Mercurial > repos > triasteran > bowtie_remove_rrna_wrapper
comparison bowtie_remove_rrna_wrapper_py2/bowtie_remove_rrna_wrapper.xml @ 20:7cbfb655e500 draft
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author | triasteran |
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date | Thu, 24 Feb 2022 15:47:30 +0000 |
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19:3532b4e69534 | 20:7cbfb655e500 |
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1 <tool id="bowtie_remove_rrna_wrapper" name="Remove rRNA using Bowtie" version="0.1.1d"> | |
2 <requirements> | |
3 <requirement type="package" version="1.3.1">bowtie</requirement> | |
4 <requirement type="package" version="2.7">python</requirement> | |
5 </requirements> | |
6 <command detect_errors="exit_code"><![CDATA[ | |
7 python2 '$__tool_directory__/bowtie_wrapper.py' | |
8 ## Set number of threads | |
9 --threads="\${GALAXY_SLOTS:-4}" | |
10 ## Outputs | |
11 --output="${output}" | |
12 #if str( $singlePaired.sPaired ) == "single" | |
13 #if $output_unmapped_reads_l | |
14 --output_unmapped_reads="${output_unmapped_reads_l}" | |
15 #end if | |
16 #if $output_suppressed_reads_l | |
17 --output_suppressed_reads="${output_suppressed_reads_l}" | |
18 #end if | |
19 --galaxy_input_format="${singlePaired.sInput1.ext}" | |
20 #else | |
21 #if $output_unmapped_reads_l and $output_unmapped_reads_r | |
22 --output_unmapped_reads_l="${output_unmapped_reads_l}" | |
23 --output_unmapped_reads_r="${output_unmapped_reads_r}" | |
24 #end if | |
25 #if $output_suppressed_reads_l and $output_suppressed_reads_l | |
26 --output_suppressed_reads_l="${output_suppressed_reads_l}" | |
27 --output_suppressed_reads_r="${output_suppressed_reads_r}" | |
28 #end if | |
29 --galaxy_input_format="${singlePaired.pInput1.ext}" | |
30 #end if | |
31 ## Inputs | |
32 --dataType="solexa" ##this indicates that nucleotide base space is used in the wrapper | |
33 --suppressHeader="${suppressHeader}" | |
34 --genomeSource="${refGenomeSource.genomeSource}" | |
35 #if $refGenomeSource.genomeSource == "history": | |
36 ##index already exists | |
37 #if $refGenomeSource.ownFile.extension.startswith( 'bowtie_' ): | |
38 ##user previously built | |
39 --ref="${refGenomeSource.ownFile.extra_files_path}/${refGenomeSource.ownFile.metadata.base_name}" | |
40 --do_not_build_index | |
41 #else: | |
42 ##build index on the fly | |
43 --ref="${refGenomeSource.ownFile}" | |
44 --indexSettings="${refGenomeSource.indexParams.indexSettings}" | |
45 #if $refGenomeSource.indexParams.indexSettings == "indexFull": | |
46 --iautoB="${refGenomeSource.indexParams.autoBehavior.autoB}" | |
47 #if $refGenomeSource.indexParams.autoBehavior.autoB == "set": | |
48 --ipacked="${refGenomeSource.indexParams.autoBehavior.packed}" | |
49 --ibmax="${refGenomeSource.indexParams.autoBehavior.bmax}" | |
50 --ibmaxdivn="${refGenomeSource.indexParams.autoBehavior.bmaxdivn}" | |
51 --idcv="${refGenomeSource.indexParams.autoBehavior.dcv}" | |
52 #end if | |
53 --inodc="${refGenomeSource.indexParams.nodc}" | |
54 --inoref="${refGenomeSource.indexParams.noref}" | |
55 --ioffrate="${refGenomeSource.indexParams.offrate}" | |
56 --iftab="${refGenomeSource.indexParams.ftab}" | |
57 --intoa="${refGenomeSource.indexParams.ntoa}" | |
58 --iendian="${refGenomeSource.indexParams.endian}" | |
59 --iseed="${refGenomeSource.indexParams.seed}" | |
60 --icutoff="${refGenomeSource.indexParams.cutoff}" | |
61 #end if | |
62 #end if | |
63 #else | |
64 ##use pre-built index | |
65 --ref="${refGenomeSource.index.fields.path}" | |
66 #end if | |
67 --paired="${singlePaired.sPaired}" | |
68 #if $singlePaired.sPaired == "single": | |
69 --input1="${singlePaired.sInput1}" | |
70 --params="${singlePaired.sParams.sSettingsType}" | |
71 #if $singlePaired.sParams.sSettingsType == "full": | |
72 --skip="${singlePaired.sParams.sSkip}" | |
73 --alignLimit="${singlePaired.sParams.sAlignLimit}" | |
74 --trimH="${singlePaired.sParams.sTrimH}" | |
75 --trimL="${singlePaired.sParams.sTrimL}" | |
76 --mismatchSeed="${singlePaired.sParams.sMismatchSeed}" | |
77 --mismatchQual="${singlePaired.sParams.sMismatchQual}" | |
78 --seedLen="${singlePaired.sParams.sSeedLen}" | |
79 --rounding="${singlePaired.sParams.sRounding}" | |
80 --maqSoapAlign="${singlePaired.sParams.sMaqSoapAlign}" | |
81 --reverseAlign="${singlePaired.sParams.sReverseAlign}" | |
82 --tryHard="${singlePaired.sParams.sTryHard}" | |
83 --valAlign="${singlePaired.sParams.sValAlign}" | |
84 --allValAligns="${singlePaired.sParams.sAllValAligns}" | |
85 --suppressAlign="${singlePaired.sParams.sSuppressAlign}" | |
86 --best="${singlePaired.sParams.sBestOption.sBest}" | |
87 #if $singlePaired.sParams.sBestOption.sBest == "doBest": | |
88 --maxBacktracks="${singlePaired.sParams.sBestOption.sdMaxBacktracks}" | |
89 --strata="${singlePaired.sParams.sBestOption.sdStrata}" | |
90 #else: | |
91 --maxBacktracks="${singlePaired.sParams.sBestOption.snMaxBacktracks}" | |
92 #end if | |
93 --offrate="${singlePaired.sParams.sOffrate}" | |
94 --seed="${singlePaired.sParams.sSeed}" | |
95 #end if | |
96 #else: | |
97 --input1="${singlePaired.pInput1}" | |
98 --input2="${singlePaired.pInput2}" | |
99 --maxInsert="${singlePaired.pMaxInsert}" | |
100 --mateOrient="${singlePaired.pMateOrient}" | |
101 --params="${singlePaired.pParams.pSettingsType}" | |
102 #if $singlePaired.pParams.pSettingsType == "full": | |
103 --skip="${singlePaired.pParams.pSkip}" | |
104 --alignLimit="${singlePaired.pParams.pAlignLimit}" | |
105 --trimH="${singlePaired.pParams.pTrimH}" | |
106 --trimL="${singlePaired.pParams.pTrimL}" | |
107 --mismatchSeed="${singlePaired.pParams.pMismatchSeed}" | |
108 --mismatchQual="${singlePaired.pParams.pMismatchQual}" | |
109 --seedLen="${singlePaired.pParams.pSeedLen}" | |
110 --rounding="${singlePaired.pParams.pRounding}" | |
111 --maqSoapAlign="${singlePaired.pParams.pMaqSoapAlign}" | |
112 --minInsert="${singlePaired.pParams.pMinInsert}" | |
113 --maxAlignAttempt="${singlePaired.pParams.pMaxAlignAttempt}" | |
114 --forwardAlign="${singlePaired.pParams.pForwardAlign}" | |
115 --reverseAlign="${singlePaired.pParams.pReverseAlign}" | |
116 --tryHard="${singlePaired.pParams.pTryHard}" | |
117 --valAlign="${singlePaired.pParams.pValAlign}" | |
118 --allValAligns="${singlePaired.pParams.pAllValAligns}" | |
119 --suppressAlign="${singlePaired.pParams.pSuppressAlign}" | |
120 --best="${singlePaired.pParams.pBestOption.pBest}" | |
121 #if $singlePaired.pParams.pBestOption.pBest == "doBest": | |
122 --maxBacktracks="${singlePaired.pParams.pBestOption.pdMaxBacktracks}" | |
123 --strata="${singlePaired.pParams.pBestOption.pdStrata}" | |
124 #else: | |
125 --maxBacktracks="${singlePaired.pParams.pBestOption.pnMaxBacktracks}" | |
126 #end if | |
127 --offrate="${singlePaired.pParams.pOffrate}" | |
128 --seed="${singlePaired.pParams.pSeed}" | |
129 #end if | |
130 #end if | |
131 ]]></command> | |
132 <inputs> | |
133 <conditional name="refGenomeSource"> | |
134 <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"> | |
135 <option value="indexed">Use a built-in index</option> | |
136 <option value="history">Use one from the history</option> | |
137 </param> | |
138 <when value="indexed"> | |
139 <param name="index" type="select" label="Select the appropriate rRNA index" help="If the rRNA index for your organism is not listed, you will need to upload a fasta file of the rRNA sequences. "> | |
140 <options from_data_table="bowtie_rrna_indexes"> | |
141 <filter type="sort_by" column="2" /> | |
142 <validator type="no_options" message="No indexes are available" /> | |
143 </options> | |
144 </param> | |
145 </when> | |
146 <when value="history"> | |
147 <param name="ownFile" type="data" format="bowtie_base_index,fasta" label="Select the reference genome" /> | |
148 <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"> | |
150 <option value="indexPreSet">Default</option> | |
151 <option value="indexFull">Set your own</option> | |
152 </param> | |
153 <when value="indexPreSet" /> | |
154 <when value="indexFull"> | |
155 <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"> | |
157 <option value="auto">Automatic behavior</option> | |
158 <option value="set">Set values (sets --noauto and allows others to be set)</option> | |
159 </param> | |
160 <when value="auto" /> | |
161 <when value="set"> | |
162 <param name="packed" type="select" label="Whether or not to use a packed representation for DNA strings (--packed)"> | |
163 <option value="unpacked">Use regular representation</option> | |
164 <option value="packed">Use packed representation</option> | |
165 </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" /> | |
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)" /> | |
168 <param name="dcv" type="integer" value="1024" label="The period for the difference-cover sample (--dcv)" /> | |
169 </when> | |
170 </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)"> | |
172 <option value="dc">Use difference-cover sample</option> | |
173 <option value="nodc">Disable difference-cover sample</option> | |
174 </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)"> | |
176 <option value="ref">Build all index files</option> | |
177 <option value="noref">Do not build paired-end alignment index files</option> | |
178 </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)" /> | |
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" /> | |
181 <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> | |
183 <option value="yes">Convert Ns to As</option> | |
184 </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"> | |
186 <option value="little">Little</option> | |
187 <option value="big">Big</option> | |
188 </param> | |
189 <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 --> | |
192 </conditional> <!-- indexParams --> | |
193 </when> <!-- history --> | |
194 </conditional> <!-- refGenomeSource --> | |
195 <conditional name="singlePaired"> | |
196 <param name="sPaired" type="select" label="Is this library mate-paired?"> | |
197 <option value="single">Single-end</option> | |
198 <option value="paired">Paired-end</option> | |
199 </param> | |
200 <when value="single"> | |
201 <param name="sInput1" type="data" format="fastqsanger,fastqillumina,fastqsolexa" label="FASTQ file" help="Must have ASCII encoded quality scores"/> | |
202 <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"> | |
204 <option value="preSet">Commonly used</option> | |
205 <option value="full" selected="true">Full parameter list</option> | |
206 </param> | |
207 <when value="preSet" /> | |
208 <when value="full"> | |
209 <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" /> | |
211 <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)" /> | |
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" /> | |
214 <param name="sMismatchQual" type="integer" value="70" label="Maximum permitted total of quality values at mismatched read positions (-e)" /> | |
215 <param name="sSeedLen" type="integer" value="25" label="Seed length (-l)" help="Minimum value is 5" /> | |
216 <param name="sRounding" type="select" label="Whether or not to round to the nearest 10 and saturating at 30 (--nomaqround)"> | |
217 <option value="round">Round to nearest 10</option> | |
218 <option value="noRound">Do not round to nearest 10</option> | |
219 </param> | |
220 <param name="sMaqSoapAlign" type="integer" value="3" label="Number of mismatches for SOAP-like alignment policy (-v)" help="-1 for default MAQ-like alignment policy" /> | |
221 <param name="sReverseAlign" type="select" label="Choose whether or not to align against the reverse-complement reference strand (--norc)"> | |
222 <option value="noReverse">Do not align against the reverse-complement reference strand</option> | |
223 <option value="reverse">Align against the reverse-complement reference strand</option> | |
224 </param> | |
225 <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"> | |
226 <option value="noTryHard">Do not try hard</option> | |
227 <option value="doTryHard">Try hard</option> | |
228 </param> | |
229 <param name="sValAlign" type="integer" value="1" label="Report up to n valid alignments per read (-k)" /> | |
230 <param name="sAllValAligns" type="select" label="Whether or not to report all valid alignments per read (-a)"> | |
231 <option value="noAllValAligns">Do not report all valid alignments</option> | |
232 <option value="doAllValAligns">Report all valid alignments</option> | |
233 </param> | |
234 <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" /> | |
235 <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)" /> | |
236 <param name="sUnmappedFile" type="boolean" truevalue="true" falsevalue="false" checked="True" label="Write all reads that could not be aligned to a file (--un)" /> | |
237 <conditional name="sBestOption"> | |
238 <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"> | |
239 <option value="noBest">Do not use best</option> | |
240 <option value="doBest">Use best</option> | |
241 </param> | |
242 <when value="noBest"> | |
243 <param name="snMaxBacktracks" type="integer" value="125" label="Maximum number of backtracks permitted when aligning a read (--maxbts)" /> | |
244 </when> | |
245 <when value="doBest"> | |
246 <param name="sdMaxBacktracks" type="integer" value="800" label="Maximum number of backtracks permitted when aligning a read (--maxbts)" /> | |
247 <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)"> | |
248 <option value="noStrata">Do not use strata option</option> | |
249 <option value="doStrata">Use strata option</option> | |
250 </param> | |
251 </when> | |
252 </conditional> <!-- bestOption --> | |
253 <param name="sOffrate" type="integer" value="-1" label="Override the offrate of the index to n (-o)" help="-1 for default" /> | |
254 <param name="sSeed" type="integer" value="-1" label="Seed for pseudo-random number generator (--seed)" help="-1 for default" /> | |
255 </when> <!-- full --> | |
256 </conditional> <!-- sParams --> | |
257 </when> <!-- single --> | |
258 <when value="paired"> | |
259 <param name="pInput1" type="data" format="fastqsanger,fastqillumina,fastqsolexa" label="Forward FASTQ file" help="Must have ASCII encoded quality scores"/> | |
260 <param name="pInput2" type="data" format="fastqsanger,fastqillumina,fastqsolexa" label="Reverse FASTQ file" help="File format must match the Forward FASTQ file"> | |
261 <options options_filter_attribute="ext" from_parameter="tool.app.datatypes_registry.datatypes_by_extension" transform_lines="obj.keys()"> | |
262 <column name="name" index="0"/> | |
263 <column name="value" index="0"/> | |
264 <filter type="param_value" ref="pInput1" ref_attribute="ext" column="0"/> | |
265 </options> | |
266 </param> | |
267 <param name="pMaxInsert" type="integer" value="1000" label="Maximum insert size for valid paired-end alignments (-X)" /> | |
268 <param name="pMateOrient" type="select" label="The upstream/downstream mate orientation for valid paired-end alignment against the forward reference strand (--fr/--rf/--ff)"> | |
269 <option value="fr">FR (for Illumina)</option> | |
270 <option value="rf">RF</option> | |
271 <option value="ff">FF (for SOLiD)</option> | |
272 </param> | |
273 <conditional name="pParams"> | |
274 <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"> | |
275 <option value="preSet">Commonly used</option> | |
276 <option value="full">Full parameter list</option> | |
277 </param> | |
278 <when value="preSet" /> | |
279 <when value="full"> | |
280 <param name="pSkip" type="integer" value="0" label="Skip the first n pairs (-s)" /> | |
281 <param name="pAlignLimit" type="integer" value="-1" label="Only align the first n pairs (-u)" help="-1 for off" /> | |
282 <param name="pTrimH" type="integer" value="0" label="Trim n bases from high-quality (left) end of each read before alignment (-5)" /> | |
283 <param name="pTrimL" type="integer" value="0" label="Trim n bases from low-quality (right) end of each read before alignment (-3)" /> | |
284 <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" /> | |
285 <param name="pMismatchQual" type="integer" value="70" label="Maximum permitted total of quality values at mismatched read positions (-e)" /> | |
286 <param name="pSeedLen" type="integer" value="25" label="Seed length (-l)" help="Minimum value is 5" /> | |
287 <param name="pRounding" type="select" label="Whether or not to round to the nearest 10 and saturating at 30 (--nomaqround)"> | |
288 <option value="round">Round to nearest 10</option> | |
289 <option value="noRound">Do not round to nearest 10</option> | |
290 </param> | |
291 <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" /> | |
292 <param name="pMinInsert" type="integer" value="0" label="Minimum insert size for valid paired-end alignments (-I)" /> | |
293 <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)" /> | |
294 <param name="pForwardAlign" type="select" label="Choose whether or not to attempt to align the forward reference strand (--nofw)"> | |
295 <option value="forward">Align against the forward reference strand</option> | |
296 <option value="noForward">Do not align against the forward reference strand</option> | |
297 </param> | |
298 <param name="pReverseAlign" type="select" label="Choose whether or not to align against the reverse-complement reference strand (--norc)"> | |
299 <option value="reverse">Align against the reverse-complement reference strand</option> | |
300 <option value="noReverse">Do not align against the reverse-complement reference strand</option> | |
301 </param> | |
302 <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"> | |
303 <option value="noTryHard">Do not try hard</option> | |
304 <option value="doTryHard">Try hard</option> | |
305 </param> | |
306 <param name="pValAlign" type="integer" value="1" label="Report up to n valid arguments per pair (-k)" /> | |
307 <param name="pAllValAligns" type="select" label="Whether or not to report all valid alignments per pair (-a)"> | |
308 <option value="noAllValAligns">Do not report all valid alignments</option> | |
309 <option value="doAllValAligns">Report all valid alignments</option> | |
310 </param> | |
311 <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" /> | |
312 <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)" /> | |
313 <param name="pUnmappedFile" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write all reads that could not be aligned to a file (--un)" /> | |
314 <conditional name="pBestOption"> | |
315 <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"> | |
316 <option value="noBest">Do not use best</option> | |
317 <option value="doBest">Use best</option> | |
318 </param> | |
319 <when value="noBest"> | |
320 <param name="pnMaxBacktracks" type="integer" value="125" label="Maximum number of backtracks permitted when aligning a read (--maxbts)" /> | |
321 </when> | |
322 <when value="doBest"> | |
323 <param name="pdMaxBacktracks" type="integer" value="800" label="Maximum number of backtracks permitted when aligning a read (--maxbts)" /> | |
324 <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)"> | |
325 <option value="noStrata">Do not use strata option</option> | |
326 <option value="doStrata">Use strata option</option> | |
327 </param> | |
328 </when> | |
329 </conditional> | |
330 <param name="pOffrate" type="integer" value="-1" label="Override the offrate of the index to n (-o)" help="-1 for default" /> | |
331 <param name="pSeed" type="integer" value="-1" label="Seed for pseudo-random number generator (--seed)" help="-1 for default" /> | |
332 </when> <!-- full --> | |
333 </conditional> <!-- pParams --> | |
334 </when> <!-- paired --> | |
335 </conditional> <!-- singlePaired --> | |
336 <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" /> | |
337 </inputs> | |
338 <outputs> | |
339 <data format="sam" name="output" label="${tool.name} on ${on_string}: mapped reads"> | |
340 <actions> | |
341 <conditional name="refGenomeSource.genomeSource"> | |
342 <when value="indexed"> | |
343 <action type="metadata" name="dbkey"> | |
344 <option type="from_data_table" name="bowtie_indexes" column="1" offset="0"> | |
345 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/> | |
346 <filter type="param_value" ref="refGenomeSource.index" column="0"/> | |
347 </option> | |
348 </action> | |
349 </when> | |
350 <when value="history"> | |
351 <action type="metadata" name="dbkey"> | |
352 <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" /> | |
353 </action> | |
354 </when> | |
355 </conditional> | |
356 </actions> | |
357 </data> | |
358 <data format="fastq" name="output_suppressed_reads_l" label="${tool.name} on ${on_string}: suppressed reads (L)"> | |
359 <filter>(( | |
360 singlePaired['sPaired'] == "single" and | |
361 singlePaired['sParams']['sSettingsType'] == "full" and | |
362 singlePaired['sParams']['sMaxFile'] is True | |
363 ) or ( | |
364 singlePaired['sPaired'] == "paired" and | |
365 singlePaired['pParams']['pSettingsType'] == "full" and | |
366 singlePaired['pParams']['pMaxFile'] is True | |
367 )) | |
368 </filter> | |
369 <actions> | |
370 <conditional name="singlePaired.sPaired"> | |
371 <when value="single"> | |
372 <action type="format"> | |
373 <option type="from_param" name="singlePaired.sInput1" param_attribute="ext" /> | |
374 </action> | |
375 </when> | |
376 <when value="paired"> | |
377 <action type="format"> | |
378 <option type="from_param" name="singlePaired.pInput1" param_attribute="ext" /> | |
379 </action> | |
380 </when> | |
381 </conditional> | |
382 </actions> | |
383 </data> | |
384 <data format="fastq" name="output_suppressed_reads_r" label="${tool.name} on ${on_string}: suppressed reads (R)"> | |
385 <filter>singlePaired['sPaired'] == "paired"</filter> | |
386 <filter>singlePaired['pParams']['pSettingsType'] == "full"</filter> | |
387 <filter>singlePaired['pParams']['pMaxFile'] is True</filter> | |
388 <actions> | |
389 <conditional name="singlePaired.sPaired"> | |
390 <when value="single"> | |
391 <action type="format"> | |
392 <option type="from_param" name="singlePaired.sInput1" param_attribute="ext" /> | |
393 </action> | |
394 </when> | |
395 <when value="paired"> | |
396 <action type="format"> | |
397 <option type="from_param" name="singlePaired.pInput1" param_attribute="ext" /> | |
398 </action> | |
399 </when> | |
400 </conditional> | |
401 </actions> | |
402 </data> | |
403 <data format="fastq" name="output_unmapped_reads_l" label="${tool.name} on ${on_string}: unmapped reads (L)"> | |
404 <filter> | |
405 (( | |
406 singlePaired['sPaired'] == "single" and | |
407 singlePaired['sParams']['sSettingsType'] == "full" and | |
408 singlePaired['sParams']['sUnmappedFile'] is True | |
409 ) or ( | |
410 singlePaired['sPaired'] == "paired" and | |
411 singlePaired['pParams']['pSettingsType'] == "full" and | |
412 singlePaired['pParams']['pUnmappedFile'] is True | |
413 )) | |
414 </filter> | |
415 <actions> | |
416 <conditional name="singlePaired.sPaired"> | |
417 <when value="single"> | |
418 <action type="format"> | |
419 <option type="from_param" name="singlePaired.sInput1" param_attribute="ext" /> | |
420 </action> | |
421 </when> | |
422 <when value="paired"> | |
423 <action type="format"> | |
424 <option type="from_param" name="singlePaired.pInput1" param_attribute="ext" /> | |
425 </action> | |
426 </when> | |
427 </conditional> | |
428 </actions> | |
429 </data> | |
430 <data format="fastq" name="output_unmapped_reads_r" label="${tool.name} on ${on_string}: unmapped reads (R)"> | |
431 <filter>singlePaired['sPaired'] == "paired"</filter> | |
432 <filter>singlePaired['pParams']['pSettingsType'] == "full"</filter> | |
433 <filter>singlePaired['pParams']['pUnmappedFile'] is True</filter> | |
434 <actions> | |
435 <conditional name="singlePaired.sPaired"> | |
436 <when value="single"> | |
437 <action type="format"> | |
438 <option type="from_param" name="singlePaired.sInput1" param_attribute="ext" /> | |
439 </action> | |
440 </when> | |
441 <when value="paired"> | |
442 <action type="format"> | |
443 <option type="from_param" name="singlePaired.pInput1" param_attribute="ext" /> | |
444 </action> | |
445 </when> | |
446 </conditional> | |
447 </actions> | |
448 </data> | |
449 </outputs> | |
450 <tests> | |
451 <test> | |
452 <!-- | |
453 Bowtie command: | |
454 bowtie -q -p 4 -S +sam-nohead chrM_base test-data/bowtie_in2.fastqsanger > bowtie_out6_u.sam | |
455 sort bowtie_out6_u.sam > bowtie_out6.sam | |
456 -p is the number of threads. You need to replace the + with 2 dashes. | |
457 chrM_base needs to be the base location/name of the index files. | |
458 --> | |
459 <param name="genomeSource" value="indexed" /> | |
460 <!-- this is the backwards-compatible "unique value" for this index, not an actual path --> | |
461 <param name="index" value="equCab2chrM" /> | |
462 <param name="sPaired" value="single" /> | |
463 <param name="sInput1" ftype="fastqsanger" value="bowtie_in2.fastqsanger" /> | |
464 <param name="sSettingsType" value="preSet" /> | |
465 <param name="suppressHeader" value="true" /> | |
466 <output name="output" ftype="sam" file="bowtie_out6.sam" sort="True" /> | |
467 </test> | |
468 <test> | |
469 <!-- | |
470 Bowtie command: | |
471 bowtie-build -f test-data/phiX.fasta phiX_base | |
472 bowtie -q -X 1000 +ff -p 4 -S +sam-nohead -n 2 -e 70 -l 28 +pairtries 100 +maxbts 800 +best +un bowtie_out8_u.fastq phiX_base -1 test-data/bowtie_in5.fastqsanger -2 test-data/bowtie_in6.fastqsanger > bowtie_out7_u.sam | |
473 sort bowtie_out7_u.sam > bowtie_out7.sam | |
474 sort bowtie_out8_u_1.sam > bowtie_out8_1.sam | |
475 sort bowtie_out8_u_2.sam > bowtie_out8_2.sam | |
476 Then also need to modify bowtie_out8_1.sam and bowtie_out8_2.sam so that all @ lines come before sequence lines. | |
477 -p is the number of threads. You need to replace the + with 2 dashes. | |
478 The two unmapped output files will be named bowtie_out8_1.fastq and bowtie_out8_2.fastq. | |
479 chrM_base is the index files' location/base name. | |
480 --> | |
481 <param name="genomeSource" value="history" /> | |
482 <param name="ownFile" value="phiX.fasta" /> | |
483 <param name="indexSettings" value="indexPreSet" /> | |
484 <param name="sPaired" value="paired" /> | |
485 <param name="pInput1" ftype="fastqsanger" value="bowtie_in5.fastqsanger" /> | |
486 <param name="pInput2" ftype="fastqsanger" value="bowtie_in6.fastqsanger" /> | |
487 <param name="pMaxInsert" value="1000" /> | |
488 <param name="pMateOrient" value="ff" /> | |
489 <param name="pSettingsType" value="full" /> | |
490 <param name="pSkip" value="0" /> | |
491 <param name="pAlignLimit" value="-1" /> | |
492 <param name="pTrimH" value="0" /> | |
493 <param name="pTrimL" value="0" /> | |
494 <param name="pMismatchSeed" value="2" /> | |
495 <param name="pMismatchQual" value="70" /> | |
496 <param name="pSeedLen" value="25" /> | |
497 <param name="pRounding" value="round" /> | |
498 <param name="pMaqSoapAlign" value="-1" /> | |
499 <param name="pMinInsert" value="0" /> | |
500 <param name="pMaxAlignAttempt" value="100" /> | |
501 <param name="pForwardAlign" value="forward" /> | |
502 <param name="pReverseAlign" value="reverse" /> | |
503 <param name="pTryHard" value="noTryHard" /> | |
504 <param name="pValAlign" value="1" /> | |
505 <param name="pAllValAligns" value="noAllValAligns" /> | |
506 <param name="pSuppressAlign" value="-1" /> | |
507 <param name="pUnmappedFile" value="true" /> | |
508 <param name="pMaxFile" value="false" /> | |
509 <param name="pBest" value="doBest" /> | |
510 <param name="pdMaxBacktracks" value="800" /> | |
511 <param name="pdStrata" value="noStrata" /> | |
512 <param name="pOffrate" value="-1" /> | |
513 <param name="pSeed" value="-1" /> | |
514 <param name="suppressHeader" value="true" /> | |
515 <output name="output" ftype="sam" file="bowtie_out7.sam" sort="True" /> | |
516 <output name="output_unmapped_reads_l" ftype="fastqsanger" file="bowtie_out8_1.fastq" sort="True" /> | |
517 <output name="output_unmapped_reads_r" ftype="fastqsanger" file="bowtie_out8_2.fastq" sort="True" /> | |
518 </test> | |
519 <!-- start testing of non-sanger variant fastq reads --> | |
520 <test> | |
521 <param name="genomeSource" value="history" /> | |
522 <param name="ownFile" value="phiX.fasta" /> | |
523 <param name="indexSettings" value="indexPreSet" /> | |
524 <param name="sPaired" value="paired" /> | |
525 <param name="pInput1" ftype="fastqillumina" value="bowtie_in5.fastqillumina" /> | |
526 <param name="pInput2" ftype="fastqillumina" value="bowtie_in6.fastqillumina" /> | |
527 <param name="pMaxInsert" value="1000" /> | |
528 <param name="pMateOrient" value="ff" /> | |
529 <param name="pSettingsType" value="full" /> | |
530 <param name="pSkip" value="0" /> | |
531 <param name="pAlignLimit" value="-1" /> | |
532 <param name="pTrimH" value="0" /> | |
533 <param name="pTrimL" value="0" /> | |
534 <param name="pMismatchSeed" value="2" /> | |
535 <param name="pMismatchQual" value="70" /> | |
536 <param name="pSeedLen" value="25" /> | |
537 <param name="pRounding" value="round" /> | |
538 <param name="pMaqSoapAlign" value="-1" /> | |
539 <param name="pMinInsert" value="0" /> | |
540 <param name="pMaxAlignAttempt" value="100" /> | |
541 <param name="pForwardAlign" value="forward" /> | |
542 <param name="pReverseAlign" value="reverse" /> | |
543 <param name="pTryHard" value="noTryHard" /> | |
544 <param name="pValAlign" value="1" /> | |
545 <param name="pAllValAligns" value="noAllValAligns" /> | |
546 <param name="pSuppressAlign" value="-1" /> | |
547 <param name="pUnmappedFile" value="true" /> | |
548 <param name="pMaxFile" value="false" /> | |
549 <param name="pBest" value="doBest" /> | |
550 <param name="pdMaxBacktracks" value="800" /> | |
551 <param name="pdStrata" value="noStrata" /> | |
552 <param name="pOffrate" value="-1" /> | |
553 <param name="pSeed" value="-1" /> | |
554 <param name="suppressHeader" value="true" /> | |
555 <output name="output" ftype="sam" file="bowtie_out7.sam" sort="True" /> | |
556 <output name="output_unmapped_reads_l" ftype="fastqillumna" file="bowtie_out8_1.fastqillumina.sorted" sort="True" /> | |
557 <output name="output_unmapped_reads_r" ftype="fastqillumna" file="bowtie_out8_2.fastqillumina.sorted" sort="True" /> | |
558 </test> | |
559 <test> | |
560 <param name="genomeSource" value="history" /> | |
561 <param name="ownFile" value="phiX.fasta" /> | |
562 <param name="indexSettings" value="indexPreSet" /> | |
563 <param name="sPaired" value="paired" /> | |
564 <param name="pInput1" ftype="fastqsolexa" value="bowtie_in5.fastqsolexa" /> | |
565 <param name="pInput2" ftype="fastqsolexa" value="bowtie_in6.fastqsolexa" /> | |
566 <param name="pMaxInsert" value="1000" /> | |
567 <param name="pMateOrient" value="ff" /> | |
568 <param name="pSettingsType" value="full" /> | |
569 <param name="pSkip" value="0" /> | |
570 <param name="pAlignLimit" value="-1" /> | |
571 <param name="pTrimH" value="0" /> | |
572 <param name="pTrimL" value="0" /> | |
573 <param name="pMismatchSeed" value="2" /> | |
574 <param name="pMismatchQual" value="70" /> | |
575 <param name="pSeedLen" value="25" /> | |
576 <param name="pRounding" value="round" /> | |
577 <param name="pMaqSoapAlign" value="-1" /> | |
578 <param name="pMinInsert" value="0" /> | |
579 <param name="pMaxAlignAttempt" value="100" /> | |
580 <param name="pForwardAlign" value="forward" /> | |
581 <param name="pReverseAlign" value="reverse" /> | |
582 <param name="pTryHard" value="noTryHard" /> | |
583 <param name="pValAlign" value="1" /> | |
584 <param name="pAllValAligns" value="noAllValAligns" /> | |
585 <param name="pSuppressAlign" value="-1" /> | |
586 <param name="pUnmappedFile" value="true" /> | |
587 <param name="pMaxFile" value="false" /> | |
588 <param name="pBest" value="doBest" /> | |
589 <param name="pdMaxBacktracks" value="800" /> | |
590 <param name="pdStrata" value="noStrata" /> | |
591 <param name="pOffrate" value="-1" /> | |
592 <param name="pSeed" value="-1" /> | |
593 <param name="suppressHeader" value="true" /> | |
594 <output name="output" ftype="sam" file="bowtie_out7.sam" sort="True" /> | |
595 <output name="output_unmapped_reads_l" ftype="fastqsolexa" file="bowtie_out8_1.fastqsolexa.sorted" sort="True" /> | |
596 <output name="output_unmapped_reads_r" ftype="fastqsolexa" file="bowtie_out8_2.fastqsolexa.sorted" sort="True" /> | |
597 </test> | |
598 <!-- end testing of non-sanger variant fastq reads --> | |
599 <test> | |
600 <!-- | |
601 Bowtie command: | |
602 bowtie -q -p 4 -S +sam-nohead -n 2 -e 70 -l 25 +maxbts 125 -y -k 1 chrM_base test-data/bowtie_in2.fastqsanger > bowtie_out9_u.sam | |
603 sort bowtie_out9_u.sam > bowtie_out9.sam | |
604 -p is the number of threads. You need to replace the + with 2 dashes. | |
605 chrM_base is the index files' location/base name. | |
606 --> | |
607 <param name="genomeSource" value="indexed" /> | |
608 <!-- this is the backwards-compatible "unique value" for this index, not an actual path --> | |
609 <param name="index" value="equCab2chrM" /> | |
610 <param name="sPaired" value="single" /> | |
611 <param name="sInput1" ftype="fastqsanger" value="bowtie_in2.fastqsanger" /> | |
612 <param name="sSettingsType" value="full" /> | |
613 <param name="sSkip" value="0" /> | |
614 <param name="sAlignLimit" value="-1" /> | |
615 <param name="sTrimH" value="0" /> | |
616 <param name="sTrimL" value="0" /> | |
617 <param name="sMismatchSeed" value="2" /> | |
618 <param name="sMismatchQual" value="70" /> | |
619 <param name="sSeedLen" value="25" /> | |
620 <param name="sRounding" value="round" /> | |
621 <param name="sMaqSoapAlign" value="-1" /> | |
622 <param name="sTryHard" value="doTryHard" /> | |
623 <param name="sValAlign" value="1" /> | |
624 <param name="sAllValAligns" value="noAllValAligns" /> | |
625 <param name="sSuppressAlign" value="-1" /> | |
626 <param name="sUnmappedFile" value="false" /> | |
627 <param name="sMaxFile" value="false" /> | |
628 <param name="sBest" value="noBest" /> | |
629 <param name="snMaxBacktracks" value="125" /> | |
630 <param name="sOffrate" value="-1" /> | |
631 <param name="sSeed" value="-1" /> | |
632 <param name="suppressHeader" value="true" /> | |
633 <output name="output" ftype="sam" file="bowtie_out9.sam" sort="True" /> | |
634 </test> | |
635 <test> | |
636 <!-- | |
637 Bowtie command: | |
638 bowtie-build +offrate 5 +ftabchars 10 +little -f test-data/phiX.fasta phiX_base | |
639 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 | |
640 sort bowtie_out10_u.sam > bowtie_out10.sam | |
641 -p is the number of threads. You need to replace the + with 2 dashes. | |
642 chrM_base is the index files' location/base name. | |
643 --> | |
644 <param name="genomeSource" value="history" /> | |
645 <param name="ownFile" value="phiX.fasta" /> | |
646 <param name="indexSettings" value="indexFull" /> | |
647 <param name="autoB" value="auto" /> | |
648 <param name="nodc" value="dc" /> | |
649 <param name="noref" value="ref" /> | |
650 <param name="offrate" value="5" /> | |
651 <param name="ftab" value="10" /> | |
652 <param name="ntoa" value="no" /> | |
653 <param name="endian" value="little" /> | |
654 <param name="seed" value="-1" /> | |
655 <param name="cutoff" value="-1" /> | |
656 <param name="sPaired" value="paired" /> | |
657 <param name="pInput1" ftype="fastqsanger" value="bowtie_in5.fastqsanger" /> | |
658 <param name="pInput2" ftype="fastqsanger" value="bowtie_in6.fastqsanger" /> | |
659 <param name="pMaxInsert" value="1000" /> | |
660 <param name="pMateOrient" value="ff" /> | |
661 <param name="pSettingsType" value="preSet" /> | |
662 <param name="suppressHeader" value="true" /> | |
663 <output name="output" ftype="sam" file="bowtie_out10.sam" sort="True" /> | |
664 </test> | |
665 </tests> | |
666 <help> | |
667 <![CDATA[ | |
668 Bowtie is a short read aligner. | |
669 ]]> | |
670 </help> | |
671 <citations> | |
672 <citation type="bibtex"> | |
673 @misc{githubbowtie, | |
674 author = {LastTODO, FirstTODO}, | |
675 year = {TODO}, | |
676 title = {bowtie}, | |
677 publisher = {GitHub}, | |
678 journal = {GitHub repository}, | |
679 url = {https://github.com/BenLangmead/bowtie}, | |
680 }</citation> | |
681 </citations> | |
682 </tool> |