrac=$singlePaired.sParams.sSnpfrac 92 --keepends=$singlePaired.sParams.sKeepends 93 #end if 94 #else: 95 --input1=$singlePaired.pInput1 96 --input2=$singlePaired.pInput2 97 --maxInsert=$singlePaired.pMaxInsert 98 --mateOrient=$singlePaired.pMateOrient 99 --params=$singlePaired.pParams.pSettingsType 100 #if $singlePaired.pParams.pSettingsType == "full": 101 --skip=$singlePaired.pParams.pSkip 102 --alignLimit=$singlePaired.pParams.pAlignLimit 103 --trimH=$singlePaired.pParams.pTrimH 104 --trimL=$singlePaired.pParams.pTrimL 105 --mismatchSeed=$singlePaired.pParams.pMismatchSeed 106 --mismatchQual=$singlePaired.pParams.pMismatchQual 107 --seedLen=$singlePaired.pParams.pSeedLen 108 --rounding=$singlePaired.pParams.pRounding 109 --maqSoapAlign=$singlePaired.pParams.pMaqSoapAlign 110 --minInsert=$singlePaired.pParams.pMinInsert 111 --maxAlignAttempt=$singlePaired.pParams.pMaxAlignAttempt 112 --forwardAlign=$singlePaired.pParams.pForwardAlign 113 --reverseAlign=$singlePaired.pParams.pReverseAlign 114 --tryHard=$singlePaired.pParams.pTryHard 115 --valAlign=$singlePaired.pParams.pValAlign 116 --allValAligns=$singlePaired.pParams.pAllValAligns 117 --suppressAlign=$singlePaired.pParams.pSuppressAlign 118 --best=$singlePaired.pParams.pBestOption.pBest 119 #if $singlePaired.pParams.pBestOption.pBest == "doBest": 120 --maxBacktracks=$singlePaired.pParams.pBestOption.pdMaxBacktracks 121 --strata=$singlePaired.pParams.pBestOption.pdStrata 122 #else: 123 --maxBacktracks=$singlePaired.pParams.pBestOption.pnMaxBacktracks 124 #end if 125 --offrate=$singlePaired.pParams.pOffrate 126 --seed=$singlePaired.pParams.pSeed 127 --snpphred=$singlePaired.pParams.pSnpphred 128 --snpfrac=$singlePaired.pParams.pSnpfrac 129 --keepends=$singlePaired.pParams.pKeepends 130 #end if 131 #end if 132 </command> 133 <inputs> 134 <conditional name="refGenomeSource"> 135 <param name="genomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options"> 136 <option value="indexed">Use a built-in index</option> 137 <option value="history">Use one from the history</option> 138 </param> 139 <when value="indexed"> 140 <param name="index" type="select" label="Select the reference genome" help="if your genome of interest is not listed - contact Galaxy team"> 141 <options from_data_table="bowtie_indexes_color"> 142 <filter type="sort_by" column="2" /> 143 <validator type="no_options" message="No indexes are available" /> 144 </options> 145 </param> 146 </when> 147 <when value="history"> 148 <param name="ownFile" type="data" format="bowtie_color_index,fasta" metadata_name="dbkey" label="Select the reference genome" /> 149 <conditional name="indexParams"> 150 <param name="indexSettings" type="select" label="Choose whether to use Default options for building indices or to Set your own" help="These settings are ignored when using a prebuilt index"> 151 <option value="indexPreSet">Default</option> 152 <option value="indexFull">Set your own</option> 153 </param> 154 <when value="indexPreSet" /> 155 <when value="indexFull"> 156 <conditional name="autoBehavior"> 157 <param name="autoB" type="select" label="Choose to use automatic or specified behavior for some parameters (-a)" help="Allows you to set --packed, --bmax, --bmaxdivn, and --dcv"> 158 <option value="auto">Automatic behavior</option> 159 <option value="set">Set values (sets --noauto and allows others to be set)</option> 160 </param> 161 <when value="auto" /> 162 <when value="set"> 163 <param name="packed" type="select" label="Whether or not to use a packed representation for DNA strings (--packed)"> 164 <option value="unpacked">Use regular representation</option> 165 <option value="packed">Use packed representation</option> 166 </param> 167 <param name="bmax" type="integer" value="-1" label="Maximum number of suffixes allowed in a block (--bmax)" help="-1 for not specified. Must be at least 1" /> 168 <param name="bmaxdivn" type="integer" value="4" label="Maximum number of suffixes allowed in a block as a fraction of the length of the reference (--bmaxdivn)" /> 169 <param name="dcv" type="integer" value="1024" label="The period for the difference-cover sample (--dcv)" /> 170 </when> 171 </conditional> 172 <param name="nodc" type="select" label="Whether or not to disable the use of the difference-cover sample (--nodc)" help="Suffix sorting becomes quadratic-time in the worst case (with a very repetitive reference)"> 173 <option value="dc">Use difference-cover sample</option> 174 <option value="nodc">Disable difference-cover sample</option> 175 </param> 176 <param name="noref" type="select" label="Whether or not to build the part of the reference index used only in paired-end alignment (-r)"> 177 <option value="ref">Build all index files</option> 178 <option value="noref">Do not build paired-end alignment index files</option> 179 </param> 180 <param name="offrate" type="integer" value="5" label="How many rows get marked during annotation of some or all of the Burrows-Wheeler rows (-o)" /> 181 <param name="ftab" type="integer" value="10" label="The size of the lookup table used to calculate an initial Burrows-Wheeler range with respect to the first n characters of the query (-t)" help="ftab is 4^(n+1) bytes" /> 182 <param name="ntoa" type="select" label="Whether or not to convert Ns in the reference sequence to As (--ntoa)"> 183 <option value="no">Do not convert Ns</option> 184 <option value="yes">Convert Ns to As</option> 185 </param> 186 <param name="endian" type="select" label="Endianness to use when serializing integers to the index file (--big/--little)" help="Little is most appropriate for Intel- and AMD-based architecture"> 187 <option value="little">Little</option> 188 <option value="big">Big</option> 189 </param> 190 <param name="seed" type="integer" value="-1" label="Seed for the pseudorandom number generator (--seed)" help="Use -1 to use default" /> 191 <param name="cutoff" type="integer" value="-1" label="Number of first bases of the reference sequence to index (--cutoff)" help="Use -1 to use default" /> 192 </when> <!-- indexFull --> 193 </conditional> <!-- indexParams --> 194 </when> <!-- history --> 195 </conditional> <!-- refGenomeSource --> 196 <conditional name="singlePaired"> 197 <param name="sPaired" type="select" label="Is this library mate-paired?"> 198 <option value="single">Single-end</option> 199 <option value="paired">Paired-end</option> 200 </param> 201 <when value="single"> 202 <param name="sInput1" type="data" format="fastqcssanger" label="FASTQ file" help="Must have Sanger-scaled quality values with ASCII offset 33"/> 203 <conditional name="sParams"> 204 <param name="sSettingsType" type="select" label="Bowtie settings to use" help="For most mapping needs use Commonly used settings. If you want full control use Full parameter list"> 205 <option value="preSet">Commonly used</option> 206 <option value="full">Full parameter list</option> 207 </param> 208 <when value="preSet" /> 209 <when value="full"> 210 <param name="sSkip" type="integer" value="0" label="Skip the first n reads (-s)" /> 211 <param name="sAlignLimit" type="integer" value="-1" label="Only align the first n reads (-u)" help="-1 for off" /> 212 <param name="sTrimH" type="integer" value="0" label="Trim n bases from high-quality (left) end of each read before alignment (-5)" /> 213 <param name="sTrimL" type="integer" value="0" label="Trim n bases from low-quality (right) end of each read before alignment (-3)" /> 214 <param name="sMismatchSeed" type="integer" value="2" label="Maximum number of mismatches permitted in the seed (-n)" help="May be 0, 1, 2, or 3" /> 215 <param name="sMismatchQual" type="integer" value="70" label="Maximum permitted total of quality values at mismatched read positions (-e)" /> 216 <param name="sSeedLen" type="integer" value="28" label="Seed length (-l)" help="Minimum value is 5" /> 217 <param name="sRounding" type="select" label="Whether or not to round to the nearest 10 and saturating at 30 (--nomaqround)"> 218 <option value="round">Round to nearest 10</option> 219 <option value="noRound">Do not round to nearest 10</option> 220 </param> 221 <param name="sMaqSoapAlign" type="integer" value="-1" label="Number of mismatches for SOAP-like alignment policy (-v)" help="-1 for default MAQ-like alignment policy" /> 222 <param name="sTryHard" type="select" label="Whether or not to try as hard as possible to find valid alignments when they exist (-y)" help="Tryhard mode is much slower than regular mode"> 223 <option value="noTryHard">Do not try hard</option> 224 <option value="doTryHard">Try hard</option> 225 </param> 226 <param name="sValAlign" type="integer" value="1" label="Report up to n valid alignments per read (-k)" /> 227 <param name="sAllValAligns" type="select" label="Whether or not to report all valid alignments per read (-a)"> 228 <option value="noAllValAligns">Do not report all valid alignments</option> 229 <option value="doAllValAligns">Report all valid alignments</option> 230 </param> 231 <param name="sSuppressAlign" type="integer" value="-1" label="Suppress all alignments for a read if more than n reportable alignments exist (-m)" help="-1 for no limit" /> 232 <param name="sMaxFile" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write all reads with a number of valid alignments exceeding the limit set with the -m option to a file (--max)" /> 233 <param name="sUnmappedFile" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write all reads that could not be aligned to a file (--un)" /> 234 <conditional name="sBestOption"> 235 <param name="sBest" type="select" label="Whether or not to make Bowtie guarantee that reported singleton alignments are 'best' in terms of stratum and in terms of the quality values at the mismatched positions (--best)" help="Removes all strand bias. Only affects which alignments are reported by Bowtie. Runs slower with best option"> 236 <option value="noBest">Do not use best</option> 237 <option value="doBest">Use best</option> 238 </param> 239 <when value="noBest"> 240 <param name="snMaxBacktracks" type="integer" value="125" label="Maximum number of backtracks permitted when aligning a read (--maxbts)" /> 241 </when> 242 <when value="doBest"> 243 <param name="sdMaxBacktracks" type="integer" value="800" label="Maximum number of backtracks permitted when aligning a read (--maxbts)" /> 244 <param name="sdStrata" type="select" label="Whether or not to report only those alignments that fall in the best stratum if many valid alignments exist and are reportable (--strata)"> 245 <option value="noStrata">Do not use strata option</option> 246 <option value="doStrata">Use strata option</option> 247 </param> 248 </when> 249 </conditional> <!-- sBestOption --> 250 <param name="sOffrate" type="integer" value="-1" label="Override the offrate of the index to n (-o)" help="-1 for default" /> 251 <param name="sSeed" type="integer" value="-1" label="Seed for pseudo-random number generator (--seed)" help="-1 for default" /> 252 <param name="sSnpphred" type="integer" value="-1" label="SNP penalty (ratio of SNPs per base in the subject genome) (--snpphred)" help="Enter this OR Ratio of SNPs per base" /> 253 <param name="sSnpfrac" type="float" value="0.001" label="Ratio of SNPs per base (estimated ratio for colorspace alignments) (--snpfrac)" help="Enter this OR SNP penalty" /> 254 <param name="sKeepends" type="select" label="Keep the extreme-ends nucleotides and qualities rather than trimming them (--col-keepends)"> 255 <option value="doKeepends">Keep ends</option> 256 <option value="noKeepends">Trim ends</option> 257 </param> 258 </when> <!-- full --> 259 </conditional> <!-- sParams --> 260 </when> <!-- single --> 261 <when value="paired"> 262 <param name="pInput1" type="data" format="fastqcssanger" label="FASTQ file" help="Must have Sanger-scaled quality values with ASCII offset 33"/> 263 <param name="pInput2" type="data" format="fastqcssanger" label="Reverse FASTQ file" help="Must have Sanger-scaled quality values with ASCII offset 33"/> 264 <param name="pMaxInsert" type="integer" value="1000" label="Maximum insert size for valid paired-end alignments (-X)" /> 265 <param name="pMateOrient" type="select" label="The upstream/downstream mate orientation for valid paired-end alignment against the forward reference strand (--fr/--rf/--ff)"> 266 <option value="ff">FF (for SOLiD)</option> 267 <option value="fr">FR (for Illumina)</option> 268 <option value="rf">RF</option> 269 </param> 270 <conditional name="pParams"> 271 <param name="pSettingsType" type="select" label="Bowtie settings to use" help="For most mapping needs use Commonly used settings. If you want full control use Full parameter list"> 272 <option value="preSet">Commonly used</option> 273 <option value="full">Full parameter list</option> 274 </param> 275 <when value="preSet" /> 276 <when value="full"> 277 <param name="pSkip" type="integer" value="0" label="Skip the first n pairs (-s)" /> 278 <param name="pAlignLimit" type="integer" value="-1" label="Only align the first n pairs (-u)" help="-1 for off" /> 279 <param name="pTrimH" type="integer" value="0" label="Trim n bases from high-quality (left) end of each read before alignment (-5)" /> 280 <param name="pTrimL" type="integer" value="0" label="Trim n bases from low-quality (right) end of each read before alignment (-3)" /> 281 <param name="pMismatchSeed" type="integer" value="2" label="Maximum number of mismatches permitted in the seed (-n)" help="May be 0, 1, 2, or 3" /> 282 <param name="pMismatchQual" type="integer" value="70" label="Maximum permitted total of quality values at mismatched read positions (-e)" /> 283 <param name="pSeedLen" type="integer" value="28" label="Seed length (-l)" help="Minimum value is 5" /> 284 <param name="pRounding" type="select" label="Whether or not to round to the nearest 10 and saturating at 30 (--nomaqround)"> 285 <option value="round">Round to nearest 10</option> 286 <option value="noRound">Do not round to nearest 10</option> 287 </param> 288 <param name="pMaqSoapAlign" type="integer" value="-1" label="Number of mismatches for SOAP-like alignment policy (-v)" help="-1 for default MAQ-like alignment policy" /> 289 <param name="pMinInsert" type="integer" value="0" label="Minimum insert size for valid paired-end alignments (-I)" /> 290 <param name="pMaxAlignAttempt" type="integer" value="100" label="Maximum number of attempts Bowtie will make to match an alignment for one mate with an alignment for the opposite mate (--pairtries)" /> 291 <param name="pForwardAlign" type="select" label="Choose whether or not to attempt to align the forward reference strand (--nofw)"> 292 <option value="forward">Align against the forward reference strand</option> 293 <option value="noForward">Do not align against the forward reference strand</option> 294 </param> 295 <param name="pReverseAlign" type="select" label="Choose whether or not to align against the reverse-complement reference strand (--norc)"> 296 <option value="reverse">Align against the reverse-complement reference strand</option> 297 <option value="noReverse">Do not align against the reverse-complement reference strand</option> 298 </param> 299 <param name="pTryHard" type="select" label="Whether or not to try as hard as possible to find valid alignments when they exist (-y)" help="Tryhard mode is much slower than regular mode"> 300 <option value="noTryHard">Do not try hard</option> 301 <option value="doTryHard">Try hard</option> 302 </param> 303 <param name="pValAlign" type="integer" value="1" label="Report up to n valid arguments per pair (-k)" /> 304 <param name="pAllValAligns" type="select" label="Whether or not to report all valid alignments per pair (-a)"> 305 <option value="noAllValAligns">Do not report all valid alignments</option> 306 <option value="doAllValAligns">Report all valid alignments</option> 307 </param> 308 <param name="pSuppressAlign" type="integer" value="-1" label="Suppress all alignments for a pair if more than n reportable alignments exist (-m)" help="-1 for no limit" /> 309 <param name="pMaxFile" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write all reads with a number of valid alignments exceeding the limit set with the -m option to a file (--max)" /> 310 <param name="pUnmappedFile" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write all reads that could not be aligned to a file (--un)" /> 311 <conditional name="pBestOption"> 312 <param name="pBest" type="select" label="Whether or not to make Bowtie guarantee that reported singleton alignments are 'best' in terms of stratum and in terms of the quality values at the mismatched positions (--best)" help="Removes all strand bias. Only affects which alignments are reported by Bowtie. Runs slower with best option"> 313 <option value="noBest">Do not use best</option> 314 <option value="doBest">Use best</option> 315 </param> 316 <when value="noBest"> 317 <param name="pnMaxBacktracks" type="integer" value="125" label="Maximum number of backtracks permitted when aligning a read (--maxbts)" /> 318 </when> 319 <when value="doBest"> 320 <param name="pdMaxBacktracks" type="integer" value="800" label="Maximum number of backtracks permitted when aligning a read (--maxbts)" /> 321 <param name="pdStrata" type="select" label="Whether or not to report only those alignments that fall in the best stratum if many valid alignments exist and are reportable (--strata)"> 322 <option value="noStrata">Do not use strata option</option> 323 <option value="doStrata">Use strata option</option> 324 </param> 325 </when> 326 </conditional> <!-- pBestOption --> 327 <param name="pOffrate" type="integer" value="-1" label="Override the offrate of the index to n (-o)" help="-1 for default" /> 328 <param name="pSeed" type="integer" value="-1" label="Seed for pseudo-random number generator (--seed)" help="-1 for default" /> 329 <param name="pSnpphred" type="integer" value="-1" label="SNP penalty (ratio of SNPs per base in the subject genome) (--snpphred)" help="Enter this OR Ratio of SNPs per base" /> 330 <param name="pSnpfrac" type="float" value="0.001" label="Ratio of SNPs per base (estimated ratio for colorspace alignments) (--snpfrac)" help="Enter this OR SNP penalty" /> 331 <param name="pKeepends" type="select" label="Keep the extreme-ends nucleotides and qualities rather than trimming them (--col-keepends)"> 332 <option value="doKeepends">Keep ends</option> 333 <option value="noKeepends">Trim ends</option> 334 </param> 335 </when> <!-- full --> 336 </conditional> <!-- pParams --> 337 </when> <!-- paired --> 338 </conditional> <!-- singlePaired --> 339 <param name="suppressHeader" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Suppress the header in the output SAM file" help="Bowtie produces SAM with several lines of header information by default" /> 340 </inputs> 341 <outputs> 342 <data format="sam" name="output" label="${tool.name} on ${on_string}: mapped reads"> 343 <actions> 344 <conditional name="refGenomeSource.genomeSource"> 345 <when value="indexed"> 346 <action type="metadata" name="dbkey"> 347 <option type="from_data_table" name="bowtie_indexes_color" column="1" offset="0"> 348 <filter type="param_value" column="0" value="#" filter_by="startswith" keep="False"/> 349 <filter type="param_value" ref="refGenomeSource.index" column="0"/> 350 </option> 351 </action> 352 </when> 353 <when value="history"> 354 <action type="metadata" name="dbkey"> 355 <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" /> 356 </action> 357 </when> 358 </conditional> 359 </actions> 360 </data> 361 <data format="fastqcssanger" name="output_suppressed_reads_l" label="${tool.name} on ${on_string}: suppressed reads (L)"> 362 <filter>(( 363 singlePaired['sPaired'] == "single" and 364 singlePaired['sParams']['sSettingsType'] == "full" and 365 singlePaired['sParams']['sMaxFile'] is True 366 ) or ( 367 singlePaired['sPaired'] == "paired" and 368 singlePaired['pParams']['pSettingsType'] == "full" and 369 singlePaired['pParams']['pMaxFile'] is True 370 )) 371 </filter> 372 </data> 373 <data format="fastqcssanger" name="output_suppressed_reads_r" label="${tool.name} on ${on_string}: suppressed reads (R)"> 374 <filter>singlePaired['sPaired'] == "paired"</filter> 375 <filter>singlePaired['pParams']['pSettingsType'] == "full"</filter> 376 <filter>singlePaired['pParams']['pMaxFile'] is True</filter> 377 </data> 378 <data format="fastqcssanger" name="output_unmapped_reads_l" label="${tool.name} on ${on_string}: unmapped reads (L)"> 379 <filter> 380 (( 381 singlePaired['sPaired'] == "single" and 382 singlePaired['sParams']['sSettingsType'] == "full" and 383 singlePaired['sParams']['sUnmappedFile'] is True 384 ) or ( 385 singlePaired['sPaired'] == "paired" and 386 singlePaired['pParams']['pSettingsType'] == "full" and 387 singlePaired['pParams']['pUnmappedFile'] is True 388 )) 389 </filter> 390 </data> 391 <data format="fastqcssanger" name="output_unmapped_reads_r" label="${tool.name} on ${on_string}: unmapped reads (R)"> 392 <filter>singlePaired['sPaired'] == "paired"</filter> 393 <filter>singlePaired['pParams']['pSettingsType'] == "full"</filter> 394 <filter>singlePaired['pParams']['pUnmappedFile'] is True</filter> 395 </data> 396 </outputs> 397 <tests> 398 <test> 399 <!-- 400 Bowtie command: 401 bowtie -q -p 4 -S +sam-nohead -C chrM_color test-data/bowtie_in1.fastqcssanger > bowtie_out1_u.sam 402 sort bowtie_out1_u.sam > bowtie_out1.sam 403 -p is the number of threads, which is hardcoded above. You need to replace the + with 2 dashes. 404 chrM_color needs to be the base location/name of the index files. 405 --> 406 <param name="genomeSource" value="indexed" /> 407 <param name="index" value="equCab2chrM" /> 408 <param name="sPaired" value="single" /> 409 <param name="sInput1" ftype="fastqcssanger" value="bowtie_in1.fastqcssanger" /> 410 <param name="sSettingsType" value="preSet" /> 411 <param name="suppressHeader" value="true" /> 412 <output name="output" ftype="sam" file="bowtie_out1.sam" sort="True" /> 413 </test> 414 <test> 415 <!-- 416 Bowtie command: 417 bowtie-build -C -f test-data/chr_m.fasta chrM_color 418 bowtie -q -X 1000 +ff -p 4 -S +sam-nohead -C -n 2 -e 70 -l 28 -X 250 +pairtries 100 +maxbts 125 -k 1 +snpfrac 0.001 +col-keepends +un bowtie_out3_u.fastq chrM_color -1 test-data/bowtie_in3.fastqcssanger -2 test-data/bowtie_in4.fastqcssanger > bowtie_out2_u.sam 419 sort bowtie_out2_u.sam > bowtie_out2.sam 420 sort bowtie_out3_u_1.sam > bowtie_out3_1.sam 421 sort bowtie_out3_u_2.sam > bowtie_out3_2.sam 422 Then also need to modify bowtie_out3_1.sam and bowtie_out3_2.sam so that all @ lines come before sequence lines. 423 The two unmapped output files will be named bowtie_out4_1.fastq and bowtie_out4_2.fastq 424 -p is the number of threads, hardcoded above. You need to replace the + with 2 dashes. 425 chrM_base is the index files' location/base name. 426 --> 427 <param name="genomeSource" value="history" /> 428 <param name="ownFile" value="chr_m.fasta" /> 429 <param name="indexSettings" value="indexPreSet" /> 430 <param name="sPaired" value="paired" /> 431 <param name="pInput1" ftype="fastqcssanger" value="bowtie_in3.fastqcssanger" /> 432 <param name="pInput2" ftype="fastqcssanger" value="bowtie_in4.fastqcssanger" /> 433 <param name="pMaxInsert" value="1000" /> 434 <param name="pMateOrient" value="ff" /> 435 <param name="pSettingsType" value="full" /> 436 <param name="pSkip" value="0" /> 437 <param name="pAlignLimit" value="-1" /> 438 <param name="pTrimH" value="0" /> 439 <param name="pTrimL" value="0" /> 440 <param name="pMismatchSeed" value="2" /> 441 <param name="pMismatchQual" value="70" /> 442 <param name="pSeedLen" value="28" /> 443 <param name="pRounding" value="round" /> 444 <param name="pMaqSoapAlign" value="-1" /> 445 <param name="pMinInsert" value="0" /> 446 <param name="pMaxAlignAttempt" value="100" /> 447 <param name="pForwardAlign" value="forward" /> 448 <param name="pReverseAlign" value="reverse" /> 449 <param name="pTryHard" value="noTryHard" /> 450 <param name="pValAlign" value="1" /> 451 <param name="pAllValAligns" value="noAllValAligns" /> 452 <param name="pSuppressAlign" value="-1" /> 453 <param name="pUnmappedFile" value="true" /> 454 <param name="pMaxFile" value="false" /> 455 <param name="pBest" value="noBest" /> 456 <param name="pnMaxBacktracks" value="125" /> 457 <param name="pOffrate" value="-1" /> 458 <param name="pSeed" value="-1" /> 459 <param name="pSnpphred" value="-1" /> 460 <param name="pSnpfrac" value="0.001" /> 461 <param name="pKeepends" value="doKeepends" /> 462 <param name="suppressHeader" value="true" /> 463 <output name="output" ftype="sam" file="bowtie_out2.sam" sort="True" /> 464 <output name="output_unmapped_reads_l" ftype="fastqcssanger" file="bowtie_out3_1.fastq" sort="True" /> 465 <output name="output_unmapped_reads_r" ftype="fastqcssanger" file="bowtie_out3_2.fastq" sort="True" /> 466 </test> 467 <test> 468 <!-- 469 Bowtie command: 470 bowtie -q -p 4 -S +sam-nohead -C -n 2 -e 70 -l 28 +maxbts 125 -k 1 +snpfrac 0.001 +col-keepends chrM_color test-data/bowtie_in1.fastqcssanger > bowtie_out4_u.sam 471 sort bowtie_out4_u.sam > bowtie_out4.sam 472 -p is the number of threads, hardcoded above. You need to replace the + with 2 dashes. 473 chrM_base is the index files' location/base name. 474 --> 475 <param name="genomeSource" value="indexed" /> 476 <param name="index" value="equCab2chrM" /> 477 <param name="sPaired" value="single" /> 478 <param name="sInput1" ftype="fastqcssanger" value="bowtie_in1.fastqcssanger" /> 479 <param name="sSettingsType" value="full" /> 480 <param name="sSkip" value="0" /> 481 <param name="sAlignLimit" value="-1" /> 482 <param name="sTrimH" value="0" /> 483 <param name="sTrimL" value="0" /> 484 <param name="sMismatchSeed" value="2" /> 485 <param name="sMismatchQual" value="70" /> 486 <param name="sSeedLen" value="28" /> 487 <param name="sRounding" value="round" /> 488 <param name="sMaqSoapAlign" value="-1" /> 489 <param name="sTryHard" value="noTryHard" /> 490 <param name="sValAlign" value="1" /> 491 <param name="sAllValAligns" value="noAllValAligns" /> 492 <param name="sSuppressAlign" value="-1" /> 493 <param name="sUnmappedFile" value="false" /> 494 <param name="sMaxFile" value="false" /> 495 <param name="sBest" value="noBest" /> 496 <param name="snMaxBacktracks" value="125" /> 497 <param name="sOffrate" value="-1" /> 498 <param name="sSeed" value="-1" /> 499 <param name="sSnpphred" value="-1" /> 500 <param name="sSnpfrac" value="0.001" /> 501 <param name="sKeepends" value="doKeepends" /> 502 <param name="suppressHeader" value="true" /> 503 <output name="output" ftype="sam" file="bowtie_out4.sam" sort="True" /> 504 </test> 505 <test> 506 <!-- 507 Bowtie command: 508 bowtie-build +noauto +bmaxdivn 4 +dcv 1024 +offrate 5 +ftabchars 10 +little -C -f test-data/chr_m.fasta chrM_color 509 bowtie -q -X 1000 +ff -p 4 -S +sam-nohead -C chrM_color -1 test-data/bowtie_in3.fastqcssanger -2 test-data/bowtie_in4.fastqcssanger > bowtie_out5_u.sam 510 sort bowtie_out5_u.sam > bowtie_out5.sam 511 -p is the number of threads, hardcoded above. You need to replace the + with 2 dashes. 512 chrM_base is the index files' location/base name. 513 --> 514 <param name="genomeSource" value="history" /> 515 <param name="ownFile" value="chr_m.fasta" /> 516 <param name="indexSettings" value="indexFull" /> 517 <param name="autoB" value="set" /> 518 <param name="packed" value="unpacked" /> 519 <param name="bmax" value="-1" /> 520 <param name="bmaxdivn" value="4" /> 521 <param name="dcv" value="1024" /> 522 <param name="nodc" value="dc" /> 523 <param name="noref" value="ref" /> 524 <param name="offrate" value="5" /> 525 <param name="ftab" value="10" /> 526 <param name="ntoa" value="no" /> 527 <param name="endian" value="little" /> 528 <param name="seed" value="-1" /> 529 <param name="cutoff" value="-1" /> 530 <param name="sPaired" value="paired" /> 531 <param name="pInput1" ftype="fastqcssanger" value="bowtie_in3.fastqcssanger" /> 532 <param name="pInput2" ftype="fastqcssanger" value="bowtie_in4.fastqcssanger" /> 533 <param name="pMaxInsert" value="1000" /> 534 <param name="pMateOrient" value="ff" /> 535 <param name="pSettingsType" value="preSet" /> 536 <param name="suppressHeader" value="true" /> 537 <output name="output" ftype="sam" file="bowtie_out5.sam" sort="True" /> 538 </test> 539 </tests> 540 541 <help> 542 543**What it does** 544 545Bowtie_ is a short read aligner designed to be ultrafast and memory-efficient. It is developed by Ben Langmead and Cole Trapnell. Please cite: Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology 10:R25. 546 547.. _Bowtie: http://bowtie-bio.sourceforge.net/index.shtml 548 549------ 550 551**Know what you are doing** 552 553.. class:: warningmark 554 555There is no such thing (yet) as an automated gearshift in short read mapping. 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. 556 557 .. __: http://bowtie-bio.sourceforge.net/index.shtml 558 559------ 560 561**Input formats** 562 563Bowtie accepts files in Sanger FASTQ format. Use the FASTQ Groomer to prepare your files. 564 565------ 566 567**A Note on Built-in Reference Genomes** 568 569Some genomes have multiple variants. If only one "type" of genome is listed, it is the Full version, which means that everything that came in the original genome data download (possibly with mitochondrial and plasmid DNA added if it wasn't already included). The Full version is available for every genome. Some genomes also come in the Canonical variant, which contains only the "canonical" (well-defined) chromosomes or segments, such as chr1-chr22, chrX, chrY, and chrM for human. Other variations include gender. These will come in the canonical form only, so the general Canonical variant is actually Canonical Female and the other is Canonical Male (identical to female excluding chrX). 570 571------ 572 573**Outputs** 574 575The output is in SAM format, and has the following columns:: 576 577 Column Description 578 -------- -------------------------------------------------------- 579 1 QNAME Query (pair) NAME 580 2 FLAG bitwise FLAG 581 3 RNAME Reference sequence NAME 582 4 POS 1-based leftmost POSition/coordinate of clipped sequence 583 5 MAPQ MAPping Quality (Phred-scaled) 584 6 CIGAR extended CIGAR string 585 7 MRNM Mate Reference sequence NaMe ('=' if same as RNAME) 586 8 MPOS 1-based Mate POSition 587 9 ISIZE Inferred insert SIZE 588 10 SEQ query SEQuence on the same strand as the reference 589 11 QUAL query QUALity (ASCII-33 gives the Phred base quality) 590 12 OPT variable OPTional fields in the format TAG:VTYPE:VALUE 591 592The flags are as follows:: 593 594 Flag Description 595 ------ ------------------------------------- 596 0x0001 the read is paired in sequencing 597 0x0002 the read is mapped in a proper pair 598 0x0004 the query sequence itself is unmapped 599 0x0008 the mate is unmapped 600 0x0010 strand of the query (1 for reverse) 601 0x0020 strand of the mate 602 0x0040 the read is the first read in a pair 603 0x0080 the read is the second read in a pair 604 0x0100 the alignment is not primary 605 606It looks like this (scroll sideways to see the entire example):: 607 608 QNAME FLAG RNAME POS MAPQ CIAGR MRNM MPOS ISIZE SEQ QUAL OPT 609 HWI-EAS91_1_30788AAXX:1:1:1761:343 4 * 0 0 * * 0 0 AAAAAAANNAAAAAAAAAAAAAAAAAAAAAAAAAAACNNANNGAGTNGNNNNNNNGCTTCCCACAGNNCTGG hhhhhhh;;hhhhhhhhhhh^hOhhhhghhhfhhhgh;;h;;hhhh;h;;;;;;;hhhhhhghhhh;;Phhh 610 HWI-EAS91_1_30788AAXX:1:1:1578:331 4 * 0 0 * * 0 0 GTATAGANNAATAAGAAAAAAAAAAATGAAGACTTTCNNANNTCTGNANNNNNNNTCTTTTTTCAGNNGTAG hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhhhh;;h;;hhhh;h;;;;;;;hhhhhhhhhhh;;hhVh 611 612------- 613 614**Bowtie settings** 615 616All of the options have a default value. You can change any of them. Most of the options in Bowtie have been implemented here. 617 618------ 619 620**Bowtie parameter list** 621 622This is an exhaustive list of Bowtie options: 623 624For indexing (bowtie-build):: 625 626 -a No auto behavior. Disable the default behavior where bowtie automatically 627 selects values for --bmax/--bmaxdivn/--dcv/--packed parameters according 628 to the memory available. [off] 629 --packed Packing. Use a packed representation for DNA strings. [auto] 630 --bmax INT Suffix maximum. The maximum number of suffixes allowed in a block. [auto] 631 --bmaxdivn INT Suffix maximum fraction. The maximum number of suffixes allowed in a block 632 expressed as a fraction of the length of the reference. [4] 633 --dcv INT Difference-cover sample. Use INT as the period for the difference-cover 634 sample. [1024] 635 --nodc INT No difference-cover sample. Disable the difference-cover sample. [off] 636 -r No reference indexes. Do not build the NAME.3.ebwt and NAME.4.ebwt portions 637 of the index. Used only for paired-end alignment. [off] 638 -o Offrate. How many Burrows-Wheeler rows get marked by the indexer. The 639 indexer will mark every 2^INT rows. The marked rows correspond to rows on 640 the genome. [5] 641 -t INT Ftab. The lookup table used to calculate an initial Burrows-Wheeler range 642 with respect to the first INT characters of the query. Ftab is 4^INT+1 643 bytes. [10] 644 --ntoa N conversion. Convert Ns to As before building the index. Otherwise, Ns are 645 simply excluded from the index and Bowtie will not find alignments that 646 overlap them. [off] 647 --big Endianness. Endianness to use when serializing integers to the index file. [off] 648 --little Endianness. [--little] 649 --seed INT Random seed. Use INT as the seed for the pseudo-random number generator. [off] 650 --cutoff INT Cutoff. Index only the first INT bases of the reference sequences (cumulative 651 across sequences) and ignore the rest. [off] 652 653For aligning (bowtie):: 654 655 -s INT Skip. Do not align the first INT reads or pairs in the input. [off] 656 -u INT Align limit. Only align the first INT reads/pairs from the input. [no limit] 657 -5 INT High-quality trim. Trim INT bases from the high-quality (left) end of each 658 read before alignment. [0] 659 -3 INT Low-quality trim. Trim INT bases from the low-quality (right) end of each 660 read before alignment. [0] 661 -n INT Mismatch seed. Maximum number of mismatches permitted in the seed (defined 662 with seed length option). Can be 0, 1, 2, or 3. [2] 663 -e INT Mismatch quality. Maximum permitted total of quality values at mismatched 664 read positions. Bowtie rounds quality values to the nearest 10 and saturates 665 at 30. [70] 666 -l INT Seed length. The number of bases on the high-quality end of the read to 667 which the -n ceiling applies. Must be at least 5. [28] 668 --nomaqround Suppress MAQ rounding. Values are internally rounded to the nearest 10 and 669 saturate at 30. This options turns off that rounding. [off] 670 -v INT MAQ- or SOAP-like alignment policy. This option turns off the default 671 MAQ-like alignment policy in favor of a SOAP-like one. End-to-end alignments 672 with at most INT mismatches. [off] 673 -I INT Minimum insert. The minimum insert size for valid paired-end alignments. 674 Does checking on untrimmed reads if -5 or -3 is used. [0] 675 -X INT Maximum insert. The maximum insert size for valid paired-end alignments. 676 Does checking on untrimmed reads if -5 or -3 is used. [250] 677 --fr Mate orientation. The upstream/downstream mate orientations for a valid 678 paired-end alignment against the forward reference strand. [--fr] 679 --rf Mate orientation. [off] 680 --ff Mate orientation. [off] 681 --pairtries INT Maximum alignment attempts for paired-end data. [100] 682 --nofw No forward aligning. Choosing this option means that Bowtie will not attempt 683 to align against the forward reference strand. [off] 684 --norc No reverse-complement aligning. Setting this will mean that Bowtie will not 685 attempt to align against the reverse-complement reference strand. [off] 686 --maxbts INT Maximum backtracks. The maximum number of backtracks permitted when aligning 687 a read in -n 2 or -n 3 mode. [125 without --best] [800 with --best] 688 -y Try hard. Try as hard as possible to find valid alignments when they exist, 689 including paired-end alignments. [off] 690 --chunkmbs INT Thread memory. The number of megabytes of memory a given thread is given to 691 store path descriptors in --best mode. [32] 692 -k INT Valid alignments. The number of valid alignments per read or pair. [off] 693 -a All valid alignments. Choosing this means that all valid alignments per read 694 or pair will be reported. [off] 695 -m INT Suppress alignments. Suppress all alignments for a particular read or pair 696 if more than INT reportable alignments exist for it. [no limit] 697 --best Best mode. Make Bowtie guarantee that reported singleton alignments are 698 "best" in terms of stratum (the number of mismatches) and quality values at 699 mismatched position. [off] 700 --strata Best strata. When running in best mode, report alignments that fall into the 701 best stratum if there are ones falling into more than one. [off] 702 -o INT Offrate override. Override the offrate of the index with INT. Some row 703 markings are discarded when index read into memory. INT must be greater than 704 the value used to build the index (default: 5). [off] 705 --seed INT Random seed. Use INT as the seed for the pseudo-random number generator. [off] 706 --snpphred INT Use INT as the SNP penalty for decoding colorspace alignments. True ratio of 707 SNPs per base in the subject genome. [see --snpfrac] 708 --snpfrac DEC Use DEC as the estimated ratio of SNPs per base when decoding colorspace 709 alignments. [0.001] 710 --col-keepends Keep the extreme-end nucleotides and qualities when decoding colorspace 711 alignments. [off] 712 713 </help> 714</tool>