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/tools/sr_mapping/bowtie_wrapper.xml

https://bitbucket.org/cistrome/cistrome-harvard/
XML | 838 lines | 766 code | 34 blank | 38 comment | 0 complexity | 449552858fd209f2ed4301bc29f8b742 MD5 | raw file
    

  1. <tool id="bowtie_wrapper" name="Map with Bowtie for Illumina" version="1.1.2">
    2. 

  2.   <requirements><requirement type='package'>bowtie</requirement></requirements>
    3. 

  3.   <description></description>
    4. 

  4.   <parallelism method="basic"></parallelism>
    5. 

  5.   <command interpreter="python">
    6. 

  6.     bowtie_wrapper.py
    7. 

  7.       ## Hackish setting of number of threads
    8. 

  8.       --threads="4"
    9. 

  9.       ## Outputs
    10. 

  10.       --output=$output
    11. 

  11.       #if str( $singlePaired.sPaired ) == "single"
    12. 

  12.         #if $output_unmapped_reads_l
    13. 

  13.           --output_unmapped_reads=$output_unmapped_reads_l
    14. 

  14.         #end if
    15. 

  15.         #if $output_suppressed_reads_l
    16. 

  16.           --output_suppressed_reads=$output_suppressed_reads_l
    17. 

  17.         #end if
    18. 

  18.         --galaxy_input_format="${singlePaired.sInput1.ext}"
    19. 

  19.       #else
    20. 

  20.         #if $output_unmapped_reads_l and $output_unmapped_reads_r
    21. 

  21.           --output_unmapped_reads_l=$output_unmapped_reads_l
    22. 

  22.           --output_unmapped_reads_r=$output_unmapped_reads_r
    23. 

  23.         #end if
    24. 

  24.         #if $output_suppressed_reads_l and $output_suppressed_reads_l
    25. 

  25.           --output_suppressed_reads_l=$output_suppressed_reads_l
    26. 

  26.           --output_suppressed_reads_r=$output_suppressed_reads_r
    27. 

  27.         #end if
    28. 

  28.         --galaxy_input_format="${singlePaired.pInput1.ext}"
    29. 

  29.       #end if
    30. 

  30.       ## Inputs
    31. 

  31.       --dataType="solexa" ##this indicates that nucleotide base space is used in the wrapper
    32. 

  32.       --suppressHeader=$suppressHeader
    33. 

  33.       --genomeSource=$refGenomeSource.genomeSource
    34. 

  34.       #if $refGenomeSource.genomeSource == "history":
    35. 

  35.         ##index already exists
    36. 

  36.         #if $refGenomeSource.ownFile.extension.startswith( 'bowtie_' ):
    37. 

  37.           ##user previously built
    38. 

  38.           --ref="${refGenomeSource.ownFile.extra_files_path}/${refGenomeSource.ownFile.metadata.base_name}"
    39. 

  39.           --do_not_build_index
    40. 

  40.         #else:
    41. 

  41.           ##build index on the fly
    42. 

  42.           --ref=$refGenomeSource.ownFile
    43. 

  43.           --indexSettings=$refGenomeSource.indexParams.indexSettings
    44. 

  44.           #if $refGenomeSource.indexParams.indexSettings == "indexFull":
    45. 

  45.             --iautoB=$refGenomeSource.indexParams.autoBehavior.autoB
    46. 

  46.             #if $refGenomeSource.indexParams.autoBehavior.autoB == "set":
    47. 

  47.               --ipacked=$refGenomeSource.indexParams.autoBehavior.packed
    48. 

  48.               --ibmax=$refGenomeSource.indexParams.autoBehavior.bmax
    49. 

  49.               --ibmaxdivn=$refGenomeSource.indexParams.autoBehavior.bmaxdivn
    50. 

  50.               --idcv=$refGenomeSource.indexParams.autoBehavior.dcv
    51. 

  51.             #end if
    52. 

  52.             --inodc=$refGenomeSource.indexParams.nodc
    53. 

  53.             --inoref=$refGenomeSource.indexParams.noref
    54. 

  54.             --ioffrate=$refGenomeSource.indexParams.offrate
    55. 

  55.             --iftab=$refGenomeSource.indexParams.ftab
    56. 

  56.             --intoa=$refGenomeSource.indexParams.ntoa
    57. 

  57.             --iendian=$refGenomeSource.indexParams.endian
    58. 

  58.             --iseed=$refGenomeSource.indexParams.seed
    59. 

  59.             --icutoff=$refGenomeSource.indexParams.cutoff 
    60. 

  60.           #end if
    61. 

  61.         #end if
    62. 

  62.       #else
    63. 

  63.         ##use pre-built index
    64. 

  64.         ##--ref="${ filter( lambda x: str( x[0] ) == str( $refGenomeSource.index ), $__app__.tool_data_tables[ 'bowtie_indexes' ].get_fields() )[0][-1] }"
    65. 

  65.         --ref="${ refGenomeSource.index.fields.path }"
    66. 

  66.       #end if
    67. 

  67.       --paired=$singlePaired.sPaired
    68. 

  68.       #if $singlePaired.sPaired == "single":
    69. 

  69.         --input1=$singlePaired.sInput1
    70. 

  70.         --params=$singlePaired.sParams.sSettingsType
    71. 

  71.         #if $singlePaired.sParams.sSettingsType == "full":
    72. 

  72.           --skip=$singlePaired.sParams.sSkip
    73. 

  73.           --alignLimit=$singlePaired.sParams.sAlignLimit
    74. 

  74.           --trimH=$singlePaired.sParams.sTrimH
    75. 

  75.           --trimL=$singlePaired.sParams.sTrimL
    76. 

  76.           --mismatchSeed=$singlePaired.sParams.sMismatchSeed
    77. 

  77.           --mismatchQual=$singlePaired.sParams.sMismatchQual
    78. 

  78.           --seedLen=$singlePaired.sParams.sSeedLen
    79. 

  79.           --rounding=$singlePaired.sParams.sRounding
    80. 

  80.           --maqSoapAlign=$singlePaired.sParams.sMaqSoapAlign
    81. 

  81.           --tryHard=$singlePaired.sParams.sTryHard
    82. 

  82.           --valAlign=$singlePaired.sParams.sValAlign
    83. 

  83.           --allValAligns=$singlePaired.sParams.sAllValAligns
    84. 

  84.           --suppressAlign=$singlePaired.sParams.sSuppressAlign
    85. 

  85.           --best=$singlePaired.sParams.sBestOption.sBest
    86. 

  86.           #if $singlePaired.sParams.sBestOption.sBest == "doBest":
    87. 

  87.             --maxBacktracks=$singlePaired.sParams.sBestOption.sdMaxBacktracks
    88. 

  88.             --strata=$singlePaired.sParams.sBestOption.sdStrata
    89. 

  89.           #else:
    90. 

  90.             --maxBacktracks=$singlePaired.sParams.sBestOption.snMaxBacktracks
    91. 

  91.           #end if
    92. 

  92.           --offrate=$singlePaired.sParams.sOffrate
    93. 

  93.           --seed=$singlePaired.sParams.sSeed
    94. 

  94.         #end if
    95. 

  95.       #else:
    96. 

  96.         --input1=$singlePaired.pInput1
    97. 

  97.         --input2=$singlePaired.pInput2
    98. 

  98.         --maxInsert=$singlePaired.pMaxInsert
    99. 

  99.         --mateOrient=$singlePaired.pMateOrient
    100. 

  100.         --params=$singlePaired.pParams.pSettingsType
    101. 

  101.         #if $singlePaired.pParams.pSettingsType == "full":
    102. 

  102.           --skip=$singlePaired.pParams.pSkip
    103. 

  103.           --alignLimit=$singlePaired.pParams.pAlignLimit
    104. 

  104.           --trimH=$singlePaired.pParams.pTrimH
    105. 

  105.           --trimL=$singlePaired.pParams.pTrimL
    106. 

  106.           --mismatchSeed=$singlePaired.pParams.pMismatchSeed
    107. 

  107.           --mismatchQual=$singlePaired.pParams.pMismatchQual
    108. 

  108.           --seedLen=$singlePaired.pParams.pSeedLen
    109. 

  109.           --rounding=$singlePaired.pParams.pRounding
    110. 

  110.           --maqSoapAlign=$singlePaired.pParams.pMaqSoapAlign
    111. 

  111.           --minInsert=$singlePaired.pParams.pMinInsert
    112. 

  112.           --maxAlignAttempt=$singlePaired.pParams.pMaxAlignAttempt
    113. 

  113.           --forwardAlign=$singlePaired.pParams.pForwardAlign
    114. 

  114.           --reverseAlign=$singlePaired.pParams.pReverseAlign
    115. 

  115.           --tryHard=$singlePaired.pParams.pTryHard
    116. 

  116.           --valAlign=$singlePaired.pParams.pValAlign
    117. 

  117.           --allValAligns=$singlePaired.pParams.pAllValAligns
    118. 

  118.           --suppressAlign=$singlePaired.pParams.pSuppressAlign
    119. 

  119.           --best=$singlePaired.pParams.pBestOption.pBest
    120. 

  120.           #if $singlePaired.pParams.pBestOption.pBest == "doBest":
    121. 

  121.             --maxBacktracks=$singlePaired.pParams.pBestOption.pdMaxBacktracks
    122. 

  122.             --strata=$singlePaired.pParams.pBestOption.pdStrata
    123. 

  123.           #else:
    124. 

  124.             --maxBacktracks=$singlePaired.pParams.pBestOption.pnMaxBacktracks
    125. 

  125.           #end if
    126. 

  126.           --offrate=$singlePaired.pParams.pOffrate
    127. 

  127.           --seed=$singlePaired.pParams.pSeed
    128. 

  128.         #end if
    129. 

  129.       #end if
    130. 

  130.   </command>
    131. 

  131.   <inputs>
    132. 

  132.     <conditional name="refGenomeSource">
    133. 

  133.       <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">
    134. 

  134.         <option value="indexed">Use a built-in index</option>
    135. 

  135.         <option value="history">Use one from the history</option>
    136. 

  136.       </param>
    137. 

  137.       <when value="indexed">
    138. 

  138.         <param name="index" type="select" label="Select a reference genome" help="if your genome of interest is not listed - contact Galaxy team">
    139. 

  139.           <options from_data_table="bowtie_indexes">
    140. 

  140.             <filter type="sort_by" column="2" />
    141. 

  141.             <validator type="no_options" message="No indexes are available" />
    142. 

  142.           </options>
    143. 

  143.         </param>
    144. 

  144.       </when>
    145. 

  145.       <when value="history">
    146. 

  146.         <param name="ownFile" type="data" format="bowtie_base_index,fasta" metadata_name="dbkey" label="Select the reference genome" />
    147. 

  147.         <conditional name="indexParams">
    148. 

  148.           <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">
    149. 

  149.             <option value="indexPreSet">Default</option>
    150. 

  150.             <option value="indexFull">Set your own</option>
    151. 

  151.           </param> 
    152. 

  152.           <when value="indexPreSet" />
    153. 

  153.           <when value="indexFull">
    154. 

  154.             <conditional name="autoBehavior">
    155. 

  155.               <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">
    156. 

  156.                 <option value="auto">Automatic behavior</option>
    157. 

  157.                 <option value="set">Set values (sets --noauto and allows others to be set)</option>
    158. 

  158.               </param>
    159. 

  159.               <when value="auto" />
    160. 

  160.               <when value="set">
    161. 

  161.                 <param name="packed" type="select" label="Whether or not to use a packed representation for DNA strings (--packed)">
    162. 

  162.                   <option value="unpacked">Use regular representation</option>
    163. 

  163.                   <option value="packed">Use packed representation</option>
    164. 

  164.                 </param>
    165. 

  165.                 <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" />
    166. 

  166.                 <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)" />
    167. 

  167.                 <param name="dcv" type="integer" value="1024" label="The period for the difference-cover sample (--dcv)" />
    168. 

  168.               </when>
    169. 

  169.             </conditional>
    170. 

  170.             <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)">
    171. 

  171.               <option value="dc">Use difference-cover sample</option>
    172. 

  172.               <option value="nodc">Disable difference-cover sample</option>
    173. 

  173.             </param>
    174. 

  174.             <param name="noref" type="select" label="Whether or not to build the part of the reference index used only in paired-end alignment (-r)">
    175. 

  175.               <option value="ref">Build all index files</option>
    176. 

  176.               <option value="noref">Do not build paired-end alignment index files</option>
    177. 

  177.             </param>
    178. 

  178.             <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)" />
    179. 

  179.             <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" />
    180. 

  180.             <param name="ntoa" type="select" label="Whether or not to convert Ns in the reference sequence to As (--ntoa)">
    181. 

  181.               <option value="no">Do not convert Ns</option>
    182. 

  182.               <option value="yes">Convert Ns to As</option>
    183. 

  183.             </param>
    184. 

  184.             <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">
    185. 

  185.               <option value="little">Little</option>
    186. 

  186.               <option value="big">Big</option>
    187. 

  187.             </param> 
    188. 

  188.             <param name="seed" type="integer" value="-1" label="Seed for the pseudorandom number generator (--seed)" help="Use -1 to use default" />
    189. 

  189.             <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" />
    190. 

  190.           </when>  <!-- indexFull -->
    191. 

  191.         </conditional>  <!-- indexParams -->
    192. 

  192.       </when>  <!-- history -->
    193. 

  193.     </conditional>  <!-- refGenomeSource -->
    194. 

  194.     <conditional name="singlePaired">
    195. 

  195.       <param name="sPaired" type="select" label="Is this library mate-paired?">
    196. 

  196.         <option value="single">Single-end</option>
    197. 

  197.         <option value="paired">Paired-end</option>
    198. 

  198.       </param>
    199. 

  199.       <when value="single">
    200. 

  200.         <param name="sInput1" type="data" format="fastqsanger,fastqillumina,fastqsolexa" label="FASTQ file" help="Must have ASCII encoded quality scores"/>
    201. 

  201.         <conditional name="sParams">
    202. 

  202.           <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">
    203. 

  203.             <option value="preSet">Commonly used</option>
    204. 

  204.             <option value="full">Full parameter list</option>
    205. 

  205.             </param>
    206. 

  206.           <when value="preSet" />
    207. 

  207.           <when value="full">
    208. 

  208.             <param name="sSkip" type="integer" value="0" label="Skip the first n reads (-s)" />  
    209. 

  209.             <param name="sAlignLimit" type="integer" value="-1" label="Only align the first n reads (-u)" help="-1 for off" />  
    210. 

  210.             <param name="sTrimH" type="integer" value="0" label="Trim n bases from high-quality (left) end of each read before alignment (-5)" />
    211. 

  211.             <param name="sTrimL" type="integer" value="0" label="Trim n bases from low-quality (right) end of each read before alignment (-3)" />
    212. 

  212.             <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" />
    213. 

  213.             <param name="sMismatchQual" type="integer" value="70" label="Maximum permitted total of quality values at mismatched read positions (-e)" />
    214. 

  214.             <param name="sSeedLen" type="integer" value="28" label="Seed length (-l)" help="Minimum value is 5" />
    215. 

  215.             <param name="sRounding" type="select" label="Whether or not to round to the nearest 10 and saturating at 30 (--nomaqround)">
    216. 

  216.               <option value="round">Round to nearest 10</option>
    217. 

  217.               <option value="noRound">Do not round to nearest 10</option>
    218. 

  218.             </param>
    219. 

  219.             <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" />
    220. 

  220.             <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">
    221. 

  221.               <option value="noTryHard">Do not try hard</option>
    222. 

  222.               <option value="doTryHard">Try hard</option>
    223. 

  223.             </param>
    224. 

  224.             <param name="sValAlign" type="integer" value="1" label="Report up to n valid alignments per read (-k)" />
    225. 

  225.             <param name="sAllValAligns" type="select" label="Whether or not to report all valid alignments per read (-a)">
    226. 

  226.               <option value="noAllValAligns">Do not report all valid alignments</option>
    227. 

  227.               <option value="doAllValAligns">Report all valid alignments</option>
    228. 

  228.             </param>
    229. 

  229.             <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" />
    230. 

  230.             <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)" />
    231. 

  231.             <param name="sUnmappedFile" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write all reads that could not be aligned to a file (--un)" />
    232. 

  232.             <conditional name="sBestOption">
    233. 

  233.               <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">
    234. 

  234.                 <option value="noBest">Do not use best</option>
    235. 

  235.                 <option value="doBest">Use best</option>
    236. 

  236.               </param>
    237. 

  237.               <when value="noBest">
    238. 

  238.                 <param name="snMaxBacktracks" type="integer" value="125" label="Maximum number of backtracks permitted when aligning a read (--maxbts)" />
    239. 

  239.               </when>
    240. 

  240.               <when value="doBest">
    241. 

  241.                 <param name="sdMaxBacktracks" type="integer" value="800" label="Maximum number of backtracks permitted when aligning a read (--maxbts)" />
    242. 

  242.                 <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)">
    243. 

  243.                   <option value="noStrata">Do not use strata option</option>
    244. 

  244.                   <option value="doStrata">Use strata option</option>
    245. 

  245.                 </param>
    246. 

  246.               </when>
    247. 

  247.             </conditional> <!-- bestOption -->
    248. 

  248.             <param name="sOffrate" type="integer" value="-1" label="Override the offrate of the index to n (-o)" help="-1 for default" />
    249. 

  249.             <param name="sSeed" type="integer" value="-1" label="Seed for pseudo-random number generator (--seed)" help="-1 for default" />
    250. 

  250.           </when> <!-- full -->
    251. 

  251.         </conditional> <!-- sParams -->
    252. 

  252.       </when> <!-- single -->
    253. 

  253.       <when value="paired">
    254. 

  254.         <param name="pInput1" type="data" format="fastqsanger,fastqillumina,fastqsolexa" label="Forward FASTQ file" help="Must have ASCII encoded quality scores"/>
    255. 

  255.         <param name="pInput2" type="data" format="fastqsanger,fastqillumina,fastqsolexa" label="Reverse FASTQ file" help="File format must match the Forward FASTQ file">
    256. 

  256.             <options options_filter_attribute="ext" from_parameter="tool.app.datatypes_registry.datatypes_by_extension" transform_lines="obj.keys()">>
    257. 

  257.                <column name="name" index="0"/>
    258. 

  258.                <column name="value" index="0"/>
    259. 

  259.                <filter type="param_value" ref="pInput1" ref_attribute="ext" column="0"/> 
    260. 

  260.            </options>
    261. 

  261.         </param>
    262. 

  262.         <param name="pMaxInsert" type="integer" value="1000" label="Maximum insert size for valid paired-end alignments (-X)" />
    263. 

  263.         <param name="pMateOrient" type="select" label="The upstream/downstream mate orientation for valid paired-end alignment against the forward reference strand (--fr/--rf/--ff)">
    264. 

  264.           <option value="fr">FR (for Illumina)</option>
    265. 

  265.           <option value="rf">RF</option>
    266. 

  266.           <option value="ff">FF (for SOLiD)</option>
    267. 

  267.         </param>
    268. 

  268.         <conditional name="pParams">
    269. 

  269.           <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">
    270. 

  270.             <option value="preSet">Commonly used</option>
    271. 

  271.             <option value="full">Full parameter list</option>
    272. 

  272.           </param>
    273. 

  273.           <when value="preSet" />
    274. 

  274.           <when value="full">
    275. 

  275.             <param name="pSkip" type="integer" value="0" label="Skip the first n pairs (-s)" />  
    276. 

  276.             <param name="pAlignLimit" type="integer" value="-1" label="Only align the first n pairs (-u)" help="-1 for off" />  
    277. 

  277.             <param name="pTrimH" type="integer" value="0" label="Trim n bases from high-quality (left) end of each read before alignment (-5)" />
    278. 

  278.             <param name="pTrimL" type="integer" value="0" label="Trim n bases from low-quality (right) end of each read before alignment (-3)" />
    279. 

  279.             <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" />
    280. 

  280.             <param name="pMismatchQual" type="integer" value="70" label="Maximum permitted total of quality values at mismatched read positions (-e)" />
    281. 

  281.             <param name="pSeedLen" type="integer" value="28" label="Seed length (-l)" help="Minimum value is 5" />
    282. 

  282.             <param name="pRounding" type="select" label="Whether or not to round to the nearest 10 and saturating at 30 (--nomaqround)">
    283. 

  283.               <option value="round">Round to nearest 10</option>
    284. 

  284.               <option value="noRound">Do not round to nearest 10</option>
    285. 

  285.             </param>
    286. 

  286.             <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" />
    287. 

  287.             <param name="pMinInsert" type="integer" value="0" label="Minimum insert size for valid paired-end alignments (-I)" />
    288. 

  288.             <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)" />
    289. 

  289.             <param name="pForwardAlign" type="select" label="Choose whether or not to attempt to align the forward reference strand (--nofw)">
    290. 

  290.               <option value="forward">Align against the forward reference strand</option>
    291. 

  291.               <option value="noForward">Do not align against the forward reference strand</option>
    292. 

  292.             </param>
    293. 

  293.             <param name="pReverseAlign" type="select" label="Choose whether or not to align against the reverse-complement reference strand (--norc)">
    294. 

  294.               <option value="reverse">Align against the reverse-complement reference strand</option>
    295. 

  295.               <option value="noReverse">Do not align against the reverse-complement reference strand</option>
    296. 

  296.             </param>
    297. 

  297.             <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">
    298. 

  298.               <option value="noTryHard">Do not try hard</option>
    299. 

  299.               <option value="doTryHard">Try hard</option>
    300. 

  300.             </param>
    301. 

  301.             <param name="pValAlign" type="integer" value="1" label="Report up to n valid arguments per pair (-k)" />
    302. 

  302.             <param name="pAllValAligns" type="select" label="Whether or not to report all valid alignments per pair (-a)">
    303. 

  303.               <option value="noAllValAligns">Do not report all valid alignments</option>
    304. 

  304.               <option value="doAllValAligns">Report all valid alignments</option>
    305. 

  305.             </param>
    306. 

  306.             <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" />
    307. 

  307.             <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)" />
    308. 

  308.             <param name="pUnmappedFile" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write all reads that could not be aligned to a file (--un)" />
    309. 

  309.             <conditional name="pBestOption">
    310. 

  310.               <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">
    311. 

  311.                 <option value="noBest">Do not use best</option>
    312. 

  312.                 <option value="doBest">Use best</option>
    313. 

  313.               </param>
    314. 

  314.               <when value="noBest">
    315. 

  315.                 <param name="pnMaxBacktracks" type="integer" value="125" label="Maximum number of backtracks permitted when aligning a read (--maxbts)" />
    316. 

  316.               </when>
    317. 

  317.               <when value="doBest">
    318. 

  318.                 <param name="pdMaxBacktracks" type="integer" value="800" label="Maximum number of backtracks permitted when aligning a read (--maxbts)" />
    319. 

  319.                 <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)">
    320. 

  320.                   <option value="noStrata">Do not use strata option</option>
    321. 

  321.                   <option value="doStrata">Use strata option</option>
    322. 

  322.                 </param>
    323. 

  323.               </when>
    324. 

  324.             </conditional>
    325. 

  325.             <param name="pOffrate" type="integer" value="-1" label="Override the offrate of the index to n (-o)" help="-1 for default" />
    326. 

  326.             <param name="pSeed" type="integer" value="-1" label="Seed for pseudo-random number generator (--seed)" help="-1 for default" />
    327. 

  327.           </when> <!-- full -->
    328. 

  328.         </conditional> <!-- pParams -->
    329. 

  329.       </when> <!-- paired -->
    330. 

  330.     </conditional> <!-- singlePaired -->
    331. 

  331.     <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" />
    332. 

  332.   </inputs>
    333. 

  333.   <outputs>
    334. 

  334.     <data format="sam" name="output" label="${tool.name} on ${on_string}: mapped reads">
    335. 

  335.       <actions>
    336. 

  336.         <conditional name="refGenomeSource.genomeSource">
    337. 

  337.           <when value="indexed">
    338. 

  338.             <action type="metadata" name="dbkey">
    339. 

  339.               <option type="from_data_table" name="bowtie_indexes" column="1" offset="0">
    340. 

  340.                 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
    341. 

  341.                 <filter type="param_value" ref="refGenomeSource.index" column="0"/>
    342. 

  342.               </option>
    343. 

  343.             </action>
    344. 

  344.           </when>
    345. 

  345.           <when value="history">
    346. 

  346.             <action type="metadata" name="dbkey">
    347. 

  347.               <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" />
    348. 

  348.             </action>
    349. 

  349.           </when>
    350. 

  350.         </conditional>
    351. 

  351.       </actions>
    352. 

  352.     </data>
    353. 

  353.     <data format="fastq" name="output_suppressed_reads_l" label="${tool.name} on ${on_string}: suppressed reads (L)">
    354. 

  354.       <filter>((
    355. 

  355.           singlePaired['sPaired'] == "single" and
    356. 

  356.           singlePaired['sParams']['sSettingsType'] == "full" and
    357. 

  357.           singlePaired['sParams']['sMaxFile'] is True
    358. 

  358.         ) or (
    359. 

  359.           singlePaired['sPaired'] == "paired" and
    360. 

  360.           singlePaired['pParams']['pSettingsType'] == "full" and
    361. 

  361.           singlePaired['pParams']['pMaxFile'] is True
    362. 

  362.         ))
    363. 

  363.       </filter>
    364. 

  364.       <actions>
    365. 

  365.         <conditional name="singlePaired.sPaired">
    366. 

  366.           <when value="single">
    367. 

  367.             <action type="format">
    368. 

  368.               <option type="from_param" name="singlePaired.sInput1" param_attribute="ext" />
    369. 

  369.             </action>
    370. 

  370.           </when>
    371. 

  371.           <when value="paired">
    372. 

  372.             <action type="format">
    373. 

  373.               <option type="from_param" name="singlePaired.pInput1" param_attribute="ext" />
    374. 

  374.             </action>
    375. 

  375.           </when>
    376. 

  376.         </conditional>
    377. 

  377.       </actions>
    378. 

  378.     </data>
    379. 

  379.     <data format="fastq" name="output_suppressed_reads_r" label="${tool.name} on ${on_string}: suppressed reads (R)">
    380. 

  380.       <filter>singlePaired['sPaired'] == "paired"</filter>
    381. 

  381.       <filter>singlePaired['pParams']['pSettingsType'] == "full"</filter>
    382. 

  382.       <filter>singlePaired['pParams']['pMaxFile'] is True</filter>
    383. 

  383.       <actions>
    384. 

  384.         <conditional name="singlePaired.sPaired">
    385. 

  385.           <when value="single">
    386. 

  386.             <action type="format">
    387. 

  387.               <option type="from_param" name="singlePaired.sInput1" param_attribute="ext" />
    388. 

  388.             </action>
    389. 

  389.           </when>
    390. 

  390.           <when value="paired">
    391. 

  391.             <action type="format">
    392. 

  392.               <option type="from_param" name="singlePaired.pInput1" param_attribute="ext" />
    393. 

  393.             </action>
    394. 

  394.           </when>
    395. 

  395.         </conditional>
    396. 

  396.       </actions>
    397. 

  397.     </data>
    398. 

  398.     <data format="fastq" name="output_unmapped_reads_l" label="${tool.name} on ${on_string}: unmapped reads (L)">
    399. 

  399.       <filter>
    400. 

  400.         ((
    401. 

  401.           singlePaired['sPaired'] == "single" and
    402. 

  402.           singlePaired['sParams']['sSettingsType'] == "full" and
    403. 

  403.           singlePaired['sParams']['sUnmappedFile'] is True
    404. 

  404.         ) or (
    405. 

  405.           singlePaired['sPaired'] == "paired" and
    406. 

  406.           singlePaired['pParams']['pSettingsType'] == "full" and
    407. 

  407.           singlePaired['pParams']['pUnmappedFile'] is True
    408. 

  408.         ))
    409. 

  409.       </filter>
    410. 

  410.       <actions>
    411. 

  411.         <conditional name="singlePaired.sPaired">
    412. 

  412.           <when value="single">
    413. 

  413.             <action type="format">
    414. 

  414.               <option type="from_param" name="singlePaired.sInput1" param_attribute="ext" />
    415. 

  415.             </action>
    416. 

  416.           </when>
    417. 

  417.           <when value="paired">
    418. 

  418.             <action type="format">
    419. 

  419.               <option type="from_param" name="singlePaired.pInput1" param_attribute="ext" />
    420. 

  420.             </action>
    421. 

  421.           </when>
    422. 

  422.         </conditional>
    423. 

  423.       </actions>
    424. 

  424.     </data>
    425. 

  425.     <data format="fastq" name="output_unmapped_reads_r" label="${tool.name} on ${on_string}: unmapped reads (R)">
    426. 

  426.       <filter>singlePaired['sPaired'] == "paired"</filter>
    427. 

  427.       <filter>singlePaired['pParams']['pSettingsType'] == "full"</filter>
    428. 

  428.       <filter>singlePaired['pParams']['pUnmappedFile'] is True</filter>
    429. 

  429.       <actions>
    430. 

  430.         <conditional name="singlePaired.sPaired">
    431. 

  431.           <when value="single">
    432. 

  432.             <action type="format">
    433. 

  433.               <option type="from_param" name="singlePaired.sInput1" param_attribute="ext" />
    434. 

  434.             </action>
    435. 

  435.           </when>
    436. 

  436.           <when value="paired">
    437. 

  437.             <action type="format">
    438. 

  438.               <option type="from_param" name="singlePaired.pInput1" param_attribute="ext" />
    439. 

  439.             </action>
    440. 

  440.           </when>
    441. 

  441.         </conditional>
    442. 

  442.       </actions>
    443. 

  443.     </data>
    444. 

  444.   </outputs>
    445. 

  445.   <tests>
    446. 

  446.     <test>
    447. 

  447.       <!--
    448. 

  448.       Bowtie command:
    449. 

  449.       bowtie -q -p 4 -S +sam-nohead chrM_base test-data/bowtie_in2.fastqsanger > bowtie_out6_u.sam
    450. 

  450.       sort bowtie_out6_u.sam > bowtie_out6.sam
    451. 

  451.       -p is the number of threads, which is hardcoded above. You need to replace the + with 2 dashes. 
    452. 

  452.       chrM_base needs to be the base location/name of the index files.
    453. 

  453.       -->
    454. 

  454.       <param name="genomeSource" value="indexed" />
    455. 

  455.       <!-- this is the backwards-compatible "unique value" for this index, not an actual path -->
    456. 

  456.       <param name="index" value="equCab2chrM" />
    457. 

  457.       <param name="sPaired" value="single" />
    458. 

  458.       <param name="sInput1" ftype="fastqsanger" value="bowtie_in2.fastqsanger" />
    459. 

  459.       <param name="sSettingsType" value="preSet" />
    460. 

  460.       <param name="suppressHeader" value="true" />
    461. 

  461.       <output name="output" ftype="sam" file="bowtie_out6.sam" sort="True" />
    462. 

  462.     </test>
    463. 

  463.     <test>
    464. 

  464.       <!--
    465. 

  465.       Bowtie command:
    466. 

  466.       bowtie-build -f test-data/phiX.fasta phiX_base
    467. 

  467.       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
    468. 

  468.       sort bowtie_out7_u.sam > bowtie_out7.sam
    469. 

  469.       sort bowtie_out8_u_1.sam > bowtie_out8_1.sam
    470. 

  470.       sort bowtie_out8_u_2.sam > bowtie_out8_2.sam
    471. 

  471.       Then also need to modify bowtie_out8_1.sam and bowtie_out8_2.sam so that all @ lines come before sequence lines.
    472. 

  472.       -p is the number of threads, hardcoded above. You need to replace the + with 2 dashes.
    473. 

  473.       The two unmapped output files will be named bowtie_out8_1.fastq and bowtie_out8_2.fastq.
    474. 

  474.       chrM_base is the index files' location/base name. 
    475. 

  475.       -->
    476. 

  476.       <param name="genomeSource" value="history" />
    477. 

  477.       <param name="ownFile" value="phiX.fasta" />
    478. 

  478.       <param name="indexSettings" value="indexPreSet" />
    479. 

  479.       <param name="sPaired" value="paired" />
    480. 

  480.       <param name="pInput1" ftype="fastqsanger" value="bowtie_in5.fastqsanger" />
    481. 

  481.       <param name="pInput2" ftype="fastqsanger" value="bowtie_in6.fastqsanger" />
    482. 

  482.       <param name="pMaxInsert" value="1000" />
    483. 

  483.       <param name="pMateOrient" value="ff" />
    484. 

  484.       <param name="pSettingsType" value="full" />
    485. 

  485.       <param name="pSkip" value="0" />
    486. 

  486.       <param name="pAlignLimit" value="-1" />
    487. 

  487.       <param name="pTrimH" value="0" />
    488. 

  488.       <param name="pTrimL" value="0" />
    489. 

  489.       <param name="pMismatchSeed" value="2" />
    490. 

  490.       <param name="pMismatchQual" value="70" />
    491. 

  491.       <param name="pSeedLen" value="28" />
    492. 

  492.       <param name="pRounding" value="round" />
    493. 

  493.       <param name="pMaqSoapAlign" value="-1" />
    494. 

  494.       <param name="pMinInsert" value="0" />
    495. 

  495.       <param name="pMaxAlignAttempt" value="100" />
    496. 

  496.       <param name="pForwardAlign" value="forward" />
    497. 

  497.       <param name="pReverseAlign" value="reverse" />
    498. 

  498.       <param name="pTryHard" value="noTryHard" />
    499. 

  499.       <param name="pValAlign" value="1" />
    500. 

  500.       <param name="pAllValAligns" value="noAllValAligns" />
    501. 

  501.       <param name="pSuppressAlign" value="-1" />
    502. 

  502.       <param name="pUnmappedFile" value="true" />
    503. 

  503.       <param name="pMaxFile" value="false" />
    504. 

  504.       <param name="pBest" value="doBest" />
    505. 

  505.       <param name="pdMaxBacktracks" value="800" />
    506. 

  506.       <param name="pdStrata" value="noStrata" />
    507. 

  507.       <param name="pOffrate" value="-1" />
    508. 

  508.       <param name="pSeed" value="-1" />
    509. 

  509.       <param name="suppressHeader" value="true" />
    510. 

  510.       <output name="output" ftype="sam" file="bowtie_out7.sam" sort="True" />
    511. 

  511.       <output name="output_unmapped_reads_l" ftype="fastqsanger" file="bowtie_out8_1.fastq" sort="True" />
    512. 

  512.       <output name="output_unmapped_reads_r" ftype="fastqsanger" file="bowtie_out8_2.fastq" sort="True" />
    513. 

  513.     </test>
    514. 

  514.     <!-- start testing of non-sanger variant fastq reads -->
    515. 

  515.     <test>
    516. 

  516.       <param name="genomeSource" value="history" />
    517. 

  517.       <param name="ownFile" value="phiX.fasta" />
    518. 

  518.       <param name="indexSettings" value="indexPreSet" />
    519. 

  519.       <param name="sPaired" value="paired" />
    520. 

  520.       <param name="pInput1" ftype="fastqillumina" value="bowtie_in5.fastqillumina" />
    521. 

  521.       <param name="pInput2" ftype="fastqillumina" value="bowtie_in6.fastqillumina" />
    522. 

  522.       <param name="pMaxInsert" value="1000" />
    523. 

  523.       <param name="pMateOrient" value="ff" />
    524. 

  524.       <param name="pSettingsType" value="full" />
    525. 

  525.       <param name="pSkip" value="0" />
    526. 

  526.       <param name="pAlignLimit" value="-1" />
    527. 

  527.       <param name="pTrimH" value="0" />
    528. 

  528.       <param name="pTrimL" value="0" />
    529. 

  529.       <param name="pMismatchSeed" value="2" />
    530. 

  530.       <param name="pMismatchQual" value="70" />
    531. 

  531.       <param name="pSeedLen" value="28" />
    532. 

  532.       <param name="pRounding" value="round" />
    533. 

  533.       <param name="pMaqSoapAlign" value="-1" />
    534. 

  534.       <param name="pMinInsert" value="0" />
    535. 

  535.       <param name="pMaxAlignAttempt" value="100" />
    536. 

  536.       <param name="pForwardAlign" value="forward" />
    537. 

  537.       <param name="pReverseAlign" value="reverse" />
    538. 

  538.       <param name="pTryHard" value="noTryHard" />
    539. 

  539.       <param name="pValAlign" value="1" />
    540. 

  540.       <param name="pAllValAligns" value="noAllValAligns" />
    541. 

  541.       <param name="pSuppressAlign" value="-1" />
    542. 

  542.       <param name="pUnmappedFile" value="true" />
    543. 

  543.       <param name="pMaxFile" value="false" />
    544. 

  544.       <param name="pBest" value="doBest" />
    545. 

  545.       <param name="pdMaxBacktracks" value="800" />
    546. 

  546.       <param name="pdStrata" value="noStrata" />
    547. 

  547.       <param name="pOffrate" value="-1" />
    548. 

  548.       <param name="pSeed" value="-1" />
    549. 

  549.       <param name="suppressHeader" value="true" />
    550. 

  550.       <output name="output" ftype="sam" file="bowtie_out7.sam" sort="True" />
    551. 

  551.       <output name="output_unmapped_reads_l" ftype="fastqillumna" file="bowtie_out8_1.fastqillumina.sorted" sort="True" />
    552. 

  552.       <output name="output_unmapped_reads_r" ftype="fastqillumna" file="bowtie_out8_2.fastqillumina.sorted" sort="True" />
    553. 

  553.     </test>
    554. 

  554.     <test>
    555. 

  555.       <param name="genomeSource" value="history" />
    556. 

  556.       <param name="ownFile" value="phiX.fasta" />
    557. 

  557.       <param name="indexSettings" value="indexPreSet" />
    558. 

  558.       <param name="sPaired" value="paired" />
    559. 

  559.       <param name="pInput1" ftype="fastqsolexa" value="bowtie_in5.fastqsolexa" />
    560. 

  560.       <param name="pInput2" ftype="fastqsolexa" value="bowtie_in6.fastqsolexa" />
    561. 

  561.       <param name="pMaxInsert" value="1000" />
    562. 

  562.       <param name="pMateOrient" value="ff" />
    563. 

  563.       <param name="pSettingsType" value="full" />
    564. 

  564.       <param name="pSkip" value="0" />
    565. 

  565.       <param name="pAlignLimit" value="-1" />
    566. 

  566.       <param name="pTrimH" value="0" />
    567. 

  567.       <param name="pTrimL" value="0" />
    568. 

  568.       <param name="pMismatchSeed" value="2" />
    569. 

  569.       <param name="pMismatchQual" value="70" />
    570. 

  570.       <param name="pSeedLen" value="28" />
    571. 

  571.       <param name="pRounding" value="round" />
    572. 

  572.       <param name="pMaqSoapAlign" value="-1" />
    573. 

  573.       <param name="pMinInsert" value="0" />
    574. 

  574.       <param name="pMaxAlignAttempt" value="100" />
    575. 

  575.       <param name="pForwardAlign" value="forward" />
    576. 

  576.       <param name="pReverseAlign" value="reverse" />
    577. 

  577.       <param name="pTryHard" value="noTryHard" />
    578. 

  578.       <param name="pValAlign" value="1" />
    579. 

  579.       <param name="pAllValAligns" value="noAllValAligns" />
    580. 

  580.       <param name="pSuppressAlign" value="-1" />
    581. 

  581.       <param name="pUnmappedFile" value="true" />
    582. 

  582.       <param name="pMaxFile" value="false" />
    583. 

  583.       <param name="pBest" value="doBest" />
    584. 

  584.       <param name="pdMaxBacktracks" value="800" />
    585. 

  585.       <param name="pdStrata" value="noStrata" />
    586. 

  586.       <param name="pOffrate" value="-1" />
    587. 

  587.       <param name="pSeed" value="-1" />
    588. 

  588.       <param name="suppressHeader" value="true" />
    589. 

  589.       <output name="output" ftype="sam" file="bowtie_out7.sam" sort="True" />
    590. 

  590.       <output name="output_unmapped_reads_l" ftype="fastqsolexa" file="bowtie_out8_1.fastqsolexa.sorted" sort="True" />
    591. 

  591.       <output name="output_unmapped_reads_r" ftype="fastqsolexa" file="bowtie_out8_2.fastqsolexa.sorted" sort="True" />
    592. 

  592.     </test>
    593. 

  593.     <!-- end testing of non-sanger variant fastq reads -->    
    594. 

  594.     <test>
    595. 

  595.       <!--
    596. 

  596.       Bowtie command:
    597. 

  597.       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
    598. 

  598.       sort bowtie_out9_u.sam > bowtie_out9.sam
    599. 

  599.       -p is the number of threads, hardcoded above. You need to replace the + with 2 dashes.
    600. 

  600.       chrM_base is the index files' location/base name. 
    601. 

  601.       -->
    602. 

  602.       <param name="genomeSource" value="indexed" />
    603. 

  603.       <!-- this is the backwards-compatible "unique value" for this index, not an actual path -->
    604. 

  604.       <param name="index" value="equCab2chrM" />
    605. 

  605.       <param name="sPaired" value="single" />
    606. 

  606.       <param name="sInput1" ftype="fastqsanger" value="bowtie_in2.fastqsanger" />
    607. 

  607.       <param name="sSettingsType" value="full" />
    608. 

  608.       <param name="sSkip" value="0" />
    609. 

  609.       <param name="sAlignLimit" value="-1" />
    610. 

  610.       <param name="sTrimH" value="0" />
    611. 

  611.       <param name="sTrimL" value="0" />
    612. 

  612.       <param name="sMismatchSeed" value="2" />
    613. 

  613.       <param name="sMismatchQual" value="70" />
    614. 

  614.       <param name="sSeedLen" value="28" />
    615. 

  615.       <param name="sRounding" value="round" />
    616. 

  616.       <param name="sMaqSoapAlign" value="-1" />
    617. 

  617.       <param name="sTryHard" value="doTryHard" />
    618. 

  618.       <param name="sValAlign" value="1" />
    619. 

  619.       <param name="sAllValAligns" value="noAllValAligns" />
    620. 

  620.       <param name="sSuppressAlign" value="-1" />
    621. 

  621.       <param name="sUnmappedFile" value="false" />
    622. 

  622.       <param name="sMaxFile" value="false" />
    623. 

  623.       <param name="sBest" value="noBest" />
    624. 

  624.       <param name="snMaxBacktracks" value="125" />
    625. 

  625.       <param name="sOffrate" value="-1" />
    626. 

  626.       <param name="sSeed" value="-1" />
    627. 

  627.       <param name="suppressHeader" value="true" />
    628. 

  628.       <output name="output" ftype="sam" file="bowtie_out9.sam" sort="True" />
    629. 

  629.     </test>
    630. 

  630.     <test>
    631. 

  631.       <!--
    632. 

  632.       Bowtie command:
    633. 

  633.       bowtie-build +offrate 5 +ftabchars 10 +little -f test-data/phiX.fasta phiX_base
    634. 

  634.       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
    635. 

  635.       sort bowtie_out10_u.sam > bowtie_out10.sam
    636. 

  636.       -p is the number of threads, hardcoded above. You need to replace the + with 2 dashes.
    637. 

  637.       chrM_base is the index files' location/base name. 
    638. 

  638.       -->
    639. 

  639.       <param name="genomeSource" value="history" />
    640. 

  640.       <param name="ownFile" value="phiX.fasta" />
    641. 

  641.       <param name="indexSettings" value="indexFull" />
    642. 

  642.       <param name="autoB" value="auto" />
    643. 

  643.       <param name="nodc" value="dc" />
    644. 

  644.       <param name="noref" value="ref" />
    645. 

  645.       <param name="offrate" value="5" />
    646. 

  646.       <param name="ftab" value="10" />
    647. 

  647.       <param name="ntoa" value="no" />
    648. 

  648.       <param name="endian" value="little" />
    649. 

  649.       <param name="seed" value="-1" />
    650. 

  650.       <param name="cutoff" value="-1" />
    651. 

  651.       <param name="sPaired" value="paired" />
    652. 

  652.       <param name="pInput1" ftype="fastqsanger" value="bowtie_in5.fastqsanger" />
    653. 

  653.       <param name="pInput2" ftype="fastqsanger" value="bowtie_in6.fastqsanger" />
    654. 

  654.       <param name="pMaxInsert" value="1000" />
    655. 

  655.       <param name="pMateOrient" value="ff" />
    656. 

  656.       <param name="pSettingsType" value="preSet" />
    657. 

  657.       <param name="suppressHeader" value="true" />
    658. 

  658.       <output name="output" ftype="sam" file="bowtie_out10.sam" sort="True" />
    659. 

  659.     </test>
    660. 

  660.   </tests>
    661. 

  661. 

  662.   <help>
    663. 

  663. 

  664. **What it does**
    665. 

  665. 

  666. Bowtie_ is a short read aligner designed to be ultrafast and memory-efficient. It is developed by Ben Langmead and Cole Trapnell. Please cite: Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology 10:R25.
    667. 

  667. 

  668. .. _Bowtie: http://bowtie-bio.sourceforge.net/index.shtml
    669. 

  669. 

  670. ------
    671. 

  671. 

  672. **Know what you are doing**
    673. 

  673. 

  674. .. class:: warningmark
    675. 

  675. 

  676. There is no such thing (yet) as an automated gearshift in short read mapping. It is all like stick-shift driving in San Francisco. In other words = running this tool with default parameters will probably not give you meaningful results. A way to deal with this is to **understand** the parameters by carefully reading the `documentation`__ and experimenting. Fortunately, Galaxy makes experimenting easy.
    677. 

  677. 

  678.  .. __: http://bowtie-bio.sourceforge.net/index.shtml
    679. 

  679. 

  680. ------
    681. 

  681. 

  682. **Input formats**
    683. 

  683. 

  684. Bowtie accepts files in Sanger FASTQ format. Use the FASTQ Groomer to prepare your files.
    685. 

  685. 

  686. ------
    687. 

  687. 

  688. **A Note on Built-in Reference Genomes**
    689. 

  689. 

  690. Some genomes have multiple variants. If only one "type" of genome is listed, it is the Full version, which means that everything that came in the original genome data download (possibly with mitochondrial and plasmid DNA added if it wasn't already included). The Full version is available for every genome. Some genomes also come in the Canonical variant, which contains only the "canonical" (well-defined) chromosomes or segments, such as chr1-chr22, chrX, chrY, and chrM for human. Other variations include gender. These will come in the canonical form only, so the general Canonical variant is actually Canonical Female and the other is Canonical Male (identical to female excluding chrX).
    691. 

    692. 

  692. ------
    693. 

  693. 

  694. **Outputs**
    695. 

  695. 

  696. The output is in SAM format, and has the following columns::
    697. 

  697. 

  698.     Column  Description
    699. 

  699.   --------  --------------------------------------------------------   
    700. 

  700.    1 QNAME  Query (pair) NAME
    701. 

  701.    2 FLAG   bitwise FLAG
    702. 

  702.    3 RNAME  Reference sequence NAME
    703. 

  703.    4 POS    1-based leftmost POSition/coordinate of clipped sequence
    704. 

  704.    5 MAPQ   MAPping Quality (Phred-scaled)
    705. 

  705.    6 CIGAR  extended CIGAR string
    706. 

  706.    7 MRNM   Mate Reference sequence NaMe ('=' if same as RNAME)
    707. 

  707.    8 MPOS   1-based Mate POSition
    708. 

  708.    9 ISIZE  Inferred insert SIZE
    709. 

  709.   10 SEQ    query SEQuence on the same strand as the reference
    710. 

  710.   11 QUAL   query QUALity (ASCII-33 gives the Phred base quality)
    711. 

  711.   12 OPT    variable OPTional fields in the format TAG:VTYPE:VALUE
    712. 

  712.   
    713. 

  713. The flags are as follows::
    714. 

  714. 

  715.     Flag  Description
    716. 

  716.   ------  -------------------------------------
    717. 

  717.   0x0001  the read is paired in sequencing
    718. 

  718.   0x0002  the read is mapped in a proper pair
    719. 

  719.   0x0004  the query sequence itself is unmapped
    720. 

  720.   0x0008  the mate is unmapped
    721. 

  721.   0x0010  strand of the query (1 for reverse)
    722. 

  722.   0x0020  strand of the mate
    723. 

  723.   0x0040  the read is the first read in a pair
    724. 

  724.   0x0080  the read is the second read in a pair
    725. 

  725.   0x0100  the alignment is not primary
    726. 

  726. 

  727. It looks like this (scroll sideways to see the entire example)::
    728. 

  728. 

  729.   QNAME	FLAG	RNAME	POS	MAPQ	CIAGR	MRNM	MPOS	ISIZE	SEQ	QUAL	OPT
    730. 

  730.   HWI-EAS91_1_30788AAXX:1:1:1761:343	4	*	0	0	*	*	0	0	AAAAAAANNAAAAAAAAAAAAAAAAAAAAAAAAAAACNNANNGAGTNGNNNNNNNGCTTCCCACAGNNCTGG	hhhhhhh;;hhhhhhhhhhh^hOhhhhghhhfhhhgh;;h;;hhhh;h;;;;;;;hhhhhhghhhh;;Phhh
    731. 

  731.   HWI-EAS91_1_30788AAXX:1:1:1578:331	4	*	0	0	*	*	0	0	GTATAGANNAATAAGAAAAAAAAAAATGAAGACTTTCNNANNTCTGNANNNNNNNTCTTTTTTCAGNNGTAG	hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhhhh;;h;;hhhh;h;;;;;;;hhhhhhhhhhh;;hhVh
    732. 

  732. 

  733. -------
    734. 

  734. 

  735. **Bowtie settings**
    736. 

  736. 

  737. All of the options have a default value. You can change any of them. Most of the options in Bowtie have been implemented here.
    738. 

  738. 

  739. ------
    740. 

  740. 

  741. **Bowtie parameter list**
    742. 

  742. 

  743. This is an exhaustive list of Bowtie options:
    744. 

  744. 

  745. For indexing (bowtie-build)::
    746. 

  746. 

  747.   -a                 No auto behavior. Disable the default behavior where bowtie automatically 
    748. 

  748.                      selects values for --bmax/--bmaxdivn/--dcv/--packed parameters according 
    749. 

  749.                      to the memory available. [off]
    750. 

  750.   --packed           Packing. Use a packed representation for DNA strings. [auto] 
    751. 

  751.   --bmax INT         Suffix maximum. The maximum number of suffixes allowed in a block. [auto]
    752. 

  752.   --bmaxdivn INT     Suffix maximum fraction. The maximum number of suffixes allowed in a block 
    753. 

  753.                      expressed as a fraction of the length of the reference. [4]
    754. 

  754.   --dcv INT          Difference-cover sample. Use INT as the period for the difference-cover 
    755. 

  755.                      sample. [1024]
    756. 

  756.   --nodc INT         No difference-cover sample. Disable the difference-cover sample. [off]
    757. 

  757.   -r                 No reference indexes. Do not build the NAME.3.ebwt and NAME.4.ebwt portions 
    758. 

  758.                      of the index. Used only for paired-end alignment. [off]
    759. 

  759.   -o                 Offrate. How many Burrows-Wheeler rows get marked by the indexer. The 
    760. 

  760.                      indexer will mark every 2^INT rows. The marked rows correspond to rows on 
    761. 

  761.                      the genome. [5]
    762. 

  762.   -t INT             Ftab. The lookup table used to calculate an initial Burrows-Wheeler range 
    763. 

  763.                      with respect to the first INT characters of the query. Ftab is 4^INT+1 
    764. 

  764.                      bytes. [10]
    765. 

  765.   --ntoa             N conversion. Convert Ns to As before building the index. Otherwise, Ns are 
    766. 

  766.                      simply excluded from the index and Bowtie will not find alignments that 
    767. 

  767.                      overlap them. [off]
    768. 

  768.   --big              Endianness. Endianness to use when serializing integers to the index file. [off]
    769. 

  769.   --little           Endianness. [--little]
    770. 

  770.   --seed INT         Random seed. Use INT as the seed for the pseudo-random number generator. [off]
    771. 

  771.   --cutoff INT       Cutoff. Index only the first INT bases of the reference sequences (cumulative 
    772. 

  772.                      across sequences) and ignore the rest. [off]
    773. 

  773. 

  774. For aligning (bowtie)::
    775. 

  775. 

  776.   -s INT             Skip. Do not align the first INT reads or pairs in the input. [off]
    777. 

  777.   -u INT             Align limit. Only align the first INT reads/pairs from the input. [no limit]
    778. 

  778.   -5 INT             High-quality trim. Trim INT bases from the high-quality (left) end of each 
    779. 

  779.                      read before alignment. [0]
    780. 

  780.   -3 INT             Low-quality trim. Trim INT bases from the low-quality (right) end of each 
    781. 

  781.                      read before alignment. [0]
    782. 

  782.   -n INT             Mismatch seed. Maximum number of mismatches permitted in the seed (defined 
    783. 

  783.                      with seed length option). Can be 0, 1, 2, or 3. [2]
    784. 

  784.   -e INT             Mismatch quality. Maximum permitted total of quality values at mismatched 
    785. 

  785.                      read positions. Bowtie rounds quality values to the nearest 10 and saturates 
    786. 

  786.                      at 30. [70]
    787. 

  787.   -l INT             Seed length. The number of bases on the high-quality end of the read to 
    788. 

  788.                      which the -n ceiling applies. Must be at least 5. [28]
    789. 

  789.   --nomaqround       Suppress MAQ rounding. Values are internally rounded to the nearest 10 and 
    790. 

  790.                      saturate at 30. This options turns off that rounding. [off] 
    791. 

  791.   -v INT             MAQ- or SOAP-like alignment policy. This option turns off the default 
    792. 

  792.                      MAQ-like alignment policy in favor of a SOAP-like one. End-to-end alignments 
    793. 

  793.                      with at most INT mismatches. [off]
    794. 

  794.   -I INT             Minimum insert. The minimum insert size for valid paired-end alignments. 
    795. 

  795.                      Does checking on untrimmed reads if -5 or -3 is used. [0]
    796. 

  796.   -X INT             Maximum insert. The maximum insert size for valid paired-end alignments. 
    797. 

  797.                      Does checking on untrimmed reads if -5 or -3 is used. [250]
    798. 

  798.   --fr               Mate orientation. The upstream/downstream mate orientations for a valid 
    799. 

  799.                      paired-end alignment against the forward reference strand. [--fr]
    800. 

  800.   --rf               Mate orientation. [off]
    801. 

  801.   --ff               Mate orientation. [off]
    802. 

  802.   --pairtries INT    Maximum alignment attempts for paired-end data. [100] 
    803. 

  803.   --nofw             No forward aligning. Choosing this option means that Bowtie will not attempt 
    804. 

  804.                      to align against the forward reference strand. [off]
    805. 

  805.   --norc             No reverse-complement aligning. Setting this will mean that Bowtie will not 
    806. 

  806.                      attempt to align against the reverse-complement reference strand. [off]
    807. 

  807.   --un FILENAME      Write all reads that could not be aligned to file [off]
    808. 

  808.   --max FILENAME     Write all reads with a number of valid alignments exceeding the limit
    809. 

  809.                      set with the -m option to file [off]
    810. 

  810.   --maxbts INT       Maximum backtracks. The maximum number of backtracks permitted when aligning 
    811. 

  811.                      a read in -n 2 or -n 3 mode. [125 without --best] [800 with --best]
    812. 

  812.   -y                 Try hard. Try as hard as possible to find valid alignments when they exist, 
    813. 

  813.                      including paired-end alignments. [off]
    814. 

  814.   --chunkmbs INT     Thread memory. The number of megabytes of memory a given thread is given to 
    815. 

  815.                      store path descriptors in --best mode. [32]
    816. 

  816.   -k INT             Valid alignments. The number of valid alignments per read or pair. [off] 
    817. 

  817.   -a                 All valid alignments. Choosing this means that all valid alignments per read 
    818. 

  818.                      or pair will be reported. [off]
    819. 

  819.   -m INT             Suppress alignments. Suppress all alignments for a particular read or pair 
    820. 

  820.                      if more than INT reportable alignments exist for it. [no limit]
    821. 

  821.   --best             Best mode. Make Bowtie guarantee that reported singleton alignments are 
    822. 

  822.                      "best" in terms of stratum (the number of mismatches) and quality values at 
    823. 

  823.                      mismatched position. [off]
    824. 

  824.   --strata           Best strata. When running in best mode, report alignments that fall into the 
    825. 

  825.                      best stratum if there are ones falling into more than one. [off]
    826. 

  826.   -o INT             Offrate override. Override the offrate of the index with INT. Some row 
    827. 

  827.                      markings are discarded when index read into memory. INT must be greater than 
    828. 

  828.                      the value used to build the index (default: 5). [off]
    829. 

  829.   --seed INT         Random seed. Use INT as the seed for the pseudo-random number generator. [off]
    830. 

  830.   --snpphred INT     Use INT as the SNP penalty for decoding colorspace alignments. True ratio of 
    831. 

  831.                      SNPs per base in the subject genome. [see --snpfrac]
    832. 

  832.   --snpfrac DEC      Use DEC as the estimated ratio of SNPs per base when decoding colorspace 
    833. 

  833.                      alignments. [0.001]
    834. 

  834.   --col-keepends     Keep the extreme-end nucleotides and qualities when decoding colorspace 
    835. 

  835.                      alignments. [off]
    836. 

  836. 

  837.   </help>
    838. 

  838. </tool>
    839. 

  839.