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comparison bowtie_wrapper.xml @ 0:4926b3e1e2fe draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
author devteam
date Mon, 09 Nov 2015 11:18:30 -0500
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children 867a8c8e870e
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-1:000000000000 0:4926b3e1e2fe
1 <tool id="bowtie_wrapper" name="Map with Bowtie for Illumina" version="1.1.3">
2 <requirements>
3 <requirement type="package" version="0.12.7">bowtie</requirement>
4 </requirements>
5 <description></description>
6 <version_command>bowtie --version</version_command>
7 <command interpreter="python">
8 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 </command>
152 <inputs>
153 <conditional name="refGenomeSource">
154 <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">
155 <option value="indexed">Use a built-in index</option>
156 <option value="history">Use one from the history</option>
157 </param>
158 <when value="indexed">
159 <param name="index" type="select" label="Select a reference genome" help="if your genome of interest is not listed - contact Galaxy team">
160 <options from_data_table="bowtie_indexes">
161 <filter type="sort_by" column="2" />
162 <validator type="no_options" message="No indexes are available" />
163 </options>
164 </param>
165 </when>
166 <when value="history">
167 <param name="ownFile" type="data" format="bowtie_base_index,fasta" metadata_name="dbkey" label="Select the reference genome" />
168 <conditional name="indexParams">
169 <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">
170 <option value="indexPreSet">Default</option>
171 <option value="indexFull">Set your own</option>
172 </param>
173 <when value="indexPreSet" />
174 <when value="indexFull">
175 <conditional name="autoBehavior">
176 <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">
177 <option value="auto">Automatic behavior</option>
178 <option value="set">Set values (sets --noauto and allows others to be set)</option>
179 </param>
180 <when value="auto" />
181 <when value="set">
182 <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">
183 <option value="unpacked">Use regular representation</option>
184 <option value="packed">Use packed representation</option>
185 </param>
186 <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" />
187 <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)" />
188 <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" />
189 </when>
190 </conditional>
191 <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)">
192 <option value="dc">Use difference-cover sample</option>
193 <option value="nodc">Disable difference-cover sample</option>
194 </param>
195 <param name="noref" type="select" label="Whether or not to build the part of the reference index used only in paired-end alignment (-r)">
196 <option value="ref">Build all index files</option>
197 <option value="noref">Do not build paired-end alignment index files</option>
198 </param>
199 <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" />
200 <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" />
201 <param name="ntoa" type="select" label="Whether or not to convert Ns in the reference sequence to As (--ntoa)">
202 <option value="no">Do not convert Ns</option>
203 <option value="yes">Convert Ns to As</option>
204 </param>
205 <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">
206 <option value="little">Little</option>
207 <option value="big">Big</option>
208 </param>
209 <param name="seed" type="integer" value="-1" label="Seed for the pseudorandom number generator (--seed)" help="Use -1 to use default" />
210 </when> <!-- indexFull -->
211 </conditional> <!-- indexParams -->
212 </when> <!-- history -->
213 </conditional> <!-- refGenomeSource -->
214 <conditional name="singlePaired">
215 <param name="sPaired" type="select" label="Is this library mate-paired?">
216 <option value="single">Single-end</option>
217 <option value="paired">Paired-end</option>
218 </param>
219 <when value="single">
220 <param name="sInput1" type="data" format="fastqsanger,fastqillumina,fastqsolexa" label="FASTQ file" help="Must have ASCII encoded quality scores"/>
221 <conditional name="sParams">
222 <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">
223 <option value="preSet">Commonly used</option>
224 <option value="full">Full parameter list</option>
225 </param>
226 <when value="preSet" />
227 <when value="full">
228 <param name="sSkip" type="integer" value="0" label="Skip the first n reads (-s)" />
229 <param name="sAlignLimit" type="integer" value="-1" label="Only align the first n reads (-u)" help="-1 for off" />
230 <param name="sTrimH" type="integer" value="0" label="Trim n bases from high-quality (left) end of each read before alignment (-5)" />
231 <param name="sTrimL" type="integer" value="0" label="Trim n bases from low-quality (right) end of each read before alignment (-3)" />
232 <conditional name="alignModeOption">
233 <param name="alignMode" type="select" label="Alignment mode">
234 <option value="nMode">Maq-like: quality-aware, limit mismatches in seed (-n)</option>
235 <option value="vMode">ignore qualities, limit end-to-end mismatches (-v)</option>
236 </param>
237 <when value="nMode">
238 <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" />
239 <param name="sMismatchQual" type="integer" value="70" min="1" label="Maximum permitted total of quality values at all mismatched read positions (-e)" />
240 <param name="sSeedLen" type="integer" value="28" min="5" label="Seed length (-l)" help="Minimum value is 5" />
241 <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">
242 <option value="round">Round to nearest 10</option>
243 <option value="noRound">Do not round to nearest 10</option>
244 </param>
245 </when>
246 <when value="vMode">
247 <param name="maxMismatches" type="integer" value="" min="0" max="3" label="Maximum number of mismatches (-v)" help="May be 0, 1, 2, or 3" />
248 </when>
249 </conditional>
250 <param name="sForwardAlign" type="select" label="Choose whether or not to attempt to align against the forward reference strand (--nofw)">
251 <option value="forward">Align against the forward reference strand</option>
252 <option value="noForward">Do not align against the forward reference strand</option>
253 </param>
254 <param name="sReverseAlign" type="select" label="Choose whether or not to attempt to align against the reverse-complement reference strand (--norc)">
255 <option value="reverse">Align against the reverse-complement reference strand</option>
256 <option value="noReverse">Do not align against the reverse-complement reference strand</option>
257 </param>
258 <conditional name="sBestOption">
259 <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">
260 <option value="noBest">Do not use best</option>
261 <option value="doBest">Use best</option>
262 </param>
263 <when value="noBest">
264 <conditional name="sTryHardOption">
265 <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">
266 <option value="noTryHard">Do not try hard</option>
267 <option value="doTryHard">Try hard</option>
268 </param>
269 <when value="noTryHard">
270 <param name="snMaxBacktracks" type="integer" value="125" min="0" label="Maximum number of backtracks permitted when aligning a read (--maxbts)" />
271 </when>
272 <when value="doTryHard" />
273 </conditional>
274 </when>
275 <when value="doBest">
276 <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)">
277 <option value="noStrata">Do not use strata option</option>
278 <option value="doStrata">Use strata option</option>
279 </param>
280 <conditional name="sTryHardOption">
281 <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">
282 <option value="noTryHard">Do not try hard</option>
283 <option value="doTryHard">Try hard</option>
284 </param>
285 <when value="noTryHard">
286 <param name="sdMaxBacktracks" type="integer" value="800" min="0" label="Maximum number of backtracks permitted when aligning a read (--maxbts)" />
287 </when>
288 <when value="doTryHard" />
289 </conditional>
290 </when>
291 </conditional> <!-- bestOption -->
292 <conditional name="sAllValAlignsOption">
293 <param name="sAllValAligns" type="select" label="Whether or not to report all valid alignments per read (-a)">
294 <option value="noAllValAligns">Do not report all valid alignments</option>
295 <option value="doAllValAligns">Report all valid alignments</option>
296 </param>
297 <when value="noAllValAligns">
298 <param name="sValAlign" type="integer" value="1" min="1" label="Report up to n valid alignments per read (-k)" />
299 </when>
300 <when value="doAllValAligns" />
301 </conditional>
302 <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" />
303 <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)" />
304 <param name="sUnmappedFile" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write all reads that could not be aligned to a file (--un)" />
305 <param name="sOffrate" type="integer" value="-1" label="Override the offrate of the index to n (-o)" help="-1 for default" />
306 <param name="sSeed" type="integer" value="-1" label="Seed for pseudo-random number generator (--seed)" help="-1 for default" />
307 </when> <!-- full -->
308 </conditional> <!-- sParams -->
309 </when> <!-- single -->
310 <when value="paired">
311 <param name="pInput1" type="data" format="fastqsanger,fastqillumina,fastqsolexa" label="Forward FASTQ file" help="Must have ASCII encoded quality scores"/>
312 <param name="pInput2" type="data" format="fastqsanger,fastqillumina,fastqsolexa" label="Reverse FASTQ file" help="File format must match the Forward FASTQ file">
313 <options options_filter_attribute="ext" from_parameter="tool.app.datatypes_registry.datatypes_by_extension" transform_lines="obj.keys()">>
314 <column name="name" index="0"/>
315 <column name="value" index="0"/>
316 <filter type="param_value" ref="pInput1" ref_attribute="ext" column="0"/>
317 </options>
318 </param>
319 <param name="pMaxInsert" type="integer" value="1000" label="Maximum insert size for valid paired-end alignments (-X)" />
320 <param name="pMateOrient" type="select" label="The upstream/downstream mate orientation for valid paired-end alignment against the forward reference strand (--fr/--rf/--ff)">
321 <option value="fr">FR (for Illumina)</option>
322 <option value="rf">RF</option>
323 <option value="ff">FF (for SOLiD)</option>
324 </param>
325 <conditional name="pParams">
326 <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">
327 <option value="preSet">Commonly used</option>
328 <option value="full">Full parameter list</option>
329 </param>
330 <when value="preSet" />
331 <when value="full">
332 <param name="pSkip" type="integer" value="0" label="Skip the first n pairs (-s)" />
333 <param name="pAlignLimit" type="integer" value="-1" label="Only align the first n pairs (-u)" help="-1 for off" />
334 <param name="pTrimH" type="integer" value="0" label="Trim n bases from high-quality (left) end of each read before alignment (-5)" />
335 <param name="pTrimL" type="integer" value="0" label="Trim n bases from low-quality (right) end of each read before alignment (-3)" />
336 <conditional name="alignModeOption">
337 <param name="alignMode" type="select" label="Alignment mode">
338 <option value="nMode">Maq-like: quality-aware, limit mismatches in seed (-n)</option>
339 <option value="vMode">ignore qualities, limit end-to-end mismatches (-v)</option>
340 </param>
341 <when value="nMode">
342 <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" />
343 <param name="pMismatchQual" type="integer" value="70" min="1" label="Maximum permitted total of quality values at all mismatched read positions (-e)" />
344 <param name="pSeedLen" type="integer" value="28" min="5" label="Seed length (-l)" help="Minimum value is 5" />
345 <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">
346 <option value="round">Round to nearest 10</option>
347 <option value="noRound">Do not round to nearest 10</option>
348 </param>
349 </when>
350 <when value="vMode">
351 <param name="maxMismatches" type="integer" value="" min="0" max="3" label="Maximum number of mismatches (-v)" help="May be 0, 1, 2, or 3" />
352 </when>
353 </conditional>
354 <param name="pMinInsert" type="integer" value="0" label="Minimum insert size for valid paired-end alignments (-I)" />
355 <param name="pForwardAlign" type="select" label="Choose whether or not to attempt to align against the forward reference strand (--nofw)">
356 <option value="forward">Align against the forward reference strand</option>
357 <option value="noForward">Do not align against the forward reference strand</option>
358 </param>
359 <param name="pReverseAlign" type="select" label="Choose whether or not to attempt to align against the reverse-complement reference strand (--norc)">
360 <option value="reverse">Align against the reverse-complement reference strand</option>
361 <option value="noReverse">Do not align against the reverse-complement reference strand</option>
362 </param>
363 <conditional name="pBestOption">
364 <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">
365 <option value="noBest">Do not use best</option>
366 <option value="doBest">Use best</option>
367 </param>
368 <when value="noBest">
369 <conditional name="pTryHardOption">
370 <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">
371 <option value="noTryHard">Do not try hard</option>
372 <option value="doTryHard">Try hard</option>
373 </param>
374 <when value="noTryHard">
375 <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)" />
376 <param name="pnMaxBacktracks" type="integer" value="125" min="0" label="Maximum number of backtracks permitted when aligning a read (--maxbts)" />
377 </when>
378 <when value="doTryHard" />
379 </conditional>
380 </when>
381 <when value="doBest">
382 <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)">
383 <option value="noStrata">Do not use strata option</option>
384 <option value="doStrata">Use strata option</option>
385 </param>
386 <conditional name="pTryHardOption">
387 <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">
388 <option value="noTryHard">Do not try hard</option>
389 <option value="doTryHard">Try hard</option>
390 </param>
391 <when value="noTryHard">
392 <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)" />
393 <param name="pdMaxBacktracks" type="integer" value="800" min="0" label="Maximum number of backtracks permitted when aligning a read (--maxbts)" />
394 </when>
395 <when value="doTryHard" />
396 </conditional>
397 </when>
398 </conditional>
399 <conditional name="pAllValAlignsOption">
400 <param name="pAllValAligns" type="select" label="Whether or not to report all valid alignments per pair (-a)">
401 <option value="noAllValAligns">Do not report all valid alignments</option>
402 <option value="doAllValAligns">Report all valid alignments</option>
403 </param>
404 <when value="noAllValAligns">
405 <param name="pValAlign" type="integer" value="1" min="1" label="Report up to n valid alignments per pair (-k)" />
406 </when>
407 <when value="doAllValAligns" />
408 </conditional>
409 <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" />
410 <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)" />
411 <param name="pUnmappedFile" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write all reads that could not be aligned to a file (--un)" />
412 <param name="pOffrate" type="integer" value="-1" label="Override the offrate of the index to n (-o)" help="-1 for default" />
413 <param name="pSeed" type="integer" value="-1" label="Seed for pseudo-random number generator (--seed)" help="-1 for default" />
414 </when> <!-- full -->
415 </conditional> <!-- pParams -->
416 </when> <!-- paired -->
417 </conditional> <!-- singlePaired -->
418 <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" />
419 </inputs>
420 <outputs>
421 <data format="sam" name="output" label="${tool.name} on ${on_string}: mapped reads">
422 <actions>
423 <conditional name="refGenomeSource.genomeSource">
424 <when value="indexed">
425 <action type="metadata" name="dbkey">
426 <option type="from_data_table" name="bowtie_indexes" column="1" offset="0">
427 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
428 <filter type="param_value" ref="refGenomeSource.index" column="0"/>
429 </option>
430 </action>
431 </when>
432 <when value="history">
433 <action type="metadata" name="dbkey">
434 <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" />
435 </action>
436 </when>
437 </conditional>
438 </actions>
439 </data>
440 <data format="fastq" name="output_suppressed_reads_l" label="${tool.name} on ${on_string}: suppressed reads (L)">
441 <filter>((
442 singlePaired['sPaired'] == "single" and
443 singlePaired['sParams']['sSettingsType'] == "full" and
444 singlePaired['sParams']['sMaxFile'] is True
445 ) or (
446 singlePaired['sPaired'] == "paired" and
447 singlePaired['pParams']['pSettingsType'] == "full" and
448 singlePaired['pParams']['pMaxFile'] is True
449 ))
450 </filter>
451 <actions>
452 <conditional name="singlePaired.sPaired">
453 <when value="single">
454 <action type="format">
455 <option type="from_param" name="singlePaired.sInput1" param_attribute="ext" />
456 </action>
457 </when>
458 <when value="paired">
459 <action type="format">
460 <option type="from_param" name="singlePaired.pInput1" param_attribute="ext" />
461 </action>
462 </when>
463 </conditional>
464 </actions>
465 </data>
466 <data format="fastq" name="output_suppressed_reads_r" label="${tool.name} on ${on_string}: suppressed reads (R)">
467 <filter>singlePaired['sPaired'] == "paired"</filter>
468 <filter>singlePaired['pParams']['pSettingsType'] == "full"</filter>
469 <filter>singlePaired['pParams']['pMaxFile'] is True</filter>
470 <actions>
471 <conditional name="singlePaired.sPaired">
472 <when value="single">
473 <action type="format">
474 <option type="from_param" name="singlePaired.sInput1" param_attribute="ext" />
475 </action>
476 </when>
477 <when value="paired">
478 <action type="format">
479 <option type="from_param" name="singlePaired.pInput1" param_attribute="ext" />
480 </action>
481 </when>
482 </conditional>
483 </actions>
484 </data>
485 <data format="fastq" name="output_unmapped_reads_l" label="${tool.name} on ${on_string}: unmapped reads (L)">
486 <filter>
487 ((
488 singlePaired['sPaired'] == "single" and
489 singlePaired['sParams']['sSettingsType'] == "full" and
490 singlePaired['sParams']['sUnmappedFile'] is True
491 ) or (
492 singlePaired['sPaired'] == "paired" and
493 singlePaired['pParams']['pSettingsType'] == "full" and
494 singlePaired['pParams']['pUnmappedFile'] is True
495 ))
496 </filter>
497 <actions>
498 <conditional name="singlePaired.sPaired">
499 <when value="single">
500 <action type="format">
501 <option type="from_param" name="singlePaired.sInput1" param_attribute="ext" />
502 </action>
503 </when>
504 <when value="paired">
505 <action type="format">
506 <option type="from_param" name="singlePaired.pInput1" param_attribute="ext" />
507 </action>
508 </when>
509 </conditional>
510 </actions>
511 </data>
512 <data format="fastq" name="output_unmapped_reads_r" label="${tool.name} on ${on_string}: unmapped reads (R)">
513 <filter>singlePaired['sPaired'] == "paired"</filter>
514 <filter>singlePaired['pParams']['pSettingsType'] == "full"</filter>
515 <filter>singlePaired['pParams']['pUnmappedFile'] is True</filter>
516 <actions>
517 <conditional name="singlePaired.sPaired">
518 <when value="single">
519 <action type="format">
520 <option type="from_param" name="singlePaired.sInput1" param_attribute="ext" />
521 </action>
522 </when>
523 <when value="paired">
524 <action type="format">
525 <option type="from_param" name="singlePaired.pInput1" param_attribute="ext" />
526 </action>
527 </when>
528 </conditional>
529 </actions>
530 </data>
531 </outputs>
532 <tests>
533 <test>
534 <!--
535 Bowtie command:
536 bowtie -q -p 4 -S +sam-nohead chrM_base test-data/bowtie_in2.fastqsanger > bowtie_out6_u.sam
537 sort bowtie_out6_u.sam > bowtie_out6.sam
538 -p is the number of threads. You need to replace the + with 2 dashes.
539 chrM_base needs to be the base location/name of the index files.
540 -->
541 <param name="genomeSource" value="indexed" />
542 <!-- this is the backwards-compatible "unique value" for this index, not an actual path -->
543 <param name="index" value="equCab2chrM" />
544 <param name="sPaired" value="single" />
545 <param name="sInput1" ftype="fastqsanger" value="bowtie_in2.fastqsanger" />
546 <param name="sSettingsType" value="preSet" />
547 <param name="suppressHeader" value="true" />
548 <output name="output" ftype="sam" file="bowtie_out6.sam" sort="True" />
549 </test>
550 <test>
551 <!--
552 Bowtie command:
553 bowtie-build -f test-data/phiX.fasta phiX_base
554 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
555 sort bowtie_out7_u.sam > bowtie_out7.sam
556 sort bowtie_out8_u_1.sam > bowtie_out8_1.sam
557 sort bowtie_out8_u_2.sam > bowtie_out8_2.sam
558 Then also need to modify bowtie_out8_1.sam and bowtie_out8_2.sam so that all @ lines come before sequence lines.
559 -p is the number of threads. You need to replace the + with 2 dashes.
560 The two unmapped output files will be named bowtie_out8_1.fastq and bowtie_out8_2.fastq.
561 chrM_base is the index files' location/base name.
562 -->
563 <param name="genomeSource" value="history" />
564 <param name="ownFile" value="phiX.fasta" />
565 <param name="indexSettings" value="indexPreSet" />
566 <param name="sPaired" value="paired" />
567 <param name="pInput1" ftype="fastqsanger" value="bowtie_in5.fastqsanger" />
568 <param name="pInput2" ftype="fastqsanger" value="bowtie_in6.fastqsanger" />
569 <param name="pMaxInsert" value="1000" />
570 <param name="pMateOrient" value="ff" />
571 <param name="pSettingsType" value="full" />
572 <param name="pSkip" value="0" />
573 <param name="pAlignLimit" value="-1" />
574 <param name="pTrimH" value="0" />
575 <param name="pTrimL" value="0" />
576 <param name="alignMode" value="nMode" />
577 <param name="pMismatchSeed" value="2" />
578 <param name="pMismatchQual" value="70" />
579 <param name="pSeedLen" value="28" />
580 <param name="pRounding" value="round" />
581 <param name="pMinInsert" value="0" />
582 <param name="pMaxAlignAttempt" value="100" />
583 <param name="pForwardAlign" value="forward" />
584 <param name="pReverseAlign" value="reverse" />
585 <param name="pTryHard" value="noTryHard" />
586 <param name="pValAlign" value="1" />
587 <param name="pAllValAligns" value="noAllValAligns" />
588 <param name="pSuppressAlign" value="-1" />
589 <param name="pUnmappedFile" value="true" />
590 <param name="pMaxFile" value="false" />
591 <param name="pBest" value="doBest" />
592 <param name="pdMaxBacktracks" value="800" />
593 <param name="pdStrata" value="noStrata" />
594 <param name="pOffrate" value="-1" />
595 <param name="pSeed" value="-1" />
596 <param name="suppressHeader" value="true" />
597 <output name="output" ftype="sam" file="bowtie_out7.sam" sort="True" />
598 <output name="output_unmapped_reads_l" ftype="fastqsanger" file="bowtie_out8_1.fastq" sort="True" />
599 <output name="output_unmapped_reads_r" ftype="fastqsanger" file="bowtie_out8_2.fastq" sort="True" />
600 </test>
601 <!-- start testing of non-sanger variant fastq reads -->
602 <test>
603 <param name="genomeSource" value="history" />
604 <param name="ownFile" value="phiX.fasta" />
605 <param name="indexSettings" value="indexPreSet" />
606 <param name="sPaired" value="paired" />
607 <param name="pInput1" ftype="fastqillumina" value="bowtie_in5.fastqillumina" />
608 <param name="pInput2" ftype="fastqillumina" value="bowtie_in6.fastqillumina" />
609 <param name="pMaxInsert" value="1000" />
610 <param name="pMateOrient" value="ff" />
611 <param name="pSettingsType" value="full" />
612 <param name="pSkip" value="0" />
613 <param name="pAlignLimit" value="-1" />
614 <param name="pTrimH" value="0" />
615 <param name="pTrimL" value="0" />
616 <param name="alignMode" value="nMode" />
617 <param name="pMismatchSeed" value="2" />
618 <param name="pMismatchQual" value="70" />
619 <param name="pSeedLen" value="28" />
620 <param name="pRounding" value="round" />
621 <param name="pMinInsert" value="0" />
622 <param name="pMaxAlignAttempt" value="100" />
623 <param name="pForwardAlign" value="forward" />
624 <param name="pReverseAlign" value="reverse" />
625 <param name="pTryHard" value="noTryHard" />
626 <param name="pValAlign" value="1" />
627 <param name="pAllValAligns" value="noAllValAligns" />
628 <param name="pSuppressAlign" value="-1" />
629 <param name="pUnmappedFile" value="true" />
630 <param name="pMaxFile" value="false" />
631 <param name="pBest" value="doBest" />
632 <param name="pdMaxBacktracks" value="800" />
633 <param name="pdStrata" value="noStrata" />
634 <param name="pOffrate" value="-1" />
635 <param name="pSeed" value="-1" />
636 <param name="suppressHeader" value="true" />
637 <output name="output" ftype="sam" file="bowtie_out7.sam" sort="True" />
638 <output name="output_unmapped_reads_l" ftype="fastqillumina" file="bowtie_out8_1.fastqillumina.sorted" sort="True" />
639 <output name="output_unmapped_reads_r" ftype="fastqillumina" file="bowtie_out8_2.fastqillumina.sorted" sort="True" />
640 </test>
641 <test>
642 <param name="genomeSource" value="history" />
643 <param name="ownFile" value="phiX.fasta" />
644 <param name="indexSettings" value="indexPreSet" />
645 <param name="sPaired" value="paired" />
646 <param name="pInput1" ftype="fastqsolexa" value="bowtie_in5.fastqsolexa" />
647 <param name="pInput2" ftype="fastqsolexa" value="bowtie_in6.fastqsolexa" />
648 <param name="pMaxInsert" value="1000" />
649 <param name="pMateOrient" value="ff" />
650 <param name="pSettingsType" value="full" />
651 <param name="pSkip" value="0" />
652 <param name="pAlignLimit" value="-1" />
653 <param name="pTrimH" value="0" />
654 <param name="pTrimL" value="0" />
655 <param name="alignMode" value="nMode" />
656 <param name="pMismatchSeed" value="2" />
657 <param name="pMismatchQual" value="70" />
658 <param name="pSeedLen" value="28" />
659 <param name="pRounding" value="round" />
660 <param name="pMinInsert" value="0" />
661 <param name="pMaxAlignAttempt" value="100" />
662 <param name="pForwardAlign" value="forward" />
663 <param name="pReverseAlign" value="reverse" />
664 <param name="pTryHard" value="noTryHard" />
665 <param name="pValAlign" value="1" />
666 <param name="pAllValAligns" value="noAllValAligns" />
667 <param name="pSuppressAlign" value="-1" />
668 <param name="pUnmappedFile" value="true" />
669 <param name="pMaxFile" value="false" />
670 <param name="pBest" value="doBest" />
671 <param name="pdMaxBacktracks" value="800" />
672 <param name="pdStrata" value="noStrata" />
673 <param name="pOffrate" value="-1" />
674 <param name="pSeed" value="-1" />
675 <param name="suppressHeader" value="true" />
676 <output name="output" ftype="sam" file="bowtie_out7.sam" sort="True" />
677 <output name="output_unmapped_reads_l" ftype="fastqsolexa" file="bowtie_out8_1.fastqsolexa.sorted" sort="True" />
678 <output name="output_unmapped_reads_r" ftype="fastqsolexa" file="bowtie_out8_2.fastqsolexa.sorted" sort="True" />
679 </test>
680 <!-- end testing of non-sanger variant fastq reads -->
681 <test>
682 <!--
683 Bowtie command:
684 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
685 sort bowtie_out9_u.sam > bowtie_out9.sam
686 -p is the number of threads. You need to replace the + with 2 dashes.
687 chrM_base is the index files' location/base name.
688 -->
689 <param name="genomeSource" value="indexed" />
690 <!-- this is the backwards-compatible "unique value" for this index, not an actual path -->
691 <param name="index" value="equCab2chrM" />
692 <param name="sPaired" value="single" />
693 <param name="sInput1" ftype="fastqsanger" value="bowtie_in2.fastqsanger" />
694 <param name="sSettingsType" value="full" />
695 <param name="sSkip" value="0" />
696 <param name="sAlignLimit" value="-1" />
697 <param name="sTrimH" value="0" />
698 <param name="sTrimL" value="0" />
699 <param name="alignMode" value="nMode" />
700 <param name="sMismatchSeed" value="2" />
701 <param name="sMismatchQual" value="70" />
702 <param name="sSeedLen" value="28" />
703 <param name="sRounding" value="round" />
704 <param name="sForwardAlign" value="forward" />
705 <param name="sReverseAlign" value="reverse" />
706 <param name="sTryHard" value="doTryHard" />
707 <param name="sValAlign" value="1" />
708 <param name="sAllValAligns" value="noAllValAligns" />
709 <param name="sSuppressAlign" value="-1" />
710 <param name="sUnmappedFile" value="false" />
711 <param name="sMaxFile" value="false" />
712 <param name="sBest" value="noBest" />
713 <param name="sOffrate" value="-1" />
714 <param name="sSeed" value="-1" />
715 <param name="suppressHeader" value="true" />
716 <output name="output" ftype="sam" file="bowtie_out9.sam" sort="True" />
717 </test>
718 <test>
719 <!--
720 Bowtie command:
721 bowtie-build +offrate 5 +ftabchars 10 +little -f test-data/phiX.fasta phiX_base
722 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
723 sort bowtie_out10_u.sam > bowtie_out10.sam
724 -p is the number of threads. You need to replace the + with 2 dashes.
725 chrM_base is the index files' location/base name.
726 -->
727 <param name="genomeSource" value="history" />
728 <param name="ownFile" value="phiX.fasta" />
729 <param name="indexSettings" value="indexFull" />
730 <param name="autoB" value="auto" />
731 <param name="nodc" value="dc" />
732 <param name="noref" value="ref" />
733 <param name="offrate" value="5" />
734 <param name="ftab" value="10" />
735 <param name="ntoa" value="no" />
736 <param name="endian" value="little" />
737 <param name="seed" value="-1" />
738 <param name="sPaired" value="paired" />
739 <param name="pInput1" ftype="fastqsanger" value="bowtie_in5.fastqsanger" />
740 <param name="pInput2" ftype="fastqsanger" value="bowtie_in6.fastqsanger" />
741 <param name="pMaxInsert" value="1000" />
742 <param name="pMateOrient" value="ff" />
743 <param name="pSettingsType" value="preSet" />
744 <param name="suppressHeader" value="true" />
745 <output name="output" ftype="sam" file="bowtie_out10.sam" sort="True" />
746 </test>
747 </tests>
748
749 <help>
750
751 **What it does**
752
753 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.
754
755 .. _Bowtie: http://bowtie-bio.sourceforge.net/index.shtml
756
757 ------
758
759 **Know what you are doing**
760
761 .. class:: warningmark
762
763 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.
764
765 .. __: http://bowtie-bio.sourceforge.net/index.shtml
766
767 ------
768
769 **Input formats**
770
771 Bowtie accepts files in Sanger FASTQ format. Use the FASTQ Groomer to prepare your files.
772
773 ------
774
775 **A Note on Built-in Reference Genomes**
776
777 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.
778
779 ------
780
781 **Outputs**
782
783 The output is in SAM format, and has the following columns::
784
785 Column Description
786 -------- --------------------------------------------------------
787 1 QNAME Query (pair) NAME
788 2 FLAG bitwise FLAG
789 3 RNAME Reference sequence NAME
790 4 POS 1-based leftmost POSition/coordinate of clipped sequence
791 5 MAPQ MAPping Quality (Phred-scaled)
792 6 CIGAR extended CIGAR string
793 7 MRNM Mate Reference sequence NaMe ('=' if same as RNAME)
794 8 MPOS 1-based Mate POSition
795 9 ISIZE Inferred insert SIZE
796 10 SEQ query SEQuence on the same strand as the reference
797 11 QUAL query QUALity (ASCII-33 gives the Phred base quality)
798 12 OPT variable OPTional fields in the format TAG:VTYPE:VALUE
799
800 The flags are as follows::
801
802 Flag Description
803 ------ -------------------------------------
804 0x0001 the read is paired in sequencing
805 0x0002 the read is mapped in a proper pair
806 0x0004 the query sequence itself is unmapped
807 0x0008 the mate is unmapped
808 0x0010 strand of the query (1 for reverse)
809 0x0020 strand of the mate
810 0x0040 the read is the first read in a pair
811 0x0080 the read is the second read in a pair
812 0x0100 the alignment is not primary
813
814 It looks like this (scroll sideways to see the entire example)::
815
816 QNAME FLAG RNAME POS MAPQ CIAGR MRNM MPOS ISIZE SEQ QUAL OPT
817 HWI-EAS91_1_30788AAXX:1:1:1761:343 4 * 0 0 * * 0 0 AAAAAAANNAAAAAAAAAAAAAAAAAAAAAAAAAAACNNANNGAGTNGNNNNNNNGCTTCCCACAGNNCTGG hhhhhhh;;hhhhhhhhhhh^hOhhhhghhhfhhhgh;;h;;hhhh;h;;;;;;;hhhhhhghhhh;;Phhh
818 HWI-EAS91_1_30788AAXX:1:1:1578:331 4 * 0 0 * * 0 0 GTATAGANNAATAAGAAAAAAAAAAATGAAGACTTTCNNANNTCTGNANNNNNNNTCTTTTTTCAGNNGTAG hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhhhh;;h;;hhhh;h;;;;;;;hhhhhhhhhhh;;hhVh
819
820 -------
821
822 **Bowtie settings**
823
824 All of the options have a default value. You can change any of them. Most of the options in Bowtie have been implemented here.
825
826 ------
827
828 **Bowtie parameter list**
829
830 This is an exhaustive list of Bowtie options:
831
832 For indexing (bowtie-build)::
833
834 -a No auto behavior. Disable the default behavior where bowtie automatically
835 selects values for --bmax/--bmaxdivn/--dcv/--packed parameters according
836 to the memory available. [off]
837 --packed Packing. Use a packed representation for DNA strings. [auto]
838 --bmax INT Suffix maximum. The maximum number of suffixes allowed in a block. [auto]
839 --bmaxdivn INT Suffix maximum fraction. The maximum number of suffixes allowed in a block
840 expressed as a fraction of the length of the reference. [4]
841 --dcv INT Difference-cover sample. Use INT as the period for the difference-cover
842 sample. [1024]
843 --nodc INT No difference-cover sample. Disable the difference-cover sample. [off]
844 -r No reference indexes. Do not build the NAME.3.ebwt and NAME.4.ebwt portions
845 of the index. Used only for paired-end alignment. [off]
846 -o Offrate. How many Burrows-Wheeler rows get marked by the indexer. The
847 indexer will mark every 2^INT rows. The marked rows correspond to rows on
848 the genome. [5]
849 -t INT The ftab lookup table used to calculate an initial Burrows-Wheeler range
850 with respect to the first INT characters of the query. Ftab size is 4^(INT+1)
851 bytes. [10]
852 --ntoa N conversion. Convert Ns to As before building the index. Otherwise, Ns are
853 simply excluded from the index and Bowtie will not find alignments that
854 overlap them. [off]
855 --big Endianness. Endianness to use when serializing integers to the index file. [off]
856 --little Endianness. [--little]
857 --seed INT Random seed. Use INT as the seed for the pseudo-random number generator. [off]
858
859 For aligning (bowtie)::
860
861 -s INT Skip. Do not align the first INT reads or pairs in the input. [off]
862 -u INT Align limit. Only align the first INT reads/pairs from the input. [no limit]
863 -5 INT High-quality trim. Trim INT bases from the high-quality (left) end of each
864 read before alignment. [0]
865 -3 INT Low-quality trim. Trim INT bases from the low-quality (right) end of each
866 read before alignment. [0]
867 -n INT Mismatch seed. Maximum number of mismatches permitted in the seed (defined
868 with seed length option). Can be 0, 1, 2, or 3. [2]
869 -e INT Mismatch quality. Maximum permitted total of quality values at mismatched
870 read positions. Bowtie rounds quality values to the nearest 10 and saturates
871 at 30. [70]
872 -l INT Seed length. The number of bases on the high-quality end of the read to
873 which the -n ceiling applies. Must be at least 5. [28]
874 --nomaqround Suppress Maq rounding. Values are internally rounded to the nearest 10 and
875 saturate at 30. This options turns off that rounding. [off]
876 -v INT Maq- or SOAP-like alignment policy. This option turns off the default
877 Maq-like alignment policy in favor of a SOAP-like one. End-to-end alignments
878 with at most INT mismatches. [off]
879 -I INT Minimum insert. The minimum insert size for valid paired-end alignments.
880 Does checking on untrimmed reads if -5 or -3 is used. [0]
881 -X INT Maximum insert. The maximum insert size for valid paired-end alignments.
882 Does checking on untrimmed reads if -5 or -3 is used. [250]
883 --fr Mate orientation. The upstream/downstream mate orientations for a valid
884 paired-end alignment against the forward reference strand. [--fr]
885 --rf Mate orientation. [off]
886 --ff Mate orientation. [off]
887 --pairtries INT Maximum alignment attempts for paired-end data. [100]
888 --nofw No forward aligning. Choosing this option means that Bowtie will not attempt
889 to align against the forward reference strand. [off]
890 --norc No reverse-complement aligning. Setting this will mean that Bowtie will not
891 attempt to align against the reverse-complement reference strand. [off]
892 --un FILENAME Write all reads that could not be aligned to file [off]
893 --max FILENAME Write all reads with a number of valid alignments exceeding the limit
894 set with the -m option to file [off]
895 --maxbts INT Maximum backtracks. The maximum number of backtracks permitted when aligning
896 a read in -n 2 or -n 3 mode. [125 without --best] [800 with --best]
897 -y Try hard. Try as hard as possible to find valid alignments when they exist,
898 including paired-end alignments. [off]
899 --chunkmbs INT Thread memory. The number of megabytes of memory a given thread is given to
900 store path descriptors in --best mode. [32]
901 -k INT Valid alignments. The number of valid alignments per read or pair. [off]
902 -a All valid alignments. Choosing this means that all valid alignments per read
903 or pair will be reported. [off]
904 -m INT Suppress alignments. Suppress all alignments for a particular read or pair
905 if more than INT reportable alignments exist for it. [no limit]
906 --best Best mode. Make Bowtie guarantee that reported singleton alignments are
907 "best" in terms of stratum (the number of mismatches) and quality values at
908 mismatched position. [off]
909 --strata Best strata. When running in best mode, report alignments that fall into the
910 best stratum if there are ones falling into more than one. [off]
911 -o INT Offrate override. Override the offrate of the index with INT. Some row
912 markings are discarded when index read into memory. INT must be greater than
913 the value used to build the index (default: 5). [off]
914 --seed INT Random seed. Use INT as the seed for the pseudo-random number generator. [off]
915 --snpphred INT Use INT as the SNP penalty for decoding colorspace alignments. True ratio of
916 SNPs per base in the subject genome. [see --snpfrac]
917 --snpfrac DEC Use DEC as the estimated ratio of SNPs per base when decoding colorspace
918 alignments. [0.001]
919 --col-keepends Keep the extreme-end nucleotides and qualities when decoding colorspace
920 alignments. [off]
921
922 </help>
923 <citations>
924 <citation type="doi">10.1186/gb-2009-10-3-r25</citation>
925 </citations>
926 </tool>