Mercurial > repos > devteam > bowtie_wrappers

annotate bowtie_wrapper.xml @ 0:4926b3e1e2fe draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
author devteam
date Mon, 09 Nov 2015 11:18:30 -0500
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children 867a8c8e870e
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4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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1 <tool id="bowtie_wrapper" name="Map with Bowtie for Illumina" version="1.1.3">
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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2 <requirements>
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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3 <requirement type="package" version="0.12.7">bowtie</requirement>
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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4 </requirements>
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5 <description></description>
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6 <version_command>bowtie --version</version_command>
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7 <command interpreter="python">
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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8 bowtie_wrapper.py
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9 ## Set number of threads
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10 --threads="\${GALAXY_SLOTS:-4}"
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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11 ## Outputs
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12 --output="${output}"
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13 #if str( $singlePaired.sPaired ) == "single"
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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14 #if $output_unmapped_reads_l
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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15 --output_unmapped_reads="${output_unmapped_reads_l}"
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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16 #end if
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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17 #if $output_suppressed_reads_l
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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18 --output_suppressed_reads="${output_suppressed_reads_l}"
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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19 #end if
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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20 --galaxy_input_format="${singlePaired.sInput1.ext}"
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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21 #else
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22 #if $output_unmapped_reads_l and $output_unmapped_reads_r
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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23 --output_unmapped_reads_l="${output_unmapped_reads_l}"
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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24 --output_unmapped_reads_r="${output_unmapped_reads_r}"
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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25 #end if
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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26 #if $output_suppressed_reads_l and $output_suppressed_reads_l
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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27 --output_suppressed_reads_l="${output_suppressed_reads_l}"
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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28 --output_suppressed_reads_r="${output_suppressed_reads_r}"
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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29 #end if
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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30 --galaxy_input_format="${singlePaired.pInput1.ext}"
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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31 #end if
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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32 ## Inputs
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33 --dataType="solexa" ##this indicates that nucleotide base space is used in the wrapper
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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34 --suppressHeader="${suppressHeader}"
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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35 --genomeSource="${refGenomeSource.genomeSource}"
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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36 #if $refGenomeSource.genomeSource == "history":
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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37 ##index already exists
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38 #if $refGenomeSource.ownFile.extension.startswith( 'bowtie_' ):
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39 ##user previously built
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40 --ref="${refGenomeSource.ownFile.extra_files_path}/${refGenomeSource.ownFile.metadata.base_name}"
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41 --do_not_build_index
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42 #else:
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43 ##build index on the fly
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44 --ref="${refGenomeSource.ownFile}"
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45 --indexSettings="${refGenomeSource.indexParams.indexSettings}"
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46 #if $refGenomeSource.indexParams.indexSettings == "indexFull":
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47 --iautoB="${refGenomeSource.indexParams.autoBehavior.autoB}"
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48 #if $refGenomeSource.indexParams.autoBehavior.autoB == "set":
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49 --ipacked="${refGenomeSource.indexParams.autoBehavior.packed}"
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50 --ibmax="${refGenomeSource.indexParams.autoBehavior.bmax}"
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51 --ibmaxdivn="${refGenomeSource.indexParams.autoBehavior.bmaxdivn}"
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52 --idcv="${refGenomeSource.indexParams.autoBehavior.dcv}"
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53 #end if
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54 --inodc="${refGenomeSource.indexParams.nodc}"
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55 --inoref="${refGenomeSource.indexParams.noref}"
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56 --ioffrate="${refGenomeSource.indexParams.offrate}"
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57 --iftab="${refGenomeSource.indexParams.ftab}"
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58 --intoa="${refGenomeSource.indexParams.ntoa}"
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59 --iendian="${refGenomeSource.indexParams.endian}"
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60 --iseed="${refGenomeSource.indexParams.seed}"
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61 #end if
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62 #end if
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63 #else
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64 ##use pre-built index
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65 --ref="${refGenomeSource.index.fields.path}"
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66 #end if
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67 --paired="${singlePaired.sPaired}"
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68 #if $singlePaired.sPaired == "single":
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69 --input1="${singlePaired.sInput1}"
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70 --params="${singlePaired.sParams.sSettingsType}"
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71 #if $singlePaired.sParams.sSettingsType == "full":
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72 --skip="${singlePaired.sParams.sSkip}"
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73 --alignLimit="${singlePaired.sParams.sAlignLimit}"
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74 --trimH="${singlePaired.sParams.sTrimH}"
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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75 --trimL="${singlePaired.sParams.sTrimL}"
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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76 #if $singlePaired.sParams.alignModeOption.alignMode == 'nMode'
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77 --mismatchSeed="${singlePaired.sParams.alignModeOption.sMismatchSeed}"
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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78 --mismatchQual="${singlePaired.sParams.alignModeOption.sMismatchQual}"
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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79 --seedLen="${singlePaired.sParams.alignModeOption.sSeedLen}"
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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80 --rounding="${singlePaired.sParams.alignModeOption.sRounding}"
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81 #else
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82 --maxMismatches="${singlePaired.sParams.alignModeOption.maxMismatches}"
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83 #end if
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84 --forwardAlign="${singlePaired.sParams.sForwardAlign}"
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85 --reverseAlign="${singlePaired.sParams.sReverseAlign}"
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86 --tryHard="${singlePaired.sParams.sBestOption.sTryHardOption.sTryHard}"
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87 --allValAligns="${singlePaired.sParams.sAllValAlignsOption.sAllValAligns}"
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88 #if $singlePaired.sParams.sAllValAlignsOption.sAllValAligns == "noAllValAligns"
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89 --valAlign="${singlePaired.sParams.sAllValAlignsOption.sValAlign}"
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90 #end if
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91 --suppressAlign="${singlePaired.sParams.sSuppressAlign}"
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92 --best="${singlePaired.sParams.sBestOption.sBest}"
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93 #if $singlePaired.sParams.sBestOption.sBest == "doBest":
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94 --strata="${singlePaired.sParams.sBestOption.sdStrata}"
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95 #if $singlePaired.sParams.sBestOption.sTryHardOption.sTryHard == "noTryHard"
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96 --maxBacktracks="${singlePaired.sParams.sBestOption.sTryHardOption.sdMaxBacktracks}"
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97 #end if
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98 #else:
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99 #if $singlePaired.sParams.sBestOption.sTryHardOption.sTryHard == "noTryHard"
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100 --maxBacktracks="${singlePaired.sParams.sBestOption.sTryHardOption.snMaxBacktracks}"
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101 #end if
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102 #end if
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103 --offrate="${singlePaired.sParams.sOffrate}"
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104 --seed="${singlePaired.sParams.sSeed}"
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105 #end if
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106 #else:
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107 --input1="${singlePaired.pInput1}"
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108 --input2="${singlePaired.pInput2}"
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109 --maxInsert="${singlePaired.pMaxInsert}"
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110 --mateOrient="${singlePaired.pMateOrient}"
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111 --params="${singlePaired.pParams.pSettingsType}"
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112 #if $singlePaired.pParams.pSettingsType == "full":
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113 --skip="${singlePaired.pParams.pSkip}"
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114 --alignLimit="${singlePaired.pParams.pAlignLimit}"
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115 --trimH="${singlePaired.pParams.pTrimH}"
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116 --trimL="${singlePaired.pParams.pTrimL}"
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117 #if $singlePaired.pParams.alignModeOption.alignMode == 'nMode'
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118 --mismatchSeed="${singlePaired.pParams.alignModeOption.pMismatchSeed}"
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119 --mismatchQual="${singlePaired.pParams.alignModeOption.pMismatchQual}"
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120 --seedLen="${singlePaired.pParams.alignModeOption.pSeedLen}"
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121 --rounding="${singlePaired.pParams.alignModeOption.pRounding}"
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122 #else
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123 --maxMismatches="${singlePaired.pParams.alignModeOption.maxMismatches}"
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124 #end if
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125 --minInsert="${singlePaired.pParams.pMinInsert}"
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126 --forwardAlign="${singlePaired.pParams.pForwardAlign}"
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127 --reverseAlign="${singlePaired.pParams.pReverseAlign}"
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128 --tryHard="${singlePaired.pParams.pBestOption.pTryHardOption.pTryHard}"
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129 --allValAligns="${singlePaired.pParams.pAllValAlignsOption.pAllValAligns}"
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130 #if $singlePaired.pParams.pAllValAlignsOption.pAllValAligns == "noAllValAligns"
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131 --valAlign="${singlePaired.pParams.pAllValAlignsOption.pValAlign}"
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132 #end if
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133 --suppressAlign="${singlePaired.pParams.pSuppressAlign}"
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134 --best="${singlePaired.pParams.pBestOption.pBest}"
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135 #if $singlePaired.pParams.pBestOption.pBest == "doBest":
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136 --strata="${singlePaired.pParams.pBestOption.pdStrata}"
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137 #if $singlePaired.pParams.pBestOption.pTryHardOption.pTryHard == "noTryHard"
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138 --maxAlignAttempt="${singlePaired.pParams.pBestOption.pTryHardOption.pMaxAlignAttempt}"
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139 --maxBacktracks="${singlePaired.pParams.pBestOption.pTryHardOption.pdMaxBacktracks}"
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140 #end if
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141 #else:
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142 #if $singlePaired.pParams.pBestOption.pTryHardOption.pTryHard == "noTryHard"
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143 --maxAlignAttempt="${singlePaired.pParams.pBestOption.pTryHardOption.pMaxAlignAttempt}"
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144 --maxBacktracks="${singlePaired.pParams.pBestOption.pTryHardOption.pnMaxBacktracks}"
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145 #end if
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146 #end if
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147 --offrate="${singlePaired.pParams.pOffrate}"
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148 --seed="${singlePaired.pParams.pSeed}"
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149 #end if
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150 #end if
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151 </command>
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152 <inputs>
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153 <conditional name="refGenomeSource">
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154 <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">
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155 <option value="indexed">Use a built-in index</option>
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156 <option value="history">Use one from the history</option>
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157 </param>
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158 <when value="indexed">
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159 <param name="index" type="select" label="Select a reference genome" help="if your genome of interest is not listed - contact Galaxy team">
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160 <options from_data_table="bowtie_indexes">
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161 <filter type="sort_by" column="2" />
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162 <validator type="no_options" message="No indexes are available" />
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163 </options>
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164 </param>
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165 </when>
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166 <when value="history">
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167 <param name="ownFile" type="data" format="bowtie_base_index,fasta" metadata_name="dbkey" label="Select the reference genome" />
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168 <conditional name="indexParams">
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169 <param name="indexSettings" type="select" label="Choose whether to use Default options for building indices or to Set your own" help="These settings are ignored when using a prebuilt index">
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170 <option value="indexPreSet">Default</option>
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171 <option value="indexFull">Set your own</option>
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172 </param>
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173 <when value="indexPreSet" />
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174 <when value="indexFull">
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175 <conditional name="autoBehavior">
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176 <param name="autoB" type="select" label="Choose to use automatic or specified behavior for some parameters (-a)" help="Allows you to set --packed, --bmax, --bmaxdivn, and --dcv">
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177 <option value="auto">Automatic behavior</option>
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178 <option value="set">Set values (sets --noauto and allows others to be set)</option>
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179 </param>
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180 <when value="auto" />
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181 <when value="set">
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182 <param name="packed" type="select" label="Whether or not to use a packed representation for DNA strings (--packed)" help="Packed representation saves memory but makes indexing 2-3 times slower">
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183 <option value="unpacked">Use regular representation</option>
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184 <option value="packed">Use packed representation</option>
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185 </param>
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186 <param name="bmax" type="integer" value="-1" label="Maximum number of suffixes allowed in a block (--bmax)" help="-1 for not specified. Must be at least 1" />
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187 <param name="bmaxdivn" type="integer" value="4" label="Maximum number of suffixes allowed in a block as a fraction of the length of the reference (--bmaxdivn)" />
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188 <param name="dcv" type="integer" value="1024" min="3" label="The period for the difference-cover sample (--dcv)" help="A larger period yields less memory overhead, but may make suffix sorting slower, especially if repeats are present" />
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189 </when>
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190 </conditional>
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191 <param name="nodc" type="select" label="Whether or not to disable the use of the difference-cover sample (--nodc)" help="Suffix sorting becomes quadratic-time in the worst case (with a very repetitive reference)">
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192 <option value="dc">Use difference-cover sample</option>
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193 <option value="nodc">Disable difference-cover sample</option>
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194 </param>
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195 <param name="noref" type="select" label="Whether or not to build the part of the reference index used only in paired-end alignment (-r)">
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196 <option value="ref">Build all index files</option>
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197 <option value="noref">Do not build paired-end alignment index files</option>
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198 </param>
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199 <param name="offrate" type="integer" value="5" min="0" label="The indexer will mark every 2^n Burrows-Wheeler rows with their corresponding location on the genome (-o)" help="Marking more rows makes reference-position lookups faster, but requires more memory to hold the annotations at runtime" />
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200 <param name="ftab" type="integer" value="10" min="1" label="The size of the ftab lookup table used to calculate an initial Burrows-Wheeler range with respect to the first n characters of the query (-t)" help="ftab size is 4^(n+1) bytes" />
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201 <param name="ntoa" type="select" label="Whether or not to convert Ns in the reference sequence to As (--ntoa)">
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202 <option value="no">Do not convert Ns</option>
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203 <option value="yes">Convert Ns to As</option>
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204 </param>
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205 <param name="endian" type="select" label="Endianness to use when serializing integers to the index file (--big/--little)" help="Little is most appropriate for Intel- and AMD-based architecture">
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206 <option value="little">Little</option>
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207 <option value="big">Big</option>
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208 </param>
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209 <param name="seed" type="integer" value="-1" label="Seed for the pseudorandom number generator (--seed)" help="Use -1 to use default" />
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210 </when> <!-- indexFull -->
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211 </conditional> <!-- indexParams -->
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212 </when> <!-- history -->
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213 </conditional> <!-- refGenomeSource -->
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214 <conditional name="singlePaired">
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215 <param name="sPaired" type="select" label="Is this library mate-paired?">
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216 <option value="single">Single-end</option>
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217 <option value="paired">Paired-end</option>
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218 </param>
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219 <when value="single">
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220 <param name="sInput1" type="data" format="fastqsanger,fastqillumina,fastqsolexa" label="FASTQ file" help="Must have ASCII encoded quality scores"/>
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221 <conditional name="sParams">
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222 <param name="sSettingsType" type="select" label="Bowtie settings to use" help="For most mapping needs use Commonly used settings. If you want full control use Full parameter list">
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223 <option value="preSet">Commonly used</option>
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224 <option value="full">Full parameter list</option>
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225 </param>
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226 <when value="preSet" />
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227 <when value="full">
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228 <param name="sSkip" type="integer" value="0" label="Skip the first n reads (-s)" />
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229 <param name="sAlignLimit" type="integer" value="-1" label="Only align the first n reads (-u)" help="-1 for off" />
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230 <param name="sTrimH" type="integer" value="0" label="Trim n bases from high-quality (left) end of each read before alignment (-5)" />
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231 <param name="sTrimL" type="integer" value="0" label="Trim n bases from low-quality (right) end of each read before alignment (-3)" />
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232 <conditional name="alignModeOption">
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233 <param name="alignMode" type="select" label="Alignment mode">
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234 <option value="nMode">Maq-like: quality-aware, limit mismatches in seed (-n)</option>
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235 <option value="vMode">ignore qualities, limit end-to-end mismatches (-v)</option>
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236 </param>
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237 <when value="nMode">
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238 <param name="sMismatchSeed" type="integer" value="2" min="0" max="3" label="Maximum number of mismatches permitted in the seed (-n)" help="May be 0, 1, 2, or 3" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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239 <param name="sMismatchQual" type="integer" value="70" min="1" label="Maximum permitted total of quality values at all mismatched read positions (-e)" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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240 <param name="sSeedLen" type="integer" value="28" min="5" label="Seed length (-l)" help="Minimum value is 5" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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241 <param name="sRounding" type="select" label="Whether or not to round to the nearest 10 and saturating at 30 (--nomaqround)" help="Maq accepts quality values in the Phred quality scale, but internally rounds values to the nearest 10, with a maximum of 30. By default, bowtie also rounds this way">
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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242 <option value="round">Round to nearest 10</option>
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243 <option value="noRound">Do not round to nearest 10</option>
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244 </param>
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245 </when>
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246 <when value="vMode">
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247 <param name="maxMismatches" type="integer" value="" min="0" max="3" label="Maximum number of mismatches (-v)" help="May be 0, 1, 2, or 3" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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248 </when>
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249 </conditional>
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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250 <param name="sForwardAlign" type="select" label="Choose whether or not to attempt to align against the forward reference strand (--nofw)">
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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251 <option value="forward">Align against the forward reference strand</option>
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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252 <option value="noForward">Do not align against the forward reference strand</option>
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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253 </param>
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254 <param name="sReverseAlign" type="select" label="Choose whether or not to attempt to align against the reverse-complement reference strand (--norc)">
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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255 <option value="reverse">Align against the reverse-complement reference strand</option>
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256 <option value="noReverse">Do not align against the reverse-complement reference strand</option>
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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257 </param>
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258 <conditional name="sBestOption">
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259 <param name="sBest" type="select" label="Whether or not to make Bowtie guarantee that reported singleton alignments are 'best' in terms of stratum and in terms of the quality values at the mismatched positions (--best)" help="Removes all strand bias. Only affects which alignments are reported by Bowtie. Runs slower with best option">
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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260 <option value="noBest">Do not use best</option>
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261 <option value="doBest">Use best</option>
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262 </param>
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263 <when value="noBest">
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264 <conditional name="sTryHardOption">
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265 <param name="sTryHard" type="select" label="Whether or not to try as hard as possible to find valid alignments when they exist (-y)" help="Tryhard mode is much slower than regular mode">
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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266 <option value="noTryHard">Do not try hard</option>
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267 <option value="doTryHard">Try hard</option>
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268 </param>
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269 <when value="noTryHard">
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270 <param name="snMaxBacktracks" type="integer" value="125" min="0" label="Maximum number of backtracks permitted when aligning a read (--maxbts)" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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271 </when>
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272 <when value="doTryHard" />
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273 </conditional>
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274 </when>
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275 <when value="doBest">
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276 <param name="sdStrata" type="select" label="Whether or not to report only those alignments that fall in the best stratum if many valid alignments exist and are reportable (--strata)">
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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277 <option value="noStrata">Do not use strata option</option>
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278 <option value="doStrata">Use strata option</option>
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279 </param>
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280 <conditional name="sTryHardOption">
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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281 <param name="sTryHard" type="select" label="Whether or not to try as hard as possible to find valid alignments when they exist (-y)" help="Tryhard mode is much slower than regular mode">
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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282 <option value="noTryHard">Do not try hard</option>
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283 <option value="doTryHard">Try hard</option>
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284 </param>
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285 <when value="noTryHard">
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286 <param name="sdMaxBacktracks" type="integer" value="800" min="0" label="Maximum number of backtracks permitted when aligning a read (--maxbts)" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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287 </when>
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288 <when value="doTryHard" />
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289 </conditional>
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290 </when>
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291 </conditional> <!-- bestOption -->
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292 <conditional name="sAllValAlignsOption">
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293 <param name="sAllValAligns" type="select" label="Whether or not to report all valid alignments per read (-a)">
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294 <option value="noAllValAligns">Do not report all valid alignments</option>
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295 <option value="doAllValAligns">Report all valid alignments</option>
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296 </param>
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297 <when value="noAllValAligns">
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298 <param name="sValAlign" type="integer" value="1" min="1" label="Report up to n valid alignments per read (-k)" />
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299 </when>
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300 <when value="doAllValAligns" />
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301 </conditional>
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302 <param name="sSuppressAlign" type="integer" value="-1" label="Suppress all alignments for a read if more than n reportable alignments exist (-m)" help="-1 for no limit" />
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303 <param name="sMaxFile" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write all reads with a number of valid alignments exceeding the limit set with the -m option to a file (--max)" />
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304 <param name="sUnmappedFile" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write all reads that could not be aligned to a file (--un)" />
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305 <param name="sOffrate" type="integer" value="-1" label="Override the offrate of the index to n (-o)" help="-1 for default" />
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306 <param name="sSeed" type="integer" value="-1" label="Seed for pseudo-random number generator (--seed)" help="-1 for default" />
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307 </when> <!-- full -->
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308 </conditional> <!-- sParams -->
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309 </when> <!-- single -->
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310 <when value="paired">
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311 <param name="pInput1" type="data" format="fastqsanger,fastqillumina,fastqsolexa" label="Forward FASTQ file" help="Must have ASCII encoded quality scores"/>
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312 <param name="pInput2" type="data" format="fastqsanger,fastqillumina,fastqsolexa" label="Reverse FASTQ file" help="File format must match the Forward FASTQ file">
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313 <options options_filter_attribute="ext" from_parameter="tool.app.datatypes_registry.datatypes_by_extension" transform_lines="obj.keys()">>
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314 <column name="name" index="0"/>
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315 <column name="value" index="0"/>
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316 <filter type="param_value" ref="pInput1" ref_attribute="ext" column="0"/>
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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317 </options>
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318 </param>
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319 <param name="pMaxInsert" type="integer" value="1000" label="Maximum insert size for valid paired-end alignments (-X)" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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320 <param name="pMateOrient" type="select" label="The upstream/downstream mate orientation for valid paired-end alignment against the forward reference strand (--fr/--rf/--ff)">
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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321 <option value="fr">FR (for Illumina)</option>
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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322 <option value="rf">RF</option>
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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323 <option value="ff">FF (for SOLiD)</option>
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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324 </param>
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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325 <conditional name="pParams">
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326 <param name="pSettingsType" type="select" label="Bowtie settings to use" help="For most mapping needs use Commonly used settings. If you want full control use Full parameter list">
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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327 <option value="preSet">Commonly used</option>
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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328 <option value="full">Full parameter list</option>
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329 </param>
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330 <when value="preSet" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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331 <when value="full">
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332 <param name="pSkip" type="integer" value="0" label="Skip the first n pairs (-s)" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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333 <param name="pAlignLimit" type="integer" value="-1" label="Only align the first n pairs (-u)" help="-1 for off" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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334 <param name="pTrimH" type="integer" value="0" label="Trim n bases from high-quality (left) end of each read before alignment (-5)" />
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335 <param name="pTrimL" type="integer" value="0" label="Trim n bases from low-quality (right) end of each read before alignment (-3)" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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336 <conditional name="alignModeOption">
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337 <param name="alignMode" type="select" label="Alignment mode">
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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338 <option value="nMode">Maq-like: quality-aware, limit mismatches in seed (-n)</option>
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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339 <option value="vMode">ignore qualities, limit end-to-end mismatches (-v)</option>
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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340 </param>
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341 <when value="nMode">
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342 <param name="pMismatchSeed" type="integer" value="2" min="0" max="3" label="Maximum number of mismatches permitted in the seed (-n)" help="May be 0, 1, 2, or 3" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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343 <param name="pMismatchQual" type="integer" value="70" min="1" label="Maximum permitted total of quality values at all mismatched read positions (-e)" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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344 <param name="pSeedLen" type="integer" value="28" min="5" label="Seed length (-l)" help="Minimum value is 5" />
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345 <param name="pRounding" type="select" label="Whether or not to round to the nearest 10 and saturating at 30 (--nomaqround)" help="Maq accepts quality values in the Phred quality scale, but internally rounds values to the nearest 10, with a maximum of 30. By default, bowtie also rounds this way">
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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346 <option value="round">Round to nearest 10</option>
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347 <option value="noRound">Do not round to nearest 10</option>
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348 </param>
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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349 </when>
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350 <when value="vMode">
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351 <param name="maxMismatches" type="integer" value="" min="0" max="3" label="Maximum number of mismatches (-v)" help="May be 0, 1, 2, or 3" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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352 </when>
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353 </conditional>
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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354 <param name="pMinInsert" type="integer" value="0" label="Minimum insert size for valid paired-end alignments (-I)" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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355 <param name="pForwardAlign" type="select" label="Choose whether or not to attempt to align against the forward reference strand (--nofw)">
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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356 <option value="forward">Align against the forward reference strand</option>
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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357 <option value="noForward">Do not align against the forward reference strand</option>
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358 </param>
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359 <param name="pReverseAlign" type="select" label="Choose whether or not to attempt to align against the reverse-complement reference strand (--norc)">
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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360 <option value="reverse">Align against the reverse-complement reference strand</option>
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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361 <option value="noReverse">Do not align against the reverse-complement reference strand</option>
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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362 </param>
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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363 <conditional name="pBestOption">
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364 <param name="pBest" type="select" label="Whether or not to make Bowtie guarantee that reported singleton alignments are 'best' in terms of stratum and in terms of the quality values at the mismatched positions (--best)" help="Removes all strand bias. Only affects which alignments are reported by Bowtie. Runs slower with best option">
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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365 <option value="noBest">Do not use best</option>
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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366 <option value="doBest">Use best</option>
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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367 </param>
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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368 <when value="noBest">
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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369 <conditional name="pTryHardOption">
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370 <param name="pTryHard" type="select" label="Whether or not to try as hard as possible to find valid alignments when they exist (-y)" help="Tryhard mode is much slower than regular mode">
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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371 <option value="noTryHard">Do not try hard</option>
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372 <option value="doTryHard">Try hard</option>
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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373 </param>
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374 <when value="noTryHard">
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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375 <param name="pMaxAlignAttempt" type="integer" value="100" min="1" label="Maximum number of attempts Bowtie will make to match an alignment for one mate with an alignment for the opposite mate (--pairtries)" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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376 <param name="pnMaxBacktracks" type="integer" value="125" min="0" label="Maximum number of backtracks permitted when aligning a read (--maxbts)" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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377 </when>
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378 <when value="doTryHard" />
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379 </conditional>
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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380 </when>
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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381 <when value="doBest">
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382 <param name="pdStrata" type="select" label="Whether or not to report only those alignments that fall in the best stratum if many valid alignments exist and are reportable (--strata)">
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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383 <option value="noStrata">Do not use strata option</option>
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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384 <option value="doStrata">Use strata option</option>
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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385 </param>
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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386 <conditional name="pTryHardOption">
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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387 <param name="pTryHard" type="select" label="Whether or not to try as hard as possible to find valid alignments when they exist (-y)" help="Tryhard mode is much slower than regular mode">
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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388 <option value="noTryHard">Do not try hard</option>
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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389 <option value="doTryHard">Try hard</option>
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parents:
diff changeset
390 </param>
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
391 <when value="noTryHard">
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
392 <param name="pMaxAlignAttempt" type="integer" value="100" min="1" label="Maximum number of attempts Bowtie will make to match an alignment for one mate with an alignment for the opposite mate (--pairtries)" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
393 <param name="pdMaxBacktracks" type="integer" value="800" min="0" label="Maximum number of backtracks permitted when aligning a read (--maxbts)" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
394 </when>
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
395 <when value="doTryHard" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
396 </conditional>
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
397 </when>
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
398 </conditional>
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
399 <conditional name="pAllValAlignsOption">
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
400 <param name="pAllValAligns" type="select" label="Whether or not to report all valid alignments per pair (-a)">
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
401 <option value="noAllValAligns">Do not report all valid alignments</option>
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
402 <option value="doAllValAligns">Report all valid alignments</option>
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
403 </param>
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
404 <when value="noAllValAligns">
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
405 <param name="pValAlign" type="integer" value="1" min="1" label="Report up to n valid alignments per pair (-k)" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
406 </when>
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
407 <when value="doAllValAligns" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
408 </conditional>
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
409 <param name="pSuppressAlign" type="integer" value="-1" label="Suppress all alignments for a pair if more than n reportable alignments exist (-m)" help="-1 for no limit" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
410 <param name="pMaxFile" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write all reads with a number of valid alignments exceeding the limit set with the -m option to a file (--max)" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
411 <param name="pUnmappedFile" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write all reads that could not be aligned to a file (--un)" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
412 <param name="pOffrate" type="integer" value="-1" label="Override the offrate of the index to n (-o)" help="-1 for default" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
413 <param name="pSeed" type="integer" value="-1" label="Seed for pseudo-random number generator (--seed)" help="-1 for default" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
414 </when> <!-- full -->
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
415 </conditional> <!-- pParams -->
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
416 </when> <!-- paired -->
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
417 </conditional> <!-- singlePaired -->
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
418 <param name="suppressHeader" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Suppress the header in the output SAM file (--sam-nohead)" help="Bowtie produces SAM with several lines of header information by default" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
419 </inputs>
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
420 <outputs>
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
421 <data format="sam" name="output" label="${tool.name} on ${on_string}: mapped reads">
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
422 <actions>
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
423 <conditional name="refGenomeSource.genomeSource">
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
424 <when value="indexed">
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
425 <action type="metadata" name="dbkey">
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
426 <option type="from_data_table" name="bowtie_indexes" column="1" offset="0">
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
427 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
428 <filter type="param_value" ref="refGenomeSource.index" column="0"/>
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
429 </option>
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
430 </action>
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
431 </when>
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
432 <when value="history">
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
433 <action type="metadata" name="dbkey">
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
434 <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
435 </action>
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
436 </when>
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
437 </conditional>
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
438 </actions>
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
439 </data>
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
440 <data format="fastq" name="output_suppressed_reads_l" label="${tool.name} on ${on_string}: suppressed reads (L)">
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
441 <filter>((
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
442 singlePaired['sPaired'] == "single" and
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
443 singlePaired['sParams']['sSettingsType'] == "full" and
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
444 singlePaired['sParams']['sMaxFile'] is True
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
445 ) or (
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
446 singlePaired['sPaired'] == "paired" and
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
447 singlePaired['pParams']['pSettingsType'] == "full" and
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
448 singlePaired['pParams']['pMaxFile'] is True
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
449 ))
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
450 </filter>
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
451 <actions>
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
452 <conditional name="singlePaired.sPaired">
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
453 <when value="single">
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
454 <action type="format">
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
455 <option type="from_param" name="singlePaired.sInput1" param_attribute="ext" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
456 </action>
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
457 </when>
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
458 <when value="paired">
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
459 <action type="format">
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
460 <option type="from_param" name="singlePaired.pInput1" param_attribute="ext" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
461 </action>
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
462 </when>
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
463 </conditional>
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
464 </actions>
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
465 </data>
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
466 <data format="fastq" name="output_suppressed_reads_r" label="${tool.name} on ${on_string}: suppressed reads (R)">
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
467 <filter>singlePaired['sPaired'] == "paired"</filter>
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
468 <filter>singlePaired['pParams']['pSettingsType'] == "full"</filter>
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
469 <filter>singlePaired['pParams']['pMaxFile'] is True</filter>
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
470 <actions>
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
471 <conditional name="singlePaired.sPaired">
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
472 <when value="single">
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
473 <action type="format">
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
474 <option type="from_param" name="singlePaired.sInput1" param_attribute="ext" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
475 </action>
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
476 </when>
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
477 <when value="paired">
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
478 <action type="format">
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
479 <option type="from_param" name="singlePaired.pInput1" param_attribute="ext" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
480 </action>
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
481 </when>
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
482 </conditional>
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
483 </actions>
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
484 </data>
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
485 <data format="fastq" name="output_unmapped_reads_l" label="${tool.name} on ${on_string}: unmapped reads (L)">
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
486 <filter>
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
487 ((
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
488 singlePaired['sPaired'] == "single" and
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
489 singlePaired['sParams']['sSettingsType'] == "full" and
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
490 singlePaired['sParams']['sUnmappedFile'] is True
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
491 ) or (
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
492 singlePaired['sPaired'] == "paired" and
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
493 singlePaired['pParams']['pSettingsType'] == "full" and
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
494 singlePaired['pParams']['pUnmappedFile'] is True
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
495 ))
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
496 </filter>
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
497 <actions>
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
498 <conditional name="singlePaired.sPaired">
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
499 <when value="single">
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
500 <action type="format">
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
501 <option type="from_param" name="singlePaired.sInput1" param_attribute="ext" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
502 </action>
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
503 </when>
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
504 <when value="paired">
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
505 <action type="format">
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
506 <option type="from_param" name="singlePaired.pInput1" param_attribute="ext" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
507 </action>
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
508 </when>
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
509 </conditional>
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
510 </actions>
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
511 </data>
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
512 <data format="fastq" name="output_unmapped_reads_r" label="${tool.name} on ${on_string}: unmapped reads (R)">
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
513 <filter>singlePaired['sPaired'] == "paired"</filter>
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
514 <filter>singlePaired['pParams']['pSettingsType'] == "full"</filter>
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
515 <filter>singlePaired['pParams']['pUnmappedFile'] is True</filter>
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
516 <actions>
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
517 <conditional name="singlePaired.sPaired">
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
518 <when value="single">
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
519 <action type="format">
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
520 <option type="from_param" name="singlePaired.sInput1" param_attribute="ext" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
521 </action>
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
522 </when>
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
523 <when value="paired">
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
524 <action type="format">
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
525 <option type="from_param" name="singlePaired.pInput1" param_attribute="ext" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
526 </action>
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
527 </when>
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
528 </conditional>
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
529 </actions>
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
530 </data>
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
531 </outputs>
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
532 <tests>
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
533 <test>
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
534 <!--
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
535 Bowtie command:
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
536 bowtie -q -p 4 -S +sam-nohead chrM_base test-data/bowtie_in2.fastqsanger > bowtie_out6_u.sam
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
537 sort bowtie_out6_u.sam > bowtie_out6.sam
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
538 -p is the number of threads. You need to replace the + with 2 dashes.
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
539 chrM_base needs to be the base location/name of the index files.
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
540 -->
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
541 <param name="genomeSource" value="indexed" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
542 <!-- this is the backwards-compatible "unique value" for this index, not an actual path -->
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
543 <param name="index" value="equCab2chrM" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
544 <param name="sPaired" value="single" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
545 <param name="sInput1" ftype="fastqsanger" value="bowtie_in2.fastqsanger" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
546 <param name="sSettingsType" value="preSet" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
547 <param name="suppressHeader" value="true" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
548 <output name="output" ftype="sam" file="bowtie_out6.sam" sort="True" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
549 </test>
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
550 <test>
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
551 <!--
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
552 Bowtie command:
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
553 bowtie-build -f test-data/phiX.fasta phiX_base
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
554 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
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
555 sort bowtie_out7_u.sam > bowtie_out7.sam
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
556 sort bowtie_out8_u_1.sam > bowtie_out8_1.sam
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
557 sort bowtie_out8_u_2.sam > bowtie_out8_2.sam
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
558 Then also need to modify bowtie_out8_1.sam and bowtie_out8_2.sam so that all @ lines come before sequence lines.
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
559 -p is the number of threads. You need to replace the + with 2 dashes.
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
560 The two unmapped output files will be named bowtie_out8_1.fastq and bowtie_out8_2.fastq.
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
561 chrM_base is the index files' location/base name.
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
562 -->
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
563 <param name="genomeSource" value="history" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
564 <param name="ownFile" value="phiX.fasta" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
565 <param name="indexSettings" value="indexPreSet" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
566 <param name="sPaired" value="paired" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
567 <param name="pInput1" ftype="fastqsanger" value="bowtie_in5.fastqsanger" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
568 <param name="pInput2" ftype="fastqsanger" value="bowtie_in6.fastqsanger" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
569 <param name="pMaxInsert" value="1000" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
570 <param name="pMateOrient" value="ff" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
571 <param name="pSettingsType" value="full" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
572 <param name="pSkip" value="0" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
573 <param name="pAlignLimit" value="-1" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
574 <param name="pTrimH" value="0" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
575 <param name="pTrimL" value="0" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
576 <param name="alignMode" value="nMode" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
577 <param name="pMismatchSeed" value="2" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
578 <param name="pMismatchQual" value="70" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
579 <param name="pSeedLen" value="28" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
580 <param name="pRounding" value="round" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
581 <param name="pMinInsert" value="0" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
582 <param name="pMaxAlignAttempt" value="100" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
583 <param name="pForwardAlign" value="forward" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
584 <param name="pReverseAlign" value="reverse" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
585 <param name="pTryHard" value="noTryHard" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
586 <param name="pValAlign" value="1" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
587 <param name="pAllValAligns" value="noAllValAligns" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
588 <param name="pSuppressAlign" value="-1" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
589 <param name="pUnmappedFile" value="true" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
590 <param name="pMaxFile" value="false" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
591 <param name="pBest" value="doBest" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
592 <param name="pdMaxBacktracks" value="800" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
593 <param name="pdStrata" value="noStrata" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
594 <param name="pOffrate" value="-1" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
595 <param name="pSeed" value="-1" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
596 <param name="suppressHeader" value="true" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
597 <output name="output" ftype="sam" file="bowtie_out7.sam" sort="True" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
598 <output name="output_unmapped_reads_l" ftype="fastqsanger" file="bowtie_out8_1.fastq" sort="True" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
599 <output name="output_unmapped_reads_r" ftype="fastqsanger" file="bowtie_out8_2.fastq" sort="True" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
600 </test>
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
601 <!-- start testing of non-sanger variant fastq reads -->
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
602 <test>
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
603 <param name="genomeSource" value="history" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
604 <param name="ownFile" value="phiX.fasta" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
605 <param name="indexSettings" value="indexPreSet" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
606 <param name="sPaired" value="paired" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
607 <param name="pInput1" ftype="fastqillumina" value="bowtie_in5.fastqillumina" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
608 <param name="pInput2" ftype="fastqillumina" value="bowtie_in6.fastqillumina" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
609 <param name="pMaxInsert" value="1000" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
610 <param name="pMateOrient" value="ff" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
611 <param name="pSettingsType" value="full" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
612 <param name="pSkip" value="0" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
613 <param name="pAlignLimit" value="-1" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
614 <param name="pTrimH" value="0" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
615 <param name="pTrimL" value="0" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
616 <param name="alignMode" value="nMode" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
617 <param name="pMismatchSeed" value="2" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
618 <param name="pMismatchQual" value="70" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
619 <param name="pSeedLen" value="28" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
620 <param name="pRounding" value="round" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
621 <param name="pMinInsert" value="0" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
622 <param name="pMaxAlignAttempt" value="100" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
623 <param name="pForwardAlign" value="forward" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
624 <param name="pReverseAlign" value="reverse" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
625 <param name="pTryHard" value="noTryHard" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
626 <param name="pValAlign" value="1" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
627 <param name="pAllValAligns" value="noAllValAligns" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
628 <param name="pSuppressAlign" value="-1" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
629 <param name="pUnmappedFile" value="true" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
630 <param name="pMaxFile" value="false" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
631 <param name="pBest" value="doBest" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
632 <param name="pdMaxBacktracks" value="800" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
633 <param name="pdStrata" value="noStrata" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
634 <param name="pOffrate" value="-1" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
635 <param name="pSeed" value="-1" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
636 <param name="suppressHeader" value="true" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
637 <output name="output" ftype="sam" file="bowtie_out7.sam" sort="True" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
638 <output name="output_unmapped_reads_l" ftype="fastqillumina" file="bowtie_out8_1.fastqillumina.sorted" sort="True" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
639 <output name="output_unmapped_reads_r" ftype="fastqillumina" file="bowtie_out8_2.fastqillumina.sorted" sort="True" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
640 </test>
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
641 <test>
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
642 <param name="genomeSource" value="history" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
643 <param name="ownFile" value="phiX.fasta" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
644 <param name="indexSettings" value="indexPreSet" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
645 <param name="sPaired" value="paired" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
646 <param name="pInput1" ftype="fastqsolexa" value="bowtie_in5.fastqsolexa" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
647 <param name="pInput2" ftype="fastqsolexa" value="bowtie_in6.fastqsolexa" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
648 <param name="pMaxInsert" value="1000" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
649 <param name="pMateOrient" value="ff" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
650 <param name="pSettingsType" value="full" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
651 <param name="pSkip" value="0" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
652 <param name="pAlignLimit" value="-1" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
653 <param name="pTrimH" value="0" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
654 <param name="pTrimL" value="0" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
655 <param name="alignMode" value="nMode" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
656 <param name="pMismatchSeed" value="2" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
657 <param name="pMismatchQual" value="70" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
658 <param name="pSeedLen" value="28" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
659 <param name="pRounding" value="round" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
660 <param name="pMinInsert" value="0" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
661 <param name="pMaxAlignAttempt" value="100" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
662 <param name="pForwardAlign" value="forward" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
663 <param name="pReverseAlign" value="reverse" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
664 <param name="pTryHard" value="noTryHard" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
665 <param name="pValAlign" value="1" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
666 <param name="pAllValAligns" value="noAllValAligns" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
667 <param name="pSuppressAlign" value="-1" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
668 <param name="pUnmappedFile" value="true" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
669 <param name="pMaxFile" value="false" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
670 <param name="pBest" value="doBest" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
671 <param name="pdMaxBacktracks" value="800" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
672 <param name="pdStrata" value="noStrata" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
673 <param name="pOffrate" value="-1" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
674 <param name="pSeed" value="-1" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
675 <param name="suppressHeader" value="true" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
676 <output name="output" ftype="sam" file="bowtie_out7.sam" sort="True" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
677 <output name="output_unmapped_reads_l" ftype="fastqsolexa" file="bowtie_out8_1.fastqsolexa.sorted" sort="True" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
678 <output name="output_unmapped_reads_r" ftype="fastqsolexa" file="bowtie_out8_2.fastqsolexa.sorted" sort="True" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
679 </test>
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
680 <!-- end testing of non-sanger variant fastq reads -->
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
681 <test>
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
682 <!--
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
683 Bowtie command:
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
684 bowtie -q -p 4 -S +sam-nohead -n 2 -e 70 -l 28 -y -k 1 chrM_base test-data/bowtie_in2.fastqsanger > bowtie_out9_u.sam
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
685 sort bowtie_out9_u.sam > bowtie_out9.sam
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
686 -p is the number of threads. You need to replace the + with 2 dashes.
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
687 chrM_base is the index files' location/base name.
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
688 -->
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
689 <param name="genomeSource" value="indexed" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
690 <!-- this is the backwards-compatible "unique value" for this index, not an actual path -->
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
691 <param name="index" value="equCab2chrM" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
692 <param name="sPaired" value="single" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
693 <param name="sInput1" ftype="fastqsanger" value="bowtie_in2.fastqsanger" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
694 <param name="sSettingsType" value="full" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
695 <param name="sSkip" value="0" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
696 <param name="sAlignLimit" value="-1" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
697 <param name="sTrimH" value="0" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
698 <param name="sTrimL" value="0" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
699 <param name="alignMode" value="nMode" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
700 <param name="sMismatchSeed" value="2" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
701 <param name="sMismatchQual" value="70" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
702 <param name="sSeedLen" value="28" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
703 <param name="sRounding" value="round" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
704 <param name="sForwardAlign" value="forward" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
705 <param name="sReverseAlign" value="reverse" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
706 <param name="sTryHard" value="doTryHard" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
707 <param name="sValAlign" value="1" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
708 <param name="sAllValAligns" value="noAllValAligns" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
709 <param name="sSuppressAlign" value="-1" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
710 <param name="sUnmappedFile" value="false" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
711 <param name="sMaxFile" value="false" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
712 <param name="sBest" value="noBest" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
713 <param name="sOffrate" value="-1" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
714 <param name="sSeed" value="-1" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
715 <param name="suppressHeader" value="true" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
716 <output name="output" ftype="sam" file="bowtie_out9.sam" sort="True" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
717 </test>
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
718 <test>
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
719 <!--
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
720 Bowtie command:
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
721 bowtie-build +offrate 5 +ftabchars 10 +little -f test-data/phiX.fasta phiX_base
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
722 bowtie -q -X 1000 +ff -p 4 -S +sam-nohead phiX_base -1 test-data/bowtie_in5.fastqsanger -2 test-data/bowtie_in6.fastqsanger > bowtie_out10_u.sam
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
723 sort bowtie_out10_u.sam > bowtie_out10.sam
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
724 -p is the number of threads. You need to replace the + with 2 dashes.
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
725 chrM_base is the index files' location/base name.
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
726 -->
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
727 <param name="genomeSource" value="history" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
728 <param name="ownFile" value="phiX.fasta" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
729 <param name="indexSettings" value="indexFull" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
730 <param name="autoB" value="auto" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
731 <param name="nodc" value="dc" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
732 <param name="noref" value="ref" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
733 <param name="offrate" value="5" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
734 <param name="ftab" value="10" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
735 <param name="ntoa" value="no" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
736 <param name="endian" value="little" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
737 <param name="seed" value="-1" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
738 <param name="sPaired" value="paired" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
739 <param name="pInput1" ftype="fastqsanger" value="bowtie_in5.fastqsanger" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
740 <param name="pInput2" ftype="fastqsanger" value="bowtie_in6.fastqsanger" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
741 <param name="pMaxInsert" value="1000" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
742 <param name="pMateOrient" value="ff" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
743 <param name="pSettingsType" value="preSet" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
744 <param name="suppressHeader" value="true" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
745 <output name="output" ftype="sam" file="bowtie_out10.sam" sort="True" />
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
746 </test>
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
747 </tests>
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
748
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
749 <help>
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
750
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
751 **What it does**
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
752
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
753 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.
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
754
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
755 .. _Bowtie: http://bowtie-bio.sourceforge.net/index.shtml
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
756
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
757 ------
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
758
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
759 **Know what you are doing**
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
760
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
761 .. class:: warningmark
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
762
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
763 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.
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
764
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
765 .. __: http://bowtie-bio.sourceforge.net/index.shtml
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
766
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
767 ------
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
768
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
769 **Input formats**
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
770
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
771 Bowtie accepts files in Sanger FASTQ format. Use the FASTQ Groomer to prepare your files.
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
772
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
773 ------
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
774
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
775 **A Note on Built-in Reference Genomes**
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
776
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
777 The default variant for all genomes is "Full", defined as all primary chromosomes (or scaffolds/contigs) including mitochondrial plus associated unmapped, plasmid, and other segments. When only one version of a genome is available in this tool, it represents the default "Full" variant. Some genomes will have more than one variant available. The "Canonical Male" or sometimes simply "Canonical" variant contains the primary chromosomes for a genome. For example a human "Canonical" variant contains chr1-chr22, chrX, chrY, and chrM. The "Canonical Female" variant contains the primary chromosomes excluding chrY.
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
778
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
779 ------
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
780
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
781 **Outputs**
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
782
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
783 The output is in SAM format, and has the following columns::
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
784
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
785 Column Description
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
786 -------- --------------------------------------------------------
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
787 1 QNAME Query (pair) NAME
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
788 2 FLAG bitwise FLAG
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
789 3 RNAME Reference sequence NAME
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
790 4 POS 1-based leftmost POSition/coordinate of clipped sequence
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
791 5 MAPQ MAPping Quality (Phred-scaled)
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
792 6 CIGAR extended CIGAR string
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
793 7 MRNM Mate Reference sequence NaMe ('=' if same as RNAME)
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
794 8 MPOS 1-based Mate POSition
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
795 9 ISIZE Inferred insert SIZE
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
796 10 SEQ query SEQuence on the same strand as the reference
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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parents:
diff changeset
797 11 QUAL query QUALity (ASCII-33 gives the Phred base quality)
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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parents:
diff changeset
798 12 OPT variable OPTional fields in the format TAG:VTYPE:VALUE
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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parents:
diff changeset
799
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
800 The flags are as follows::
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
801
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
802 Flag Description
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
803 ------ -------------------------------------
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
804 0x0001 the read is paired in sequencing
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
805 0x0002 the read is mapped in a proper pair
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
806 0x0004 the query sequence itself is unmapped
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
807 0x0008 the mate is unmapped
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
808 0x0010 strand of the query (1 for reverse)
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
809 0x0020 strand of the mate
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
810 0x0040 the read is the first read in a pair
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
811 0x0080 the read is the second read in a pair
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
812 0x0100 the alignment is not primary
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
813
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
814 It looks like this (scroll sideways to see the entire example)::
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
815
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
816 QNAME FLAG RNAME POS MAPQ CIAGR MRNM MPOS ISIZE SEQ QUAL OPT
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
817 HWI-EAS91_1_30788AAXX:1:1:1761:343 4 * 0 0 * * 0 0 AAAAAAANNAAAAAAAAAAAAAAAAAAAAAAAAAAACNNANNGAGTNGNNNNNNNGCTTCCCACAGNNCTGG hhhhhhh;;hhhhhhhhhhh^hOhhhhghhhfhhhgh;;h;;hhhh;h;;;;;;;hhhhhhghhhh;;Phhh
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
818 HWI-EAS91_1_30788AAXX:1:1:1578:331 4 * 0 0 * * 0 0 GTATAGANNAATAAGAAAAAAAAAAATGAAGACTTTCNNANNTCTGNANNNNNNNTCTTTTTTCAGNNGTAG hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhhhh;;h;;hhhh;h;;;;;;;hhhhhhhhhhh;;hhVh
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
819
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
820 -------
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
821
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
822 **Bowtie settings**
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
823
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
824 All of the options have a default value. You can change any of them. Most of the options in Bowtie have been implemented here.
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
825
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
826 ------
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
827
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
828 **Bowtie parameter list**
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
829
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
830 This is an exhaustive list of Bowtie options:
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
831
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
832 For indexing (bowtie-build)::
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
833
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
834 -a No auto behavior. Disable the default behavior where bowtie automatically
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
835 selects values for --bmax/--bmaxdivn/--dcv/--packed parameters according
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
836 to the memory available. [off]
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
837 --packed Packing. Use a packed representation for DNA strings. [auto]
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
838 --bmax INT Suffix maximum. The maximum number of suffixes allowed in a block. [auto]
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
839 --bmaxdivn INT Suffix maximum fraction. The maximum number of suffixes allowed in a block
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
840 expressed as a fraction of the length of the reference. [4]
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
841 --dcv INT Difference-cover sample. Use INT as the period for the difference-cover
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
842 sample. [1024]
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
843 --nodc INT No difference-cover sample. Disable the difference-cover sample. [off]
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
844 -r No reference indexes. Do not build the NAME.3.ebwt and NAME.4.ebwt portions
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
845 of the index. Used only for paired-end alignment. [off]
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
846 -o Offrate. How many Burrows-Wheeler rows get marked by the indexer. The
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
847 indexer will mark every 2^INT rows. The marked rows correspond to rows on
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
848 the genome. [5]
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
849 -t INT The ftab lookup table used to calculate an initial Burrows-Wheeler range
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
850 with respect to the first INT characters of the query. Ftab size is 4^(INT+1)
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
851 bytes. [10]
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
852 --ntoa N conversion. Convert Ns to As before building the index. Otherwise, Ns are
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
853 simply excluded from the index and Bowtie will not find alignments that
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
854 overlap them. [off]
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
855 --big Endianness. Endianness to use when serializing integers to the index file. [off]
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
856 --little Endianness. [--little]
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
857 --seed INT Random seed. Use INT as the seed for the pseudo-random number generator. [off]
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
858
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
859 For aligning (bowtie)::
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
860
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
861 -s INT Skip. Do not align the first INT reads or pairs in the input. [off]
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
862 -u INT Align limit. Only align the first INT reads/pairs from the input. [no limit]
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
863 -5 INT High-quality trim. Trim INT bases from the high-quality (left) end of each
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
864 read before alignment. [0]
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
865 -3 INT Low-quality trim. Trim INT bases from the low-quality (right) end of each
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
866 read before alignment. [0]
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
867 -n INT Mismatch seed. Maximum number of mismatches permitted in the seed (defined
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
868 with seed length option). Can be 0, 1, 2, or 3. [2]
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
869 -e INT Mismatch quality. Maximum permitted total of quality values at mismatched
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
870 read positions. Bowtie rounds quality values to the nearest 10 and saturates
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
871 at 30. [70]
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
872 -l INT Seed length. The number of bases on the high-quality end of the read to
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
873 which the -n ceiling applies. Must be at least 5. [28]
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
874 --nomaqround Suppress Maq rounding. Values are internally rounded to the nearest 10 and
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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875 saturate at 30. This options turns off that rounding. [off]
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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876 -v INT Maq- or SOAP-like alignment policy. This option turns off the default
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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877 Maq-like alignment policy in favor of a SOAP-like one. End-to-end alignments
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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diff changeset
878 with at most INT mismatches. [off]
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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879 -I INT Minimum insert. The minimum insert size for valid paired-end alignments.
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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880 Does checking on untrimmed reads if -5 or -3 is used. [0]
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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881 -X INT Maximum insert. The maximum insert size for valid paired-end alignments.
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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882 Does checking on untrimmed reads if -5 or -3 is used. [250]
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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883 --fr Mate orientation. The upstream/downstream mate orientations for a valid
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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884 paired-end alignment against the forward reference strand. [--fr]
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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diff changeset
885 --rf Mate orientation. [off]
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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886 --ff Mate orientation. [off]
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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887 --pairtries INT Maximum alignment attempts for paired-end data. [100]
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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888 --nofw No forward aligning. Choosing this option means that Bowtie will not attempt
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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diff changeset
889 to align against the forward reference strand. [off]
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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890 --norc No reverse-complement aligning. Setting this will mean that Bowtie will not
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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891 attempt to align against the reverse-complement reference strand. [off]
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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diff changeset
892 --un FILENAME Write all reads that could not be aligned to file [off]
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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893 --max FILENAME Write all reads with a number of valid alignments exceeding the limit
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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894 set with the -m option to file [off]
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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895 --maxbts INT Maximum backtracks. The maximum number of backtracks permitted when aligning
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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diff changeset
896 a read in -n 2 or -n 3 mode. [125 without --best] [800 with --best]
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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897 -y Try hard. Try as hard as possible to find valid alignments when they exist,
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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898 including paired-end alignments. [off]
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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899 --chunkmbs INT Thread memory. The number of megabytes of memory a given thread is given to
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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diff changeset
900 store path descriptors in --best mode. [32]
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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diff changeset
901 -k INT Valid alignments. The number of valid alignments per read or pair. [off]
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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902 -a All valid alignments. Choosing this means that all valid alignments per read
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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903 or pair will be reported. [off]
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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diff changeset
904 -m INT Suppress alignments. Suppress all alignments for a particular read or pair
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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905 if more than INT reportable alignments exist for it. [no limit]
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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906 --best Best mode. Make Bowtie guarantee that reported singleton alignments are
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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diff changeset
907 "best" in terms of stratum (the number of mismatches) and quality values at
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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908 mismatched position. [off]
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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909 --strata Best strata. When running in best mode, report alignments that fall into the
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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910 best stratum if there are ones falling into more than one. [off]
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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911 -o INT Offrate override. Override the offrate of the index with INT. Some row
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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912 markings are discarded when index read into memory. INT must be greater than
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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913 the value used to build the index (default: 5). [off]
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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914 --seed INT Random seed. Use INT as the seed for the pseudo-random number generator. [off]
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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915 --snpphred INT Use INT as the SNP penalty for decoding colorspace alignments. True ratio of
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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916 SNPs per base in the subject genome. [see --snpfrac]
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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diff changeset
917 --snpfrac DEC Use DEC as the estimated ratio of SNPs per base when decoding colorspace
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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918 alignments. [0.001]
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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919 --col-keepends Keep the extreme-end nucleotides and qualities when decoding colorspace
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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920 alignments. [off]
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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921
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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922 </help>
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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923 <citations>
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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924 <citation type="doi">10.1186/gb-2009-10-3-r25</citation>
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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925 </citations>
4926b3e1e2fe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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926 </tool>