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

リビジョン 2, 41.3 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central
行番号 
1<tool id="bowtie_color_wrapper" name="Map with Bowtie for SOLiD" version="1.0.0">
2  <requirements><requirement type='package'>bowtie</requirement></requirements>
3  <description></description>
4  <command interpreter="python">
5    bowtie_wrapper.py
6    --threads="4"
7    --dataType="solid"
8    --output=$output
9    --suppressHeader=$suppressHeader
10    --genomeSource=$refGenomeSource.genomeSource
11    #if $refGenomeSource.genomeSource == "history":
12       #if $refGenomeSource.ownFile.extension.startswith( 'bowtie_' ):
13       --ref="${refGenomeSource.ownFile.extra_files_path}/${refGenomeSource.ownFile.metadata.base_name}"
14       --do_not_build_index
15       #else:
16     --ref=$refGenomeSource.ownFile
17     --indexSettings=$refGenomeSource.indexParams.indexSettings
18     #if $refGenomeSource.indexParams.indexSettings == "indexFull":
19      --iautoB=$refGenomeSource.indexParams.autoBehavior.autoB
20      #if $refGenomeSource.indexParams.autoBehavior.autoB == "set":
21       --ipacked=$refGenomeSource.indexParams.autoBehavior.packed
22       --ibmax=$refGenomeSource.indexParams.autoBehavior.bmax
23       --ibmaxdivn=$refGenomeSource.indexParams.autoBehavior.bmaxdivn
24       --idcv=$refGenomeSource.indexParams.autoBehavior.dcv
25      #else:
26       --ipacked="None"
27       --ibmax="None"
28       --ibmaxdivn="None"
29       --idcv="None"
30      #end if
31      --inodc=$refGenomeSource.indexParams.nodc
32      --inoref=$refGenomeSource.indexParams.noref
33      --ioffrate=$refGenomeSource.indexParams.offrate
34      --iftab=$refGenomeSource.indexParams.ftab
35      --intoa=$refGenomeSource.indexParams.ntoa
36      --iendian=$refGenomeSource.indexParams.endian
37      --iseed=$refGenomeSource.indexParams.seed
38      --icutoff=$refGenomeSource.indexParams.cutoff
39     #else:
40      --iautoB="None"
41      --ipacked="None"
42      --ibmax="None"
43      --ibmaxdivn="None"
44      --idcv="None"
45      --inodc="None"
46      --inoref="None"
47      --ioffrate="None"
48      --iftab="None"
49      --intoa="None"
50      --iendian="None"
51      --iseed="None"
52      --icutoff="None"
53     #end if
54     #end if
55    #else:
56     --ref=$refGenomeSource.index
57     --indexSettings="None"
58     --iautoB="None"
59     --ipacked="None"
60     --ibmax="None"
61     --ibmaxdivn="None"
62     --idcv="None"
63     --inodc="None"
64     --inoref="None"
65     --ioffrate="None"
66     --iftab="None"
67     --intoa="None"
68     --iendian="None"
69     --iseed="None"
70     --icutoff="None"
71    #end if
72    --paired=$singlePaired.sPaired
73    #if $singlePaired.sPaired == "single":
74     --input1=$singlePaired.sInput1
75     --input2="None"
76     --params=$singlePaired.sParams.sSettingsType
77     #if $singlePaired.sParams.sSettingsType == "full":
78      --skip=$singlePaired.sParams.sSkip
79      --alignLimit=$singlePaired.sParams.sAlignLimit
80      --trimH=$singlePaired.sParams.sTrimH
81      --trimL=$singlePaired.sParams.sTrimL
82      --mismatchSeed=$singlePaired.sParams.sMismatchSeed
83      --mismatchQual=$singlePaired.sParams.sMismatchQual
84      --seedLen=$singlePaired.sParams.sSeedLen
85      --rounding=$singlePaired.sParams.sRounding
86      --maqSoapAlign=$singlePaired.sParams.sMaqSoapAlign
87      --tryHard=$singlePaired.sParams.sTryHard
88      --valAlign=$singlePaired.sParams.sValAlign
89      --allValAligns=$singlePaired.sParams.sAllValAligns
90      --suppressAlign=$singlePaired.sParams.sSuppressAlign
91      --best=$singlePaired.sParams.sBestOption.sBest
92      #if $singlePaired.sParams.sBestOption.sBest == "doBest":
93       --maxBacktracks=$singlePaired.sParams.sBestOption.sdMaxBacktracks
94       --strata=$singlePaired.sParams.sBestOption.sdStrata
95      #else:
96       --maxBacktracks=$singlePaired.sParams.sBestOption.snMaxBacktracks
97       --strata="None"
98      #end if
99      --offrate=$singlePaired.sParams.sOffrate
100      --seed=$singlePaired.sParams.sSeed
101      --snpphred=$singlePaired.sParams.sSnpphred
102      --snpfrac=$singlePaired.sParams.sSnpfrac
103      --keepends=$singlePaired.sParams.sKeepends
104     #else:
105      --skip="None"
106      --alignLimit="None"
107      --trimH="None"
108      --trimL="None"
109      --mismatchSeed="None"
110      --mismatchQual="None"
111      --seedLen="None"
112      --rounding="None"
113      --maqSoapAlign="None"
114      --tryHard="None"
115      --valAlign="None"
116      --allValAligns="None"
117      --suppressAlign="None"
118      --best="None"
119      --maxBacktracks="None"
120      --strata="None"
121      --offrate="None"
122      --seed="None"
123      --snpphred="None"
124      --snpfrac="None"
125      --keepends="None"
126     #end if
127     --minInsert="None"
128     --maxInsert="None"
129     --mateOrient="None"
130     --maxAlignAttempt="None"
131     --forwardAlign="None"
132     --reverseAlign="None"
133    #else:
134     --input1=$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      --snpphred=$singlePaired.pParams.pSnpphred
168      --snpfrac=$singlePaired.pParams.pSnpfrac
169      --keepends=$singlePaired.pParams.pKeepends
170     #else:
171      --skip="None"
172      --alignLimit="None"
173      --trimH="None"
174      --trimL="None"
175      --mismatchSeed="None"
176      --mismatchQual="None"
177      --seedLen="None"
178      --rounding="None"
179      --maqSoapAlign="None"
180      --minInsert="None"
181      --maxAlignAttempt="None"
182      --forwardAlign="None"
183      --reverseAlign="None"
184      --tryHard="None"
185      --valAlign="None"
186      --allValAligns="None"
187      --suppressAlign="None"
188      --best="None"
189      --maxBacktracks="None"
190      --strata="None"
191      --offrate="None"
192      --seed="None"
193      --snpphred="None"
194      --snpfrac="None"
195      --keepends="None"
196     #end if
197    #end if
198  </command>
199  <inputs>
200    <conditional name="refGenomeSource">
201      <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">
202        <option value="indexed">Use a built-in index</option>
203        <option value="history">Use one from the history</option>
204      </param>
205      <when value="indexed">
206        <param name="index" type="select" label="Select the reference genome" help="if your genome of interest is not listed - contact Galaxy team">
207          <options from_file="bowtie_indices_color.loc">
208            <column name="value" index="1" />
209            <column name="name" index="0" />
210          </options>
211        </param>
212      </when>
213      <when value="history">
214        <param name="ownFile" type="data" format="bowtie_color_index,fasta" metadata_name="dbkey" label="Select the reference genome" />
215        <conditional name="indexParams">
216          <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">
217            <option value="indexPreSet">Default</option>
218            <option value="indexFull">Set your own</option>
219          </param>
220          <when value="indexPreSet" />
221          <when value="indexFull">
222            <conditional name="autoBehavior">
223              <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">
224                <option value="auto">Automatic behavior</option>
225                <option value="set">Set values (sets --noauto and allows others to be set)</option>
226              </param>
227              <when value="auto" />
228              <when value="set">
229                <param name="packed" type="select" label="Whether or not to use a packed representation for DNA strings (--packed)">
230                  <option value="unpacked">Use regular representation</option>
231                  <option value="packed">Use packed representation</option>
232                </param>
233                <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" />
234                <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)" />
235                <param name="dcv" type="integer" value="1024" label="The period for the difference-cover sample (--dcv)" />
236              </when>
237            </conditional>
238            <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)">
239              <option value="dc">Use difference-cover sample</option>
240              <option value="nodc">Disable difference-cover sample</option>
241            </param>
242            <param name="noref" type="select" label="Whether or not to build the part of the reference index used only in paired-end alignment (-r)">
243              <option value="ref">Build all index files</option>
244              <option value="noref">Do not build paired-end alignment index files</option>
245            </param>
246            <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)" />
247            <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" />
248            <param name="ntoa" type="select" label="Whether or not to convert Ns in the reference sequence to As (--ntoa)">
249              <option value="no">Do not convert Ns</option>
250              <option value="yes">Convert Ns to As</option>
251            </param>
252            <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">
253              <option value="little">Little</option>
254              <option value="big">Big</option>
255            </param>
256            <param name="seed" type="integer" value="-1" label="Seed for the pseudorandom number generator (--seed)" help="Use -1 to use default" />
257            <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" />
258          </when>  <!-- cIndexFull -->
259        </conditional>  <!-- cIndexParams -->
260      </when>  <!-- cHistory -->
261    </conditional>  <!-- cRefGenomeSource -->
262    <conditional name="singlePaired">
263      <param name="sPaired" type="select" label="Is this library mate-paired?">
264        <option value="single">Single-end</option>
265        <option value="paired">Paired-end</option>
266      </param>
267      <when value="single">
268        <param name="sInput1" type="data" format="fastqcssanger" label="FASTQ file" help="Must have Sanger-scaled quality values with ASCII offset 33"/>
269        <conditional name="sParams">
270          <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">
271            <option value="preSet">Commonly used</option>
272            <option value="full">Full parameter list</option>
273          </param>
274          <when value="preSet" />
275          <when value="full">
276            <param name="sSkip" type="integer" value="0" label="Skip the first n reads (-s)" /> 
277            <param name="sAlignLimit" type="integer" value="-1" label="Only align the first n reads (-u)" help="-1 for off" /> 
278            <param name="sTrimH" type="integer" value="0" label="Trim n bases from high-quality (left) end of each read before alignment (-5)" />
279            <param name="sTrimL" type="integer" value="0" label="Trim n bases from low-quality (right) end of each read before alignment (-3)" />
280            <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" />
281            <param name="sMismatchQual" type="integer" value="70" label="Maximum permitted total of quality values at mismatched read positions (-e)" />
282            <param name="sSeedLen" type="integer" value="28" label="Seed length (-l)" help="Minimum value is 5" />
283            <param name="sRounding" type="select" label="Whether or not to round to the nearest 10 and saturating at 30 (--nomaqround)">
284              <option value="round">Round to nearest 10</option>
285              <option value="noRound">Do not round to nearest 10</option>
286            </param>
287            <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" />
288            <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">
289              <option value="noTryHard">Do not try hard</option>
290              <option value="doTryHard">Try hard</option>
291            </param>
292            <param name="sValAlign" type="integer" value="1" label="Report up to n valid alignments per read (-k)" />
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            <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" />
298            <conditional name="sBestOption">
299              <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">
300                <option value="noBest">Do not use best</option>
301                <option value="doBest">Use best</option>
302              </param>
303              <when value="noBest">
304                <param name="snMaxBacktracks" type="integer" value="125" label="Maximum number of backtracks permitted when aligning a read (--maxbts)" />
305              </when>
306              <when value="doBest">
307                <param name="sdMaxBacktracks" type="integer" value="800" label="Maximum number of backtracks permitted when aligning a read (--maxbts)" />
308                <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)">
309                  <option value="noStrata">Do not use strata option</option>
310                  <option value="doStrata">Use strata option</option>
311                </param>
312              </when>
313            </conditional> <!-- csBestOption -->
314            <param name="sOffrate" type="integer" value="-1" label="Override the offrate of the index to n (-o)" help="-1 for default" />
315            <param name="sSeed" type="integer" value="-1" label="Seed for pseudo-random number generator (--seed)" help="-1 for default" />
316            <param name="sSnpphred" type="integer" value="-1" label="SNP penalty (ratio of SNPs per base in the subject genome) (--snpphred)" help="Enter this OR Ratio of SNPs per base" />
317            <param name="sSnpfrac" type="float" value="0.001" label="Ratio of SNPs per base (estimated ratio for colorspace alignments) (--snpfrac)" help="Enter this OR SNP penalty" />
318            <param name="sKeepends" type="select" label="Keep the extreme-ends nucleotides and qualities rather than trimming them (--col-keepends)">
319              <option value="doKeepends">Keep ends</option>
320              <option value="noKeepends">Trim ends</option>
321            </param>
322          </when> <!-- csFull -->
323        </conditional> <!-- csParams -->
324      </when> <!-- cSingle -->
325      <when value="paired">
326        <param name="pInput1" type="data" format="fastqcssanger" label="FASTQ file" help="Must have Sanger-scaled quality values with ASCII offset 33"/>
327        <param name="pInput2" type="data" format="fastqcssanger" label="Reverse FASTQ file" help="Must have Sanger-scaled quality values with ASCII offset 33"/>
328        <param name="pMaxInsert" type="integer" value="1000" label="Maximum insert size for valid paired-end alignments (-X)" />
329        <param name="pMateOrient" type="select" label="The upstream/downstream mate orientation for valid paired-end alignment against the forward reference strand (--fr/--rf/--ff)">
330          <option value="ff">FF (for SOLiD)</option>
331          <option value="fr">FR (for Illumina)</option>
332          <option value="rf">RF</option>
333        </param>
334        <conditional name="pParams">
335          <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">
336            <option value="preSet">Commonly used</option>
337            <option value="full">Full parameter list</option>
338          </param>
339          <when value="preSet" />
340          <when value="full">
341            <param name="pSkip" type="integer" value="0" label="Skip the first n pairs (-s)" /> 
342            <param name="pAlignLimit" type="integer" value="-1" label="Only align the first n pairs (-u)" help="-1 for off" /> 
343            <param name="pTrimH" type="integer" value="0" label="Trim n bases from high-quality (left) end of each read before alignment (-5)" />
344            <param name="pTrimL" type="integer" value="0" label="Trim n bases from low-quality (right) end of each read before alignment (-3)" />
345            <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" />
346            <param name="pMismatchQual" type="integer" value="70" label="Maximum permitted total of quality values at mismatched read positions (-e)" />
347            <param name="pSeedLen" type="integer" value="28" label="Seed length (-l)" help="Minimum value is 5" />
348            <param name="pRounding" type="select" label="Whether or not to round to the nearest 10 and saturating at 30 (--nomaqround)">
349              <option value="round">Round to nearest 10</option>
350              <option value="noRound">Do not round to nearest 10</option>
351            </param>
352            <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" />
353            <param name="pMinInsert" type="integer" value="0" label="Minimum insert size for valid paired-end alignments (-I)" />
354            <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)" />
355            <param name="pForwardAlign" type="select" label="Choose whether or not to attempt to align 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 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            <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">
364              <option value="noTryHard">Do not try hard</option>
365              <option value="doTryHard">Try hard</option>
366            </param>
367            <param name="pValAlign" type="integer" value="1" label="Report up to n valid arguments per pair (-k)" />
368            <param name="pAllValAligns" type="select" label="Whether or not to report all valid alignments per pair (-a)">
369              <option value="noAllValAligns">Do not report all valid alignments</option>
370              <option value="doAllValAligns">Report all valid alignments</option>
371            </param>
372            <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" />
373            <conditional name="pBestOption">
374              <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">
375                <option value="noBest">Do not use best</option>
376                <option value="doBest">Use best</option>
377              </param>
378              <when value="noBest">
379                <param name="pnMaxBacktracks" type="integer" value="125" label="Maximum number of backtracks permitted when aligning a read (--maxbts)" />
380              </when>
381              <when value="doBest">
382                <param name="pdMaxBacktracks" type="integer" value="800" label="Maximum number of backtracks permitted when aligning a read (--maxbts)" />
383                <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)">
384                  <option value="noStrata">Do not use strata option</option>
385                  <option value="doStrata">Use strata option</option>
386                </param>
387              </when>
388            </conditional>  <!-- cpBestOption -->
389            <param name="pOffrate" type="integer" value="-1" label="Override the offrate of the index to n (-o)" help="-1 for default" />
390            <param name="pSeed" type="integer" value="-1" label="Seed for pseudo-random number generator (--seed)" help="-1 for default" />
391            <param name="pSnpphred" type="integer" value="-1" label="SNP penalty (ratio of SNPs per base in the subject genome) (--snpphred)" help="Enter this OR Ratio of SNPs per base" />
392            <param name="pSnpfrac" type="float" value="0.001" label="Ratio of SNPs per base (estimated ratio for colorspace alignments) (--snpfrac)" help="Enter this OR SNP penalty" />
393            <param name="pKeepends" type="select" label="Keep the extreme-ends nucleotides and qualities rather than trimming them (--col-keepends)">
394              <option value="doKeepends">Keep ends</option>
395              <option value="noKeepends">Trim ends</option>
396            </param>
397          </when> <!-- cpFull -->
398        </conditional> <!-- cpParams -->
399      </when> <!-- cPaired -->
400    </conditional> <!-- cSinglePaired -->
401    <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" />
402  </inputs>
403  <outputs>
404    <data format="sam" name="output" >
405      <actions>
406        <conditional name="refGenomeSource.genomeSource">
407          <when value="indexed">
408            <action type="metadata" name="dbkey">
409              <option type="from_file" name="bowtie_indices_color.loc" column="0" offset="0">
410                <filter type="param_value" column="0" value="#" filter_by="startswith" keep="False"/>
411                <filter type="param_value" ref="refGenomeSource.index" column="1"/>
412              </option>
413            </action>
414          </when>
415        </conditional>
416        <!-- Special casing equCab2chrM to equCab2 -->
417        <action type="metadata" name="dbkey">
418          <option type="from_param" name="refGenomeSource.genomeSource" column="0" offset="0">
419            <filter type="insert_column" column="0" value="equCab2chrM"/>
420            <filter type="insert_column" column="0" value="equCab2"/>
421            <filter type="metadata_value" ref="output" name="dbkey" column="1" />
422          </option>
423        </action>
424      </actions>
425    </data>
426  </outputs>
427  <tests>
428    <test>
429      <!--
430      Bowtie command:
431      bowtie -p 4 -S +sam-nohead -q -C chrM_color test-data/bowtie_in1.fastqcssanger > test-data/bowtie_out1.sam
432      -p is the number of threads, which is hardcoded above. You need to replace the + with 2 dashes.
433      chrM_color needs to be the base location/name of the index files.
434      -->
435      <param name="genomeSource" value="indexed" />
436      <param name="index" value="equCab2chrM" />
437      <param name="sPaired" value="single" />
438      <param name="sInput1" ftype="fastqcssanger" value="bowtie_in1.fastqcssanger" />
439      <param name="sSettingsType" value="preSet" />
440      <param name="suppressHeader" value="true" />
441      <output name="output" ftype="sam" file="bowtie_out1.sam" />
442    </test>
443    <test>
444      <!--
445      Bowtie command:
446      bowtie-build -f -C test-data/chr_m.fasta chrM_color
447      bowtie -X 1000 +ff -n 2 -e 70 -l 28 -X 250 +pairtries 100 +maxbts 125 -k 1 -C +snpfrac 0.001 +col-keepends -p 4 -S +sam-nohead -q chrM_color -1 test-data/bowtie_in3.fastqcssanger -2 test-data/bowtie_in4.fastqcssanger > test-data/bowtie_out3.sam
448      -p is the number of threads, hardcoded above. You need to replace the + with 2 dashes.
449      chrM_base is the index files' location/base name.
450      -->
451      <param name="genomeSource" value="history" />
452      <param name="ownFile" value="chr_m.fasta" />
453      <param name="indexSettings" value="indexPreSet" />
454      <param name="sPaired" value="paired" />
455      <param name="pInput1" ftype="fastqcssanger" value="bowtie_in3.fastqcssanger" />
456      <param name="pInput2" ftype="fastqcssanger" value="bowtie_in4.fastqcssanger" />
457      <param name="pMaxInsert" value="1000" />
458      <param name="pMateOrient" value="ff" />
459      <param name="pSettingsType" value="full" />
460      <param name="pSkip" value="0" />
461      <param name="pAlignLimit" value="-1" />
462      <param name="pTrimH" value="0" />
463      <param name="pTrimL" value="0" />
464      <param name="pMismatchSeed" value="2" />
465      <param name="pMismatchQual" value="70" />
466      <param name="pSeedLen" value="28" />
467      <param name="pRounding" value="round" />
468      <param name="pMaqSoapAlign" value="-1" />
469      <param name="pMinInsert" value="0" />
470      <param name="pMaxAlignAttempt" value="100" />
471      <param name="pForwardAlign" value="forward" />
472      <param name="pReverseAlign" value="reverse" />
473      <param name="pTryHard" value="noTryHard" />
474      <param name="pValAlign" value="1" />
475      <param name="pAllValAligns" value="noAllValAligns" />
476      <param name="pSuppressAlign" value="-1" />
477      <param name="pBest" value="noBest" />
478      <param name="pnMaxBacktracks" value="125" />
479      <param name="pOffrate" value="-1" />
480      <param name="pSeed" value="-1" />
481      <param name="pSnpphred" value="-1" />
482      <param name="pSnpfrac" value="0.001" />
483      <param name="pKeepends" value="doKeepends" />
484      <param name="suppressHeader" value="true" />
485      <output name="output" ftype="sam" file="bowtie_out3.sam" />
486    </test>
487    <test>
488      <!--
489      Bowtie command:
490      bowtie -n 2 -e 70 -l 28 +maxbts 125 -k 1 -C +snpfrac 0.001 +col-keepends -p 4 -S +sam-nohead -q chrM_color test-data/bowtie_in1.fastqcssanger > test-data/bowtie_out5.sam
491      -p is the number of threads, hardcoded above. You need to replace the + with 2 dashes.
492      chrM_base is the index files' location/base name.
493      -->
494      <param name="genomeSource" value="indexed" />
495      <param name="index" value="equCab2chrM" />
496      <param name="sPaired" value="single" />
497      <param name="sInput1" ftype="fastqcssanger" value="bowtie_in1.fastqcssanger" />
498      <param name="sSettingsType" value="full" />
499      <param name="sSkip" value="0" />
500      <param name="sAlignLimit" value="-1" />
501      <param name="sTrimH" value="0" />
502      <param name="sTrimL" value="0" />
503      <param name="sMismatchSeed" value="2" />
504      <param name="sMismatchQual" value="70" />
505      <param name="sSeedLen" value="28" />
506      <param name="sRounding" value="round" />
507      <param name="sMaqSoapAlign" value="-1" />
508      <param name="sTryHard" value="noTryHard" />
509      <param name="sValAlign" value="1" />
510      <param name="sAllValAligns" value="noAllValAligns" />
511      <param name="sSuppressAlign" value="-1" />
512      <param name="sBest" value="noBest" />
513      <param name="snMaxBacktracks" value="125" />
514      <param name="sOffrate" value="-1" />
515      <param name="sSeed" value="-1" />
516      <param name="sSnpphred" value="-1" />
517      <param name="sSnpfrac" value="0.001" />
518      <param name="sKeepends" value="doKeepends" />
519      <param name="suppressHeader" value="true" />
520      <output name="output" ftype="sam" file="bowtie_out5.sam" />
521    </test>
522    <test>
523      <!--
524      Bowtie command:
525      bowtie-build +noauto +bmaxdivn 4 +dcv 1024 +offrate 5 +ftabchars 10 +little -C -f test-data/chr_m.fasta chrM_color
526      bowtie -X 1000 +ff -p 4 -S +sam-nohead -q -C chrM_color -1 test-data/bowtie_in3.fastqcssanger -2 test-data/bowtie_in4.fastqcssanger > test-data/bowtie_out7.sam
527      -p is the number of threads, hardcoded above. You need to replace the + with 2 dashes.
528      chrM_base is the index files' location/base name.
529      -->
530      <param name="genomeSource" value="history" />
531      <param name="ownFile" value="chr_m.fasta" />
532      <param name="indexSettings" value="indexFull" />
533      <param name="autoB" value="set" />
534      <param name="packed" value="unpacked" />
535      <param name="bmax" value="-1" />
536      <param name="bmaxdivn" value="4" />
537      <param name="dcv" value="1024" />
538      <param name="nodc" value="dc" />
539      <param name="noref" value="ref" />
540      <param name="offrate" value="5" />
541      <param name="ftab" value="10" />
542      <param name="ntoa" value="no" />
543      <param name="endian" value="little" />
544      <param name="seed" value="-1" />
545      <param name="cutoff" value="-1" />
546      <param name="sPaired" value="paired" />
547      <param name="pInput1" ftype="fastqcssanger" value="bowtie_in3.fastqcssanger" />
548      <param name="pInput2" ftype="fastqcssanger" value="bowtie_in4.fastqcssanger" />
549      <param name="pMaxInsert" value="1000" />
550      <param name="pMateOrient" value="ff" />
551      <param name="pSettingsType" value="preSet" />
552      <param name="suppressHeader" value="true" />
553      <output name="output" ftype="sam" file="bowtie_out7.sam" />
554    </test>
555  </tests>
556
557  <help>
558
559**What it does**
560
561Bowtie_ 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.
562
563.. _Bowtie: http://bowtie-bio.sourceforge.net/index.shtml
564
565------
566
567**Know what you are doing**
568
569.. class:: warningmark
570
571There 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.
572
573 .. __: http://bowtie-bio.sourceforge.net/index.shtml
574
575------
576
577**Input formats**
578
579Bowtie accepts files in Sanger FASTQ format. Use the FASTQ Groomer to prepare your files.
580
581------
582
583**Outputs**
584
585The output is in SAM format, and has the following columns::
586
587    Column  Description
588  --------  --------------------------------------------------------
589   1 QNAME  Query (pair) NAME
590   2 FLAG   bitwise FLAG
591   3 RNAME  Reference sequence NAME
592   4 POS    1-based leftmost POSition/coordinate of clipped sequence
593   5 MAPQ   MAPping Quality (Phred-scaled)
594   6 CIGAR  extended CIGAR string
595   7 MRNM   Mate Reference sequence NaMe ('=' if same as RNAME)
596   8 MPOS   1-based Mate POSition
597   9 ISIZE  Inferred insert SIZE
598  10 SEQ    query SEQuence on the same strand as the reference
599  11 QUAL   query QUALity (ASCII-33 gives the Phred base quality)
600  12 OPT    variable OPTional fields in the format TAG:VTYPE:VALUE
601
602The flags are as follows::
603
604    Flag  Description
605  ------  -------------------------------------
606  0x0001  the read is paired in sequencing
607  0x0002  the read is mapped in a proper pair
608  0x0004  the query sequence itself is unmapped
609  0x0008  the mate is unmapped
610  0x0010  strand of the query (1 for reverse)
611  0x0020  strand of the mate
612  0x0040  the read is the first read in a pair
613  0x0080  the read is the second read in a pair
614  0x0100  the alignment is not primary
615
616It looks like this (scroll sideways to see the entire example)::
617
618  QNAME FLAG    RNAME   POS     MAPQ    CIAGR   MRNM    MPOS    ISIZE   SEQ     QUAL    OPT
619  HWI-EAS91_1_30788AAXX:1:1:1761:343    4       *       0       0       *       *       0       0       AAAAAAANNAAAAAAAAAAAAAAAAAAAAAAAAAAACNNANNGAGTNGNNNNNNNGCTTCCCACAGNNCTGG        hhhhhhh;;hhhhhhhhhhh^hOhhhhghhhfhhhgh;;h;;hhhh;h;;;;;;;hhhhhhghhhh;;Phhh
620  HWI-EAS91_1_30788AAXX:1:1:1578:331    4       *       0       0       *       *       0       0       GTATAGANNAATAAGAAAAAAAAAAATGAAGACTTTCNNANNTCTGNANNNNNNNTCTTTTTTCAGNNGTAG        hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhhhh;;h;;hhhh;h;;;;;;;hhhhhhhhhhh;;hhVh
621
622-------
623
624**Bowtie settings**
625
626All of the options have a default value. You can change any of them. Most of the options in Bowtie have been implemented here.
627
628------
629
630**Bowtie parameter list**
631
632This is an exhaustive list of Bowtie options:
633
634For indexing (bowtie-build)::
635
636  -a               No auto behavior. Disable the default behavior where bowtie automatically
637                   selects values for --bmax/--bmaxdivn/--dcv/--packed parameters according
638                   to the memory available. [off]
639  --packed         Packing. Use a packed representation for DNA strings. [auto]
640  --bmax INT       Suffix maximum. The maximum number of suffixes allowed in a block. [auto]
641  --bmaxdivn INT   Suffix maximum fraction. The maximum number of suffixes allowed in a block
642                   expressed as a fraction of the length of the reference. [4]
643  --dcv INT        Difference-cover sample. Use INT as the period for the difference-cover
644                   sample. [1024]
645  --nodc INT       No difference-cover sample. Disable the difference-cover sample. [off]
646  -r               No reference indexes. Do not build the NAME.3.ebwt and NAME.4.ebwt portions
647                   of the index. Used only for paired-end alignment. [off]
648  -o               Offrate. How many Burrows-Wheeler rows get marked by the indexer. The
649                   indexer will mark every 2^INT rows. The marked rows correspond to rows on
650                   the genome. [5]
651  -t INT           Ftab. The lookup table used to calculate an initial Burrows-Wheeler range
652                   with respect to the first INT characters of the query. Ftab is 4^INT+1
653                   bytes. [10]
654  --ntoa           N conversion. Convert Ns to As before building the index. Otherwise, Ns are
655                   simply excluded from the index and Bowtie will not find alignments that
656                   overlap them. [off]
657  --big            Endianness. Endianness to use when serializing integers to the index file. [off]
658  --little         Endianness. [--little]
659  --seed INT       Random seed. Use INT as the seed for the pseudo-random number generator. [off]
660  --cutoff INT     Cutoff. Index only the first INT bases of the reference sequences (cumulative
661                   across sequences) and ignore the rest. [off]
662
663For aligning (bowtie)::
664
665  -s INT           Skip. Do not align the first INT reads or pairs in the input. [off]
666  -u INT           Align limit. Only align the first INT reads/pairs from the input. [no limit]
667  -5 INT           High-quality trim. Trim INT bases from the high-quality (left) end of each
668                   read before alignment. [0]
669  -3 INT           Low-quality trim. Trim INT bases from the low-quality (right) end of each
670                   read before alignment. [0]
671  -n INT           Mismatch seed. Maximum number of mismatches permitted in the seed (defined
672                   with seed length option). Can be 0, 1, 2, or 3. [2]
673  -e INT           Mismatch quality. Maximum permitted total of quality values at mismatched
674                   read positions. Bowtie rounds quality values to the nearest 10 and saturates
675                   at 30. [70]
676  -l INT           Seed length. The number of bases on the high-quality end of the read to
677                   which the -n ceiling applies. Must be at least 5. [28]
678  --nomaqround     Suppress MAQ rounding. Values are internally rounded to the nearest 10 and
679                   saturate at 30. This options turns off that rounding. [off]
680  -v INT           MAQ- or SOAP-like alignment policy. This option turns off the default
681                   MAQ-like alignment policy in favor of a SOAP-like one. End-to-end alignments
682                   with at most INT mismatches. [off]
683  -I INT           Minimum insert. The minimum insert size for valid paired-end alignments.
684                   Does checking on untrimmed reads if -5 or -3 is used. [0]
685  -X INT           Maximum insert. The maximum insert size for valid paired-end alignments.
686                   Does checking on untrimmed reads if -5 or -3 is used. [250]
687  --fr             Mate orientation. The upstream/downstream mate orientations for a valid
688                   paired-end alignment against the forward reference strand. [--fr]
689  --rf             Mate orientation. [off]
690  --ff             Mate orientation. [off]
691  --pairtries INT  Maximum alignment attempts for paired-end data. [100]
692  --nofw           No forward aligning. Choosing this option means that Bowtie will not attempt
693                   to align against the forward reference strand. [off]
694  --norc           No reverse-complement aligning. Setting this will mean that Bowtie will not
695                   attempt to align against the reverse-complement reference strand. [off]
696  --maxbts INT     Maximum backtracks. The maximum number of backtracks permitted when aligning
697                   a read in -n 2 or -n 3 mode. [125 without --best] [800 with --best]
698  -y               Try hard. Try as hard as possible to find valid alignments when they exist,
699                   including paired-end alignments. [off]
700  --chunkmbs INT   Thread memory. The number of megabytes of memory a given thread is given to
701                   store path descriptors in --best mode. [32]
702  -k INT           Valid alignments. The number of valid alignments per read or pair. [off]
703  -a               All valid alignments. Choosing this means that all valid alignments per read
704                   or pair will be reported. [off]
705  -m INT           Suppress alignments. Suppress all alignments for a particular read or pair
706                   if more than INT reportable alignments exist for it. [no limit]
707  --best           Best mode. Make Bowtie guarantee that reported singleton alignments are
708                   "best" in terms of stratum (the number of mismatches) and quality values at
709                   mismatched position. [off]
710  --strata         Best strata. When running in best mode, report alignments that fall into the
711                   best stratum if there are ones falling into more than one. [off]
712  -o INT           Offrate override. Override the offrate of the index with INT. Some row
713                   markings are discarded when index read into memory. INT must be greater than
714                   the value used to build the index (default: 5). [off]
715  --seed INT       Random seed. Use INT as the seed for the pseudo-random number generator. [off]
716  --snpphred INT   Use INT as the SNP penalty for decoding colorspace alignments. True ratio of
717                   SNPs per base in the subject genome. [see --snpfrac]
718  --snpfrac DEC    Use DEC as the estimated ratio of SNPs per base when decoding colorspace
719                   alignments. [0.001]
720  --col-keepends   Keep the extreme-end nucleotides and qualities when decoding colorspace
721                   alignments. [off]
722
723  </help>
724</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。