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comparison bowtie_transcriptome_wrapper/bowtie_transcriptomic_wrapper.xml @ 0:1b109d213a42 draft

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author jackcurragh
date Tue, 15 Mar 2022 10:06:15 +0000
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1 <tool id="bowtie_transcriptomic_wrapper" name="Align to transcriptome using Bowtie" version="1.2.0">
2 <description></description>
3 <requirements>
4 <requirement type="package" version="1.2.0">bowtie</requirement>
5 </requirements>
6 <version_command>bowtie --version</version_command>
7 <command>
8 python '$__tool_directory__/bowtie_wrapper.py'
9 ## Set number of threads
10 --threads="\${GALAXY_SLOTS:-4}"
11 ## Outputs
12 --output="${output}"
13 #if str( $singlePaired.sPaired ) == "single"
14 #if $output_unmapped_reads_l
15 --output_unmapped_reads="${output_unmapped_reads_l}"
16 #end if
17 #if $output_suppressed_reads_l
18 --output_suppressed_reads="${output_suppressed_reads_l}"
19 #end if
20 --galaxy_input_format="${singlePaired.sInput1.ext}"
21 #else
22 #if $output_unmapped_reads_l and $output_unmapped_reads_r
23 --output_unmapped_reads_l="${output_unmapped_reads_l}"
24 --output_unmapped_reads_r="${output_unmapped_reads_r}"
25 #end if
26 #if $output_suppressed_reads_l and $output_suppressed_reads_l
27 --output_suppressed_reads_l="${output_suppressed_reads_l}"
28 --output_suppressed_reads_r="${output_suppressed_reads_r}"
29 #end if
30 --galaxy_input_format="${singlePaired.pInput1.ext}"
31 #end if
32 ## Inputs
33 --dataType="solexa" ##this indicates that nucleotide base space is used in the wrapper
34 --suppressHeader="${suppressHeader}"
35 --genomeSource="${refGenomeSource.genomeSource}"
36 #if $refGenomeSource.genomeSource == "history":
37 ##index already exists
38 #if $refGenomeSource.ownFile.extension.startswith( 'bowtie_' ):
39 ##user previously built
40 --ref="${refGenomeSource.ownFile.extra_files_path}/${refGenomeSource.ownFile.metadata.base_name}"
41 --do_not_build_index
42 #else:
43 ##build index on the fly
44 --ref="${refGenomeSource.ownFile}"
45 --indexSettings="${refGenomeSource.indexParams.indexSettings}"
46 #if $refGenomeSource.indexParams.indexSettings == "indexFull":
47 --iautoB="${refGenomeSource.indexParams.autoBehavior.autoB}"
48 #if $refGenomeSource.indexParams.autoBehavior.autoB == "set":
49 --ipacked="${refGenomeSource.indexParams.autoBehavior.packed}"
50 --ibmax="${refGenomeSource.indexParams.autoBehavior.bmax}"
51 --ibmaxdivn="${refGenomeSource.indexParams.autoBehavior.bmaxdivn}"
52 --idcv="${refGenomeSource.indexParams.autoBehavior.dcv}"
53 #end if
54 --inodc="${refGenomeSource.indexParams.nodc}"
55 --inoref="${refGenomeSource.indexParams.noref}"
56 --ioffrate="${refGenomeSource.indexParams.offrate}"
57 --iftab="${refGenomeSource.indexParams.ftab}"
58 --intoa="${refGenomeSource.indexParams.ntoa}"
59 --iendian="${refGenomeSource.indexParams.endian}"
60 --iseed="${refGenomeSource.indexParams.seed}"
61 #end if
62 #end if
63 #else
64 ##use pre-built index
65 --ref="${refGenomeSource.index.fields.path}"
66 #end if
67 --paired="${singlePaired.sPaired}"
68 #if $singlePaired.sPaired == "single":
69 --input1="${singlePaired.sInput1}"
70 --params="${singlePaired.sParams.sSettingsType}"
71 #if $singlePaired.sParams.sSettingsType == "full":
72 --skip="${singlePaired.sParams.sSkip}"
73 --alignLimit="${singlePaired.sParams.sAlignLimit}"
74 --trimH="${singlePaired.sParams.sTrimH}"
75 --trimL="${singlePaired.sParams.sTrimL}"
76 #if $singlePaired.sParams.alignModeOption.alignMode == 'nMode'
77 --mismatchSeed="${singlePaired.sParams.alignModeOption.sMismatchSeed}"
78 --mismatchQual="${singlePaired.sParams.alignModeOption.sMismatchQual}"
79 --seedLen="${singlePaired.sParams.alignModeOption.sSeedLen}"
80 --rounding="${singlePaired.sParams.alignModeOption.sRounding}"
81 #else
82 --maxMismatches="${singlePaired.sParams.alignModeOption.maxMismatches}"
83 #end if
84 --forwardAlign="${singlePaired.sParams.sForwardAlign}"
85 --reverseAlign="${singlePaired.sParams.sReverseAlign}"
86 --tryHard="${singlePaired.sParams.sBestOption.sTryHardOption.sTryHard}"
87 --allValAligns="${singlePaired.sParams.sAllValAlignsOption.sAllValAligns}"
88 #if $singlePaired.sParams.sAllValAlignsOption.sAllValAligns == "noAllValAligns"
89 --valAlign="${singlePaired.sParams.sAllValAlignsOption.sValAlign}"
90 #end if
91 --suppressAlign="${singlePaired.sParams.sSuppressAlign}"
92 --best="${singlePaired.sParams.sBestOption.sBest}"
93 #if $singlePaired.sParams.sBestOption.sBest == "doBest":
94 --strata="${singlePaired.sParams.sBestOption.sdStrata}"
95 #if $singlePaired.sParams.sBestOption.sTryHardOption.sTryHard == "noTryHard"
96 --maxBacktracks="${singlePaired.sParams.sBestOption.sTryHardOption.sdMaxBacktracks}"
97 #end if
98 #else:
99 #if $singlePaired.sParams.sBestOption.sTryHardOption.sTryHard == "noTryHard"
100 --maxBacktracks="${singlePaired.sParams.sBestOption.sTryHardOption.snMaxBacktracks}"
101 #end if
102 #end if
103 --offrate="${singlePaired.sParams.sOffrate}"
104 --seed="${singlePaired.sParams.sSeed}"
105 #end if
106 #else:
107 --input1="${singlePaired.pInput1}"
108 --input2="${singlePaired.pInput2}"
109 --maxInsert="${singlePaired.pMaxInsert}"
110 --mateOrient="${singlePaired.pMateOrient}"
111 --params="${singlePaired.pParams.pSettingsType}"
112 #if $singlePaired.pParams.pSettingsType == "full":
113 --skip="${singlePaired.pParams.pSkip}"
114 --alignLimit="${singlePaired.pParams.pAlignLimit}"
115 --trimH="${singlePaired.pParams.pTrimH}"
116 --trimL="${singlePaired.pParams.pTrimL}"
117 #if $singlePaired.pParams.alignModeOption.alignMode == 'nMode'
118 --mismatchSeed="${singlePaired.pParams.alignModeOption.pMismatchSeed}"
119 --mismatchQual="${singlePaired.pParams.alignModeOption.pMismatchQual}"
120 --seedLen="${singlePaired.pParams.alignModeOption.pSeedLen}"
121 --rounding="${singlePaired.pParams.alignModeOption.pRounding}"
122 #else
123 --maxMismatches="${singlePaired.pParams.alignModeOption.maxMismatches}"
124 #end if
125 --minInsert="${singlePaired.pParams.pMinInsert}"
126 --forwardAlign="${singlePaired.pParams.pForwardAlign}"
127 --reverseAlign="${singlePaired.pParams.pReverseAlign}"
128 --tryHard="${singlePaired.pParams.pBestOption.pTryHardOption.pTryHard}"
129 --allValAligns="${singlePaired.pParams.pAllValAlignsOption.pAllValAligns}"
130 #if $singlePaired.pParams.pAllValAlignsOption.pAllValAligns == "noAllValAligns"
131 --valAlign="${singlePaired.pParams.pAllValAlignsOption.pValAlign}"
132 #end if
133 --suppressAlign="${singlePaired.pParams.pSuppressAlign}"
134 --best="${singlePaired.pParams.pBestOption.pBest}"
135 #if $singlePaired.pParams.pBestOption.pBest == "doBest":
136 --strata="${singlePaired.pParams.pBestOption.pdStrata}"
137 #if $singlePaired.pParams.pBestOption.pTryHardOption.pTryHard == "noTryHard"
138 --maxAlignAttempt="${singlePaired.pParams.pBestOption.pTryHardOption.pMaxAlignAttempt}"
139 --maxBacktracks="${singlePaired.pParams.pBestOption.pTryHardOption.pdMaxBacktracks}"
140 #end if
141 #else:
142 #if $singlePaired.pParams.pBestOption.pTryHardOption.pTryHard == "noTryHard"
143 --maxAlignAttempt="${singlePaired.pParams.pBestOption.pTryHardOption.pMaxAlignAttempt}"
144 --maxBacktracks="${singlePaired.pParams.pBestOption.pTryHardOption.pnMaxBacktracks}"
145 #end if
146 #end if
147 --offrate="${singlePaired.pParams.pOffrate}"
148 --seed="${singlePaired.pParams.pSeed}"
149 #end if
150 #end if
151 #if $save_mapping_stats
152 --output_mapping_stats="$mapping_stats"
153 #end if
154 </command>
155 <inputs>
156 <conditional name="refGenomeSource">
157 <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">
158 <option value="indexed">Use a built-in index</option>
159 <option value="history">Use one from the history</option>
160 </param>
161 <when value="indexed">
162 <param name="index" type="select" label="Select a reference genome" help="if your genome of interest is not listed - contact Galaxy team">
163 <options from_data_table="bowtie_indexes">
164 <filter type="sort_by" column="2" />
165 <validator type="no_options" message="No indexes are available" />
166 </options>
167 </param>
168 </when>
169 <when value="history">
170 <param name="ownFile" type="data" format="bowtie_base_index,fasta" label="Select the reference genome" />
171 <conditional name="indexParams">
172 <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">
173 <option value="indexPreSet">Default</option>
174 <option value="indexFull">Set your own</option>
175 </param>
176 <when value="indexPreSet" />
177 <when value="indexFull">
178 <conditional name="autoBehavior">
179 <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">
180 <option value="auto">Automatic behavior</option>
181 <option value="set">Set values (sets --noauto and allows others to be set)</option>
182 </param>
183 <when value="auto" />
184 <when value="set">
185 <param name="packed" type="select" label="Whether or not to use a packed representation for DNA strings (--packed)" help="Packed representation saves memory but makes indexing 2-3 times slower">
186 <option value="unpacked">Use regular representation</option>
187 <option value="packed">Use packed representation</option>
188 </param>
189 <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" />
190 <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)" />
191 <param name="dcv" type="integer" value="1024" min="3" label="The period for the difference-cover sample (--dcv)" help="A larger period yields less memory overhead, but may make suffix sorting slower, especially if repeats are present" />
192 </when>
193 </conditional>
194 <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)">
195 <option value="dc">Use difference-cover sample</option>
196 <option value="nodc">Disable difference-cover sample</option>
197 </param>
198 <param name="noref" type="select" label="Whether or not to build the part of the reference index used only in paired-end alignment (-r)">
199 <option value="ref">Build all index files</option>
200 <option value="noref">Do not build paired-end alignment index files</option>
201 </param>
202 <param name="offrate" type="integer" value="5" min="0" label="The indexer will mark every 2^n Burrows-Wheeler rows with their corresponding location on the genome (-o)" help="Marking more rows makes reference-position lookups faster, but requires more memory to hold the annotations at runtime" />
203 <param name="ftab" type="integer" value="10" min="1" label="The size of the ftab lookup table used to calculate an initial Burrows-Wheeler range with respect to the first n characters of the query (-t)" help="ftab size is 4^(n+1) bytes" />
204 <param name="ntoa" type="select" label="Whether or not to convert Ns in the reference sequence to As (--ntoa)">
205 <option value="no">Do not convert Ns</option>
206 <option value="yes">Convert Ns to As</option>
207 </param>
208 <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">
209 <option value="little">Little</option>
210 <option value="big">Big</option>
211 </param>
212 <param name="seed" type="integer" value="-1" label="Seed for the pseudorandom number generator (--seed)" help="Use -1 to use default" />
213 </when> <!-- indexFull -->
214 </conditional> <!-- indexParams -->
215 </when> <!-- history -->
216 </conditional> <!-- refGenomeSource -->
217 <conditional name="singlePaired">
218 <param name="sPaired" type="select" label="Is this library mate-paired?">
219 <option value="single">Single-end</option>
220 <option value="paired">Paired-end</option>
221 </param>
222 <when value="single">
223 <param name="sInput1" type="data" format="fastqsanger,fastqillumina,fastqsolexa" label="FASTQ file" help="Must have ASCII encoded quality scores"/>
224 <conditional name="sParams">
225 <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">
226 <option value="preSet">Commonly used</option>
227 <option value="full" selected="true">Full parameter list</option>
228 </param>
229 <when value="preSet" />
230 <when value="full">
231 <param name="sSkip" type="integer" value="0" label="Skip the first n reads (-s)" />
232 <param name="sAlignLimit" type="integer" value="-1" label="Only align the first n reads (-u)" help="-1 for off" />
233 <param name="sTrimH" type="integer" value="0" label="Trim n bases from high-quality (left) end of each read before alignment (-5)" />
234 <param name="sTrimL" type="integer" value="0" label="Trim n bases from low-quality (right) end of each read before alignment (-3)" />
235 <conditional name="alignModeOption">
236 <param name="alignMode" type="select" label="Alignment mode">
237 <option value="nMode">Maq-like: quality-aware, limit mismatches in seed (-n)</option>
238 <option value="vMode" selected="true">ignore qualities, limit end-to-end mismatches (-v)</option>
239 </param>
240 <when value="nMode">
241 <param name="sMismatchSeed" type="integer" value="2" min="0" max="3" label="Maximum number of mismatches permitted in the seed (-n)" help="May be 0, 1, 2, or 3" />
242 <param name="sMismatchQual" type="integer" value="70" min="1" label="Maximum permitted total of quality values at all mismatched read positions (-e)" />
243 <param name="sSeedLen" type="integer" value="28" min="5" label="Seed length (-l)" help="Minimum value is 5" />
244 <param name="sRounding" type="select" label="Whether or not to round to the nearest 10 and saturating at 30 (--nomaqround)" help="Maq accepts quality values in the Phred quality scale, but internally rounds values to the nearest 10, with a maximum of 30. By default, bowtie also rounds this way">
245 <option value="round">Round to nearest 10</option>
246 <option value="noRound">Do not round to nearest 10</option>
247 </param>
248 </when>
249 <when value="vMode">
250 <param name="maxMismatches" type="integer" value="3" min="0" max="3" label="Maximum number of mismatches (-v)" help="May be 0, 1, 2, or 3" />
251 <param name="sSeedLen" type="integer" value="25" min="5" label="Seed length (-l)" help="Minimum value is 5" />
252 </when>
253 </conditional>
254 <param name="sForwardAlign" type="select" label="Choose whether or not to attempt to align against the forward reference strand (--nofw)">
255 <option value="forward">Align against the forward reference strand</option>
256 <option value="noForward">Do not align against the forward reference strand</option>
257 </param>
258 <param name="sReverseAlign" type="select" label="Choose whether or not to attempt to align against the reverse-complement reference strand (--norc)">
259 <option value="reverse">Align against the reverse-complement reference strand</option>
260 <option value="noReverse">Do not align against the reverse-complement reference strand</option>
261 </param>
262 <conditional name="sBestOption">
263 <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">
264 <option value="noBest">Do not use best</option>
265 <option value="doBest">Use best</option>
266 </param>
267 <when value="noBest">
268 <conditional name="sTryHardOption">
269 <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">
270 <option value="noTryHard">Do not try hard</option>
271 <option value="doTryHard">Try hard</option>
272 </param>
273 <when value="noTryHard">
274 <param name="snMaxBacktracks" type="integer" value="125" min="0" label="Maximum number of backtracks permitted when aligning a read (--maxbts)" />
275 </when>
276 <when value="doTryHard" />
277 </conditional>
278 </when>
279 <when value="doBest">
280 <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)">
281 <option value="noStrata">Do not use strata option</option>
282 <option value="doStrata">Use strata option</option>
283 </param>
284 <conditional name="sTryHardOption">
285 <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">
286 <option value="noTryHard">Do not try hard</option>
287 <option value="doTryHard">Try hard</option>
288 </param>
289 <when value="noTryHard">
290 <param name="sdMaxBacktracks" type="integer" value="800" min="0" label="Maximum number of backtracks permitted when aligning a read (--maxbts)" />
291 </when>
292 <when value="doTryHard" />
293 </conditional>
294 </when>
295 </conditional> <!-- bestOption -->
296 <conditional name="sAllValAlignsOption">
297 <param name="sAllValAligns" type="select" label="Whether or not to report all valid alignments per read (-a)">
298 <option value="noAllValAligns">Do not report all valid alignments</option>
299 <option value="doAllValAligns" selected="true">Report all valid alignments</option>
300 </param>
301 <when value="noAllValAligns">
302 <param name="sValAlign" type="integer" value="1" min="1" label="Report up to n valid alignments per read (-k)" />
303 </when>
304 <when value="doAllValAligns" />
305 </conditional>
306 <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" />
307 <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)" />
308 <param name="sUnmappedFile" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write all reads that could not be aligned to a file (--un)" />
309 <param name="sOffrate" type="integer" value="-1" label="Override the offrate of the index to n (-o)" help="-1 for default" />
310 <param name="sSeed" type="integer" value="-1" label="Seed for pseudo-random number generator (--seed)" help="-1 for default" />
311 </when> <!-- full -->
312 </conditional> <!-- sParams -->
313 </when> <!-- single -->
314 <when value="paired">
315 <param name="pInput1" type="data" format="fastqsanger,fastqillumina,fastqsolexa" label="Forward FASTQ file" help="Must have ASCII encoded quality scores"/>
316 <param name="pInput2" type="data" format="fastqsanger,fastqillumina,fastqsolexa" label="Reverse FASTQ file" help="File format must match the Forward FASTQ file">
317 <options options_filter_attribute="ext" from_parameter="tool.app.datatypes_registry.datatypes_by_extension" transform_lines="obj.keys()">
318 <column name="name" index="0"/>
319 <column name="value" index="0"/>
320 <filter type="param_value" ref="pInput1" ref_attribute="ext" column="0"/>
321 </options>
322 </param>
323 <param name="pMaxInsert" type="integer" value="1000" label="Maximum insert size for valid paired-end alignments (-X)" />
324 <param name="pMateOrient" type="select" label="The upstream/downstream mate orientation for valid paired-end alignment against the forward reference strand (--fr/--rf/--ff)">
325 <option value="fr">FR (for Illumina)</option>
326 <option value="rf">RF</option>
327 <option value="ff">FF (for SOLiD)</option>
328 </param>
329 <conditional name="pParams">
330 <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">
331 <option value="preSet">Commonly used</option>
332 <option value="full">Full parameter list</option>
333 </param>
334 <when value="preSet" />
335 <when value="full">
336 <param name="pSkip" type="integer" value="0" label="Skip the first n pairs (-s)" />
337 <param name="pAlignLimit" type="integer" value="-1" label="Only align the first n pairs (-u)" help="-1 for off" />
338 <param name="pTrimH" type="integer" value="0" label="Trim n bases from high-quality (left) end of each read before alignment (-5)" />
339 <param name="pTrimL" type="integer" value="0" label="Trim n bases from low-quality (right) end of each read before alignment (-3)" />
340 <conditional name="alignModeOption">
341 <param name="alignMode" type="select" label="Alignment mode">
342 <option value="nMode">Maq-like: quality-aware, limit mismatches in seed (-n)</option>
343 <option value="vMode">ignore qualities, limit end-to-end mismatches (-v)</option>
344 </param>
345 <when value="nMode">
346 <param name="pMismatchSeed" type="integer" value="2" min="0" max="3" label="Maximum number of mismatches permitted in the seed (-n)" help="May be 0, 1, 2, or 3" />
347 <param name="pMismatchQual" type="integer" value="70" min="1" label="Maximum permitted total of quality values at all mismatched read positions (-e)" />
348 <param name="pSeedLen" type="integer" value="28" min="5" label="Seed length (-l)" help="Minimum value is 5" />
349 <param name="pRounding" type="select" label="Whether or not to round to the nearest 10 and saturating at 30 (--nomaqround)" help="Maq accepts quality values in the Phred quality scale, but internally rounds values to the nearest 10, with a maximum of 30. By default, bowtie also rounds this way">
350 <option value="round">Round to nearest 10</option>
351 <option value="noRound">Do not round to nearest 10</option>
352 </param>
353 </when>
354 <when value="vMode">
355 <param name="maxMismatches" type="integer" value="" min="0" max="3" label="Maximum number of mismatches (-v)" help="May be 0, 1, 2, or 3" />
356 </when>
357 </conditional>
358 <param name="pMinInsert" type="integer" value="0" label="Minimum insert size for valid paired-end alignments (-I)" />
359 <param name="pForwardAlign" type="select" label="Choose whether or not to attempt to align against the forward reference strand (--nofw)">
360 <option value="forward">Align against the forward reference strand</option>
361 <option value="noForward">Do not align against the forward reference strand</option>
362 </param>
363 <param name="pReverseAlign" type="select" label="Choose whether or not to attempt to align against the reverse-complement reference strand (--norc)">
364 <option value="reverse">Align against the reverse-complement reference strand</option>
365 <option value="noReverse" selected="true">Do not align against the reverse-complement reference strand</option>
366 </param>
367 <conditional name="pBestOption">
368 <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">
369 <option value="noBest">Do not use best</option>
370 <option value="doBest">Use best</option>
371 </param>
372 <when value="noBest">
373 <conditional name="pTryHardOption">
374 <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">
375 <option value="noTryHard">Do not try hard</option>
376 <option value="doTryHard">Try hard</option>
377 </param>
378 <when value="noTryHard">
379 <param name="pMaxAlignAttempt" type="integer" value="100" min="1" label="Maximum number of attempts Bowtie will make to match an alignment for one mate with an alignment for the opposite mate (--pairtries)" />
380 <param name="pnMaxBacktracks" type="integer" value="125" min="0" label="Maximum number of backtracks permitted when aligning a read (--maxbts)" />
381 </when>
382 <when value="doTryHard" />
383 </conditional>
384 </when>
385 <when value="doBest">
386 <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)">
387 <option value="noStrata">Do not use strata option</option>
388 <option value="doStrata">Use strata option</option>
389 </param>
390 <conditional name="pTryHardOption">
391 <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">
392 <option value="noTryHard">Do not try hard</option>
393 <option value="doTryHard">Try hard</option>
394 </param>
395 <when value="noTryHard">
396 <param name="pMaxAlignAttempt" type="integer" value="100" min="1" label="Maximum number of attempts Bowtie will make to match an alignment for one mate with an alignment for the opposite mate (--pairtries)" />
397 <param name="pdMaxBacktracks" type="integer" value="800" min="0" label="Maximum number of backtracks permitted when aligning a read (--maxbts)" />
398 </when>
399 <when value="doTryHard" />
400 </conditional>
401 </when>
402 </conditional>
403 <conditional name="pAllValAlignsOption">
404 <param name="pAllValAligns" type="select" label="Whether or not to report all valid alignments per pair (-a)">
405 <option value="noAllValAligns">Do not report all valid alignments</option>
406 <option value="doAllValAligns">Report all valid alignments</option>
407 </param>
408 <when value="noAllValAligns">
409 <param name="pValAlign" type="integer" value="1" min="1" label="Report up to n valid alignments per pair (-k)" />
410 </when>
411 <when value="doAllValAligns" />
412 </conditional>
413 <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" />
414 <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)" />
415 <param name="pUnmappedFile" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write all reads that could not be aligned to a file (--un)" />
416 <param name="pOffrate" type="integer" value="-1" label="Override the offrate of the index to n (-o)" help="-1 for default" />
417 <param name="pSeed" type="integer" value="-1" label="Seed for pseudo-random number generator (--seed)" help="-1 for default" />
418 </when> <!-- full -->
419 </conditional> <!-- pParams -->
420 </when> <!-- paired -->
421 </conditional> <!-- singlePaired -->
422 <param name="save_mapping_stats" type="boolean" checked="False" label="Save the bowtie mapping statistics to the history" />
423 <param name="suppressHeader" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Suppress the header in the output SAM file (--sam-nohead)" help="Bowtie produces SAM with several lines of header information by default" />
424 </inputs>
425 <outputs>
426 <data format="sam" name="output" label="${tool.name} on ${on_string}: mapped reads">
427 <actions>
428 <conditional name="refGenomeSource.genomeSource">
429 <when value="indexed">
430 <action type="metadata" name="dbkey">
431 <option type="from_data_table" name="bowtie_indexes" column="1" offset="0">
432 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
433 <filter type="param_value" ref="refGenomeSource.index" column="0"/>
434 </option>
435 </action>
436 </when>
437 <when value="history">
438 <action type="metadata" name="dbkey">
439 <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" />
440 </action>
441 </when>
442 </conditional>
443 </actions>
444 </data>
445 <data format="txt" name="mapping_stats" label="${tool.name} on ${on_string}: mapping stats">
446 <filter>save_mapping_stats is True</filter>
447 </data>
448 <data format="fastq" name="output_suppressed_reads_l" label="${tool.name} on ${on_string}: suppressed reads (L)">
449 <filter>((
450 singlePaired['sPaired'] == "single" and
451 singlePaired['sParams']['sSettingsType'] == "full" and
452 singlePaired['sParams']['sMaxFile'] is True
453 ) or (
454 singlePaired['sPaired'] == "paired" and
455 singlePaired['pParams']['pSettingsType'] == "full" and
456 singlePaired['pParams']['pMaxFile'] is True
457 ))
458 </filter>
459 <actions>
460 <conditional name="singlePaired.sPaired">
461 <when value="single">
462 <action type="format">
463 <option type="from_param" name="singlePaired.sInput1" param_attribute="ext" />
464 </action>
465 </when>
466 <when value="paired">
467 <action type="format">
468 <option type="from_param" name="singlePaired.pInput1" param_attribute="ext" />
469 </action>
470 </when>
471 </conditional>
472 </actions>
473 </data>
474 <data format="fastq" name="output_suppressed_reads_r" label="${tool.name} on ${on_string}: suppressed reads (R)">
475 <filter>singlePaired['sPaired'] == "paired"</filter>
476 <filter>singlePaired['pParams']['pSettingsType'] == "full"</filter>
477 <filter>singlePaired['pParams']['pMaxFile'] is True</filter>
478 <actions>
479 <conditional name="singlePaired.sPaired">
480 <when value="single">
481 <action type="format">
482 <option type="from_param" name="singlePaired.sInput1" param_attribute="ext" />
483 </action>
484 </when>
485 <when value="paired">
486 <action type="format">
487 <option type="from_param" name="singlePaired.pInput1" param_attribute="ext" />
488 </action>
489 </when>
490 </conditional>
491 </actions>
492 </data>
493 <data format="fastq" name="output_unmapped_reads_l" label="${tool.name} on ${on_string}: unmapped reads (L)">
494 <filter>
495 ((
496 singlePaired['sPaired'] == "single" and
497 singlePaired['sParams']['sSettingsType'] == "full" and
498 singlePaired['sParams']['sUnmappedFile'] is True
499 ) or (
500 singlePaired['sPaired'] == "paired" and
501 singlePaired['pParams']['pSettingsType'] == "full" and
502 singlePaired['pParams']['pUnmappedFile'] is True
503 ))
504 </filter>
505 <actions>
506 <conditional name="singlePaired.sPaired">
507 <when value="single">
508 <action type="format">
509 <option type="from_param" name="singlePaired.sInput1" param_attribute="ext" />
510 </action>
511 </when>
512 <when value="paired">
513 <action type="format">
514 <option type="from_param" name="singlePaired.pInput1" param_attribute="ext" />
515 </action>
516 </when>
517 </conditional>
518 </actions>
519 </data>
520 <data format="fastq" name="output_unmapped_reads_r" label="${tool.name} on ${on_string}: unmapped reads (R)">
521 <filter>singlePaired['sPaired'] == "paired"</filter>
522 <filter>singlePaired['pParams']['pSettingsType'] == "full"</filter>
523 <filter>singlePaired['pParams']['pUnmappedFile'] is True</filter>
524 <actions>
525 <conditional name="singlePaired.sPaired">
526 <when value="single">
527 <action type="format">
528 <option type="from_param" name="singlePaired.sInput1" param_attribute="ext" />
529 </action>
530 </when>
531 <when value="paired">
532 <action type="format">
533 <option type="from_param" name="singlePaired.pInput1" param_attribute="ext" />
534 </action>
535 </when>
536 </conditional>
537 </actions>
538 </data>
539 </outputs>
540 <tests>
541 <test>
542 <!--
543 Bowtie command:
544 bowtie -q -p 4 -S +sam-nohead chrM_base test-data/bowtie_in2.fastqsanger > bowtie_out6_u.sam
545 sort bowtie_out6_u.sam > bowtie_out6.sam
546 -p is the number of threads. You need to replace the + with 2 dashes.
547 chrM_base needs to be the base location/name of the index files.
548 -->
549 <param name="genomeSource" value="indexed" />
550 <!-- this is the backwards-compatible "unique value" for this index, not an actual path -->
551 <param name="index" value="equCab2chrM" />
552 <param name="sPaired" value="single" />
553 <param name="sInput1" ftype="fastqsanger" value="bowtie_in2.fastqsanger" />
554 <param name="sSettingsType" value="preSet" />
555 <param name="suppressHeader" value="true" />
556 <output name="output" ftype="sam" file="bowtie_out6.sam" sort="True">
557 <metadata name="dbkey" value="equCab2" />
558 </output>
559 </test>
560 <test>
561 <!--
562 Bowtie command:
563 bowtie-build -f test-data/phiX.fasta phiX_base
564 bowtie -q -X 1000 +ff -p 4 -S +sam-nohead -n 2 -e 70 -l 28 +pairtries 100 +maxbts 800 +best +un bowtie_out8_u.fastq phiX_base -1 test-data/bowtie_in5.fastqsanger -2 test-data/bowtie_in6.fastqsanger > bowtie_out7_u.sam
565 sort bowtie_out7_u.sam > bowtie_out7.sam
566 sort bowtie_out8_u_1.sam > bowtie_out8_1.sam
567 sort bowtie_out8_u_2.sam > bowtie_out8_2.sam
568 Then also need to modify bowtie_out8_1.sam and bowtie_out8_2.sam so that all @ lines come before sequence lines.
569 -p is the number of threads. You need to replace the + with 2 dashes.
570 The two unmapped output files will be named bowtie_out8_1.fastq and bowtie_out8_2.fastq.
571 chrM_base is the index files' location/base name.
572 -->
573 <param name="genomeSource" value="history" />
574 <param name="ownFile" value="phiX.fasta" />
575 <param name="indexSettings" value="indexPreSet" />
576 <param name="sPaired" value="paired" />
577 <param name="pInput1" ftype="fastqsanger" value="bowtie_in5.fastqsanger" />
578 <param name="pInput2" ftype="fastqsanger" value="bowtie_in6.fastqsanger" />
579 <param name="pMaxInsert" value="1000" />
580 <param name="pMateOrient" value="ff" />
581 <param name="pSettingsType" value="full" />
582 <param name="pSkip" value="0" />
583 <param name="pAlignLimit" value="-1" />
584 <param name="pTrimH" value="0" />
585 <param name="pTrimL" value="0" />
586 <param name="alignMode" value="nMode" />
587 <param name="pMismatchSeed" value="2" />
588 <param name="pMismatchQual" value="70" />
589 <param name="pSeedLen" value="28" />
590 <param name="pRounding" value="round" />
591 <param name="pMinInsert" value="0" />
592 <param name="pMaxAlignAttempt" value="100" />
593 <param name="pForwardAlign" value="forward" />
594 <param name="pReverseAlign" value="reverse" />
595 <param name="pTryHard" value="noTryHard" />
596 <param name="pValAlign" value="1" />
597 <param name="pAllValAligns" value="noAllValAligns" />
598 <param name="pSuppressAlign" value="-1" />
599 <param name="pUnmappedFile" value="true" />
600 <param name="pMaxFile" value="false" />
601 <param name="pBest" value="doBest" />
602 <param name="pdMaxBacktracks" value="800" />
603 <param name="pdStrata" value="noStrata" />
604 <param name="pOffrate" value="-1" />
605 <param name="pSeed" value="-1" />
606 <param name="suppressHeader" value="true" />
607 <output name="output" ftype="sam" file="bowtie_out7.sam" sort="True" />
608 <output name="output_unmapped_reads_l" ftype="fastqsanger" file="bowtie_out8_1.fastq" sort="True" />
609 <output name="output_unmapped_reads_r" ftype="fastqsanger" file="bowtie_out8_2.fastq" sort="True" />
610 </test>
611 <!-- start testing of non-sanger variant fastq reads -->
612 <test>
613 <param name="genomeSource" value="history" />
614 <param name="ownFile" value="phiX.fasta" />
615 <param name="indexSettings" value="indexPreSet" />
616 <param name="sPaired" value="paired" />
617 <param name="pInput1" ftype="fastqillumina" value="bowtie_in5.fastqillumina" />
618 <param name="pInput2" ftype="fastqillumina" value="bowtie_in6.fastqillumina" />
619 <param name="pMaxInsert" value="1000" />
620 <param name="pMateOrient" value="ff" />
621 <param name="pSettingsType" value="full" />
622 <param name="pSkip" value="0" />
623 <param name="pAlignLimit" value="-1" />
624 <param name="pTrimH" value="0" />
625 <param name="pTrimL" value="0" />
626 <param name="alignMode" value="nMode" />
627 <param name="pMismatchSeed" value="2" />
628 <param name="pMismatchQual" value="70" />
629 <param name="pSeedLen" value="28" />
630 <param name="pRounding" value="round" />
631 <param name="pMinInsert" value="0" />
632 <param name="pMaxAlignAttempt" value="100" />
633 <param name="pForwardAlign" value="forward" />
634 <param name="pReverseAlign" value="reverse" />
635 <param name="pTryHard" value="noTryHard" />
636 <param name="pValAlign" value="1" />
637 <param name="pAllValAligns" value="noAllValAligns" />
638 <param name="pSuppressAlign" value="-1" />
639 <param name="pUnmappedFile" value="true" />
640 <param name="pMaxFile" value="false" />
641 <param name="pBest" value="doBest" />
642 <param name="pdMaxBacktracks" value="800" />
643 <param name="pdStrata" value="noStrata" />
644 <param name="pOffrate" value="-1" />
645 <param name="pSeed" value="-1" />
646 <param name="suppressHeader" value="true" />
647 <output name="output" ftype="sam" file="bowtie_out7.sam" sort="True" />
648 <output name="output_unmapped_reads_l" ftype="fastqillumina" file="bowtie_out8_1.fastqillumina.sorted" sort="True" />
649 <output name="output_unmapped_reads_r" ftype="fastqillumina" file="bowtie_out8_2.fastqillumina.sorted" sort="True" />
650 </test>
651 <test>
652 <param name="genomeSource" value="history" />
653 <param name="ownFile" value="phiX.fasta" />
654 <param name="indexSettings" value="indexPreSet" />
655 <param name="sPaired" value="paired" />
656 <param name="pInput1" ftype="fastqsolexa" value="bowtie_in5.fastqsolexa" />
657 <param name="pInput2" ftype="fastqsolexa" value="bowtie_in6.fastqsolexa" />
658 <param name="pMaxInsert" value="1000" />
659 <param name="pMateOrient" value="ff" />
660 <param name="pSettingsType" value="full" />
661 <param name="pSkip" value="0" />
662 <param name="pAlignLimit" value="-1" />
663 <param name="pTrimH" value="0" />
664 <param name="pTrimL" value="0" />
665 <param name="alignMode" value="nMode" />
666 <param name="pMismatchSeed" value="2" />
667 <param name="pMismatchQual" value="70" />
668 <param name="pSeedLen" value="28" />
669 <param name="pRounding" value="round" />
670 <param name="pMinInsert" value="0" />
671 <param name="pMaxAlignAttempt" value="100" />
672 <param name="pForwardAlign" value="forward" />
673 <param name="pReverseAlign" value="reverse" />
674 <param name="pTryHard" value="noTryHard" />
675 <param name="pValAlign" value="1" />
676 <param name="pAllValAligns" value="noAllValAligns" />
677 <param name="pSuppressAlign" value="-1" />
678 <param name="pUnmappedFile" value="true" />
679 <param name="pMaxFile" value="false" />
680 <param name="pBest" value="doBest" />
681 <param name="pdMaxBacktracks" value="800" />
682 <param name="pdStrata" value="noStrata" />
683 <param name="pOffrate" value="-1" />
684 <param name="pSeed" value="-1" />
685 <param name="suppressHeader" value="true" />
686 <output name="output" ftype="sam" file="bowtie_out7.sam" sort="True" />
687 <output name="output_unmapped_reads_l" ftype="fastqsolexa" file="bowtie_out8_1.fastqsolexa.sorted" sort="True" />
688 <output name="output_unmapped_reads_r" ftype="fastqsolexa" file="bowtie_out8_2.fastqsolexa.sorted" sort="True" />
689 </test>
690 <!-- end testing of non-sanger variant fastq reads -->
691 <test>
692 <!--
693 Bowtie command:
694 bowtie -q -p 4 -S +sam-nohead -n 2 -e 70 -l 28 -y -k 1 chrM_base test-data/bowtie_in2.fastqsanger > bowtie_out9_u.sam
695 sort bowtie_out9_u.sam > bowtie_out9.sam
696 -p is the number of threads. You need to replace the + with 2 dashes.
697 chrM_base is the index files' location/base name.
698 -->
699 <param name="genomeSource" value="indexed" />
700 <!-- this is the backwards-compatible "unique value" for this index, not an actual path -->
701 <param name="index" value="equCab2chrM" />
702 <param name="sPaired" value="single" />
703 <param name="sInput1" ftype="fastqsanger" value="bowtie_in2.fastqsanger" />
704 <param name="sSettingsType" value="full" />
705 <param name="sSkip" value="0" />
706 <param name="sAlignLimit" value="-1" />
707 <param name="sTrimH" value="0" />
708 <param name="sTrimL" value="0" />
709 <param name="alignMode" value="nMode" />
710 <param name="sMismatchSeed" value="2" />
711 <param name="sMismatchQual" value="70" />
712 <param name="sSeedLen" value="28" />
713 <param name="sRounding" value="round" />
714 <param name="sForwardAlign" value="forward" />
715 <param name="sReverseAlign" value="reverse" />
716 <param name="sTryHard" value="doTryHard" />
717 <param name="sValAlign" value="1" />
718 <param name="sAllValAligns" value="noAllValAligns" />
719 <param name="sSuppressAlign" value="-1" />
720 <param name="sUnmappedFile" value="false" />
721 <param name="sMaxFile" value="false" />
722 <param name="sBest" value="noBest" />
723 <param name="sOffrate" value="-1" />
724 <param name="sSeed" value="-1" />
725 <param name="suppressHeader" value="true" />
726 <output name="output" ftype="sam" file="bowtie_out9.sam" sort="True">
727 <metadata name="dbkey" value="equCab2" />
728 </output>
729 </test>
730 <test>
731 <!--
732 Bowtie command:
733 bowtie-build +offrate 5 +ftabchars 10 +little -f test-data/phiX.fasta phiX_base
734 bowtie -q -X 1000 +ff -p 4 -S +sam-nohead phiX_base -1 test-data/bowtie_in5.fastqsanger -2 test-data/bowtie_in6.fastqsanger > bowtie_out10_u.sam
735 sort bowtie_out10_u.sam > bowtie_out10.sam
736 -p is the number of threads. You need to replace the + with 2 dashes.
737 chrM_base is the index files' location/base name.
738 -->
739 <param name="genomeSource" value="history" />
740 <param name="ownFile" value="phiX.fasta" />
741 <param name="indexSettings" value="indexFull" />
742 <param name="autoB" value="auto" />
743 <param name="nodc" value="dc" />
744 <param name="noref" value="ref" />
745 <param name="offrate" value="5" />
746 <param name="ftab" value="10" />
747 <param name="ntoa" value="no" />
748 <param name="endian" value="little" />
749 <param name="seed" value="-1" />
750 <param name="sPaired" value="paired" />
751 <param name="pInput1" ftype="fastqsanger" value="bowtie_in5.fastqsanger" />
752 <param name="pInput2" ftype="fastqsanger" value="bowtie_in6.fastqsanger" />
753 <param name="pMaxInsert" value="1000" />
754 <param name="pMateOrient" value="ff" />
755 <param name="pSettingsType" value="preSet" />
756 <param name="suppressHeader" value="true" />
757 <output name="output" ftype="sam" file="bowtie_out10.sam" sort="True" />
758 </test>
759 <test>
760 <!--
761 Bowtie command:
762 bowtie-build +offrate 5 +ftabchars 10 +little -f test-data/phiX.fasta phiX_base
763 bowtie -q -X 1000 +ff -p 4 -S +sam-nohead phiX_base -1 test-data/bowtie_in5.fastqsanger -2 test-data/bowtie_in6.fastqsanger > bowtie_out10_u.sam
764 sort bowtie_out10_u.sam > bowtie_out10.sam
765 -p is the number of threads. You need to replace the + with 2 dashes.
766 chrM_base is the index files' location/base name.
767 -->
768 <param name="genomeSource" value="history" />
769 <param name="ownFile" value="phiX.fasta" />
770 <param name="indexSettings" value="indexFull" />
771 <param name="autoB" value="auto" />
772 <param name="nodc" value="dc" />
773 <param name="noref" value="ref" />
774 <param name="offrate" value="5" />
775 <param name="ftab" value="10" />
776 <param name="ntoa" value="no" />
777 <param name="endian" value="little" />
778 <param name="seed" value="-1" />
779 <param name="sPaired" value="paired" />
780 <param name="pInput1" ftype="fastqsanger" value="bowtie_in5.fastqsanger" />
781 <param name="pInput2" ftype="fastqsanger" value="bowtie_in6.fastqsanger" />
782 <param name="pMaxInsert" value="1000" />
783 <param name="pMateOrient" value="ff" />
784 <param name="pSettingsType" value="preSet" />
785 <param name="suppressHeader" value="true" />
786 <param name="save_mapping_stats" value="true" />
787 <output name="output" ftype="sam" file="bowtie_out10.sam" sort="True" />
788 <output name="mapping_stats" ftype="txt" file="bowtie_out11.txt" sort="True" />
789 </test>
790 </tests>
791
792 <help>
793
794 **What it does**
795
796 Bowtie_ 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.
797
798 .. _Bowtie: http://bowtie-bio.sourceforge.net/index.shtml
799
800 ------
801
802 **Know what you are doing**
803
804 .. class:: warningmark
805
806 There 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.
807
808 .. __: http://bowtie-bio.sourceforge.net/index.shtml
809
810 ------
811
812 **Input formats**
813
814 Bowtie accepts files in Sanger FASTQ format. Use the FASTQ Groomer to prepare your files.
815
816 ------
817
818 **A Note on Built-in Reference Genomes**
819
820 The default variant for all genomes is "Full", defined as all primary chromosomes (or scaffolds/contigs) including mitochondrial plus associated unmapped, plasmid, and other segments. When only one version of a genome is available in this tool, it represents the default "Full" variant. Some genomes will have more than one variant available. The "Canonical Male" or sometimes simply "Canonical" variant contains the primary chromosomes for a genome. For example a human "Canonical" variant contains chr1-chr22, chrX, chrY, and chrM. The "Canonical Female" variant contains the primary chromosomes excluding chrY.
821
822 ------
823
824 **Outputs**
825
826 The output is in SAM format, and has the following columns::
827
828 Column Description
829 -------- --------------------------------------------------------
830 1 QNAME Query (pair) NAME
831 2 FLAG bitwise FLAG
832 3 RNAME Reference sequence NAME
833 4 POS 1-based leftmost POSition/coordinate of clipped sequence
834 5 MAPQ MAPping Quality (Phred-scaled)
835 6 CIGAR extended CIGAR string
836 7 MRNM Mate Reference sequence NaMe ('=' if same as RNAME)
837 8 MPOS 1-based Mate POSition
838 9 ISIZE Inferred insert SIZE
839 10 SEQ query SEQuence on the same strand as the reference
840 11 QUAL query QUALity (ASCII-33 gives the Phred base quality)
841 12 OPT variable OPTional fields in the format TAG:VTYPE:VALUE
842
843 The flags are as follows::
844
845 Flag Description
846 ------ -------------------------------------
847 0x0001 the read is paired in sequencing
848 0x0002 the read is mapped in a proper pair
849 0x0004 the query sequence itself is unmapped
850 0x0008 the mate is unmapped
851 0x0010 strand of the query (1 for reverse)
852 0x0020 strand of the mate
853 0x0040 the read is the first read in a pair
854 0x0080 the read is the second read in a pair
855 0x0100 the alignment is not primary
856
857 It looks like this (scroll sideways to see the entire example)::
858
859 QNAME FLAG RNAME POS MAPQ CIAGR MRNM MPOS ISIZE SEQ QUAL OPT
860 HWI-EAS91_1_30788AAXX:1:1:1761:343 4 * 0 0 * * 0 0 AAAAAAANNAAAAAAAAAAAAAAAAAAAAAAAAAAACNNANNGAGTNGNNNNNNNGCTTCCCACAGNNCTGG hhhhhhh;;hhhhhhhhhhh^hOhhhhghhhfhhhgh;;h;;hhhh;h;;;;;;;hhhhhhghhhh;;Phhh
861 HWI-EAS91_1_30788AAXX:1:1:1578:331 4 * 0 0 * * 0 0 GTATAGANNAATAAGAAAAAAAAAAATGAAGACTTTCNNANNTCTGNANNNNNNNTCTTTTTTCAGNNGTAG hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhhhh;;h;;hhhh;h;;;;;;;hhhhhhhhhhh;;hhVh
862
863 -------
864
865 **Bowtie settings**
866
867 All of the options have a default value. You can change any of them. Most of the options in Bowtie have been implemented here.
868
869 ------
870
871 **Bowtie parameter list**
872
873 This is an exhaustive list of Bowtie options:
874
875 For indexing (bowtie-build)::
876
877 -a No auto behavior. Disable the default behavior where bowtie automatically
878 selects values for --bmax/--bmaxdivn/--dcv/--packed parameters according
879 to the memory available. [off]
880 --packed Packing. Use a packed representation for DNA strings. [auto]
881 --bmax INT Suffix maximum. The maximum number of suffixes allowed in a block. [auto]
882 --bmaxdivn INT Suffix maximum fraction. The maximum number of suffixes allowed in a block
883 expressed as a fraction of the length of the reference. [4]
884 --dcv INT Difference-cover sample. Use INT as the period for the difference-cover
885 sample. [1024]
886 --nodc INT No difference-cover sample. Disable the difference-cover sample. [off]
887 -r No reference indexes. Do not build the NAME.3.ebwt and NAME.4.ebwt portions
888 of the index. Used only for paired-end alignment. [off]
889 -o Offrate. How many Burrows-Wheeler rows get marked by the indexer. The
890 indexer will mark every 2^INT rows. The marked rows correspond to rows on
891 the genome. [5]
892 -t INT The ftab lookup table used to calculate an initial Burrows-Wheeler range
893 with respect to the first INT characters of the query. Ftab size is 4^(INT+1)
894 bytes. [10]
895 --ntoa N conversion. Convert Ns to As before building the index. Otherwise, Ns are
896 simply excluded from the index and Bowtie will not find alignments that
897 overlap them. [off]
898 --big Endianness. Endianness to use when serializing integers to the index file. [off]
899 --little Endianness. [--little]
900 --seed INT Random seed. Use INT as the seed for the pseudo-random number generator. [off]
901
902 For aligning (bowtie)::
903
904 -s INT Skip. Do not align the first INT reads or pairs in the input. [off]
905 -u INT Align limit. Only align the first INT reads/pairs from the input. [no limit]
906 -5 INT High-quality trim. Trim INT bases from the high-quality (left) end of each
907 read before alignment. [0]
908 -3 INT Low-quality trim. Trim INT bases from the low-quality (right) end of each
909 read before alignment. [0]
910 -n INT Mismatch seed. Maximum number of mismatches permitted in the seed (defined
911 with seed length option). Can be 0, 1, 2, or 3. [2]
912 -e INT Mismatch quality. Maximum permitted total of quality values at mismatched
913 read positions. Bowtie rounds quality values to the nearest 10 and saturates
914 at 30. [70]
915 -l INT Seed length. The number of bases on the high-quality end of the read to
916 which the -n ceiling applies. Must be at least 5. [28]
917 --nomaqround Suppress Maq rounding. Values are internally rounded to the nearest 10 and
918 saturate at 30. This options turns off that rounding. [off]
919 -v INT Maq- or SOAP-like alignment policy. This option turns off the default
920 Maq-like alignment policy in favor of a SOAP-like one. End-to-end alignments
921 with at most INT mismatches. [off]
922 -I INT Minimum insert. The minimum insert size for valid paired-end alignments.
923 Does checking on untrimmed reads if -5 or -3 is used. [0]
924 -X INT Maximum insert. The maximum insert size for valid paired-end alignments.
925 Does checking on untrimmed reads if -5 or -3 is used. [250]
926 --fr Mate orientation. The upstream/downstream mate orientations for a valid
927 paired-end alignment against the forward reference strand. [--fr]
928 --rf Mate orientation. [off]
929 --ff Mate orientation. [off]
930 --pairtries INT Maximum alignment attempts for paired-end data. [100]
931 --nofw No forward aligning. Choosing this option means that Bowtie will not attempt
932 to align against the forward reference strand. [off]
933 --norc No reverse-complement aligning. Setting this will mean that Bowtie will not
934 attempt to align against the reverse-complement reference strand. [off]
935 --un FILENAME Write all reads that could not be aligned to file [off]
936 --max FILENAME Write all reads with a number of valid alignments exceeding the limit
937 set with the -m option to file [off]
938 --maxbts INT Maximum backtracks. The maximum number of backtracks permitted when aligning
939 a read in -n 2 or -n 3 mode. [125 without --best] [800 with --best]
940 -y Try hard. Try as hard as possible to find valid alignments when they exist,
941 including paired-end alignments. [off]
942 --chunkmbs INT Thread memory. The number of megabytes of memory a given thread is given to
943 store path descriptors in --best mode. [32]
944 -k INT Valid alignments. The number of valid alignments per read or pair. [off]
945 -a All valid alignments. Choosing this means that all valid alignments per read
946 or pair will be reported. [off]
947 -m INT Suppress alignments. Suppress all alignments for a particular read or pair
948 if more than INT reportable alignments exist for it. [no limit]
949 --best Best mode. Make Bowtie guarantee that reported singleton alignments are
950 "best" in terms of stratum (the number of mismatches) and quality values at
951 mismatched position. [off]
952 --strata Best strata. When running in best mode, report alignments that fall into the
953 best stratum if there are ones falling into more than one. [off]
954 -o INT Offrate override. Override the offrate of the index with INT. Some row
955 markings are discarded when index read into memory. INT must be greater than
956 the value used to build the index (default: 5). [off]
957 --seed INT Random seed. Use INT as the seed for the pseudo-random number generator. [off]
958 --snpphred INT Use INT as the SNP penalty for decoding colorspace alignments. True ratio of
959 SNPs per base in the subject genome. [see --snpfrac]
960 --snpfrac DEC Use DEC as the estimated ratio of SNPs per base when decoding colorspace
961 alignments. [0.001]
962 --col-keepends Keep the extreme-end nucleotides and qualities when decoding colorspace
963 alignments. [off]
964
965 </help>
966 <citations>
967 <citation type="doi">10.1186/gb-2009-10-3-r25</citation>
968 </citations>
969 </tool>