Mercurial > repos > devteam > bowtie_wrappers
comparison bowtie_wrapper.xml @ 4:df86f29bedee draft
planemo upload commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
author | devteam |
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date | Tue, 21 Jul 2015 13:04:45 -0400 |
parents | 42c4463baaad |
children | 306077e393d4 |
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3:9ca609a2a421 | 4:df86f29bedee |
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1 <tool id="bowtie_wrapper" name="Map with Bowtie for Illumina" version="1.1.2"> | 1 <tool id="bowtie_wrapper" name="Map with Bowtie for Illumina" version="1.1.3"> |
2 <requirements> | 2 <requirements> |
3 <requirement type='package' version="0.12.7">bowtie</requirement> | 3 <requirement type="package" version="0.12.7">bowtie</requirement> |
4 </requirements> | 4 </requirements> |
5 <description></description> | 5 <description></description> |
6 <parallelism method="basic"></parallelism> | 6 <version_command>bowtie --version</version_command> |
7 <command interpreter="python"> | 7 <command interpreter="python"> |
8 bowtie_wrapper.py | 8 bowtie_wrapper.py |
9 ## Set number of threads | 9 ## Set number of threads |
10 --threads="\${GALAXY_SLOTS:-4}" | 10 --threads="\${GALAXY_SLOTS:-4}" |
11 ## Outputs | 11 ## Outputs |
56 --ioffrate="${refGenomeSource.indexParams.offrate}" | 56 --ioffrate="${refGenomeSource.indexParams.offrate}" |
57 --iftab="${refGenomeSource.indexParams.ftab}" | 57 --iftab="${refGenomeSource.indexParams.ftab}" |
58 --intoa="${refGenomeSource.indexParams.ntoa}" | 58 --intoa="${refGenomeSource.indexParams.ntoa}" |
59 --iendian="${refGenomeSource.indexParams.endian}" | 59 --iendian="${refGenomeSource.indexParams.endian}" |
60 --iseed="${refGenomeSource.indexParams.seed}" | 60 --iseed="${refGenomeSource.indexParams.seed}" |
61 --icutoff="${refGenomeSource.indexParams.cutoff}" | |
62 #end if | 61 #end if |
63 #end if | 62 #end if |
64 #else | 63 #else |
65 ##use pre-built index | 64 ##use pre-built index |
66 --ref="${refGenomeSource.index.fields.path}" | 65 --ref="${refGenomeSource.index.fields.path}" |
72 #if $singlePaired.sParams.sSettingsType == "full": | 71 #if $singlePaired.sParams.sSettingsType == "full": |
73 --skip="${singlePaired.sParams.sSkip}" | 72 --skip="${singlePaired.sParams.sSkip}" |
74 --alignLimit="${singlePaired.sParams.sAlignLimit}" | 73 --alignLimit="${singlePaired.sParams.sAlignLimit}" |
75 --trimH="${singlePaired.sParams.sTrimH}" | 74 --trimH="${singlePaired.sParams.sTrimH}" |
76 --trimL="${singlePaired.sParams.sTrimL}" | 75 --trimL="${singlePaired.sParams.sTrimL}" |
77 --mismatchSeed="${singlePaired.sParams.sMismatchSeed}" | 76 #if $singlePaired.sParams.alignModeOption.alignMode == 'nMode' |
78 --mismatchQual="${singlePaired.sParams.sMismatchQual}" | 77 --mismatchSeed="${singlePaired.sParams.alignModeOption.sMismatchSeed}" |
79 --seedLen="${singlePaired.sParams.sSeedLen}" | 78 --mismatchQual="${singlePaired.sParams.alignModeOption.sMismatchQual}" |
80 --rounding="${singlePaired.sParams.sRounding}" | 79 --seedLen="${singlePaired.sParams.alignModeOption.sSeedLen}" |
81 --maqSoapAlign="${singlePaired.sParams.sMaqSoapAlign}" | 80 --rounding="${singlePaired.sParams.alignModeOption.sRounding}" |
82 --tryHard="${singlePaired.sParams.sTryHard}" | 81 #else |
83 --valAlign="${singlePaired.sParams.sValAlign}" | 82 --maxMismatches="${singlePaired.sParams.alignModeOption.maxMismatches}" |
84 --allValAligns="${singlePaired.sParams.sAllValAligns}" | 83 #end if |
84 --forwardAlign="${singlePaired.sParams.sForwardAlign}" | |
85 --reverseAlign="${singlePaired.sParams.sReverseAlign}" | |
86 --tryHard="${singlePaired.sParams.sBestOption.sTryHardOption.sTryHard}" | |
87 --allValAligns="${singlePaired.sParams.sAllValAlignsOption.sAllValAligns}" | |
88 #if $singlePaired.sParams.sAllValAlignsOption.sAllValAligns == "noAllValAligns" | |
89 --valAlign="${singlePaired.sParams.sAllValAlignsOption.sValAlign}" | |
90 #end if | |
85 --suppressAlign="${singlePaired.sParams.sSuppressAlign}" | 91 --suppressAlign="${singlePaired.sParams.sSuppressAlign}" |
86 --best="${singlePaired.sParams.sBestOption.sBest}" | 92 --best="${singlePaired.sParams.sBestOption.sBest}" |
87 #if $singlePaired.sParams.sBestOption.sBest == "doBest": | 93 #if $singlePaired.sParams.sBestOption.sBest == "doBest": |
88 --maxBacktracks="${singlePaired.sParams.sBestOption.sdMaxBacktracks}" | |
89 --strata="${singlePaired.sParams.sBestOption.sdStrata}" | 94 --strata="${singlePaired.sParams.sBestOption.sdStrata}" |
95 #if $singlePaired.sParams.sBestOption.sTryHardOption.sTryHard == "noTryHard" | |
96 --maxBacktracks="${singlePaired.sParams.sBestOption.sTryHardOption.sdMaxBacktracks}" | |
97 #end if | |
90 #else: | 98 #else: |
91 --maxBacktracks="${singlePaired.sParams.sBestOption.snMaxBacktracks}" | 99 #if $singlePaired.sParams.sBestOption.sTryHardOption.sTryHard == "noTryHard" |
100 --maxBacktracks="${singlePaired.sParams.sBestOption.sTryHardOption.snMaxBacktracks}" | |
101 #end if | |
92 #end if | 102 #end if |
93 --offrate="${singlePaired.sParams.sOffrate}" | 103 --offrate="${singlePaired.sParams.sOffrate}" |
94 --seed="${singlePaired.sParams.sSeed}" | 104 --seed="${singlePaired.sParams.sSeed}" |
95 #end if | 105 #end if |
96 #else: | 106 #else: |
102 #if $singlePaired.pParams.pSettingsType == "full": | 112 #if $singlePaired.pParams.pSettingsType == "full": |
103 --skip="${singlePaired.pParams.pSkip}" | 113 --skip="${singlePaired.pParams.pSkip}" |
104 --alignLimit="${singlePaired.pParams.pAlignLimit}" | 114 --alignLimit="${singlePaired.pParams.pAlignLimit}" |
105 --trimH="${singlePaired.pParams.pTrimH}" | 115 --trimH="${singlePaired.pParams.pTrimH}" |
106 --trimL="${singlePaired.pParams.pTrimL}" | 116 --trimL="${singlePaired.pParams.pTrimL}" |
107 --mismatchSeed="${singlePaired.pParams.pMismatchSeed}" | 117 #if $singlePaired.pParams.alignModeOption.alignMode == 'nMode' |
108 --mismatchQual="${singlePaired.pParams.pMismatchQual}" | 118 --mismatchSeed="${singlePaired.pParams.alignModeOption.pMismatchSeed}" |
109 --seedLen="${singlePaired.pParams.pSeedLen}" | 119 --mismatchQual="${singlePaired.pParams.alignModeOption.pMismatchQual}" |
110 --rounding="${singlePaired.pParams.pRounding}" | 120 --seedLen="${singlePaired.pParams.alignModeOption.pSeedLen}" |
111 --maqSoapAlign="${singlePaired.pParams.pMaqSoapAlign}" | 121 --rounding="${singlePaired.pParams.alignModeOption.pRounding}" |
122 #else | |
123 --maxMismatches="${singlePaired.pParams.alignModeOption.maxMismatches}" | |
124 #end if | |
112 --minInsert="${singlePaired.pParams.pMinInsert}" | 125 --minInsert="${singlePaired.pParams.pMinInsert}" |
113 --maxAlignAttempt="${singlePaired.pParams.pMaxAlignAttempt}" | |
114 --forwardAlign="${singlePaired.pParams.pForwardAlign}" | 126 --forwardAlign="${singlePaired.pParams.pForwardAlign}" |
115 --reverseAlign="${singlePaired.pParams.pReverseAlign}" | 127 --reverseAlign="${singlePaired.pParams.pReverseAlign}" |
116 --tryHard="${singlePaired.pParams.pTryHard}" | 128 --tryHard="${singlePaired.pParams.pBestOption.pTryHardOption.pTryHard}" |
117 --valAlign="${singlePaired.pParams.pValAlign}" | 129 --allValAligns="${singlePaired.pParams.pAllValAlignsOption.pAllValAligns}" |
118 --allValAligns="${singlePaired.pParams.pAllValAligns}" | 130 #if $singlePaired.pParams.pAllValAlignsOption.pAllValAligns == "noAllValAligns" |
131 --valAlign="${singlePaired.pParams.pAllValAlignsOption.pValAlign}" | |
132 #end if | |
119 --suppressAlign="${singlePaired.pParams.pSuppressAlign}" | 133 --suppressAlign="${singlePaired.pParams.pSuppressAlign}" |
120 --best="${singlePaired.pParams.pBestOption.pBest}" | 134 --best="${singlePaired.pParams.pBestOption.pBest}" |
121 #if $singlePaired.pParams.pBestOption.pBest == "doBest": | 135 #if $singlePaired.pParams.pBestOption.pBest == "doBest": |
122 --maxBacktracks="${singlePaired.pParams.pBestOption.pdMaxBacktracks}" | |
123 --strata="${singlePaired.pParams.pBestOption.pdStrata}" | 136 --strata="${singlePaired.pParams.pBestOption.pdStrata}" |
137 #if $singlePaired.pParams.pBestOption.pTryHardOption.pTryHard == "noTryHard" | |
138 --maxAlignAttempt="${singlePaired.pParams.pBestOption.pTryHardOption.pMaxAlignAttempt}" | |
139 --maxBacktracks="${singlePaired.pParams.pBestOption.pTryHardOption.pdMaxBacktracks}" | |
140 #end if | |
124 #else: | 141 #else: |
125 --maxBacktracks="${singlePaired.pParams.pBestOption.pnMaxBacktracks}" | 142 #if $singlePaired.pParams.pBestOption.pTryHardOption.pTryHard == "noTryHard" |
143 --maxAlignAttempt="${singlePaired.pParams.pBestOption.pTryHardOption.pMaxAlignAttempt}" | |
144 --maxBacktracks="${singlePaired.pParams.pBestOption.pTryHardOption.pnMaxBacktracks}" | |
145 #end if | |
126 #end if | 146 #end if |
127 --offrate="${singlePaired.pParams.pOffrate}" | 147 --offrate="${singlePaired.pParams.pOffrate}" |
128 --seed="${singlePaired.pParams.pSeed}" | 148 --seed="${singlePaired.pParams.pSeed}" |
129 #end if | 149 #end if |
130 #end if | 150 #end if |
147 <param name="ownFile" type="data" format="bowtie_base_index,fasta" metadata_name="dbkey" label="Select the reference genome" /> | 167 <param name="ownFile" type="data" format="bowtie_base_index,fasta" metadata_name="dbkey" label="Select the reference genome" /> |
148 <conditional name="indexParams"> | 168 <conditional name="indexParams"> |
149 <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"> | 169 <param name="indexSettings" type="select" label="Choose whether to use Default options for building indices or to Set your own" help="These settings are ignored when using a prebuilt index"> |
150 <option value="indexPreSet">Default</option> | 170 <option value="indexPreSet">Default</option> |
151 <option value="indexFull">Set your own</option> | 171 <option value="indexFull">Set your own</option> |
152 </param> | 172 </param> |
153 <when value="indexPreSet" /> | 173 <when value="indexPreSet" /> |
154 <when value="indexFull"> | 174 <when value="indexFull"> |
155 <conditional name="autoBehavior"> | 175 <conditional name="autoBehavior"> |
156 <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"> | 176 <param name="autoB" type="select" label="Choose to use automatic or specified behavior for some parameters (-a)" help="Allows you to set --packed, --bmax, --bmaxdivn, and --dcv"> |
157 <option value="auto">Automatic behavior</option> | 177 <option value="auto">Automatic behavior</option> |
158 <option value="set">Set values (sets --noauto and allows others to be set)</option> | 178 <option value="set">Set values (sets --noauto and allows others to be set)</option> |
159 </param> | 179 </param> |
160 <when value="auto" /> | 180 <when value="auto" /> |
161 <when value="set"> | 181 <when value="set"> |
162 <param name="packed" type="select" label="Whether or not to use a packed representation for DNA strings (--packed)"> | 182 <param name="packed" type="select" label="Whether or not to use a packed representation for DNA strings (--packed)" help="Packed representation saves memory but makes indexing 2-3 times slower"> |
163 <option value="unpacked">Use regular representation</option> | 183 <option value="unpacked">Use regular representation</option> |
164 <option value="packed">Use packed representation</option> | 184 <option value="packed">Use packed representation</option> |
165 </param> | 185 </param> |
166 <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" /> | 186 <param name="bmax" type="integer" value="-1" label="Maximum number of suffixes allowed in a block (--bmax)" help="-1 for not specified. Must be at least 1" /> |
167 <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)" /> | 187 <param name="bmaxdivn" type="integer" value="4" label="Maximum number of suffixes allowed in a block as a fraction of the length of the reference (--bmaxdivn)" /> |
168 <param name="dcv" type="integer" value="1024" label="The period for the difference-cover sample (--dcv)" /> | 188 <param name="dcv" type="integer" value="1024" min="3" label="The period for the difference-cover sample (--dcv)" help="A larger period yields less memory overhead, but may make suffix sorting slower, especially if repeats are present" /> |
169 </when> | 189 </when> |
170 </conditional> | 190 </conditional> |
171 <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)"> | 191 <param name="nodc" type="select" label="Whether or not to disable the use of the difference-cover sample (--nodc)" help="Suffix sorting becomes quadratic-time in the worst case (with a very repetitive reference)"> |
172 <option value="dc">Use difference-cover sample</option> | 192 <option value="dc">Use difference-cover sample</option> |
173 <option value="nodc">Disable difference-cover sample</option> | 193 <option value="nodc">Disable difference-cover sample</option> |
174 </param> | 194 </param> |
175 <param name="noref" type="select" label="Whether or not to build the part of the reference index used only in paired-end alignment (-r)"> | 195 <param name="noref" type="select" label="Whether or not to build the part of the reference index used only in paired-end alignment (-r)"> |
176 <option value="ref">Build all index files</option> | 196 <option value="ref">Build all index files</option> |
177 <option value="noref">Do not build paired-end alignment index files</option> | 197 <option value="noref">Do not build paired-end alignment index files</option> |
178 </param> | 198 </param> |
179 <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)" /> | 199 <param name="offrate" type="integer" value="5" min="0" label="The indexer will mark every 2^n Burrows-Wheeler rows with their corresponding location on the genome (-o)" help="Marking more rows makes reference-position lookups faster, but requires more memory to hold the annotations at runtime" /> |
180 <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" /> | 200 <param name="ftab" type="integer" value="10" min="1" label="The size of the ftab lookup table used to calculate an initial Burrows-Wheeler range with respect to the first n characters of the query (-t)" help="ftab size is 4^(n+1) bytes" /> |
181 <param name="ntoa" type="select" label="Whether or not to convert Ns in the reference sequence to As (--ntoa)"> | 201 <param name="ntoa" type="select" label="Whether or not to convert Ns in the reference sequence to As (--ntoa)"> |
182 <option value="no">Do not convert Ns</option> | 202 <option value="no">Do not convert Ns</option> |
183 <option value="yes">Convert Ns to As</option> | 203 <option value="yes">Convert Ns to As</option> |
184 </param> | 204 </param> |
185 <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"> | 205 <param name="endian" type="select" label="Endianness to use when serializing integers to the index file (--big/--little)" help="Little is most appropriate for Intel- and AMD-based architecture"> |
186 <option value="little">Little</option> | 206 <option value="little">Little</option> |
187 <option value="big">Big</option> | 207 <option value="big">Big</option> |
188 </param> | 208 </param> |
189 <param name="seed" type="integer" value="-1" label="Seed for the pseudorandom number generator (--seed)" help="Use -1 to use default" /> | 209 <param name="seed" type="integer" value="-1" label="Seed for the pseudorandom number generator (--seed)" help="Use -1 to use default" /> |
190 <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" /> | |
191 </when> <!-- indexFull --> | 210 </when> <!-- indexFull --> |
192 </conditional> <!-- indexParams --> | 211 </conditional> <!-- indexParams --> |
193 </when> <!-- history --> | 212 </when> <!-- history --> |
194 </conditional> <!-- refGenomeSource --> | 213 </conditional> <!-- refGenomeSource --> |
195 <conditional name="singlePaired"> | 214 <conditional name="singlePaired"> |
201 <param name="sInput1" type="data" format="fastqsanger,fastqillumina,fastqsolexa" label="FASTQ file" help="Must have ASCII encoded quality scores"/> | 220 <param name="sInput1" type="data" format="fastqsanger,fastqillumina,fastqsolexa" label="FASTQ file" help="Must have ASCII encoded quality scores"/> |
202 <conditional name="sParams"> | 221 <conditional name="sParams"> |
203 <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"> | 222 <param name="sSettingsType" type="select" label="Bowtie settings to use" help="For most mapping needs use Commonly used settings. If you want full control use Full parameter list"> |
204 <option value="preSet">Commonly used</option> | 223 <option value="preSet">Commonly used</option> |
205 <option value="full">Full parameter list</option> | 224 <option value="full">Full parameter list</option> |
206 </param> | 225 </param> |
207 <when value="preSet" /> | 226 <when value="preSet" /> |
208 <when value="full"> | 227 <when value="full"> |
209 <param name="sSkip" type="integer" value="0" label="Skip the first n reads (-s)" /> | 228 <param name="sSkip" type="integer" value="0" label="Skip the first n reads (-s)" /> |
210 <param name="sAlignLimit" type="integer" value="-1" label="Only align the first n reads (-u)" help="-1 for off" /> | 229 <param name="sAlignLimit" type="integer" value="-1" label="Only align the first n reads (-u)" help="-1 for off" /> |
211 <param name="sTrimH" type="integer" value="0" label="Trim n bases from high-quality (left) end of each read before alignment (-5)" /> | 230 <param name="sTrimH" type="integer" value="0" label="Trim n bases from high-quality (left) end of each read before alignment (-5)" /> |
212 <param name="sTrimL" type="integer" value="0" label="Trim n bases from low-quality (right) end of each read before alignment (-3)" /> | 231 <param name="sTrimL" type="integer" value="0" label="Trim n bases from low-quality (right) end of each read before alignment (-3)" /> |
213 <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" /> | 232 <conditional name="alignModeOption"> |
214 <param name="sMismatchQual" type="integer" value="70" label="Maximum permitted total of quality values at mismatched read positions (-e)" /> | 233 <param name="alignMode" type="select" label="Alignment mode"> |
215 <param name="sSeedLen" type="integer" value="28" label="Seed length (-l)" help="Minimum value is 5" /> | 234 <option value="nMode">Maq-like: quality-aware, limit mismatches in seed (-n)</option> |
216 <param name="sRounding" type="select" label="Whether or not to round to the nearest 10 and saturating at 30 (--nomaqround)"> | 235 <option value="vMode">ignore qualities, limit end-to-end mismatches (-v)</option> |
217 <option value="round">Round to nearest 10</option> | 236 </param> |
218 <option value="noRound">Do not round to nearest 10</option> | 237 <when value="nMode"> |
238 <param name="sMismatchSeed" type="integer" value="2" min="0" max="3" label="Maximum number of mismatches permitted in the seed (-n)" help="May be 0, 1, 2, or 3" /> | |
239 <param name="sMismatchQual" type="integer" value="70" min="1" label="Maximum permitted total of quality values at all mismatched read positions (-e)" /> | |
240 <param name="sSeedLen" type="integer" value="28" min="5" label="Seed length (-l)" help="Minimum value is 5" /> | |
241 <param name="sRounding" type="select" label="Whether or not to round to the nearest 10 and saturating at 30 (--nomaqround)" help="Maq accepts quality values in the Phred quality scale, but internally rounds values to the nearest 10, with a maximum of 30. By default, bowtie also rounds this way"> | |
242 <option value="round">Round to nearest 10</option> | |
243 <option value="noRound">Do not round to nearest 10</option> | |
244 </param> | |
245 </when> | |
246 <when value="vMode"> | |
247 <param name="maxMismatches" type="integer" value="" min="0" max="3" label="Maximum number of mismatches (-v)" help="May be 0, 1, 2, or 3" /> | |
248 </when> | |
249 </conditional> | |
250 <param name="sForwardAlign" type="select" label="Choose whether or not to attempt to align against the forward reference strand (--nofw)"> | |
251 <option value="forward">Align against the forward reference strand</option> | |
252 <option value="noForward">Do not align against the forward reference strand</option> | |
219 </param> | 253 </param> |
220 <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" /> | 254 <param name="sReverseAlign" type="select" label="Choose whether or not to attempt to align against the reverse-complement reference strand (--norc)"> |
221 <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"> | 255 <option value="reverse">Align against the reverse-complement reference strand</option> |
222 <option value="noTryHard">Do not try hard</option> | 256 <option value="noReverse">Do not align against the reverse-complement reference strand</option> |
223 <option value="doTryHard">Try hard</option> | |
224 </param> | 257 </param> |
225 <param name="sValAlign" type="integer" value="1" label="Report up to n valid alignments per read (-k)" /> | |
226 <param name="sAllValAligns" type="select" label="Whether or not to report all valid alignments per read (-a)"> | |
227 <option value="noAllValAligns">Do not report all valid alignments</option> | |
228 <option value="doAllValAligns">Report all valid alignments</option> | |
229 </param> | |
230 <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" /> | |
231 <param name="sMaxFile" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write all reads with a number of valid alignments exceeding the limit set with the -m option to a file (--max)" /> | |
232 <param name="sUnmappedFile" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write all reads that could not be aligned to a file (--un)" /> | |
233 <conditional name="sBestOption"> | 258 <conditional name="sBestOption"> |
234 <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"> | 259 <param name="sBest" type="select" label="Whether or not to make Bowtie guarantee that reported singleton alignments are 'best' in terms of stratum and in terms of the quality values at the mismatched positions (--best)" help="Removes all strand bias. Only affects which alignments are reported by Bowtie. Runs slower with best option"> |
235 <option value="noBest">Do not use best</option> | 260 <option value="noBest">Do not use best</option> |
236 <option value="doBest">Use best</option> | 261 <option value="doBest">Use best</option> |
237 </param> | 262 </param> |
238 <when value="noBest"> | 263 <when value="noBest"> |
239 <param name="snMaxBacktracks" type="integer" value="125" label="Maximum number of backtracks permitted when aligning a read (--maxbts)" /> | 264 <conditional name="sTryHardOption"> |
265 <param name="sTryHard" type="select" label="Whether or not to try as hard as possible to find valid alignments when they exist (-y)" help="Tryhard mode is much slower than regular mode"> | |
266 <option value="noTryHard">Do not try hard</option> | |
267 <option value="doTryHard">Try hard</option> | |
268 </param> | |
269 <when value="noTryHard"> | |
270 <param name="snMaxBacktracks" type="integer" value="125" min="0" label="Maximum number of backtracks permitted when aligning a read (--maxbts)" /> | |
271 </when> | |
272 <when value="doTryHard" /> | |
273 </conditional> | |
240 </when> | 274 </when> |
241 <when value="doBest"> | 275 <when value="doBest"> |
242 <param name="sdMaxBacktracks" type="integer" value="800" label="Maximum number of backtracks permitted when aligning a read (--maxbts)" /> | |
243 <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)"> | 276 <param name="sdStrata" type="select" label="Whether or not to report only those alignments that fall in the best stratum if many valid alignments exist and are reportable (--strata)"> |
244 <option value="noStrata">Do not use strata option</option> | 277 <option value="noStrata">Do not use strata option</option> |
245 <option value="doStrata">Use strata option</option> | 278 <option value="doStrata">Use strata option</option> |
246 </param> | 279 </param> |
280 <conditional name="sTryHardOption"> | |
281 <param name="sTryHard" type="select" label="Whether or not to try as hard as possible to find valid alignments when they exist (-y)" help="Tryhard mode is much slower than regular mode"> | |
282 <option value="noTryHard">Do not try hard</option> | |
283 <option value="doTryHard">Try hard</option> | |
284 </param> | |
285 <when value="noTryHard"> | |
286 <param name="sdMaxBacktracks" type="integer" value="800" min="0" label="Maximum number of backtracks permitted when aligning a read (--maxbts)" /> | |
287 </when> | |
288 <when value="doTryHard" /> | |
289 </conditional> | |
247 </when> | 290 </when> |
248 </conditional> <!-- bestOption --> | 291 </conditional> <!-- bestOption --> |
292 <conditional name="sAllValAlignsOption"> | |
293 <param name="sAllValAligns" type="select" label="Whether or not to report all valid alignments per read (-a)"> | |
294 <option value="noAllValAligns">Do not report all valid alignments</option> | |
295 <option value="doAllValAligns">Report all valid alignments</option> | |
296 </param> | |
297 <when value="noAllValAligns"> | |
298 <param name="sValAlign" type="integer" value="1" min="1" label="Report up to n valid alignments per read (-k)" /> | |
299 </when> | |
300 <when value="doAllValAligns" /> | |
301 </conditional> | |
302 <param name="sSuppressAlign" type="integer" value="-1" label="Suppress all alignments for a read if more than n reportable alignments exist (-m)" help="-1 for no limit" /> | |
303 <param name="sMaxFile" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write all reads with a number of valid alignments exceeding the limit set with the -m option to a file (--max)" /> | |
304 <param name="sUnmappedFile" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write all reads that could not be aligned to a file (--un)" /> | |
249 <param name="sOffrate" type="integer" value="-1" label="Override the offrate of the index to n (-o)" help="-1 for default" /> | 305 <param name="sOffrate" type="integer" value="-1" label="Override the offrate of the index to n (-o)" help="-1 for default" /> |
250 <param name="sSeed" type="integer" value="-1" label="Seed for pseudo-random number generator (--seed)" help="-1 for default" /> | 306 <param name="sSeed" type="integer" value="-1" label="Seed for pseudo-random number generator (--seed)" help="-1 for default" /> |
251 </when> <!-- full --> | 307 </when> <!-- full --> |
252 </conditional> <!-- sParams --> | 308 </conditional> <!-- sParams --> |
253 </when> <!-- single --> | 309 </when> <!-- single --> |
255 <param name="pInput1" type="data" format="fastqsanger,fastqillumina,fastqsolexa" label="Forward FASTQ file" help="Must have ASCII encoded quality scores"/> | 311 <param name="pInput1" type="data" format="fastqsanger,fastqillumina,fastqsolexa" label="Forward FASTQ file" help="Must have ASCII encoded quality scores"/> |
256 <param name="pInput2" type="data" format="fastqsanger,fastqillumina,fastqsolexa" label="Reverse FASTQ file" help="File format must match the Forward FASTQ file"> | 312 <param name="pInput2" type="data" format="fastqsanger,fastqillumina,fastqsolexa" label="Reverse FASTQ file" help="File format must match the Forward FASTQ file"> |
257 <options options_filter_attribute="ext" from_parameter="tool.app.datatypes_registry.datatypes_by_extension" transform_lines="obj.keys()">> | 313 <options options_filter_attribute="ext" from_parameter="tool.app.datatypes_registry.datatypes_by_extension" transform_lines="obj.keys()">> |
258 <column name="name" index="0"/> | 314 <column name="name" index="0"/> |
259 <column name="value" index="0"/> | 315 <column name="value" index="0"/> |
260 <filter type="param_value" ref="pInput1" ref_attribute="ext" column="0"/> | 316 <filter type="param_value" ref="pInput1" ref_attribute="ext" column="0"/> |
261 </options> | 317 </options> |
262 </param> | 318 </param> |
263 <param name="pMaxInsert" type="integer" value="1000" label="Maximum insert size for valid paired-end alignments (-X)" /> | 319 <param name="pMaxInsert" type="integer" value="1000" label="Maximum insert size for valid paired-end alignments (-X)" /> |
264 <param name="pMateOrient" type="select" label="The upstream/downstream mate orientation for valid paired-end alignment against the forward reference strand (--fr/--rf/--ff)"> | 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)"> |
265 <option value="fr">FR (for Illumina)</option> | 321 <option value="fr">FR (for Illumina)</option> |
271 <option value="preSet">Commonly used</option> | 327 <option value="preSet">Commonly used</option> |
272 <option value="full">Full parameter list</option> | 328 <option value="full">Full parameter list</option> |
273 </param> | 329 </param> |
274 <when value="preSet" /> | 330 <when value="preSet" /> |
275 <when value="full"> | 331 <when value="full"> |
276 <param name="pSkip" type="integer" value="0" label="Skip the first n pairs (-s)" /> | 332 <param name="pSkip" type="integer" value="0" label="Skip the first n pairs (-s)" /> |
277 <param name="pAlignLimit" type="integer" value="-1" label="Only align the first n pairs (-u)" help="-1 for off" /> | 333 <param name="pAlignLimit" type="integer" value="-1" label="Only align the first n pairs (-u)" help="-1 for off" /> |
278 <param name="pTrimH" type="integer" value="0" label="Trim n bases from high-quality (left) end of each read before alignment (-5)" /> | 334 <param name="pTrimH" type="integer" value="0" label="Trim n bases from high-quality (left) end of each read before alignment (-5)" /> |
279 <param name="pTrimL" type="integer" value="0" label="Trim n bases from low-quality (right) end of each read before alignment (-3)" /> | 335 <param name="pTrimL" type="integer" value="0" label="Trim n bases from low-quality (right) end of each read before alignment (-3)" /> |
280 <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" /> | 336 <conditional name="alignModeOption"> |
281 <param name="pMismatchQual" type="integer" value="70" label="Maximum permitted total of quality values at mismatched read positions (-e)" /> | 337 <param name="alignMode" type="select" label="Alignment mode"> |
282 <param name="pSeedLen" type="integer" value="28" label="Seed length (-l)" help="Minimum value is 5" /> | 338 <option value="nMode">Maq-like: quality-aware, limit mismatches in seed (-n)</option> |
283 <param name="pRounding" type="select" label="Whether or not to round to the nearest 10 and saturating at 30 (--nomaqround)"> | 339 <option value="vMode">ignore qualities, limit end-to-end mismatches (-v)</option> |
284 <option value="round">Round to nearest 10</option> | 340 </param> |
285 <option value="noRound">Do not round to nearest 10</option> | 341 <when value="nMode"> |
286 </param> | 342 <param name="pMismatchSeed" type="integer" value="2" min="0" max="3" label="Maximum number of mismatches permitted in the seed (-n)" help="May be 0, 1, 2, or 3" /> |
287 <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" /> | 343 <param name="pMismatchQual" type="integer" value="70" min="1" label="Maximum permitted total of quality values at all mismatched read positions (-e)" /> |
344 <param name="pSeedLen" type="integer" value="28" min="5" label="Seed length (-l)" help="Minimum value is 5" /> | |
345 <param name="pRounding" type="select" label="Whether or not to round to the nearest 10 and saturating at 30 (--nomaqround)" help="Maq accepts quality values in the Phred quality scale, but internally rounds values to the nearest 10, with a maximum of 30. By default, bowtie also rounds this way"> | |
346 <option value="round">Round to nearest 10</option> | |
347 <option value="noRound">Do not round to nearest 10</option> | |
348 </param> | |
349 </when> | |
350 <when value="vMode"> | |
351 <param name="maxMismatches" type="integer" value="" min="0" max="3" label="Maximum number of mismatches (-v)" help="May be 0, 1, 2, or 3" /> | |
352 </when> | |
353 </conditional> | |
288 <param name="pMinInsert" type="integer" value="0" label="Minimum insert size for valid paired-end alignments (-I)" /> | 354 <param name="pMinInsert" type="integer" value="0" label="Minimum insert size for valid paired-end alignments (-I)" /> |
289 <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 against the forward reference strand (--nofw)"> |
290 <param name="pForwardAlign" type="select" label="Choose whether or not to attempt to align the forward reference strand (--nofw)"> | |
291 <option value="forward">Align against the forward reference strand</option> | 356 <option value="forward">Align against the forward reference strand</option> |
292 <option value="noForward">Do not align against the forward reference strand</option> | 357 <option value="noForward">Do not align against the forward reference strand</option> |
293 </param> | 358 </param> |
294 <param name="pReverseAlign" type="select" label="Choose whether or not to align against the reverse-complement reference strand (--norc)"> | 359 <param name="pReverseAlign" type="select" label="Choose whether or not to attempt to align against the reverse-complement reference strand (--norc)"> |
295 <option value="reverse">Align against the reverse-complement reference strand</option> | 360 <option value="reverse">Align against the reverse-complement reference strand</option> |
296 <option value="noReverse">Do not align against the reverse-complement reference strand</option> | 361 <option value="noReverse">Do not align against the reverse-complement reference strand</option> |
297 </param> | 362 </param> |
298 <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"> | |
299 <option value="noTryHard">Do not try hard</option> | |
300 <option value="doTryHard">Try hard</option> | |
301 </param> | |
302 <param name="pValAlign" type="integer" value="1" label="Report up to n valid arguments per pair (-k)" /> | |
303 <param name="pAllValAligns" type="select" label="Whether or not to report all valid alignments per pair (-a)"> | |
304 <option value="noAllValAligns">Do not report all valid alignments</option> | |
305 <option value="doAllValAligns">Report all valid alignments</option> | |
306 </param> | |
307 <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" /> | |
308 <param name="pMaxFile" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write all reads with a number of valid alignments exceeding the limit set with the -m option to a file (--max)" /> | |
309 <param name="pUnmappedFile" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write all reads that could not be aligned to a file (--un)" /> | |
310 <conditional name="pBestOption"> | 363 <conditional name="pBestOption"> |
311 <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"> | 364 <param name="pBest" type="select" label="Whether or not to make Bowtie guarantee that reported singleton alignments are 'best' in terms of stratum and in terms of the quality values at the mismatched positions (--best)" help="Removes all strand bias. Only affects which alignments are reported by Bowtie. Runs slower with best option"> |
312 <option value="noBest">Do not use best</option> | 365 <option value="noBest">Do not use best</option> |
313 <option value="doBest">Use best</option> | 366 <option value="doBest">Use best</option> |
314 </param> | 367 </param> |
315 <when value="noBest"> | 368 <when value="noBest"> |
316 <param name="pnMaxBacktracks" type="integer" value="125" label="Maximum number of backtracks permitted when aligning a read (--maxbts)" /> | 369 <conditional name="pTryHardOption"> |
370 <param name="pTryHard" type="select" label="Whether or not to try as hard as possible to find valid alignments when they exist (-y)" help="Tryhard mode is much slower than regular mode"> | |
371 <option value="noTryHard">Do not try hard</option> | |
372 <option value="doTryHard">Try hard</option> | |
373 </param> | |
374 <when value="noTryHard"> | |
375 <param name="pMaxAlignAttempt" type="integer" value="100" min="1" label="Maximum number of attempts Bowtie will make to match an alignment for one mate with an alignment for the opposite mate (--pairtries)" /> | |
376 <param name="pnMaxBacktracks" type="integer" value="125" min="0" label="Maximum number of backtracks permitted when aligning a read (--maxbts)" /> | |
377 </when> | |
378 <when value="doTryHard" /> | |
379 </conditional> | |
317 </when> | 380 </when> |
318 <when value="doBest"> | 381 <when value="doBest"> |
319 <param name="pdMaxBacktracks" type="integer" value="800" label="Maximum number of backtracks permitted when aligning a read (--maxbts)" /> | |
320 <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)"> | 382 <param name="pdStrata" type="select" label="Whether or not to report only those alignments that fall in the best stratum if many valid alignments exist and are reportable (--strata)"> |
321 <option value="noStrata">Do not use strata option</option> | 383 <option value="noStrata">Do not use strata option</option> |
322 <option value="doStrata">Use strata option</option> | 384 <option value="doStrata">Use strata option</option> |
323 </param> | 385 </param> |
386 <conditional name="pTryHardOption"> | |
387 <param name="pTryHard" type="select" label="Whether or not to try as hard as possible to find valid alignments when they exist (-y)" help="Tryhard mode is much slower than regular mode"> | |
388 <option value="noTryHard">Do not try hard</option> | |
389 <option value="doTryHard">Try hard</option> | |
390 </param> | |
391 <when value="noTryHard"> | |
392 <param name="pMaxAlignAttempt" type="integer" value="100" min="1" label="Maximum number of attempts Bowtie will make to match an alignment for one mate with an alignment for the opposite mate (--pairtries)" /> | |
393 <param name="pdMaxBacktracks" type="integer" value="800" min="0" label="Maximum number of backtracks permitted when aligning a read (--maxbts)" /> | |
394 </when> | |
395 <when value="doTryHard" /> | |
396 </conditional> | |
324 </when> | 397 </when> |
325 </conditional> | 398 </conditional> |
399 <conditional name="pAllValAlignsOption"> | |
400 <param name="pAllValAligns" type="select" label="Whether or not to report all valid alignments per pair (-a)"> | |
401 <option value="noAllValAligns">Do not report all valid alignments</option> | |
402 <option value="doAllValAligns">Report all valid alignments</option> | |
403 </param> | |
404 <when value="noAllValAligns"> | |
405 <param name="pValAlign" type="integer" value="1" min="1" label="Report up to n valid alignments per pair (-k)" /> | |
406 </when> | |
407 <when value="doAllValAligns" /> | |
408 </conditional> | |
409 <param name="pSuppressAlign" type="integer" value="-1" label="Suppress all alignments for a pair if more than n reportable alignments exist (-m)" help="-1 for no limit" /> | |
410 <param name="pMaxFile" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write all reads with a number of valid alignments exceeding the limit set with the -m option to a file (--max)" /> | |
411 <param name="pUnmappedFile" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write all reads that could not be aligned to a file (--un)" /> | |
326 <param name="pOffrate" type="integer" value="-1" label="Override the offrate of the index to n (-o)" help="-1 for default" /> | 412 <param name="pOffrate" type="integer" value="-1" label="Override the offrate of the index to n (-o)" help="-1 for default" /> |
327 <param name="pSeed" type="integer" value="-1" label="Seed for pseudo-random number generator (--seed)" help="-1 for default" /> | 413 <param name="pSeed" type="integer" value="-1" label="Seed for pseudo-random number generator (--seed)" help="-1 for default" /> |
328 </when> <!-- full --> | 414 </when> <!-- full --> |
329 </conditional> <!-- pParams --> | 415 </conditional> <!-- pParams --> |
330 </when> <!-- paired --> | 416 </when> <!-- paired --> |
331 </conditional> <!-- singlePaired --> | 417 </conditional> <!-- singlePaired --> |
332 <param name="suppressHeader" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Suppress the header in the output SAM file" help="Bowtie produces SAM with several lines of header information by default" /> | 418 <param name="suppressHeader" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Suppress the header in the output SAM file (--sam-nohead)" help="Bowtie produces SAM with several lines of header information by default" /> |
333 </inputs> | 419 </inputs> |
334 <outputs> | 420 <outputs> |
335 <data format="sam" name="output" label="${tool.name} on ${on_string}: mapped reads"> | 421 <data format="sam" name="output" label="${tool.name} on ${on_string}: mapped reads"> |
336 <actions> | 422 <actions> |
337 <conditional name="refGenomeSource.genomeSource"> | 423 <conditional name="refGenomeSource.genomeSource"> |
447 <test> | 533 <test> |
448 <!-- | 534 <!-- |
449 Bowtie command: | 535 Bowtie command: |
450 bowtie -q -p 4 -S +sam-nohead chrM_base test-data/bowtie_in2.fastqsanger > bowtie_out6_u.sam | 536 bowtie -q -p 4 -S +sam-nohead chrM_base test-data/bowtie_in2.fastqsanger > bowtie_out6_u.sam |
451 sort bowtie_out6_u.sam > bowtie_out6.sam | 537 sort bowtie_out6_u.sam > bowtie_out6.sam |
452 -p is the number of threads. You need to replace the + with 2 dashes. | 538 -p is the number of threads. You need to replace the + with 2 dashes. |
453 chrM_base needs to be the base location/name of the index files. | 539 chrM_base needs to be the base location/name of the index files. |
454 --> | 540 --> |
455 <param name="genomeSource" value="indexed" /> | 541 <param name="genomeSource" value="indexed" /> |
456 <!-- this is the backwards-compatible "unique value" for this index, not an actual path --> | 542 <!-- this is the backwards-compatible "unique value" for this index, not an actual path --> |
457 <param name="index" value="equCab2chrM" /> | 543 <param name="index" value="equCab2chrM" /> |
470 sort bowtie_out8_u_1.sam > bowtie_out8_1.sam | 556 sort bowtie_out8_u_1.sam > bowtie_out8_1.sam |
471 sort bowtie_out8_u_2.sam > bowtie_out8_2.sam | 557 sort bowtie_out8_u_2.sam > bowtie_out8_2.sam |
472 Then also need to modify bowtie_out8_1.sam and bowtie_out8_2.sam so that all @ lines come before sequence lines. | 558 Then also need to modify bowtie_out8_1.sam and bowtie_out8_2.sam so that all @ lines come before sequence lines. |
473 -p is the number of threads. You need to replace the + with 2 dashes. | 559 -p is the number of threads. You need to replace the + with 2 dashes. |
474 The two unmapped output files will be named bowtie_out8_1.fastq and bowtie_out8_2.fastq. | 560 The two unmapped output files will be named bowtie_out8_1.fastq and bowtie_out8_2.fastq. |
475 chrM_base is the index files' location/base name. | 561 chrM_base is the index files' location/base name. |
476 --> | 562 --> |
477 <param name="genomeSource" value="history" /> | 563 <param name="genomeSource" value="history" /> |
478 <param name="ownFile" value="phiX.fasta" /> | 564 <param name="ownFile" value="phiX.fasta" /> |
479 <param name="indexSettings" value="indexPreSet" /> | 565 <param name="indexSettings" value="indexPreSet" /> |
480 <param name="sPaired" value="paired" /> | 566 <param name="sPaired" value="paired" /> |
485 <param name="pSettingsType" value="full" /> | 571 <param name="pSettingsType" value="full" /> |
486 <param name="pSkip" value="0" /> | 572 <param name="pSkip" value="0" /> |
487 <param name="pAlignLimit" value="-1" /> | 573 <param name="pAlignLimit" value="-1" /> |
488 <param name="pTrimH" value="0" /> | 574 <param name="pTrimH" value="0" /> |
489 <param name="pTrimL" value="0" /> | 575 <param name="pTrimL" value="0" /> |
576 <param name="alignMode" value="nMode" /> | |
490 <param name="pMismatchSeed" value="2" /> | 577 <param name="pMismatchSeed" value="2" /> |
491 <param name="pMismatchQual" value="70" /> | 578 <param name="pMismatchQual" value="70" /> |
492 <param name="pSeedLen" value="28" /> | 579 <param name="pSeedLen" value="28" /> |
493 <param name="pRounding" value="round" /> | 580 <param name="pRounding" value="round" /> |
494 <param name="pMaqSoapAlign" value="-1" /> | |
495 <param name="pMinInsert" value="0" /> | 581 <param name="pMinInsert" value="0" /> |
496 <param name="pMaxAlignAttempt" value="100" /> | 582 <param name="pMaxAlignAttempt" value="100" /> |
497 <param name="pForwardAlign" value="forward" /> | 583 <param name="pForwardAlign" value="forward" /> |
498 <param name="pReverseAlign" value="reverse" /> | 584 <param name="pReverseAlign" value="reverse" /> |
499 <param name="pTryHard" value="noTryHard" /> | 585 <param name="pTryHard" value="noTryHard" /> |
525 <param name="pSettingsType" value="full" /> | 611 <param name="pSettingsType" value="full" /> |
526 <param name="pSkip" value="0" /> | 612 <param name="pSkip" value="0" /> |
527 <param name="pAlignLimit" value="-1" /> | 613 <param name="pAlignLimit" value="-1" /> |
528 <param name="pTrimH" value="0" /> | 614 <param name="pTrimH" value="0" /> |
529 <param name="pTrimL" value="0" /> | 615 <param name="pTrimL" value="0" /> |
616 <param name="alignMode" value="nMode" /> | |
530 <param name="pMismatchSeed" value="2" /> | 617 <param name="pMismatchSeed" value="2" /> |
531 <param name="pMismatchQual" value="70" /> | 618 <param name="pMismatchQual" value="70" /> |
532 <param name="pSeedLen" value="28" /> | 619 <param name="pSeedLen" value="28" /> |
533 <param name="pRounding" value="round" /> | 620 <param name="pRounding" value="round" /> |
534 <param name="pMaqSoapAlign" value="-1" /> | |
535 <param name="pMinInsert" value="0" /> | 621 <param name="pMinInsert" value="0" /> |
536 <param name="pMaxAlignAttempt" value="100" /> | 622 <param name="pMaxAlignAttempt" value="100" /> |
537 <param name="pForwardAlign" value="forward" /> | 623 <param name="pForwardAlign" value="forward" /> |
538 <param name="pReverseAlign" value="reverse" /> | 624 <param name="pReverseAlign" value="reverse" /> |
539 <param name="pTryHard" value="noTryHard" /> | 625 <param name="pTryHard" value="noTryHard" /> |
547 <param name="pdStrata" value="noStrata" /> | 633 <param name="pdStrata" value="noStrata" /> |
548 <param name="pOffrate" value="-1" /> | 634 <param name="pOffrate" value="-1" /> |
549 <param name="pSeed" value="-1" /> | 635 <param name="pSeed" value="-1" /> |
550 <param name="suppressHeader" value="true" /> | 636 <param name="suppressHeader" value="true" /> |
551 <output name="output" ftype="sam" file="bowtie_out7.sam" sort="True" /> | 637 <output name="output" ftype="sam" file="bowtie_out7.sam" sort="True" /> |
552 <output name="output_unmapped_reads_l" ftype="fastqillumna" file="bowtie_out8_1.fastqillumina.sorted" sort="True" /> | 638 <output name="output_unmapped_reads_l" ftype="fastqillumina" file="bowtie_out8_1.fastqillumina.sorted" sort="True" /> |
553 <output name="output_unmapped_reads_r" ftype="fastqillumna" file="bowtie_out8_2.fastqillumina.sorted" sort="True" /> | 639 <output name="output_unmapped_reads_r" ftype="fastqillumina" file="bowtie_out8_2.fastqillumina.sorted" sort="True" /> |
554 </test> | 640 </test> |
555 <test> | 641 <test> |
556 <param name="genomeSource" value="history" /> | 642 <param name="genomeSource" value="history" /> |
557 <param name="ownFile" value="phiX.fasta" /> | 643 <param name="ownFile" value="phiX.fasta" /> |
558 <param name="indexSettings" value="indexPreSet" /> | 644 <param name="indexSettings" value="indexPreSet" /> |
564 <param name="pSettingsType" value="full" /> | 650 <param name="pSettingsType" value="full" /> |
565 <param name="pSkip" value="0" /> | 651 <param name="pSkip" value="0" /> |
566 <param name="pAlignLimit" value="-1" /> | 652 <param name="pAlignLimit" value="-1" /> |
567 <param name="pTrimH" value="0" /> | 653 <param name="pTrimH" value="0" /> |
568 <param name="pTrimL" value="0" /> | 654 <param name="pTrimL" value="0" /> |
655 <param name="alignMode" value="nMode" /> | |
569 <param name="pMismatchSeed" value="2" /> | 656 <param name="pMismatchSeed" value="2" /> |
570 <param name="pMismatchQual" value="70" /> | 657 <param name="pMismatchQual" value="70" /> |
571 <param name="pSeedLen" value="28" /> | 658 <param name="pSeedLen" value="28" /> |
572 <param name="pRounding" value="round" /> | 659 <param name="pRounding" value="round" /> |
573 <param name="pMaqSoapAlign" value="-1" /> | |
574 <param name="pMinInsert" value="0" /> | 660 <param name="pMinInsert" value="0" /> |
575 <param name="pMaxAlignAttempt" value="100" /> | 661 <param name="pMaxAlignAttempt" value="100" /> |
576 <param name="pForwardAlign" value="forward" /> | 662 <param name="pForwardAlign" value="forward" /> |
577 <param name="pReverseAlign" value="reverse" /> | 663 <param name="pReverseAlign" value="reverse" /> |
578 <param name="pTryHard" value="noTryHard" /> | 664 <param name="pTryHard" value="noTryHard" /> |
589 <param name="suppressHeader" value="true" /> | 675 <param name="suppressHeader" value="true" /> |
590 <output name="output" ftype="sam" file="bowtie_out7.sam" sort="True" /> | 676 <output name="output" ftype="sam" file="bowtie_out7.sam" sort="True" /> |
591 <output name="output_unmapped_reads_l" ftype="fastqsolexa" file="bowtie_out8_1.fastqsolexa.sorted" sort="True" /> | 677 <output name="output_unmapped_reads_l" ftype="fastqsolexa" file="bowtie_out8_1.fastqsolexa.sorted" sort="True" /> |
592 <output name="output_unmapped_reads_r" ftype="fastqsolexa" file="bowtie_out8_2.fastqsolexa.sorted" sort="True" /> | 678 <output name="output_unmapped_reads_r" ftype="fastqsolexa" file="bowtie_out8_2.fastqsolexa.sorted" sort="True" /> |
593 </test> | 679 </test> |
594 <!-- end testing of non-sanger variant fastq reads --> | 680 <!-- end testing of non-sanger variant fastq reads --> |
595 <test> | 681 <test> |
596 <!-- | 682 <!-- |
597 Bowtie command: | 683 Bowtie command: |
598 bowtie -q -p 4 -S +sam-nohead -n 2 -e 70 -l 28 +maxbts 125 -y -k 1 chrM_base test-data/bowtie_in2.fastqsanger > bowtie_out9_u.sam | 684 bowtie -q -p 4 -S +sam-nohead -n 2 -e 70 -l 28 -y -k 1 chrM_base test-data/bowtie_in2.fastqsanger > bowtie_out9_u.sam |
599 sort bowtie_out9_u.sam > bowtie_out9.sam | 685 sort bowtie_out9_u.sam > bowtie_out9.sam |
600 -p is the number of threads. You need to replace the + with 2 dashes. | 686 -p is the number of threads. You need to replace the + with 2 dashes. |
601 chrM_base is the index files' location/base name. | 687 chrM_base is the index files' location/base name. |
602 --> | 688 --> |
603 <param name="genomeSource" value="indexed" /> | 689 <param name="genomeSource" value="indexed" /> |
604 <!-- this is the backwards-compatible "unique value" for this index, not an actual path --> | 690 <!-- this is the backwards-compatible "unique value" for this index, not an actual path --> |
605 <param name="index" value="equCab2chrM" /> | 691 <param name="index" value="equCab2chrM" /> |
606 <param name="sPaired" value="single" /> | 692 <param name="sPaired" value="single" /> |
608 <param name="sSettingsType" value="full" /> | 694 <param name="sSettingsType" value="full" /> |
609 <param name="sSkip" value="0" /> | 695 <param name="sSkip" value="0" /> |
610 <param name="sAlignLimit" value="-1" /> | 696 <param name="sAlignLimit" value="-1" /> |
611 <param name="sTrimH" value="0" /> | 697 <param name="sTrimH" value="0" /> |
612 <param name="sTrimL" value="0" /> | 698 <param name="sTrimL" value="0" /> |
699 <param name="alignMode" value="nMode" /> | |
613 <param name="sMismatchSeed" value="2" /> | 700 <param name="sMismatchSeed" value="2" /> |
614 <param name="sMismatchQual" value="70" /> | 701 <param name="sMismatchQual" value="70" /> |
615 <param name="sSeedLen" value="28" /> | 702 <param name="sSeedLen" value="28" /> |
616 <param name="sRounding" value="round" /> | 703 <param name="sRounding" value="round" /> |
617 <param name="sMaqSoapAlign" value="-1" /> | 704 <param name="sForwardAlign" value="forward" /> |
705 <param name="sReverseAlign" value="reverse" /> | |
618 <param name="sTryHard" value="doTryHard" /> | 706 <param name="sTryHard" value="doTryHard" /> |
619 <param name="sValAlign" value="1" /> | 707 <param name="sValAlign" value="1" /> |
620 <param name="sAllValAligns" value="noAllValAligns" /> | 708 <param name="sAllValAligns" value="noAllValAligns" /> |
621 <param name="sSuppressAlign" value="-1" /> | 709 <param name="sSuppressAlign" value="-1" /> |
622 <param name="sUnmappedFile" value="false" /> | 710 <param name="sUnmappedFile" value="false" /> |
623 <param name="sMaxFile" value="false" /> | 711 <param name="sMaxFile" value="false" /> |
624 <param name="sBest" value="noBest" /> | 712 <param name="sBest" value="noBest" /> |
625 <param name="snMaxBacktracks" value="125" /> | |
626 <param name="sOffrate" value="-1" /> | 713 <param name="sOffrate" value="-1" /> |
627 <param name="sSeed" value="-1" /> | 714 <param name="sSeed" value="-1" /> |
628 <param name="suppressHeader" value="true" /> | 715 <param name="suppressHeader" value="true" /> |
629 <output name="output" ftype="sam" file="bowtie_out9.sam" sort="True" /> | 716 <output name="output" ftype="sam" file="bowtie_out9.sam" sort="True" /> |
630 </test> | 717 </test> |
633 Bowtie command: | 720 Bowtie command: |
634 bowtie-build +offrate 5 +ftabchars 10 +little -f test-data/phiX.fasta phiX_base | 721 bowtie-build +offrate 5 +ftabchars 10 +little -f test-data/phiX.fasta phiX_base |
635 bowtie -q -X 1000 +ff -p 4 -S +sam-nohead phiX_base -1 test-data/bowtie_in5.fastqsanger -2 test-data/bowtie_in6.fastqsanger > bowtie_out10_u.sam | 722 bowtie -q -X 1000 +ff -p 4 -S +sam-nohead phiX_base -1 test-data/bowtie_in5.fastqsanger -2 test-data/bowtie_in6.fastqsanger > bowtie_out10_u.sam |
636 sort bowtie_out10_u.sam > bowtie_out10.sam | 723 sort bowtie_out10_u.sam > bowtie_out10.sam |
637 -p is the number of threads. You need to replace the + with 2 dashes. | 724 -p is the number of threads. You need to replace the + with 2 dashes. |
638 chrM_base is the index files' location/base name. | 725 chrM_base is the index files' location/base name. |
639 --> | 726 --> |
640 <param name="genomeSource" value="history" /> | 727 <param name="genomeSource" value="history" /> |
641 <param name="ownFile" value="phiX.fasta" /> | 728 <param name="ownFile" value="phiX.fasta" /> |
642 <param name="indexSettings" value="indexFull" /> | 729 <param name="indexSettings" value="indexFull" /> |
643 <param name="autoB" value="auto" /> | 730 <param name="autoB" value="auto" /> |
646 <param name="offrate" value="5" /> | 733 <param name="offrate" value="5" /> |
647 <param name="ftab" value="10" /> | 734 <param name="ftab" value="10" /> |
648 <param name="ntoa" value="no" /> | 735 <param name="ntoa" value="no" /> |
649 <param name="endian" value="little" /> | 736 <param name="endian" value="little" /> |
650 <param name="seed" value="-1" /> | 737 <param name="seed" value="-1" /> |
651 <param name="cutoff" value="-1" /> | |
652 <param name="sPaired" value="paired" /> | 738 <param name="sPaired" value="paired" /> |
653 <param name="pInput1" ftype="fastqsanger" value="bowtie_in5.fastqsanger" /> | 739 <param name="pInput1" ftype="fastqsanger" value="bowtie_in5.fastqsanger" /> |
654 <param name="pInput2" ftype="fastqsanger" value="bowtie_in6.fastqsanger" /> | 740 <param name="pInput2" ftype="fastqsanger" value="bowtie_in6.fastqsanger" /> |
655 <param name="pMaxInsert" value="1000" /> | 741 <param name="pMaxInsert" value="1000" /> |
656 <param name="pMateOrient" value="ff" /> | 742 <param name="pMateOrient" value="ff" /> |
695 **Outputs** | 781 **Outputs** |
696 | 782 |
697 The output is in SAM format, and has the following columns:: | 783 The output is in SAM format, and has the following columns:: |
698 | 784 |
699 Column Description | 785 Column Description |
700 -------- -------------------------------------------------------- | 786 -------- -------------------------------------------------------- |
701 1 QNAME Query (pair) NAME | 787 1 QNAME Query (pair) NAME |
702 2 FLAG bitwise FLAG | 788 2 FLAG bitwise FLAG |
703 3 RNAME Reference sequence NAME | 789 3 RNAME Reference sequence NAME |
704 4 POS 1-based leftmost POSition/coordinate of clipped sequence | 790 4 POS 1-based leftmost POSition/coordinate of clipped sequence |
705 5 MAPQ MAPping Quality (Phred-scaled) | 791 5 MAPQ MAPping Quality (Phred-scaled) |
708 8 MPOS 1-based Mate POSition | 794 8 MPOS 1-based Mate POSition |
709 9 ISIZE Inferred insert SIZE | 795 9 ISIZE Inferred insert SIZE |
710 10 SEQ query SEQuence on the same strand as the reference | 796 10 SEQ query SEQuence on the same strand as the reference |
711 11 QUAL query QUALity (ASCII-33 gives the Phred base quality) | 797 11 QUAL query QUALity (ASCII-33 gives the Phred base quality) |
712 12 OPT variable OPTional fields in the format TAG:VTYPE:VALUE | 798 12 OPT variable OPTional fields in the format TAG:VTYPE:VALUE |
713 | 799 |
714 The flags are as follows:: | 800 The flags are as follows:: |
715 | 801 |
716 Flag Description | 802 Flag Description |
717 ------ ------------------------------------- | 803 ------ ------------------------------------- |
718 0x0001 the read is paired in sequencing | 804 0x0001 the read is paired in sequencing |
758 -r No reference indexes. Do not build the NAME.3.ebwt and NAME.4.ebwt portions | 844 -r No reference indexes. Do not build the NAME.3.ebwt and NAME.4.ebwt portions |
759 of the index. Used only for paired-end alignment. [off] | 845 of the index. Used only for paired-end alignment. [off] |
760 -o Offrate. How many Burrows-Wheeler rows get marked by the indexer. The | 846 -o Offrate. How many Burrows-Wheeler rows get marked by the indexer. The |
761 indexer will mark every 2^INT rows. The marked rows correspond to rows on | 847 indexer will mark every 2^INT rows. The marked rows correspond to rows on |
762 the genome. [5] | 848 the genome. [5] |
763 -t INT Ftab. The lookup table used to calculate an initial Burrows-Wheeler range | 849 -t INT The ftab lookup table used to calculate an initial Burrows-Wheeler range |
764 with respect to the first INT characters of the query. Ftab is 4^INT+1 | 850 with respect to the first INT characters of the query. Ftab size is 4^(INT+1) |
765 bytes. [10] | 851 bytes. [10] |
766 --ntoa N conversion. Convert Ns to As before building the index. Otherwise, Ns are | 852 --ntoa N conversion. Convert Ns to As before building the index. Otherwise, Ns are |
767 simply excluded from the index and Bowtie will not find alignments that | 853 simply excluded from the index and Bowtie will not find alignments that |
768 overlap them. [off] | 854 overlap them. [off] |
769 --big Endianness. Endianness to use when serializing integers to the index file. [off] | 855 --big Endianness. Endianness to use when serializing integers to the index file. [off] |
770 --little Endianness. [--little] | 856 --little Endianness. [--little] |
771 --seed INT Random seed. Use INT as the seed for the pseudo-random number generator. [off] | 857 --seed INT Random seed. Use INT as the seed for the pseudo-random number generator. [off] |
772 --cutoff INT Cutoff. Index only the first INT bases of the reference sequences (cumulative | |
773 across sequences) and ignore the rest. [off] | |
774 | 858 |
775 For aligning (bowtie):: | 859 For aligning (bowtie):: |
776 | 860 |
777 -s INT Skip. Do not align the first INT reads or pairs in the input. [off] | 861 -s INT Skip. Do not align the first INT reads or pairs in the input. [off] |
778 -u INT Align limit. Only align the first INT reads/pairs from the input. [no limit] | 862 -u INT Align limit. Only align the first INT reads/pairs from the input. [no limit] |
785 -e INT Mismatch quality. Maximum permitted total of quality values at mismatched | 869 -e INT Mismatch quality. Maximum permitted total of quality values at mismatched |
786 read positions. Bowtie rounds quality values to the nearest 10 and saturates | 870 read positions. Bowtie rounds quality values to the nearest 10 and saturates |
787 at 30. [70] | 871 at 30. [70] |
788 -l INT Seed length. The number of bases on the high-quality end of the read to | 872 -l INT Seed length. The number of bases on the high-quality end of the read to |
789 which the -n ceiling applies. Must be at least 5. [28] | 873 which the -n ceiling applies. Must be at least 5. [28] |
790 --nomaqround Suppress MAQ rounding. Values are internally rounded to the nearest 10 and | 874 --nomaqround Suppress Maq rounding. Values are internally rounded to the nearest 10 and |
791 saturate at 30. This options turns off that rounding. [off] | 875 saturate at 30. This options turns off that rounding. [off] |
792 -v INT MAQ- or SOAP-like alignment policy. This option turns off the default | 876 -v INT Maq- or SOAP-like alignment policy. This option turns off the default |
793 MAQ-like alignment policy in favor of a SOAP-like one. End-to-end alignments | 877 Maq-like alignment policy in favor of a SOAP-like one. End-to-end alignments |
794 with at most INT mismatches. [off] | 878 with at most INT mismatches. [off] |
795 -I INT Minimum insert. The minimum insert size for valid paired-end alignments. | 879 -I INT Minimum insert. The minimum insert size for valid paired-end alignments. |
796 Does checking on untrimmed reads if -5 or -3 is used. [0] | 880 Does checking on untrimmed reads if -5 or -3 is used. [0] |
797 -X INT Maximum insert. The maximum insert size for valid paired-end alignments. | 881 -X INT Maximum insert. The maximum insert size for valid paired-end alignments. |
798 Does checking on untrimmed reads if -5 or -3 is used. [250] | 882 Does checking on untrimmed reads if -5 or -3 is used. [250] |
833 --snpfrac DEC Use DEC as the estimated ratio of SNPs per base when decoding colorspace | 917 --snpfrac DEC Use DEC as the estimated ratio of SNPs per base when decoding colorspace |
834 alignments. [0.001] | 918 alignments. [0.001] |
835 --col-keepends Keep the extreme-end nucleotides and qualities when decoding colorspace | 919 --col-keepends Keep the extreme-end nucleotides and qualities when decoding colorspace |
836 alignments. [off] | 920 alignments. [off] |
837 | 921 |
838 </help> | 922 </help> |
923 <citations> | |
924 <citation type="doi">10.1186/gb-2009-10-3-r25</citation> | |
925 </citations> | |
839 </tool> | 926 </tool> |