root/galaxy-central/tools/sr_mapping/bowtie_wrapper.xml

リビジョン 2, 39.2 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central
行番号 
1<tool id="bowtie_wrapper" name="Map with Bowtie for Illumina" version="1.0.6">
2  <requirements><requirement type='package'>bowtie</requirement></requirements>
3  <description></description>
4  <command interpreter="python">
5    bowtie_wrapper.py
6    --threads="4"
7    --dataType="solexa"
8    --output=$output
9    --suppressHeader=$suppressHeader
10    --genomeSource=$refGenomeSource.genomeSource
11    --snpphred="None"
12    --snpfrac="None"
13    --keepends="None"
14    #if $refGenomeSource.genomeSource == "history":
15       #if $refGenomeSource.ownFile.extension.startswith( 'bowtie_' ):
16       --ref="${refGenomeSource.ownFile.extra_files_path}/${refGenomeSource.ownFile.metadata.base_name}"
17       --do_not_build_index
18       #else:
19     --ref=$refGenomeSource.ownFile
20     --indexSettings=$refGenomeSource.indexParams.indexSettings
21     #if $refGenomeSource.indexParams.indexSettings == "indexFull":
22      --iautoB=$refGenomeSource.indexParams.autoBehavior.autoB
23      #if $refGenomeSource.indexParams.autoBehavior.autoB == "set":
24       --ipacked=$refGenomeSource.indexParams.autoBehavior.packed
25       --ibmax=$refGenomeSource.indexParams.autoBehavior.bmax
26       --ibmaxdivn=$refGenomeSource.indexParams.autoBehavior.bmaxdivn
27       --idcv=$refGenomeSource.indexParams.autoBehavior.dcv
28      #else:
29       --ipacked="None"
30       --ibmax="None"
31       --ibmaxdivn="None"
32       --idcv="None"
33      #end if
34      --inodc=$refGenomeSource.indexParams.nodc
35      --inoref=$refGenomeSource.indexParams.noref
36      --ioffrate=$refGenomeSource.indexParams.offrate
37      --iftab=$refGenomeSource.indexParams.ftab
38      --intoa=$refGenomeSource.indexParams.ntoa
39      --iendian=$refGenomeSource.indexParams.endian
40      --iseed=$refGenomeSource.indexParams.seed
41      --icutoff=$refGenomeSource.indexParams.cutoff
42     #else:
43      --iautoB="None"
44      --ipacked="None"
45      --ibmax="None"
46      --ibmaxdivn="None"
47      --idcv="None"
48      --inodc="None"
49      --inoref="None"
50      --ioffrate="None"
51      --iftab="None"
52      --intoa="None"
53      --iendian="None"
54      --iseed="None"
55      --icutoff="None"
56     #end if
57     #end if
58    #else:
59     --ref=$refGenomeSource.index
60     --indexSettings="None"
61     --iautoB="None"
62     --ipacked="None"
63     --ibmax="None"
64     --ibmaxdivn="None"
65     --idcv="None"
66     --inodc="None"
67     --inoref="None"
68     --ioffrate="None"
69     --iftab="None"
70     --intoa="None"
71     --iendian="None"
72     --iseed="None"
73     --icutoff="None"
74    #end if
75    --paired=$singlePaired.sPaired
76    #if $singlePaired.sPaired == "single":
77     --input1=$singlePaired.sInput1
78     --input2="None"
79     --params=$singlePaired.sParams.sSettingsType
80     #if $singlePaired.sParams.sSettingsType == "full":
81      --skip=$singlePaired.sParams.sSkip
82      --alignLimit=$singlePaired.sParams.sAlignLimit
83      --trimH=$singlePaired.sParams.sTrimH
84      --trimL=$singlePaired.sParams.sTrimL
85      --mismatchSeed=$singlePaired.sParams.sMismatchSeed
86      --mismatchQual=$singlePaired.sParams.sMismatchQual
87      --seedLen=$singlePaired.sParams.sSeedLen
88      --rounding=$singlePaired.sParams.sRounding
89      --maqSoapAlign=$singlePaired.sParams.sMaqSoapAlign
90      --tryHard=$singlePaired.sParams.sTryHard
91      --valAlign=$singlePaired.sParams.sValAlign
92      --allValAligns=$singlePaired.sParams.sAllValAligns
93      --suppressAlign=$singlePaired.sParams.sSuppressAlign
94      --best=$singlePaired.sParams.sBestOption.sBest
95      #if $singlePaired.sParams.sBestOption.sBest == "doBest":
96       --maxBacktracks=$singlePaired.sParams.sBestOption.sdMaxBacktracks
97       --strata=$singlePaired.sParams.sBestOption.sdStrata
98      #else:
99       --maxBacktracks=$singlePaired.sParams.sBestOption.snMaxBacktracks
100       --strata="None"
101      #end if
102      --offrate=$singlePaired.sParams.sOffrate
103      --seed=$singlePaired.sParams.sSeed
104     #else:
105      --skip="None"
106      --alignLimit="None"
107      --trimH="None"
108      --trimL="None"
109      --mismatchSeed="None"
110      --mismatchQual="None"
111      --seedLen="None"
112      --rounding="None"
113      --maqSoapAlign="None"
114      --tryHard="None"
115      --valAlign="None"
116      --allValAligns="None"
117      --suppressAlign="None"
118      --best="None"
119      --maxBacktracks="None"
120      --strata="None"
121      --offrate="None"
122      --seed="None"
123      --snpphred="None"
124      --snpfrac="None"
125      --keepends="None"
126     #end if
127     --minInsert="None"
128     --maxInsert="None"
129     --mateOrient="None"
130     --maxAlignAttempt="None"
131     --forwardAlign="None"
132     --reverseAlign="None"
133    #else:
134     --input1=$singlePaired.pInput1
135     --input2=$singlePaired.pInput2
136     --maxInsert=$singlePaired.pMaxInsert
137     --mateOrient=$singlePaired.pMateOrient
138     --params=$singlePaired.pParams.pSettingsType
139     #if $singlePaired.pParams.pSettingsType == "full":
140      --skip=$singlePaired.pParams.pSkip
141      --alignLimit=$singlePaired.pParams.pAlignLimit
142      --trimH=$singlePaired.pParams.pTrimH
143      --trimL=$singlePaired.pParams.pTrimL
144      --mismatchSeed=$singlePaired.pParams.pMismatchSeed
145      --mismatchQual=$singlePaired.pParams.pMismatchQual
146      --seedLen=$singlePaired.pParams.pSeedLen
147      --rounding=$singlePaired.pParams.pRounding
148      --maqSoapAlign=$singlePaired.pParams.pMaqSoapAlign
149      --minInsert=$singlePaired.pParams.pMinInsert
150      --maxAlignAttempt=$singlePaired.pParams.pMaxAlignAttempt
151      --forwardAlign=$singlePaired.pParams.pForwardAlign
152      --reverseAlign=$singlePaired.pParams.pReverseAlign
153      --tryHard=$singlePaired.pParams.pTryHard
154      --valAlign=$singlePaired.pParams.pValAlign
155      --allValAligns=$singlePaired.pParams.pAllValAligns
156      --suppressAlign=$singlePaired.pParams.pSuppressAlign
157      --best=$singlePaired.pParams.pBestOption.pBest
158      #if $singlePaired.pParams.pBestOption.pBest == "doBest":
159       --maxBacktracks=$singlePaired.pParams.pBestOption.pdMaxBacktracks
160       --strata=$singlePaired.pParams.pBestOption.pdStrata
161      #else:
162       --maxBacktracks=$singlePaired.pParams.pBestOption.pnMaxBacktracks
163       --strata="None"
164      #end if
165      --offrate=$singlePaired.pParams.pOffrate
166      --seed=$singlePaired.pParams.pSeed
167     #else:
168      --skip="None"
169      --alignLimit="None"
170      --trimH="None"
171      --trimL="None"
172      --mismatchSeed="None"
173      --mismatchQual="None"
174      --seedLen="None"
175      --rounding="None"
176      --maqSoapAlign="None"
177      --tryHard="None"
178      --valAlign="None"
179      --allValAligns="None"
180      --suppressAlign="None"
181      --best="None"
182      --maxBacktracks="None"
183      --strata="None"
184      --offrate="None"
185      --seed="None"
186      --minInsert="None"
187      --maxAlignAttempt="None"
188      --forwardAlign="None"
189      --reverseAlign="None"
190     #end if
191    #end if
192  </command>
193  <inputs>
194    <conditional name="refGenomeSource">
195      <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">
196        <option value="indexed">Use a built-in index</option>
197        <option value="history">Use one from the history</option>
198      </param>
199      <when value="indexed">
200        <param name="index" type="select" label="Select a reference genome" help="if your genome of interest is not listed - contact Galaxy team">
201          <options from_data_table="bowtie_indexes"/>
202          <!--
203          <options from_file="bowtie_indices.loc">
204            <column name="value" index="1" />
205            <column name="name" index="0" />
206          </options>
207          -->
208        </param>
209      </when>
210      <when value="history">
211        <param name="ownFile" type="data" format="bowtie_base_index,fasta" metadata_name="dbkey" label="Select the reference genome" />
212        <conditional name="indexParams">
213          <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">
214            <option value="indexPreSet">Default</option>
215            <option value="indexFull">Set your own</option>
216          </param>
217          <when value="indexPreSet" />
218          <when value="indexFull">
219            <conditional name="autoBehavior">
220              <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">
221                <option value="auto">Automatic behavior</option>
222                <option value="set">Set values (sets --noauto and allows others to be set)</option>
223              </param>
224              <when value="auto" />
225              <when value="set">
226                <param name="packed" type="select" label="Whether or not to use a packed representation for DNA strings (--packed)">
227                  <option value="unpacked">Use regular representation</option>
228                  <option value="packed">Use packed representation</option>
229                </param>
230                <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" />
231                <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)" />
232                <param name="dcv" type="integer" value="1024" label="The period for the difference-cover sample (--dcv)" />
233              </when>
234            </conditional>
235            <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)">
236              <option value="dc">Use difference-cover sample</option>
237              <option value="nodc">Disable difference-cover sample</option>
238            </param>
239            <param name="noref" type="select" label="Whether or not to build the part of the reference index used only in paired-end alignment (-r)">
240              <option value="ref">Build all index files</option>
241              <option value="noref">Do not build paired-end alignment index files</option>
242            </param>
243            <param name="offrate" type="integer" value="5" label="How many rows get marked during annotation of some or all of the Burrows-Wheeler rows (-o)" />
244            <param name="ftab" type="integer" value="10" label="The size of the lookup table used to calculate an initial Burrows-Wheeler range with respect to the first n characters of the query (-t)" help="ftab is 4^(n+1) bytes" />
245            <param name="ntoa" type="select" label="Whether or not to convert Ns in the reference sequence to As (--ntoa)">
246              <option value="no">Do not convert Ns</option>
247              <option value="yes">Convert Ns to As</option>
248            </param>
249            <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">
250              <option value="little">Little</option>
251              <option value="big">Big</option>
252            </param>
253            <param name="seed" type="integer" value="-1" label="Seed for the pseudorandom number generator (--seed)" help="Use -1 to use default" />
254            <param name="cutoff" type="integer" value="-1" label="Number of first bases of the reference sequence to index (--cutoff)" help="Use -1 to use default" />
255          </when>  <!-- indexFull -->
256        </conditional>  <!-- indexParams -->
257      </when>  <!-- history -->
258    </conditional>  <!-- refGenomeSource -->
259    <conditional name="singlePaired">
260      <param name="sPaired" type="select" label="Is this library mate-paired?">
261        <option value="single">Single-end</option>
262        <option value="paired">Paired-end</option>
263      </param>
264      <when value="single">
265        <param name="sInput1" type="data" format="fastqsanger" label="FASTQ file" help="Must have Sanger-scaled quality values with ASCII offset 33"/>
266        <conditional name="sParams">
267          <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">
268            <option value="preSet">Commonly used</option>
269            <option value="full">Full parameter list</option>
270            </param>
271          <when value="preSet" />
272          <when value="full">
273            <param name="sSkip" type="integer" value="0" label="Skip the first n reads (-s)" /> 
274            <param name="sAlignLimit" type="integer" value="-1" label="Only align the first n reads (-u)" help="-1 for off" /> 
275            <param name="sTrimH" type="integer" value="0" label="Trim n bases from high-quality (left) end of each read before alignment (-5)" />
276            <param name="sTrimL" type="integer" value="0" label="Trim n bases from low-quality (right) end of each read before alignment (-3)" />
277            <param name="sMismatchSeed" type="integer" value="2" label="Maximum number of mismatches permitted in the seed (-n)" help="May be 0, 1, 2, or 3" />
278            <param name="sMismatchQual" type="integer" value="70" label="Maximum permitted total of quality values at mismatched read positions (-e)" />
279            <param name="sSeedLen" type="integer" value="28" label="Seed length (-l)" help="Minimum value is 5" />
280            <param name="sRounding" type="select" label="Whether or not to round to the nearest 10 and saturating at 30 (--nomaqround)">
281              <option value="round">Round to nearest 10</option>
282              <option value="noRound">Do not round to nearest 10</option>
283            </param>
284            <param name="sMaqSoapAlign" type="integer" value="-1" label="Number of mismatches for SOAP-like alignment policy (-v)" help="-1 for default MAQ-like alignment policy" />
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            <param name="sValAlign" type="integer" value="1" label="Report up to n valid alignments per read (-k)" />
290            <param name="sAllValAligns" type="select" label="Whether or not to report all valid alignments per read (-a)">
291              <option value="noAllValAligns">Do not report all valid alignments</option>
292              <option value="doAllValAligns">Report all valid alignments</option>
293            </param>
294            <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" />
295            <conditional name="sBestOption">
296              <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">
297                <option value="noBest">Do not use best</option>
298                <option value="doBest">Use best</option>
299              </param>
300              <when value="noBest">
301                <param name="snMaxBacktracks" type="integer" value="125" label="Maximum number of backtracks permitted when aligning a read (--maxbts)" />
302              </when>
303              <when value="doBest">
304                <param name="sdMaxBacktracks" type="integer" value="800" label="Maximum number of backtracks permitted when aligning a read (--maxbts)" />
305                <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)">
306                  <option value="noStrata">Do not use strata option</option>
307                  <option value="doStrata">Use strata option</option>
308                </param>
309              </when>
310            </conditional> <!-- bestOption -->
311            <param name="sOffrate" type="integer" value="-1" label="Override the offrate of the index to n (-o)" help="-1 for default" />
312            <param name="sSeed" type="integer" value="-1" label="Seed for pseudo-random number generator (--seed)" help="-1 for default" />
313          </when> <!-- full -->
314        </conditional> <!-- sParams -->
315      </when> <!-- single -->
316      <when value="paired">
317        <param name="pInput1" type="data" format="fastqsanger" label="Forward FASTQ file" help="Must have Sanger-scaled quality values with ASCII offset 33"/>
318        <param name="pInput2" type="data" format="fastqsanger" label="Reverse FASTQ file" help="Must have Sanger-scaled quality values with ASCII offset 33"/>
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            <param name="pMismatchSeed" type="integer" value="2" label="Maximum number of mismatches permitted in the seed (-n)" help="May be 0, 1, 2, or 3" />
337            <param name="pMismatchQual" type="integer" value="70" label="Maximum permitted total of quality values at mismatched read positions (-e)" />
338            <param name="pSeedLen" type="integer" value="28" label="Seed length (-l)" help="Minimum value is 5" />
339            <param name="pRounding" type="select" label="Whether or not to round to the nearest 10 and saturating at 30 (--nomaqround)">
340              <option value="round">Round to nearest 10</option>
341              <option value="noRound">Do not round to nearest 10</option>
342            </param>
343            <param name="pMaqSoapAlign" type="integer" value="-1" label="Number of mismatches for SOAP-like alignment policy (-v)" help="-1 for default MAQ-like alignment policy" />
344            <param name="pMinInsert" type="integer" value="0" label="Minimum insert size for valid paired-end alignments (-I)" />
345            <param name="pMaxAlignAttempt" type="integer" value="100" label="Maximum number of attempts Bowtie will make to match an alignment for one mate with an alignment for the opposite mate (--pairtries)" />
346            <param name="pForwardAlign" type="select" label="Choose whether or not to attempt to align the forward reference strand (--nofw)">
347              <option value="forward">Align against the forward reference strand</option>
348              <option value="noForward">Do not align against the forward reference strand</option>
349            </param>
350            <param name="pReverseAlign" type="select" label="Choose whether or not to align against the reverse-complement reference strand (--norc)">
351              <option value="reverse">Align against the reverse-complement reference strand</option>
352              <option value="noReverse">Do not align against the reverse-complement reference strand</option>
353            </param>
354            <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">
355              <option value="noTryHard">Do not try hard</option>
356              <option value="doTryHard">Try hard</option>
357            </param>
358            <param name="pValAlign" type="integer" value="1" label="Report up to n valid arguments per pair (-k)" />
359            <param name="pAllValAligns" type="select" label="Whether or not to report all valid alignments per pair (-a)">
360              <option value="noAllValAligns">Do not report all valid alignments</option>
361              <option value="doAllValAligns">Report all valid alignments</option>
362            </param>
363            <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" />
364            <conditional name="pBestOption">
365              <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">
366                <option value="noBest">Do not use best</option>
367                <option value="doBest">Use best</option>
368              </param>
369              <when value="noBest">
370                <param name="pnMaxBacktracks" type="integer" value="125" label="Maximum number of backtracks permitted when aligning a read (--maxbts)" />
371              </when>
372              <when value="doBest">
373                <param name="pdMaxBacktracks" type="integer" value="800" label="Maximum number of backtracks permitted when aligning a read (--maxbts)" />
374                <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)">
375                  <option value="noStrata">Do not use strata option</option>
376                  <option value="doStrata">Use strata option</option>
377                </param>
378              </when>
379            </conditional>
380            <param name="pOffrate" type="integer" value="-1" label="Override the offrate of the index to n (-o)" help="-1 for default" />
381            <param name="pSeed" type="integer" value="-1" label="Seed for pseudo-random number generator (--seed)" help="-1 for default" />
382          </when> <!-- full -->
383        </conditional> <!-- pParams -->
384      </when> <!-- paired -->
385    </conditional> <!-- singlePaired -->
386    <param name="suppressHeader" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Suppress the header in the output SAM file" help="Bowtie produces SAM with several lines of header information by default" />
387  </inputs>
388  <outputs>
389    <data format="sam" name="output" >
390      <actions>
391        <conditional name="refGenomeSource.genomeSource">
392          <when value="indexed">
393            <action type="metadata" name="dbkey">
394              <option type="from_file" name="bowtie_indices.loc" column="0" offset="0">
395                <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
396                <filter type="param_value" ref="refGenomeSource.index" column="1"/>
397              </option>
398            </action>
399          </when>
400        </conditional>
401        <!-- Special casing equCab2chrM to equCab2 -->
402        <action type="metadata" name="dbkey">
403          <option type="from_param" name="refGenomeSource.genomeSource" column="0" offset="0">
404            <filter type="insert_column" column="0" value="equCab2chrM"/>
405            <filter type="insert_column" column="0" value="equCab2"/>
406            <filter type="metadata_value" ref="output" name="dbkey" column="1" />
407          </option>
408        </action>
409      </actions>
410    </data>
411  </outputs>
412  <tests>
413    <test>
414      <!--
415      Bowtie command:
416      bowtie -p 4 -S +sam-nohead -q chrM_base test-data/bowtie_in2.fastqsanger > test-data/bowtie_out2.sam
417      -p is the number of threads, which is hardcoded above. You need to replace the + with 2 dashes.
418      chrM_base needs to be the base location/name of the index files.
419      -->
420      <param name="genomeSource" value="indexed" />
421      <param name="index" value="equCab2chrM" />
422      <param name="sPaired" value="single" />
423      <param name="sInput1" ftype="fastqsanger" value="bowtie_in2.fastqsanger" />
424      <param name="sSettingsType" value="preSet" />
425      <param name="suppressHeader" value="true" />
426      <output name="output" ftype="sam" file="bowtie_out2.sam" />
427    </test>
428    <test>
429      <!--
430      Bowtie command:
431      bowtie-build -f test-data/chr_m.fasta chrM_base
432      bowtie -X 1000 +fr -n 2 -e 70 -l 28 +pairtries 100 +maxbts 800 -k 1 +best -p 4 -S +sam-nohead -q chrM_base -1 test-data/bowtie_in5.fastqsanger -2 test-data/bowtie_in6.fastqsanger > test-data/bowtie_out4.sam
433      -p is the number of threads, hardcoded above. You need to replace the + with 2 dashes.
434      chrM_base is the index files' location/base name.
435      -->
436      <param name="genomeSource" value="history" />
437      <param name="ownFile" value="chr_m.fasta" />
438      <param name="indexSettings" value="indexPreSet" />
439      <param name="sPaired" value="paired" />
440      <param name="pInput1" ftype="fastqsanger" value="bowtie_in5.fastqsanger" />
441      <param name="pInput2" ftype="fastqsanger" value="bowtie_in6.fastqsanger" />
442      <param name="pMaxInsert" value="1000" />
443      <param name="pMateOrient" value="fr" />
444      <param name="pSettingsType" value="full" />
445      <param name="pSkip" value="0" />
446      <param name="pAlignLimit" value="-1" />
447      <param name="pTrimH" value="0" />
448      <param name="pTrimL" value="0" />
449      <param name="pMismatchSeed" value="2" />
450      <param name="pMismatchQual" value="70" />
451      <param name="pSeedLen" value="28" />
452      <param name="pRounding" value="round" />
453      <param name="pMaqSoapAlign" value="-1" />
454      <param name="pMinInsert" value="0" />
455      <param name="pMaxAlignAttempt" value="100" />
456      <param name="pForwardAlign" value="forward" />
457      <param name="pReverseAlign" value="reverse" />
458      <param name="pTryHard" value="noTryHard" />
459      <param name="pValAlign" value="1" />
460      <param name="pAllValAligns" value="noAllValAligns" />
461      <param name="pSuppressAlign" value="-1" />
462      <param name="pBest" value="doBest" />
463      <param name="pdMaxBacktracks" value="800" />
464      <param name="pdStrata" value="noStrata" />
465      <param name="pOffrate" value="-1" />
466      <param name="pSeed" value="-1" />
467      <param name="suppressHeader" value="true" />
468      <output name="output" ftype="sam" file="bowtie_out4.sam" />
469    </test>
470    <test>
471      <!--
472      Bowtie command:
473      bowtie -n 2 -e 70 -l 28 -k 1 +maxbts 125 -y -p 4 -S +sam-nohead -q chrM_base test-data/bowtie_in2.fastqsanger > test-data/bowtie_out6.sam
474      -p is the number of threads, hardcoded above. You need to replace the + with 2 dashes.
475      chrM_base is the index files' location/base name.
476      -->
477      <param name="genomeSource" value="indexed" />
478      <param name="index" value="equCab2chrM" />
479      <param name="sPaired" value="single" />
480      <param name="sInput1" ftype="fastqsanger" value="bowtie_in2.fastqsanger" />
481      <param name="sSettingsType" value="full" />
482      <param name="sSkip" value="0" />
483      <param name="sAlignLimit" value="-1" />
484      <param name="sTrimH" value="0" />
485      <param name="sTrimL" value="0" />
486      <param name="sMismatchSeed" value="2" />
487      <param name="sMismatchQual" value="70" />
488      <param name="sSeedLen" value="28" />
489      <param name="sRounding" value="round" />
490      <param name="sMaqSoapAlign" value="-1" />
491      <param name="sTryHard" value="doTryHard" />
492      <param name="sValAlign" value="1" />
493      <param name="sAllValAligns" value="noAllValAligns" />
494      <param name="sSuppressAlign" value="-1" />
495      <param name="sBest" value="noBest" />
496      <param name="snMaxBacktracks" value="125" />
497      <param name="sOffrate" value="-1" />
498      <param name="sSeed" value="-1" />
499      <param name="suppressHeader" value="true" />
500      <output name="output" ftype="sam" file="bowtie_out6.sam" />
501    </test>
502    <test>
503      <!--
504      Bowtie command:
505      bowtie-build +offrate 5 +ftabchars 10 +little -f test-data/chr_m.fasta chrM_base
506      bowtie -X 1000 +fr -p 4 -S +sam-nohead -q chrM_base -1 test-data/bowtie_in5.fastqsanger -2 test-data/bowtie_in6.fastqsanger > test-data/bowtie_out8.sam
507      -p is the number of threads, hardcoded above. You need to replace the + with 2 dashes.
508      chrM_base is the index files' location/base name.
509      -->
510      <param name="genomeSource" value="history" />
511      <param name="ownFile" value="chr_m.fasta" />
512      <param name="indexSettings" value="indexFull" />
513      <param name="autoB" value="auto" />
514      <param name="nodc" value="dc" />
515      <param name="noref" value="ref" />
516      <param name="offrate" value="5" />
517      <param name="ftab" value="10" />
518      <param name="ntoa" value="no" />
519      <param name="endian" value="little" />
520      <param name="seed" value="-1" />
521      <param name="cutoff" value="-1" />
522      <param name="sPaired" value="paired" />
523      <param name="pInput1" ftype="fastqsanger" value="bowtie_in5.fastqsanger" />
524      <param name="pInput2" ftype="fastqsanger" value="bowtie_in6.fastqsanger" />
525      <param name="pMaxInsert" value="1000" />
526      <param name="pMateOrient" value="fr" />
527      <param name="pSettingsType" value="preSet" />
528      <param name="suppressHeader" value="true" />
529      <output name="output" ftype="sam" file="bowtie_out8.sam" />
530    </test>
531  </tests>
532
533  <help>
534
535**What it does**
536
537Bowtie_ 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.
538
539.. _Bowtie: http://bowtie-bio.sourceforge.net/index.shtml
540
541------
542
543**Know what you are doing**
544
545.. class:: warningmark
546
547There 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.
548
549 .. __: http://bowtie-bio.sourceforge.net/index.shtml
550
551------
552
553**Input formats**
554
555Bowtie accepts files in Sanger FASTQ format. Use the FASTQ Groomer to prepare your files.
556
557------
558
559**Outputs**
560
561The output is in SAM format, and has the following columns::
562
563    Column  Description
564  --------  --------------------------------------------------------   
565   1 QNAME  Query (pair) NAME
566   2 FLAG   bitwise FLAG
567   3 RNAME  Reference sequence NAME
568   4 POS    1-based leftmost POSition/coordinate of clipped sequence
569   5 MAPQ   MAPping Quality (Phred-scaled)
570   6 CIGAR  extended CIGAR string
571   7 MRNM   Mate Reference sequence NaMe ('=' if same as RNAME)
572   8 MPOS   1-based Mate POSition
573   9 ISIZE  Inferred insert SIZE
574  10 SEQ    query SEQuence on the same strand as the reference
575  11 QUAL   query QUALity (ASCII-33 gives the Phred base quality)
576  12 OPT    variable OPTional fields in the format TAG:VTYPE:VALUE
577 
578The flags are as follows::
579
580    Flag  Description
581  ------  -------------------------------------
582  0x0001  the read is paired in sequencing
583  0x0002  the read is mapped in a proper pair
584  0x0004  the query sequence itself is unmapped
585  0x0008  the mate is unmapped
586  0x0010  strand of the query (1 for reverse)
587  0x0020  strand of the mate
588  0x0040  the read is the first read in a pair
589  0x0080  the read is the second read in a pair
590  0x0100  the alignment is not primary
591
592It looks like this (scroll sideways to see the entire example)::
593
594  QNAME FLAG    RNAME   POS     MAPQ    CIAGR   MRNM    MPOS    ISIZE   SEQ     QUAL    OPT
595  HWI-EAS91_1_30788AAXX:1:1:1761:343    4       *       0       0       *       *       0       0       AAAAAAANNAAAAAAAAAAAAAAAAAAAAAAAAAAACNNANNGAGTNGNNNNNNNGCTTCCCACAGNNCTGG        hhhhhhh;;hhhhhhhhhhh^hOhhhhghhhfhhhgh;;h;;hhhh;h;;;;;;;hhhhhhghhhh;;Phhh
596  HWI-EAS91_1_30788AAXX:1:1:1578:331    4       *       0       0       *       *       0       0       GTATAGANNAATAAGAAAAAAAAAAATGAAGACTTTCNNANNTCTGNANNNNNNNTCTTTTTTCAGNNGTAG        hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhhhh;;h;;hhhh;h;;;;;;;hhhhhhhhhhh;;hhVh
597
598-------
599
600**Bowtie settings**
601
602All of the options have a default value. You can change any of them. Most of the options in Bowtie have been implemented here.
603
604------
605
606**Bowtie parameter list**
607
608This is an exhaustive list of Bowtie options:
609
610For indexing (bowtie-build)::
611
612  -a               No auto behavior. Disable the default behavior where bowtie automatically
613                   selects values for --bmax/--bmaxdivn/--dcv/--packed parameters according
614                   to the memory available. [off]
615  --packed         Packing. Use a packed representation for DNA strings. [auto]
616  --bmax INT       Suffix maximum. The maximum number of suffixes allowed in a block. [auto]
617  --bmaxdivn INT   Suffix maximum fraction. The maximum number of suffixes allowed in a block
618                   expressed as a fraction of the length of the reference. [4]
619  --dcv INT        Difference-cover sample. Use INT as the period for the difference-cover
620                   sample. [1024]
621  --nodc INT       No difference-cover sample. Disable the difference-cover sample. [off]
622  -r               No reference indexes. Do not build the NAME.3.ebwt and NAME.4.ebwt portions
623                   of the index. Used only for paired-end alignment. [off]
624  -o               Offrate. How many Burrows-Wheeler rows get marked by the indexer. The
625                   indexer will mark every 2^INT rows. The marked rows correspond to rows on
626                   the genome. [5]
627  -t INT           Ftab. The lookup table used to calculate an initial Burrows-Wheeler range
628                   with respect to the first INT characters of the query. Ftab is 4^INT+1
629                   bytes. [10]
630  --ntoa           N conversion. Convert Ns to As before building the index. Otherwise, Ns are
631                   simply excluded from the index and Bowtie will not find alignments that
632                   overlap them. [off]
633  --big            Endianness. Endianness to use when serializing integers to the index file. [off]
634  --little         Endianness. [--little]
635  --seed INT       Random seed. Use INT as the seed for the pseudo-random number generator. [off]
636  --cutoff INT     Cutoff. Index only the first INT bases of the reference sequences (cumulative
637                   across sequences) and ignore the rest. [off]
638
639For aligning (bowtie)::
640
641  -s INT           Skip. Do not align the first INT reads or pairs in the input. [off]
642  -u INT           Align limit. Only align the first INT reads/pairs from the input. [no limit]
643  -5 INT           High-quality trim. Trim INT bases from the high-quality (left) end of each
644                   read before alignment. [0]
645  -3 INT           Low-quality trim. Trim INT bases from the low-quality (right) end of each
646                   read before alignment. [0]
647  -n INT           Mismatch seed. Maximum number of mismatches permitted in the seed (defined
648                   with seed length option). Can be 0, 1, 2, or 3. [2]
649  -e INT           Mismatch quality. Maximum permitted total of quality values at mismatched
650                   read positions. Bowtie rounds quality values to the nearest 10 and saturates
651                   at 30. [70]
652  -l INT           Seed length. The number of bases on the high-quality end of the read to
653                   which the -n ceiling applies. Must be at least 5. [28]
654  --nomaqround     Suppress MAQ rounding. Values are internally rounded to the nearest 10 and
655                   saturate at 30. This options turns off that rounding. [off]
656  -v INT           MAQ- or SOAP-like alignment policy. This option turns off the default
657                   MAQ-like alignment policy in favor of a SOAP-like one. End-to-end alignments
658                   with at most INT mismatches. [off]
659  -I INT           Minimum insert. The minimum insert size for valid paired-end alignments.
660                   Does checking on untrimmed reads if -5 or -3 is used. [0]
661  -X INT           Maximum insert. The maximum insert size for valid paired-end alignments.
662                   Does checking on untrimmed reads if -5 or -3 is used. [250]
663  --fr             Mate orientation. The upstream/downstream mate orientations for a valid
664                   paired-end alignment against the forward reference strand. [--fr]
665  --rf             Mate orientation. [off]
666  --ff             Mate orientation. [off]
667  --pairtries INT  Maximum alignment attempts for paired-end data. [100]
668  --nofw           No forward aligning. Choosing this option means that Bowtie will not attempt
669                   to align against the forward reference strand. [off]
670  --norc           No reverse-complement aligning. Setting this will mean that Bowtie will not
671                   attempt to align against the reverse-complement reference strand. [off]
672  --maxbts INT     Maximum backtracks. The maximum number of backtracks permitted when aligning
673                   a read in -n 2 or -n 3 mode. [125 without --best] [800 with --best]
674  -y               Try hard. Try as hard as possible to find valid alignments when they exist,
675                   including paired-end alignments. [off]
676  --chunkmbs INT   Thread memory. The number of megabytes of memory a given thread is given to
677                   store path descriptors in --best mode. [32]
678  -k INT           Valid alignments. The number of valid alignments per read or pair. [off]
679  -a               All valid alignments. Choosing this means that all valid alignments per read
680                   or pair will be reported. [off]
681  -m INT           Suppress alignments. Suppress all alignments for a particular read or pair
682                   if more than INT reportable alignments exist for it. [no limit]
683  --best           Best mode. Make Bowtie guarantee that reported singleton alignments are
684                   "best" in terms of stratum (the number of mismatches) and quality values at
685                   mismatched position. [off]
686  --strata         Best strata. When running in best mode, report alignments that fall into the
687                   best stratum if there are ones falling into more than one. [off]
688  -o INT           Offrate override. Override the offrate of the index with INT. Some row
689                   markings are discarded when index read into memory. INT must be greater than
690                   the value used to build the index (default: 5). [off]
691  --seed INT       Random seed. Use INT as the seed for the pseudo-random number generator. [off]
692  --snpphred INT   Use INT as the SNP penalty for decoding colorspace alignments. True ratio of
693                   SNPs per base in the subject genome. [see --snpfrac]
694  --snpfrac DEC    Use DEC as the estimated ratio of SNPs per base when decoding colorspace
695                   alignments. [0.001]
696  --col-keepends   Keep the extreme-end nucleotides and qualities when decoding colorspace
697                   alignments. [off]
698
699  </help>
700</tool>
Note: リポジトリブラウザについてのヘルプは TracBrowser を参照してください。