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Migrated tool version 0.0.19 from old tool shed archive to new tool shed repository
author nilshomer
date Tue, 07 Jun 2011 17:28:45 -0400
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1 <tool id="tmap_wrapper" name="Map with TMAP" version="0.0.19">
2 <description>for Ion Torrent</description>
3 <parallelism method="basic"></parallelism>
4 <command interpreter="python">
5 tmap_wrapper.py
6
7 ## reference source
8 --fileSource=$genomeSource.refGenomeSource
9 #if $genomeSource.refGenomeSource == "history":
10 ##build index on the fly
11 --ref="${genomeSource.ownFile}"
12 --dbkey=$dbkey
13 #else:
14 ##use precomputed indexes
15 --ref="${ filter( lambda x: str( x[0] ) == str( $genomeSource.indices ), $__app__.tool_data_tables[ 'tmap_indexes' ].get_fields() )[0][-1] }"
16 --do_not_build_index
17 #end if
18
19 ## input fastq
20 --fastq=$input
21
22 ## output file
23 --output=$output
24
25 ## run parameters
26 --params=$params.source_select
27 #if $params.source_select != "pre_set":
28 --mapall=$params.mapall.source_select
29 #if $params.mapall.source_select == "true":
30 --threads=$params.mapall.threads
31 --matchScore=$params.mapall.matchScore
32 --mismatchPenalty=$params.mapall.mismatchPenalty
33 --gapOpenPenalty=$params.mapall.gapOpenPenalty
34 --gapExtensPenalty=$params.mapall.gapExtensPenalty
35 --flowPenalty=$params.mapall.flowPenalty
36 --flowOrder=$params.mappll.flowOrder
37 --bandWidth=$params.mapall.bandWidth
38 --globalMap=$params.mapall.globalMap
39 --duplicateWindow=$params.mapall.duplicateWindow
40 --scoringThreshold=$params.mapall.scoringThreshold
41 --queueSize=$params.mapall.queueSize
42 --outputFilter=$params.mapall.outputFilter
43 --rgTag=$params.mapall.rgTag.source_select
44 #if $params.mapall.rgTag.source_select == "true":
45 --rgTagID=$params.mapall.rgTag.rgTagID
46 --rgTagCN=$params.mapall.rgTag.rgTagCN
47 --rgTagDS=$params.mapall.rgTag.rgTagDS
48 --rgTagDT=$params.mapall.rgTag.rgTagDT
49 --rgTagLB=$params.mapall.rgTag.rgTagLB
50 --rgTagPI=$params.mapall.rgTag.rgTagPI
51 --rgTagPL=$params.mapall.rgTag.rgTagPL
52 --rgTagPU=$params.mapall.rgTag.rgTagPU
53 --rgTagSM=$params.mapall.rgTag.rgTagSM
54 #end if
55 --filterIndependently=$params.mapall.filterIndependently
56 #end if
57 --map1=$params.map1.source_select
58 #if $params.map1.source_select == "true":
59 --map1SeedLength=$params.map1.map1SeedLength
60 --map1SeedMismatches=$params.map1.map1SeedMismatches
61 --map1SecondarySeedLength=$params.map1.map1SecondarySeedLength
62 --map1NumEdits=$params.map1.map1NumEdits
63 --map1BaseError=$params.map1.map1BaseError
64 --map1Mismatches=$params.map1.map1Mismatches
65 --map1GapOpens=$params.map1.map1GapOpens
66 --map1GapExtensions=$params.map1.map1GapExtensions
67 --map1MaxCALsDeletion=$params.map1.map1MaxCALsDeletion
68 --map1EndIndels=$params.map1.map1EndIndels
69 --map1MaxOptimalCALs=$params.map1.map1MaxOptimalCALs
70 --map1MaxNodes=$params.map1.map1MaxNodes
71 #end if
72 --map2=$params.map2.source_select
73 #if $params.map2.source_select == "true":
74 --map2Coefficient=$params.map2.map2Coefficient
75 --map2SeedIntervalSize=$params.map2.map2SeedIntervalSize
76 --map2ZBest=$params.map2.map2ZBest
77 --map2ReverseTrigger=$params.map2.map2ReverseTrigger
78 #end if
79 --map3=$params.map3.source_select
80 #if $params.map3.source_select == "true":
81 --map3SeedLength=$params.map3.map3SeedLength
82 --map3SeedMaxHits=$params.map3.map3SeedMaxHits
83 --map3SeedWindow=$params.map3.map3SeedWindow
84 --map3HPEnumeration=$params.map3.map3HPEnumeration
85 #end if
86 --MAP1=$params.MAP1.source_select
87 #if $params.MAP1.source_select == "true":
88 --MAP1SeedLength=$params.MAP1.MAP1SeedLength
89 --MAP1SeedMismatches=$params.MAP1.MAP1SeedMismatches
90 --MAP1SecondarySeedLength=$params.MAP1.MAP1SecondarySeedLength
91 --MAP1NumEdits=$params.MAP1.MAP1NumEdits
92 --MAP1BaseError=$params.MAP1.MAP1BaseError
93 --MAP1Mismatches=$params.MAP1.MAP1Mismatches
94 --MAP1GapOpens=$params.MAP1.MAP1GapOpens
95 --MAP1GapExtensions=$params.MAP1.MAP1GapExtensions
96 --MAP1MaxCALsDeletion=$params.MAP1.MAP1MaxCALsDeletion
97 --MAP1EndIndels=$params.MAP1.MAP1EndIndels
98 --MAP1MaxOptimalCALs=$params.MAP1.MAP1MaxOptimalCALs
99 --MAP1MaxNodes=$params.MAP1.MAP1MaxNodes
100 #end if
101 --MAP2=$params.MAP2.source_select
102 #if $params.MAP2.source_select == "true":
103 --MAP2Coefficient=$params.MAP2.MAP2Coefficient
104 --MAP2SeedIntervalSize=$params.MAP2.MAP2SeedIntervalSize
105 --MAP2ZBest=$params.MAP2.MAP2ZBest
106 --MAP2ReverseTrigger=$params.MAP2.MAP2ReverseTrigger
107 #end if
108 --MAP3=$params.MAP3.source_select
109 #if $params.MAP3.source_select == "true":
110 --MAP3SeedLength=$params.MAP3.MAP3SeedLength
111 --MAP3SeedMaxHits=$params.MAP3.MAP3SeedMaxHits
112 --MAP3SeedWindow=$params.MAP3.MAP3SeedWindow
113 --MAP3HPEnumeration=$params.MAP3.MAP3HPEnumeration
114 #end if
115 #else:
116 --threads="4"
117 --map1="false"
118 --map2="false"
119 --map3="false"
120 --MAP1="false"
121 --MAP2="false"
122 --MAP3="false"
123 #end if
124
125 ## suppress output SAM header
126 --suppressHeader=$suppressHeader
127 </command>
128 <requirements>
129 <requirement type='package'>tmap</requirement>
130 </requirements>
131 <inputs>
132 <conditional name="genomeSource">
133 <param name="refGenomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?">
134 <option value="indexed">Use a built-in index</option>
135 <option value="history">Use one from the history</option>
136 </param>
137 <when value="indexed">
138 <param name="indices" type="select" label="Select a reference genome">
139 <options from_data_table="tmap_indexes">
140 <filter type="sort_by" column="3" />
141 <validator type="no_options" message="No indexes are available for the selected input dataset" />
142 </options>
143 </param>
144 </when>
145 <when value="history">
146 <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" />
147 </when>
148 </conditional>
149 <param name="input" type="data" format="fastqsanger" label="FASTQ file" help="Must have Sanger-scaled quality values with ASCII offset 33" />
150 <conditional name="params">
151 <param name="source_select" type="select" label="TMAP settings to use" help="For most mapping needs use Commonly Used settings. If you want full control use Full Parameter List">
152 <option value="pre_set">Commonly Used</option>
153 <option value="full">Full Parameter List</option>
154 </param>
155 <when value="pre_set" />
156 <when value="full">
157 <conditional name="mapall">
158 <param name="source_select" type="select" label="Global options to use">
159 <option value="false" selected="true">Commonly Used</option>
160 <option value="true">Full Parameter List</option>
161 </param>
162 <when value="false" />
163 <when value="true">
164 <param name="threads" type="integer" value="4" label="The number of threads (-n)" />
165 <param name="matchScore" type="integer" value="3" label="Match score (-A)" />
166 <param name="mismatchPenalty" type="integer" value="5" label="Mismatch penalty (-M)" />
167 <param name="gapOpenPenalty" type="integer" value="2" label="Gap open penalty (-O)" />
168 <param name="gapExtensPenalty" type="integer" value="2" label="Gap extension penalty (-E)" />
169 <param name="flowPenalty" type="integer" value="2" label="The score penalty (-X)" />
170 <param name="flowOrder" type="text" value="" label="The flow order ([ACGT]{4+} or sff" />
171 <param name="bandWidth" type="integer" value="50" label="The band width (-w)" />
172 <param name="globalMap" type="integer" value="2" label="The soft clipping type (-g)" help="The soft-clipping type (0 - allow on the right and left, 1 - allow on the left, 2 - allow on the right, 3 - do not allow soft-clipping)" />
173 <param name="duplicateWindow" type="integer" value="128" label="The duplicate window (-W)" help="Remove duplicate alignments from different algorithms within this bp window (-1 to disable)"/>
174 <param name="scoringThreshold" type="integer" value="1" label="The scoring threshold (-T)" help="The score threshold divided by the match score" />
175 <param name="queueSize" type="integer" value="262144" label="The queue size (-q)" help="The queue size for the reads" />
176 <param name="outputFilter" type="integer" value="1" label="The output filter (-a)" help="The output filter (0 - unique best hits, 1 - random best hit, 2 - all best htis, 3 - all alignments)" />
177 <conditional name="rgTag">
178 <param name="source_select" type="select" label="Include Custom Read Group Tags">
179 <option value="false" selected="true">Default</option>
180 <option value="true">Custom</option>
181 </param>
182 <when value="false" />
183 <when value="true">
184 <param name="rgTagID" type="text" value="" label="The Read Group ID (-R)" help="The RG ID used in the RG record in the SAM header" />
185 <param name="rgTagCN" type="text" value="" label="The Read Group CN (-R)" help="The RG CN used in the RG record in the SAM header" />
186 <param name="rgTagDS" type="text" value="" label="The Read Group DS (-R)" help="The RG DS used in the RG record in the SAM header" />
187 <param name="rgTagDT" type="text" value="" label="The Read Group DT (-R)" help="The RG DT used in the RG record in the SAM header" />
188 <param name="rgTagLB" type="text" value="" label="The Read Group LB (-R)" help="The RG LB used in the RG record in the SAM header" />
189 <param name="rgTagPI" type="text" value="" label="The Read Group PI (-R)" help="The RG PI used in the RG record in the SAM header" />
190 <param name="rgTagPL" type="text" value="" label="The Read Group PL (-R)" help="The RG PL used in the RG record in the SAM header" />
191 <param name="rgTagPU" type="text" value="" label="The Read Group PU (-R)" help="The RG PU used in the RG record in the SAM header" />
192 <param name="rgTagSM" type="text" value="" label="The Read Group SM (-R)" help="The RG SM used in the RG record in the SAM header" />
193 </when>
194 </conditional>
195 <param name="filterIndependently" type="boolean" truevalue="true" falsevalue="false" checked="no" label="Filter algorithm independently (-I)" help="apply the output filter for each algorithm separately" />
196 </when>
197 </conditional>
198 <conditional name="map1">
199 <param name="source_select" type="select" label="Map1 Stage One" help="Turn on mapping algorithm #1 in the first stage">
200 <option value="true">Turn On</option>
201 <option value="false" selected="true">Turn Off</option>
202 </param>
203 <when value="true">
204 <param name="map1SeedLength" type="integer" value="32" label="The k-mer length to seed CALs (-1 to disable) (-l)" />
205 <param name="map1SeedMismatches" type="integer" value="2" label="The maximum number of mismatches in the seed (-s)" />
206 <param name="map1SecondarySeedLength" type="integer" value="64" label="The secondary seed length (-1 to disable) (-L)" />
207 <param name="map1NumEdits" type="float" value="-1" label="The maximum number of edits or false-negative probability assuming the maximum error rate (-1 to auto-tune) (-p)" />
208 <param name="map1BaseError" type="float" value="0.02" label="The the assumed per-base maximum error rate (-P)" />
209 <param name="map1Mismatches" type="float" value="3" label="The maximum number of or (read length) fraction of mismatches (-m)" />
210 <param name="map1GapOpens" type="float" value="1" label="The maximum number of or (read length) fraction of indel starts (-o)" />
211 <param name="map1GapExtensions" type="float" value="6" label="The maximum number of or (read length) fraction of indel extensions (-e)" />
212 <param name="map1MaxCALsDeletion" type="integer" value="10" label="The maximum number of CALs to extend a deletion (-d)" />
213 <param name="map1EndIndels" type="integer" value="5" label="Indels are not allowed within this number of bps from the end of the read (-i)" />
214 <param name="map1MaxOptimalCALs" type="integer" value="32" label="Stop searching when INT optimal CALs have been found (-b)" />
215 <param name="map1MaxNodes" type="integer" value="2000000" label="The maximum number of alignment nodes (-Q)" />
216 </when>
217 <when value="false" />
218 </conditional>
219 <conditional name="map2">
220 <param name="source_select" type="select" label="Map2 Stage One" help="Turn on mapping algorithm #2 in the first stage">
221 <option value="true">Turn On</option>
222 <option value="false" selected="true">Turn Off</option>
223 </param>
224 <when value="true">
225 <param name="map2Coefficient" type="float" value="5.5" label="The coefficient of length-threshold adjustment (-c)" />
226 <param name="map2SeedIntervalSize" type="integer" value="3" label="The maximum seeding interval size (-S)" />
227 <param name="map2ZBest" type="integer" value="1" label="Keep the z-best nodes during prefix trie traversal (-b)" />
228 <param name="map2ReverseTrigger" type="integer" value="5" label="The # seeds to trigger reverse alignment (-N)" />
229 </when>
230 <when value="false" />
231 </conditional>
232 <conditional name="map3">
233 <param name="source_select" type="select" label="Map3 Stage One" help="Turn on mapping algorithm #3 in the first stage">
234 <option value="true">Turn On</option>
235 <option value="false" selected="true">Turn Off</option>
236 </param>
237 <when value="true">
238 <param name="map3SeedLength" type="integer" value="-1" label="The k-mer length to seed CALs (-1 tunes to the genome size) (-l)" />
239 <param name="map3SeedMaxHits" type="integer" value="12" label="The maximum number of hits returned by a seed (-S)" />
240 <param name="map3SeedWindow" type="integer" value="25" label="The window of bases in which to group seeds (-b)" />
241 <param name="map3HPEnumeration" type="integer" value="0" label="The single homopolymer error difference for enumeration (-H)" />
242 </when>
243 <when value="false" />
244 </conditional>
245 <conditional name="MAP1">
246 <param name="source_select" type="select" label="Map1 Stage Two" help="Turn on mapping algorithm #1 in the second stage">
247 <option value="true">Turn On</option>
248 <option value="false" selected="true">Turn Off</option>
249 </param>
250 <when value="true">
251 <param name="MAP1SeedLength" type="integer" value="32" label="The k-mer length to seed CALs (-1 to disable) (-l)" />
252 <param name="MAP1SeedMismatches" type="integer" value="2" label="The maximum number of mismatches in the seed (-s)" />
253 <param name="MAP1SecondarySeedLength" type="integer" value="64" label="The secondary seed length (-1 to disable) (-L)" />
254 <param name="MAP1NumEdits" type="float" value="-1" label="The maximum number of edits or false-negative probability assuming the maximum error rate (-1 to auto-tune) (-p)" />
255 <param name="MAP1BaseError" type="float" value="0.02" label="The the assumed per-base maximum error rate (-P)" />
256 <param name="MAP1Mismatches" type="float" value="3" label="The maximum number of or (read length) fraction of mismatches (-m)" />
257 <param name="MAP1GapOpens" type="float" value="1" label="The maximum number of or (read length) fraction of indel starts (-o)" />
258 <param name="MAP1GapExtensions" type="float" value="6" label="The maximum number of or (read length) fraction of indel extensions (-e)" />
259 <param name="MAP1MaxCALsDeletion" type="integer" value="10" label="The maximum number of CALs to extend a deletion (-d)" />
260 <param name="MAP1EndIndels" type="integer" value="5" label="Indels are not allowed within this number of bps from the end of the read (-i)" />
261 <param name="MAP1MaxOptimalCALs" type="integer" value="32" label="Stop searching when INT optimal CALs have been found (-b)" />
262 <param name="MAP1MaxNodes" type="integer" value="2000000" label="The maximum number of alignment nodes (-Q)" />
263 </when>
264 <when value="false" />
265 </conditional>
266 <conditional name="MAP2">
267 <param name="source_select" type="select" label="Map2 Stage Two" help="Turn on mapping algorithm #2 in the second stage">
268 <option value="true">Turn On</option>
269 <option value="false" selected="true">Turn Off</option>
270 </param>
271 <when value="true">
272 <param name="MAP2Coefficient" type="float" value="5.5" label="The coefficient of length-threshold adjustment (-c)" />
273 <param name="MAP2SeedIntervalSize" type="integer" value="3" label="The maximum seeding interval size (-S)" />
274 <param name="MAP2ZBest" type="integer" value="1" label="Keep the z-best nodes during prefix trie traversal (-b)" />
275 <param name="MAP2ReverseTrigger" type="integer" value="5" label="The # seeds to trigger reverse alignment (-N)" />
276 </when>
277 <when value="false" />
278 </conditional>
279 <conditional name="MAP3">
280 <param name="source_select" type="select" label="Map3 Stage Two" help="Turn on mapping algorithm #3 in the second stage">
281 <option value="true">Turn On</option>
282 <option value="false" selected="true">Turn Off</option>
283 </param>
284 <when value="true">
285 <param name="MAP3SeedLength" type="integer" value="-1" label="The k-mer length to seed CALs (-1 tunes to the genome size) (-l)" />
286 <param name="MAP3SeedMaxHits" type="integer" value="12" label="The maximum number of hits returned by a seed (-S)" />
287 <param name="MAP3SeedWindow" type="integer" value="25" label="The window of bases in which to group seeds (-b)" />
288 <param name="MAP3HPEnumeration" type="integer" value="0" label="The single homopolymer error difference for enumeration (-H)" />
289 </when>
290 <when value="false" />
291 </conditional>
292 </when>
293 </conditional>
294 <param name="suppressHeader" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Suppress the header in the output SAM file" help="TMAP produces SAM with several lines of header information" />
295 </inputs>
296 <outputs>
297 <data format="sam" name="output" label="${tool.name} on ${on_string}: mapped reads">
298 <actions>
299 <conditional name="genomeSource.refGenomeSource">
300 <when value="indexed">
301 <action type="metadata" name="dbkey">
302 <option type="from_data_table" name="tmap_indexes" column="0">
303 <filter type="param_value" ref="genomeSource.indices" column="1"/>
304 </option>
305 </action>
306 </when>
307 </conditional>
308 </actions>
309 </data>
310 </outputs>
311 <help>
312
313 **What it does**
314
315 TMAP is a fast light-weight tool that aligns DNA sequences (small queries) to a sequence database (large sequences), such as the human reference genome. TMAP follows a two-stage approach, with a set of algorithms and associated settings for each stage. If there are no mappings for a read by applying the algorithms in the first stage, then the algorithms in the second stage are applied. For example, a set of algorithms to quickly align near-perfect reads may be used in the first stage, while a set of sensitive algorithms may be used to map difficult reads in the second stage.
316
317 It combines multiple mapping algorithms to give sensitive and accurate alignments quickly. It uses three core algorithms, BWA-short, BWA-long, and a variant of the SSAHA algorithm. These algorithms are described in the following publications:
318 - Li, H. and Durbin, R. (2009). Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 25, 1754–1760.
319 - Li, H. and Durbin, R. (2010). Fast and accurate long-read alignment with Burrows-Wheeler
320 - Ning, Z., Cox, A., and Mullikin, J. (2001). SSAHA: a fast search method for large DNA databases. Genome Res., 11, 1725–1729.
321
322 ------
323
324 **Know what you are doing**
325
326 .. class:: warningmark
327
328 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.
329
330 .. __: http://www.iontorrent.com/
331
332 ------
333
334 **Input formats**
335
336 TMAP accepts files in Sanger FASTQ format. Use the FASTQ Groomer to prepare your files.
337
338 ------
339
340 **A Note on Built-in Reference Genomes**
341
342 Some genomes have multiple variants. If only one "type" of genome is listed, it is the Full version, which means that everything that came in the original genome data download (possibly with mitochondrial and plasmid DNA added if it wasn't already included). The Full version is available for every genome. Some genomes also come in the Canonical variant, which contains only the "canonical" (well-defined) chromosomes or segments, such as chr1-chr22, chrX, chrY, and chrM for human. Other variations include gender. These will come in the canonical form only, so the general Canonical variant is actually Canonical Female and the other is Canonical Male (identical to female excluding chrX).
343
344 ------
345
346 **Outputs**
347
348 The output is in SAM format, and has the following columns::
349
350 Column Description
351 -------- --------------------------------------------------------
352 1 QNAME Query (pair) NAME
353 2 FLAG bitwise FLAG
354 3 RNAME Reference sequence NAME
355 4 POS 1-based leftmost POSition/coordinate of clipped sequence
356 5 MAPQ MAPping Quality (Phred-scaled)
357 6 CIGAR extended CIGAR string
358 7 MRNM Mate Reference sequence NaMe ('=' if same as RNAME)
359 8 MPOS 1-based Mate POSition
360 9 ISIZE Inferred insert SIZE
361 10 SEQ query SEQuence on the same strand as the reference
362 11 QUAL query QUALity (ASCII-33 gives the Phred base quality)
363 12 OPT variable OPTional fields in the format TAG:VTYPE:VALU
364
365 The flags are as follows::
366
367 Flag Description
368 ------ -------------------------------------
369 0x0001 the read is paired in sequencing
370 0x0002 the read is mapped in a proper pair
371 0x0004 the query sequence itself is unmapped
372 0x0008 the mate is unmapped
373 0x0010 strand of the query (1 for reverse)
374 0x0020 strand of the mate
375 0x0040 the read is the first read in a pair
376 0x0080 the read is the second read in a pair
377 0x0100 the alignment is not primary
378
379 It looks like this (scroll sideways to see the entire example)::
380
381 QNAME FLAG RNAME POS MAPQ CIAGR MRNM MPOS ISIZE SEQ QUAL OPT
382 HWI-EAS91_1_30788AAXX:1:1:1761:343 4 * 0 0 * * 0 0 AAAAAAANNAAAAAAAAAAAAAAAAAAAAAAAAAAACNNANNGAGTNGNNNNNNNGCTTCCCACAGNNCTGG hhhhhhh;;hhhhhhhhhhh^hOhhhhghhhfhhhgh;;h;;hhhh;h;;;;;;;hhhhhhghhhh;;Phhh
383 HWI-EAS91_1_30788AAXX:1:1:1578:331 4 * 0 0 * * 0 0 GTATAGANNAATAAGAAAAAAAAAAATGAAGACTTTCNNANNTCTGNANNNNNNNTCTTTTTTCAGNNGTAG hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhhhh;;h;;hhhh;h;;;;;;;hhhhhhhhhhh;;hhVh
384
385 -------
386
387 **TMAP settings**
388
389 All of the options have a default value. You can change most of them. Most of the options in TMAP have been implemented here.
390
391 ------
392
393 **TMAP parameter list**
394
395 This is an exhaustive list of TMAP options implemented here:
396
397 For the **global** options::
398
399 -A INT score for a match [5]
400 -M INT the mismatch penalty [3]
401 -O INT the indel start penalty [3]
402 -E INT the indel extend penalty [1]
403 -X INT the flow score penalty [7]
404 -w INT the band width [50]
405 -g map the full read [false]
406 -W INT remove duplicate alignments from different algorithms within this bp window (-1 to disable) [128]
407 -T INT score threshold divided by the match score [30]
408 -q INT the queue size for the reads (-1 disables) [65536]
409 -n INT the number of threads [1]
410 -a INT output filter [1]
411 0 - unique best hits
412 1 - random best hit
413 2 - all best hits
414 3 - all alignments
415 -R STRING the RG tags to add to the SAM header [(null)]
416
417 For **mapall** options::
418
419 -I apply the output filter for each algorithm separately [false]
420
421 For **map1** options::
422
423 -l INT the k-mer length to seed CALs (-1 to disable) [32]
424 -s INT maximum number of mismatches in the seed [3]
425 -m NUM maximum number of or (read length) fraction of mismatches [number: 2]
426 -o NUM maximum number of or (read length) fraction of indel starts [number: 1]
427 -e NUM maximum number of or (read length) fraction of indel extensions [number: 6]
428 -d INT the maximum number of CALs to extend a deletion [10]
429 -i INT indels are not allowed within INT number of bps from the end of the read [5]
430 -b INT stop searching when INT optimal CALs have been found [32]
431 -Q INT maximum number of alignment nodes [2000000]
432
433 For **map2** options::
434
435 -c FLOAT coefficient of length-threshold adjustment [5.5]
436 -S INT maximum seeding interval size [3]
437 -b INT Z-best [1]
438 -N INT # seeds to trigger reverse alignment [5]
439
440 For **map3** options::
441
442 -l INT the k-mer length to seed CALs (-1 tunes to the genome size) [-1]
443 -S INT the maximum number of hits returned by a seed [8]
444 -b INT the window of bases in which to group seeds [50]
445 -H INT single homopolymer error difference for enumeration [0]
446
447 </help>
448 </tool>
449
450