annotate bowtie_transcriptome_wrapper/bowtie_transcriptomic_wrapper.xml @ 2:cd79614871c2 draft

index table name has changed absolute path to indexes are added
author triasteran
date Sun, 27 Mar 2022 16:22:48 +0000
parents 14fb4b4872e3
children 14deb381fa27
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cd79614871c2 index table name has changed
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1 <tool id="bowtie_transcriptomic_wrapper" name="Align to transcriptome using Bowtie" version="1.3.0ind">
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jackcurragh
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2 <description></description>
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3 <requirements>
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4 <requirement type="package" version="1.2.0">bowtie</requirement>
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5 </requirements>
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6 <version_command>bowtie --version</version_command>
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7 <command>
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8 python '$__tool_directory__/bowtie_transcriptome_wrapper.py'
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9 ## Set number of threads
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10 --threads="\${GALAXY_SLOTS:-4}"
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11 ## Outputs
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12 --output="${output}"
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13 #if str( $singlePaired.sPaired ) == "single"
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14 #if $output_unmapped_reads_l
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15 --output_unmapped_reads="${output_unmapped_reads_l}"
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16 #end if
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jackcurragh
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17 #if $output_suppressed_reads_l
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18 --output_suppressed_reads="${output_suppressed_reads_l}"
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19 #end if
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20 --galaxy_input_format="${singlePaired.sInput1.ext}"
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jackcurragh
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21 #else
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22 #if $output_unmapped_reads_l and $output_unmapped_reads_r
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23 --output_unmapped_reads_l="${output_unmapped_reads_l}"
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24 --output_unmapped_reads_r="${output_unmapped_reads_r}"
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jackcurragh
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25 #end if
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jackcurragh
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26 #if $output_suppressed_reads_l and $output_suppressed_reads_l
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27 --output_suppressed_reads_l="${output_suppressed_reads_l}"
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28 --output_suppressed_reads_r="${output_suppressed_reads_r}"
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29 #end if
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30 --galaxy_input_format="${singlePaired.pInput1.ext}"
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31 #end if
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jackcurragh
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32 ## Inputs
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33 --dataType="solexa" ##this indicates that nucleotide base space is used in the wrapper
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34 --suppressHeader="${suppressHeader}"
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35 --genomeSource="${refGenomeSource.genomeSource}"
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jackcurragh
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36 #if $refGenomeSource.genomeSource == "history":
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jackcurragh
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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}/${refGenomeSource.ownFile.metadata.base_name}"
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41 --do_not_build_index
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jackcurragh
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42 #else:
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jackcurragh
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43 ##build index on the fly
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44 --ref="${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}"
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75 --trimL="${singlePaired.sParams.sTrimL}"
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jackcurragh
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76 #if $singlePaired.sParams.alignModeOption.alignMode == 'nMode'
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77 --mismatchSeed="${singlePaired.sParams.alignModeOption.sMismatchSeed}"
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78 --mismatchQual="${singlePaired.sParams.alignModeOption.sMismatchQual}"
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79 --seedLen="${singlePaired.sParams.alignModeOption.sSeedLen}"
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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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jackcurragh
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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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jackcurragh
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133 --suppressAlign="${singlePaired.pParams.pSuppressAlign}"
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jackcurragh
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134 --best="${singlePaired.pParams.pBestOption.pBest}"
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jackcurragh
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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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jackcurragh
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140 #end if
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jackcurragh
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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="${singlePaired.pParams.pBestOption.pTryHardOption.pnMaxBacktracks}"
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145 #end if
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jackcurragh
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146 #end if
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jackcurragh
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147 --offrate="${singlePaired.pParams.pOffrate}"
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jackcurragh
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148 --seed="${singlePaired.pParams.pSeed}"
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jackcurragh
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149 #end if
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jackcurragh
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150 #end if
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jackcurragh
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151 #if $save_mapping_stats
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152 --output_mapping_stats="$mapping_stats"
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153 #end if
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154 </command>
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155 <inputs>
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156 <conditional name="refGenomeSource">
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157 <param name="genomeSource" type="select" label="Will you select a reference from your history or use a built-in index?" help="Built-ins were indexed using default options">
0
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158 <option value="indexed">Use a built-in index</option>
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159 <option value="history">Use one from the history</option>
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160 </param>
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jackcurragh
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161 <when value="indexed">
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162 <param name="index" type="select" label="Select a reference" help="if your reference of interest is not listed - contact RiboGalaxy team">
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163 <options from_data_table="bowtie_indexes_transcriptome">
0
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164 <filter type="sort_by" column="2" />
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165 <validator type="no_options" message="No indexes are available" />
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166 </options>
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167 </param>
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168 </when>
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169 <when value="history">
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170 <param name="ownFile" type="data" format="bowtie_base_index,fasta" label="Select the reference" />
0
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171 <conditional name="indexParams">
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172 <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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173 <option value="indexPreSet">Default</option>
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174 <option value="indexFull">Set your own</option>
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175 </param>
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176 <when value="indexPreSet" />
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177 <when value="indexFull">
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178 <conditional name="autoBehavior">
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179 <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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180 <option value="auto">Automatic behavior</option>
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181 <option value="set">Set values (sets --noauto and allows others to be set)</option>
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182 </param>
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jackcurragh
parents:
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183 <when value="auto" />
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jackcurragh
parents:
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184 <when value="set">
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jackcurragh
parents:
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185 <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">
1b109d213a42 Uploaded
jackcurragh
parents:
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186 <option value="unpacked">Use regular representation</option>
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jackcurragh
parents:
diff changeset
187 <option value="packed">Use packed representation</option>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
188 </param>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
189 <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" />
1b109d213a42 Uploaded
jackcurragh
parents:
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190 <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)" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
191 <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" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
192 </when>
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jackcurragh
parents:
diff changeset
193 </conditional>
1b109d213a42 Uploaded
jackcurragh
parents:
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194 <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)">
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
195 <option value="dc">Use difference-cover sample</option>
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jackcurragh
parents:
diff changeset
196 <option value="nodc">Disable difference-cover sample</option>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
197 </param>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
198 <param name="noref" type="select" label="Whether or not to build the part of the reference index used only in paired-end alignment (-r)">
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
199 <option value="ref">Build all index files</option>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
200 <option value="noref">Do not build paired-end alignment index files</option>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
201 </param>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
202 <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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jackcurragh
parents:
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203 <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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jackcurragh
parents:
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204 <param name="ntoa" type="select" label="Whether or not to convert Ns in the reference sequence to As (--ntoa)">
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
205 <option value="no">Do not convert Ns</option>
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jackcurragh
parents:
diff changeset
206 <option value="yes">Convert Ns to As</option>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
207 </param>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
208 <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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jackcurragh
parents:
diff changeset
209 <option value="little">Little</option>
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jackcurragh
parents:
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210 <option value="big">Big</option>
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jackcurragh
parents:
diff changeset
211 </param>
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jackcurragh
parents:
diff changeset
212 <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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jackcurragh
parents:
diff changeset
213 </when> <!-- indexFull -->
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jackcurragh
parents:
diff changeset
214 </conditional> <!-- indexParams -->
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jackcurragh
parents:
diff changeset
215 </when> <!-- history -->
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jackcurragh
parents:
diff changeset
216 </conditional> <!-- refGenomeSource -->
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jackcurragh
parents:
diff changeset
217 <conditional name="singlePaired">
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
218 <param name="sPaired" type="select" label="Is this library mate-paired?">
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jackcurragh
parents:
diff changeset
219 <option value="single">Single-end</option>
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jackcurragh
parents:
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220 <option value="paired">Paired-end</option>
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jackcurragh
parents:
diff changeset
221 </param>
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jackcurragh
parents:
diff changeset
222 <when value="single">
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jackcurragh
parents:
diff changeset
223 <param name="sInput1" type="data" format="fastqsanger,fastqillumina,fastqsolexa" label="FASTQ file" help="Must have ASCII encoded quality scores"/>
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jackcurragh
parents:
diff changeset
224 <conditional name="sParams">
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jackcurragh
parents:
diff changeset
225 <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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jackcurragh
parents:
diff changeset
226 <option value="preSet">Commonly used</option>
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jackcurragh
parents:
diff changeset
227 <option value="full" selected="true">Full parameter list</option>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
228 </param>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
229 <when value="preSet" />
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jackcurragh
parents:
diff changeset
230 <when value="full">
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jackcurragh
parents:
diff changeset
231 <param name="sSkip" type="integer" value="0" label="Skip the first n reads (-s)" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
232 <param name="sAlignLimit" type="integer" value="-1" label="Only align the first n reads (-u)" help="-1 for off" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
233 <param name="sTrimH" type="integer" value="0" label="Trim n bases from high-quality (left) end of each read before alignment (-5)" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
234 <param name="sTrimL" type="integer" value="0" label="Trim n bases from low-quality (right) end of each read before alignment (-3)" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
235 <conditional name="alignModeOption">
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
236 <param name="alignMode" type="select" label="Alignment mode">
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
237 <option value="nMode">Maq-like: quality-aware, limit mismatches in seed (-n)</option>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
238 <option value="vMode" selected="true">ignore qualities, limit end-to-end mismatches (-v)</option>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
239 </param>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
240 <when value="nMode">
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jackcurragh
parents:
diff changeset
241 <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" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
242 <param name="sMismatchQual" type="integer" value="70" min="1" label="Maximum permitted total of quality values at all mismatched read positions (-e)" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
243 <param name="sSeedLen" type="integer" value="28" min="5" label="Seed length (-l)" help="Minimum value is 5" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
244 <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">
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jackcurragh
parents:
diff changeset
245 <option value="round">Round to nearest 10</option>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
246 <option value="noRound">Do not round to nearest 10</option>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
247 </param>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
248 </when>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
249 <when value="vMode">
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
250 <param name="maxMismatches" type="integer" value="3" min="0" max="3" label="Maximum number of mismatches (-v)" help="May be 0, 1, 2, or 3" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
251 <param name="sSeedLen" type="integer" value="25" min="5" label="Seed length (-l)" help="Minimum value is 5" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
252 </when>
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jackcurragh
parents:
diff changeset
253 </conditional>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
254 <param name="sForwardAlign" type="select" label="Choose whether or not to attempt to align against the forward reference strand (--nofw)">
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
255 <option value="forward">Align against the forward reference strand</option>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
256 <option value="noForward">Do not align against the forward reference strand</option>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
257 </param>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
258 <param name="sReverseAlign" type="select" label="Choose whether or not to attempt to align against the reverse-complement reference strand (--norc)">
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
259 <option value="reverse">Align against the reverse-complement reference strand</option>
1
14fb4b4872e3 Uploaded
jackcurragh
parents: 0
diff changeset
260 <option value="noReverse" selected="true">Do not align against the reverse-complement reference strand</option>
0
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
261 </param>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
262 <conditional name="sBestOption">
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
263 <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">
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jackcurragh
parents:
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264 <option value="noBest">Do not use best</option>
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jackcurragh
parents:
diff changeset
265 <option value="doBest">Use best</option>
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jackcurragh
parents:
diff changeset
266 </param>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
267 <when value="noBest">
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jackcurragh
parents:
diff changeset
268 <conditional name="sTryHardOption">
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jackcurragh
parents:
diff changeset
269 <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">
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jackcurragh
parents:
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270 <option value="noTryHard">Do not try hard</option>
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jackcurragh
parents:
diff changeset
271 <option value="doTryHard">Try hard</option>
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jackcurragh
parents:
diff changeset
272 </param>
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jackcurragh
parents:
diff changeset
273 <when value="noTryHard">
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jackcurragh
parents:
diff changeset
274 <param name="snMaxBacktracks" type="integer" value="125" min="0" label="Maximum number of backtracks permitted when aligning a read (--maxbts)" />
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jackcurragh
parents:
diff changeset
275 </when>
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jackcurragh
parents:
diff changeset
276 <when value="doTryHard" />
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jackcurragh
parents:
diff changeset
277 </conditional>
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jackcurragh
parents:
diff changeset
278 </when>
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jackcurragh
parents:
diff changeset
279 <when value="doBest">
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jackcurragh
parents:
diff changeset
280 <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)">
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
281 <option value="noStrata">Do not use strata option</option>
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jackcurragh
parents:
diff changeset
282 <option value="doStrata">Use strata option</option>
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jackcurragh
parents:
diff changeset
283 </param>
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jackcurragh
parents:
diff changeset
284 <conditional name="sTryHardOption">
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jackcurragh
parents:
diff changeset
285 <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">
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jackcurragh
parents:
diff changeset
286 <option value="noTryHard">Do not try hard</option>
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jackcurragh
parents:
diff changeset
287 <option value="doTryHard">Try hard</option>
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jackcurragh
parents:
diff changeset
288 </param>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
289 <when value="noTryHard">
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jackcurragh
parents:
diff changeset
290 <param name="sdMaxBacktracks" type="integer" value="800" min="0" label="Maximum number of backtracks permitted when aligning a read (--maxbts)" />
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jackcurragh
parents:
diff changeset
291 </when>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
292 <when value="doTryHard" />
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jackcurragh
parents:
diff changeset
293 </conditional>
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jackcurragh
parents:
diff changeset
294 </when>
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jackcurragh
parents:
diff changeset
295 </conditional> <!-- bestOption -->
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jackcurragh
parents:
diff changeset
296 <conditional name="sAllValAlignsOption">
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jackcurragh
parents:
diff changeset
297 <param name="sAllValAligns" type="select" label="Whether or not to report all valid alignments per read (-a)">
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
298 <option value="noAllValAligns">Do not report all valid alignments</option>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
299 <option value="doAllValAligns" selected="true">Report all valid alignments</option>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
300 </param>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
301 <when value="noAllValAligns">
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jackcurragh
parents:
diff changeset
302 <param name="sValAlign" type="integer" value="1" min="1" label="Report up to n valid alignments per read (-k)" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
303 </when>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
304 <when value="doAllValAligns" />
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jackcurragh
parents:
diff changeset
305 </conditional>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
306 <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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jackcurragh
parents:
diff changeset
307 <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)" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
308 <param name="sUnmappedFile" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write all reads that could not be aligned to a file (--un)" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
309 <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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jackcurragh
parents:
diff changeset
310 <param name="sSeed" type="integer" value="-1" label="Seed for pseudo-random number generator (--seed)" help="-1 for default" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
311 </when> <!-- full -->
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jackcurragh
parents:
diff changeset
312 </conditional> <!-- sParams -->
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
313 </when> <!-- single -->
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jackcurragh
parents:
diff changeset
314 <when value="paired">
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jackcurragh
parents:
diff changeset
315 <param name="pInput1" type="data" format="fastqsanger,fastqillumina,fastqsolexa" label="Forward FASTQ file" help="Must have ASCII encoded quality scores"/>
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jackcurragh
parents:
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316 <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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jackcurragh
parents:
diff changeset
317 <options options_filter_attribute="ext" from_parameter="tool.app.datatypes_registry.datatypes_by_extension" transform_lines="obj.keys()">
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jackcurragh
parents:
diff changeset
318 <column name="name" index="0"/>
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jackcurragh
parents:
diff changeset
319 <column name="value" index="0"/>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
320 <filter type="param_value" ref="pInput1" ref_attribute="ext" column="0"/>
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jackcurragh
parents:
diff changeset
321 </options>
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jackcurragh
parents:
diff changeset
322 </param>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
323 <param name="pMaxInsert" type="integer" value="1000" label="Maximum insert size for valid paired-end alignments (-X)" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
324 <param name="pMateOrient" type="select" label="The upstream/downstream mate orientation for valid paired-end alignment against the forward reference strand (--fr/--rf/--ff)">
1b109d213a42 Uploaded
jackcurragh
parents:
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325 <option value="fr">FR (for Illumina)</option>
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jackcurragh
parents:
diff changeset
326 <option value="rf">RF</option>
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jackcurragh
parents:
diff changeset
327 <option value="ff">FF (for SOLiD)</option>
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jackcurragh
parents:
diff changeset
328 </param>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
329 <conditional name="pParams">
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jackcurragh
parents:
diff changeset
330 <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">
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jackcurragh
parents:
diff changeset
331 <option value="preSet">Commonly used</option>
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jackcurragh
parents:
diff changeset
332 <option value="full">Full parameter list</option>
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jackcurragh
parents:
diff changeset
333 </param>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
334 <when value="preSet" />
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jackcurragh
parents:
diff changeset
335 <when value="full">
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jackcurragh
parents:
diff changeset
336 <param name="pSkip" type="integer" value="0" label="Skip the first n pairs (-s)" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
337 <param name="pAlignLimit" type="integer" value="-1" label="Only align the first n pairs (-u)" help="-1 for off" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
338 <param name="pTrimH" type="integer" value="0" label="Trim n bases from high-quality (left) end of each read before alignment (-5)" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
339 <param name="pTrimL" type="integer" value="0" label="Trim n bases from low-quality (right) end of each read before alignment (-3)" />
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jackcurragh
parents:
diff changeset
340 <conditional name="alignModeOption">
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
341 <param name="alignMode" type="select" label="Alignment mode">
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
342 <option value="nMode">Maq-like: quality-aware, limit mismatches in seed (-n)</option>
1
14fb4b4872e3 Uploaded
jackcurragh
parents: 0
diff changeset
343 <option value="vMode" selected="true">ignore qualities, limit end-to-end mismatches (-v)</option>
0
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
344 </param>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
345 <when value="nMode">
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jackcurragh
parents:
diff changeset
346 <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" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
347 <param name="pMismatchQual" type="integer" value="70" min="1" label="Maximum permitted total of quality values at all mismatched read positions (-e)" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
348 <param name="pSeedLen" type="integer" value="28" min="5" label="Seed length (-l)" help="Minimum value is 5" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
349 <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">
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
350 <option value="round">Round to nearest 10</option>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
351 <option value="noRound">Do not round to nearest 10</option>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
352 </param>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
353 </when>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
354 <when value="vMode">
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
355 <param name="maxMismatches" type="integer" value="" min="0" max="3" label="Maximum number of mismatches (-v)" help="May be 0, 1, 2, or 3" />
1
14fb4b4872e3 Uploaded
jackcurragh
parents: 0
diff changeset
356 <param name="pSeedLen" type="integer" value="25" min="5" label="Seed length (-l)" help="Minimum value is 5" />
0
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
357 </when>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
358 </conditional>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
359 <param name="pMinInsert" type="integer" value="0" label="Minimum insert size for valid paired-end alignments (-I)" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
360 <param name="pForwardAlign" type="select" label="Choose whether or not to attempt to align against the forward reference strand (--nofw)">
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
361 <option value="forward">Align against the forward reference strand</option>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
362 <option value="noForward">Do not align against the forward reference strand</option>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
363 </param>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
364 <param name="pReverseAlign" type="select" label="Choose whether or not to attempt to align against the reverse-complement reference strand (--norc)">
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
365 <option value="reverse">Align against the reverse-complement reference strand</option>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
366 <option value="noReverse" selected="true">Do not align against the reverse-complement reference strand</option>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
367 </param>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
368 <conditional name="pBestOption">
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
369 <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">
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
370 <option value="noBest">Do not use best</option>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
371 <option value="doBest">Use best</option>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
372 </param>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
373 <when value="noBest">
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
374 <conditional name="pTryHardOption">
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
375 <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">
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
376 <option value="noTryHard">Do not try hard</option>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
377 <option value="doTryHard">Try hard</option>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
378 </param>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
379 <when value="noTryHard">
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
380 <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)" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
381 <param name="pnMaxBacktracks" type="integer" value="125" min="0" label="Maximum number of backtracks permitted when aligning a read (--maxbts)" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
382 </when>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
383 <when value="doTryHard" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
384 </conditional>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
385 </when>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
386 <when value="doBest">
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
387 <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)">
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
388 <option value="noStrata">Do not use strata option</option>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
389 <option value="doStrata">Use strata option</option>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
390 </param>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
391 <conditional name="pTryHardOption">
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
392 <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">
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
393 <option value="noTryHard">Do not try hard</option>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
394 <option value="doTryHard">Try hard</option>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
395 </param>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
396 <when value="noTryHard">
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
397 <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)" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
398 <param name="pdMaxBacktracks" type="integer" value="800" min="0" label="Maximum number of backtracks permitted when aligning a read (--maxbts)" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
399 </when>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
400 <when value="doTryHard" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
401 </conditional>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
402 </when>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
403 </conditional>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
404 <conditional name="pAllValAlignsOption">
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
405 <param name="pAllValAligns" type="select" label="Whether or not to report all valid alignments per pair (-a)">
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
406 <option value="noAllValAligns">Do not report all valid alignments</option>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
407 <option value="doAllValAligns">Report all valid alignments</option>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
408 </param>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
409 <when value="noAllValAligns">
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
410 <param name="pValAlign" type="integer" value="1" min="1" label="Report up to n valid alignments per pair (-k)" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
411 </when>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
412 <when value="doAllValAligns" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
413 </conditional>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
414 <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" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
415 <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)" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
416 <param name="pUnmappedFile" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write all reads that could not be aligned to a file (--un)" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
417 <param name="pOffrate" type="integer" value="-1" label="Override the offrate of the index to n (-o)" help="-1 for default" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
418 <param name="pSeed" type="integer" value="-1" label="Seed for pseudo-random number generator (--seed)" help="-1 for default" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
419 </when> <!-- full -->
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
420 </conditional> <!-- pParams -->
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
421 </when> <!-- paired -->
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
422 </conditional> <!-- singlePaired -->
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
423 <param name="save_mapping_stats" type="boolean" checked="False" label="Save the bowtie mapping statistics to the history" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
424 <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" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
425 </inputs>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
426 <outputs>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
427 <data format="sam" name="output" label="${tool.name} on ${on_string}: mapped reads">
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
428 <actions>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
429 <conditional name="refGenomeSource.genomeSource">
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
430 <when value="indexed">
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
431 <action type="metadata" name="dbkey">
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
432 <option type="from_data_table" name="bowtie_indexes" column="1" offset="0">
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
433 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
434 <filter type="param_value" ref="refGenomeSource.index" column="0"/>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
435 </option>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
436 </action>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
437 </when>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
438 <when value="history">
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
439 <action type="metadata" name="dbkey">
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
440 <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
441 </action>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
442 </when>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
443 </conditional>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
444 </actions>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
445 </data>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
446 <data format="txt" name="mapping_stats" label="${tool.name} on ${on_string}: mapping stats">
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
447 <filter>save_mapping_stats is True</filter>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
448 </data>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
449 <data format="fastq" name="output_suppressed_reads_l" label="${tool.name} on ${on_string}: suppressed reads (L)">
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
450 <filter>((
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
451 singlePaired['sPaired'] == "single" and
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
452 singlePaired['sParams']['sSettingsType'] == "full" and
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
453 singlePaired['sParams']['sMaxFile'] is True
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
454 ) or (
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
455 singlePaired['sPaired'] == "paired" and
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
456 singlePaired['pParams']['pSettingsType'] == "full" and
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
457 singlePaired['pParams']['pMaxFile'] is True
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
458 ))
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
459 </filter>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
460 <actions>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
461 <conditional name="singlePaired.sPaired">
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
462 <when value="single">
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
463 <action type="format">
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
464 <option type="from_param" name="singlePaired.sInput1" param_attribute="ext" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
465 </action>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
466 </when>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
467 <when value="paired">
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
468 <action type="format">
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
469 <option type="from_param" name="singlePaired.pInput1" param_attribute="ext" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
470 </action>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
471 </when>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
472 </conditional>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
473 </actions>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
474 </data>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
475 <data format="fastq" name="output_suppressed_reads_r" label="${tool.name} on ${on_string}: suppressed reads (R)">
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
476 <filter>singlePaired['sPaired'] == "paired"</filter>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
477 <filter>singlePaired['pParams']['pSettingsType'] == "full"</filter>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
478 <filter>singlePaired['pParams']['pMaxFile'] is True</filter>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
479 <actions>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
480 <conditional name="singlePaired.sPaired">
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
481 <when value="single">
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
482 <action type="format">
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
483 <option type="from_param" name="singlePaired.sInput1" param_attribute="ext" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
484 </action>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
485 </when>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
486 <when value="paired">
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
487 <action type="format">
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
488 <option type="from_param" name="singlePaired.pInput1" param_attribute="ext" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
489 </action>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
490 </when>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
491 </conditional>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
492 </actions>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
493 </data>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
494 <data format="fastq" name="output_unmapped_reads_l" label="${tool.name} on ${on_string}: unmapped reads (L)">
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
495 <filter>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
496 ((
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
497 singlePaired['sPaired'] == "single" and
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
498 singlePaired['sParams']['sSettingsType'] == "full" and
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
499 singlePaired['sParams']['sUnmappedFile'] is True
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
500 ) or (
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
501 singlePaired['sPaired'] == "paired" and
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
502 singlePaired['pParams']['pSettingsType'] == "full" and
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
503 singlePaired['pParams']['pUnmappedFile'] is True
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
504 ))
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
505 </filter>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
506 <actions>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
507 <conditional name="singlePaired.sPaired">
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
508 <when value="single">
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
509 <action type="format">
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
510 <option type="from_param" name="singlePaired.sInput1" param_attribute="ext" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
511 </action>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
512 </when>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
513 <when value="paired">
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
514 <action type="format">
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
515 <option type="from_param" name="singlePaired.pInput1" param_attribute="ext" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
516 </action>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
517 </when>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
518 </conditional>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
519 </actions>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
520 </data>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
521 <data format="fastq" name="output_unmapped_reads_r" label="${tool.name} on ${on_string}: unmapped reads (R)">
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
522 <filter>singlePaired['sPaired'] == "paired"</filter>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
523 <filter>singlePaired['pParams']['pSettingsType'] == "full"</filter>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
524 <filter>singlePaired['pParams']['pUnmappedFile'] is True</filter>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
525 <actions>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
526 <conditional name="singlePaired.sPaired">
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
527 <when value="single">
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
528 <action type="format">
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
529 <option type="from_param" name="singlePaired.sInput1" param_attribute="ext" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
530 </action>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
531 </when>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
532 <when value="paired">
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
533 <action type="format">
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
534 <option type="from_param" name="singlePaired.pInput1" param_attribute="ext" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
535 </action>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
536 </when>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
537 </conditional>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
538 </actions>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
539 </data>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
540 </outputs>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
541 <tests>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
542 <test>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
543 <!--
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
544 Bowtie command:
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
545 bowtie -q -p 4 -S +sam-nohead chrM_base test-data/bowtie_in2.fastqsanger > bowtie_out6_u.sam
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
546 sort bowtie_out6_u.sam > bowtie_out6.sam
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
547 -p is the number of threads. You need to replace the + with 2 dashes.
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
548 chrM_base needs to be the base location/name of the index files.
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
549 -->
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
550 <param name="genomeSource" value="indexed" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
551 <!-- this is the backwards-compatible "unique value" for this index, not an actual path -->
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
552 <param name="index" value="equCab2chrM" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
553 <param name="sPaired" value="single" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
554 <param name="sInput1" ftype="fastqsanger" value="bowtie_in2.fastqsanger" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
555 <param name="sSettingsType" value="preSet" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
556 <param name="suppressHeader" value="true" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
557 <output name="output" ftype="sam" file="bowtie_out6.sam" sort="True">
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
558 <metadata name="dbkey" value="equCab2" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
559 </output>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
560 </test>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
561 <test>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
562 <!--
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
563 Bowtie command:
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
564 bowtie-build -f test-data/phiX.fasta phiX_base
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
565 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
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
566 sort bowtie_out7_u.sam > bowtie_out7.sam
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
567 sort bowtie_out8_u_1.sam > bowtie_out8_1.sam
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
568 sort bowtie_out8_u_2.sam > bowtie_out8_2.sam
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
569 Then also need to modify bowtie_out8_1.sam and bowtie_out8_2.sam so that all @ lines come before sequence lines.
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
570 -p is the number of threads. You need to replace the + with 2 dashes.
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
571 The two unmapped output files will be named bowtie_out8_1.fastq and bowtie_out8_2.fastq.
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
572 chrM_base is the index files' location/base name.
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
573 -->
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
574 <param name="genomeSource" value="history" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
575 <param name="ownFile" value="phiX.fasta" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
576 <param name="indexSettings" value="indexPreSet" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
577 <param name="sPaired" value="paired" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
578 <param name="pInput1" ftype="fastqsanger" value="bowtie_in5.fastqsanger" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
579 <param name="pInput2" ftype="fastqsanger" value="bowtie_in6.fastqsanger" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
580 <param name="pMaxInsert" value="1000" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
581 <param name="pMateOrient" value="ff" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
582 <param name="pSettingsType" value="full" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
583 <param name="pSkip" value="0" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
584 <param name="pAlignLimit" value="-1" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
585 <param name="pTrimH" value="0" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
586 <param name="pTrimL" value="0" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
587 <param name="alignMode" value="nMode" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
588 <param name="pMismatchSeed" value="2" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
589 <param name="pMismatchQual" value="70" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
590 <param name="pSeedLen" value="28" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
591 <param name="pRounding" value="round" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
592 <param name="pMinInsert" value="0" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
593 <param name="pMaxAlignAttempt" value="100" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
594 <param name="pForwardAlign" value="forward" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
595 <param name="pReverseAlign" value="reverse" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
596 <param name="pTryHard" value="noTryHard" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
597 <param name="pValAlign" value="1" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
598 <param name="pAllValAligns" value="noAllValAligns" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
599 <param name="pSuppressAlign" value="-1" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
600 <param name="pUnmappedFile" value="true" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
601 <param name="pMaxFile" value="false" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
602 <param name="pBest" value="doBest" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
603 <param name="pdMaxBacktracks" value="800" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
604 <param name="pdStrata" value="noStrata" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
605 <param name="pOffrate" value="-1" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
606 <param name="pSeed" value="-1" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
607 <param name="suppressHeader" value="true" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
608 <output name="output" ftype="sam" file="bowtie_out7.sam" sort="True" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
609 <output name="output_unmapped_reads_l" ftype="fastqsanger" file="bowtie_out8_1.fastq" sort="True" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
610 <output name="output_unmapped_reads_r" ftype="fastqsanger" file="bowtie_out8_2.fastq" sort="True" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
611 </test>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
612 <!-- start testing of non-sanger variant fastq reads -->
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
613 <test>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
614 <param name="genomeSource" value="history" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
615 <param name="ownFile" value="phiX.fasta" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
616 <param name="indexSettings" value="indexPreSet" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
617 <param name="sPaired" value="paired" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
618 <param name="pInput1" ftype="fastqillumina" value="bowtie_in5.fastqillumina" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
619 <param name="pInput2" ftype="fastqillumina" value="bowtie_in6.fastqillumina" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
620 <param name="pMaxInsert" value="1000" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
621 <param name="pMateOrient" value="ff" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
622 <param name="pSettingsType" value="full" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
623 <param name="pSkip" value="0" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
624 <param name="pAlignLimit" value="-1" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
625 <param name="pTrimH" value="0" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
626 <param name="pTrimL" value="0" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
627 <param name="alignMode" value="nMode" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
628 <param name="pMismatchSeed" value="2" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
629 <param name="pMismatchQual" value="70" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
630 <param name="pSeedLen" value="28" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
631 <param name="pRounding" value="round" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
632 <param name="pMinInsert" value="0" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
633 <param name="pMaxAlignAttempt" value="100" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
634 <param name="pForwardAlign" value="forward" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
635 <param name="pReverseAlign" value="reverse" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
636 <param name="pTryHard" value="noTryHard" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
637 <param name="pValAlign" value="1" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
638 <param name="pAllValAligns" value="noAllValAligns" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
639 <param name="pSuppressAlign" value="-1" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
640 <param name="pUnmappedFile" value="true" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
641 <param name="pMaxFile" value="false" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
642 <param name="pBest" value="doBest" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
643 <param name="pdMaxBacktracks" value="800" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
644 <param name="pdStrata" value="noStrata" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
645 <param name="pOffrate" value="-1" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
646 <param name="pSeed" value="-1" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
647 <param name="suppressHeader" value="true" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
648 <output name="output" ftype="sam" file="bowtie_out7.sam" sort="True" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
649 <output name="output_unmapped_reads_l" ftype="fastqillumina" file="bowtie_out8_1.fastqillumina.sorted" sort="True" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
650 <output name="output_unmapped_reads_r" ftype="fastqillumina" file="bowtie_out8_2.fastqillumina.sorted" sort="True" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
651 </test>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
652 <test>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
653 <param name="genomeSource" value="history" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
654 <param name="ownFile" value="phiX.fasta" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
655 <param name="indexSettings" value="indexPreSet" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
656 <param name="sPaired" value="paired" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
657 <param name="pInput1" ftype="fastqsolexa" value="bowtie_in5.fastqsolexa" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
658 <param name="pInput2" ftype="fastqsolexa" value="bowtie_in6.fastqsolexa" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
659 <param name="pMaxInsert" value="1000" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
660 <param name="pMateOrient" value="ff" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
661 <param name="pSettingsType" value="full" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
662 <param name="pSkip" value="0" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
663 <param name="pAlignLimit" value="-1" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
664 <param name="pTrimH" value="0" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
665 <param name="pTrimL" value="0" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
666 <param name="alignMode" value="nMode" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
667 <param name="pMismatchSeed" value="2" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
668 <param name="pMismatchQual" value="70" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
669 <param name="pSeedLen" value="28" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
670 <param name="pRounding" value="round" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
671 <param name="pMinInsert" value="0" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
672 <param name="pMaxAlignAttempt" value="100" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
673 <param name="pForwardAlign" value="forward" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
674 <param name="pReverseAlign" value="reverse" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
675 <param name="pTryHard" value="noTryHard" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
676 <param name="pValAlign" value="1" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
677 <param name="pAllValAligns" value="noAllValAligns" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
678 <param name="pSuppressAlign" value="-1" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
679 <param name="pUnmappedFile" value="true" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
680 <param name="pMaxFile" value="false" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
681 <param name="pBest" value="doBest" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
682 <param name="pdMaxBacktracks" value="800" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
683 <param name="pdStrata" value="noStrata" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
684 <param name="pOffrate" value="-1" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
685 <param name="pSeed" value="-1" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
686 <param name="suppressHeader" value="true" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
687 <output name="output" ftype="sam" file="bowtie_out7.sam" sort="True" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
688 <output name="output_unmapped_reads_l" ftype="fastqsolexa" file="bowtie_out8_1.fastqsolexa.sorted" sort="True" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
689 <output name="output_unmapped_reads_r" ftype="fastqsolexa" file="bowtie_out8_2.fastqsolexa.sorted" sort="True" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
690 </test>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
691 <!-- end testing of non-sanger variant fastq reads -->
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
692 <test>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
693 <!--
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
694 Bowtie command:
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
695 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
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
696 sort bowtie_out9_u.sam > bowtie_out9.sam
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
697 -p is the number of threads. You need to replace the + with 2 dashes.
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
698 chrM_base is the index files' location/base name.
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
699 -->
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
700 <param name="genomeSource" value="indexed" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
701 <!-- this is the backwards-compatible "unique value" for this index, not an actual path -->
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
702 <param name="index" value="equCab2chrM" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
703 <param name="sPaired" value="single" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
704 <param name="sInput1" ftype="fastqsanger" value="bowtie_in2.fastqsanger" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
705 <param name="sSettingsType" value="full" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
706 <param name="sSkip" value="0" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
707 <param name="sAlignLimit" value="-1" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
708 <param name="sTrimH" value="0" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
709 <param name="sTrimL" value="0" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
710 <param name="alignMode" value="nMode" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
711 <param name="sMismatchSeed" value="2" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
712 <param name="sMismatchQual" value="70" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
713 <param name="sSeedLen" value="28" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
714 <param name="sRounding" value="round" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
715 <param name="sForwardAlign" value="forward" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
716 <param name="sReverseAlign" value="reverse" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
717 <param name="sTryHard" value="doTryHard" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
718 <param name="sValAlign" value="1" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
719 <param name="sAllValAligns" value="noAllValAligns" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
720 <param name="sSuppressAlign" value="-1" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
721 <param name="sUnmappedFile" value="false" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
722 <param name="sMaxFile" value="false" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
723 <param name="sBest" value="noBest" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
724 <param name="sOffrate" value="-1" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
725 <param name="sSeed" value="-1" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
726 <param name="suppressHeader" value="true" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
727 <output name="output" ftype="sam" file="bowtie_out9.sam" sort="True">
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
728 <metadata name="dbkey" value="equCab2" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
729 </output>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
730 </test>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
731 <test>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
732 <!--
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
733 Bowtie command:
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
734 bowtie-build +offrate 5 +ftabchars 10 +little -f test-data/phiX.fasta phiX_base
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
735 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
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
736 sort bowtie_out10_u.sam > bowtie_out10.sam
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
737 -p is the number of threads. You need to replace the + with 2 dashes.
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
738 chrM_base is the index files' location/base name.
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
739 -->
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
740 <param name="genomeSource" value="history" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
741 <param name="ownFile" value="phiX.fasta" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
742 <param name="indexSettings" value="indexFull" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
743 <param name="autoB" value="auto" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
744 <param name="nodc" value="dc" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
745 <param name="noref" value="ref" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
746 <param name="offrate" value="5" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
747 <param name="ftab" value="10" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
748 <param name="ntoa" value="no" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
749 <param name="endian" value="little" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
750 <param name="seed" value="-1" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
751 <param name="sPaired" value="paired" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
752 <param name="pInput1" ftype="fastqsanger" value="bowtie_in5.fastqsanger" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
753 <param name="pInput2" ftype="fastqsanger" value="bowtie_in6.fastqsanger" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
754 <param name="pMaxInsert" value="1000" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
755 <param name="pMateOrient" value="ff" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
756 <param name="pSettingsType" value="preSet" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
757 <param name="suppressHeader" value="true" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
758 <output name="output" ftype="sam" file="bowtie_out10.sam" sort="True" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
759 </test>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
760 <test>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
761 <!--
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
762 Bowtie command:
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
763 bowtie-build +offrate 5 +ftabchars 10 +little -f test-data/phiX.fasta phiX_base
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
764 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
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
765 sort bowtie_out10_u.sam > bowtie_out10.sam
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
766 -p is the number of threads. You need to replace the + with 2 dashes.
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
767 chrM_base is the index files' location/base name.
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
768 -->
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
769 <param name="genomeSource" value="history" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
770 <param name="ownFile" value="phiX.fasta" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
771 <param name="indexSettings" value="indexFull" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
772 <param name="autoB" value="auto" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
773 <param name="nodc" value="dc" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
774 <param name="noref" value="ref" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
775 <param name="offrate" value="5" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
776 <param name="ftab" value="10" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
777 <param name="ntoa" value="no" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
778 <param name="endian" value="little" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
779 <param name="seed" value="-1" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
780 <param name="sPaired" value="paired" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
781 <param name="pInput1" ftype="fastqsanger" value="bowtie_in5.fastqsanger" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
782 <param name="pInput2" ftype="fastqsanger" value="bowtie_in6.fastqsanger" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
783 <param name="pMaxInsert" value="1000" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
784 <param name="pMateOrient" value="ff" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
785 <param name="pSettingsType" value="preSet" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
786 <param name="suppressHeader" value="true" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
787 <param name="save_mapping_stats" value="true" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
788 <output name="output" ftype="sam" file="bowtie_out10.sam" sort="True" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
789 <output name="mapping_stats" ftype="txt" file="bowtie_out11.txt" sort="True" />
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
790 </test>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
791 </tests>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
792
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
793 <help>
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
794
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
795 **What it does**
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
796
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
797 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.
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
798
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
799 .. _Bowtie: http://bowtie-bio.sourceforge.net/index.shtml
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
800
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
801 ------
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
802
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
803 **Know what you are doing**
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
804
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
805 .. class:: warningmark
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
806
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
807 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.
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
808
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
809 .. __: http://bowtie-bio.sourceforge.net/index.shtml
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
810
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
811 ------
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
812
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
813 **Input formats**
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
814
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
815 Bowtie accepts files in Sanger FASTQ format. Use the FASTQ Groomer to prepare your files.
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
816
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
817 ------
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
818
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
819 **A Note on Built-in Reference Genomes**
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
820
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
821 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.
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
822
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
823 ------
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
824
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
825 **Outputs**
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
826
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
827 The output is in SAM format, and has the following columns::
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
828
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
829 Column Description
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
830 -------- --------------------------------------------------------
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
831 1 QNAME Query (pair) NAME
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
832 2 FLAG bitwise FLAG
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
833 3 RNAME Reference sequence NAME
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
834 4 POS 1-based leftmost POSition/coordinate of clipped sequence
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
835 5 MAPQ MAPping Quality (Phred-scaled)
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
836 6 CIGAR extended CIGAR string
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
837 7 MRNM Mate Reference sequence NaMe ('=' if same as RNAME)
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
838 8 MPOS 1-based Mate POSition
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
839 9 ISIZE Inferred insert SIZE
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
840 10 SEQ query SEQuence on the same strand as the reference
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
841 11 QUAL query QUALity (ASCII-33 gives the Phred base quality)
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
842 12 OPT variable OPTional fields in the format TAG:VTYPE:VALUE
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
843
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
844 The flags are as follows::
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
845
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
846 Flag Description
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
847 ------ -------------------------------------
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
848 0x0001 the read is paired in sequencing
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
849 0x0002 the read is mapped in a proper pair
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
850 0x0004 the query sequence itself is unmapped
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
851 0x0008 the mate is unmapped
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
852 0x0010 strand of the query (1 for reverse)
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
853 0x0020 strand of the mate
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
854 0x0040 the read is the first read in a pair
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
855 0x0080 the read is the second read in a pair
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
856 0x0100 the alignment is not primary
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
857
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
858 It looks like this (scroll sideways to see the entire example)::
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
859
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
860 QNAME FLAG RNAME POS MAPQ CIAGR MRNM MPOS ISIZE SEQ QUAL OPT
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
861 HWI-EAS91_1_30788AAXX:1:1:1761:343 4 * 0 0 * * 0 0 AAAAAAANNAAAAAAAAAAAAAAAAAAAAAAAAAAACNNANNGAGTNGNNNNNNNGCTTCCCACAGNNCTGG hhhhhhh;;hhhhhhhhhhh^hOhhhhghhhfhhhgh;;h;;hhhh;h;;;;;;;hhhhhhghhhh;;Phhh
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
862 HWI-EAS91_1_30788AAXX:1:1:1578:331 4 * 0 0 * * 0 0 GTATAGANNAATAAGAAAAAAAAAAATGAAGACTTTCNNANNTCTGNANNNNNNNTCTTTTTTCAGNNGTAG hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhhhh;;h;;hhhh;h;;;;;;;hhhhhhhhhhh;;hhVh
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
863
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
864 -------
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
865
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
866 **Bowtie settings**
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
867
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
868 All of the options have a default value. You can change any of them. Most of the options in Bowtie have been implemented here.
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
869
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
870 ------
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
871
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
872 **Bowtie parameter list**
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
873
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
874 This is an exhaustive list of Bowtie options:
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
875
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
876 For indexing (bowtie-build)::
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
877
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
878 -a No auto behavior. Disable the default behavior where bowtie automatically
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
879 selects values for --bmax/--bmaxdivn/--dcv/--packed parameters according
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
880 to the memory available. [off]
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
881 --packed Packing. Use a packed representation for DNA strings. [auto]
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
882 --bmax INT Suffix maximum. The maximum number of suffixes allowed in a block. [auto]
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
883 --bmaxdivn INT Suffix maximum fraction. The maximum number of suffixes allowed in a block
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
884 expressed as a fraction of the length of the reference. [4]
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
885 --dcv INT Difference-cover sample. Use INT as the period for the difference-cover
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
886 sample. [1024]
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
887 --nodc INT No difference-cover sample. Disable the difference-cover sample. [off]
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
888 -r No reference indexes. Do not build the NAME.3.ebwt and NAME.4.ebwt portions
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
889 of the index. Used only for paired-end alignment. [off]
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
890 -o Offrate. How many Burrows-Wheeler rows get marked by the indexer. The
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
891 indexer will mark every 2^INT rows. The marked rows correspond to rows on
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
892 the genome. [5]
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
893 -t INT The ftab lookup table used to calculate an initial Burrows-Wheeler range
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
894 with respect to the first INT characters of the query. Ftab size is 4^(INT+1)
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
895 bytes. [10]
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jackcurragh
parents:
diff changeset
896 --ntoa N conversion. Convert Ns to As before building the index. Otherwise, Ns are
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jackcurragh
parents:
diff changeset
897 simply excluded from the index and Bowtie will not find alignments that
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jackcurragh
parents:
diff changeset
898 overlap them. [off]
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
899 --big Endianness. Endianness to use when serializing integers to the index file. [off]
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
900 --little Endianness. [--little]
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jackcurragh
parents:
diff changeset
901 --seed INT Random seed. Use INT as the seed for the pseudo-random number generator. [off]
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
902
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
903 For aligning (bowtie)::
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
904
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
905 -s INT Skip. Do not align the first INT reads or pairs in the input. [off]
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
906 -u INT Align limit. Only align the first INT reads/pairs from the input. [no limit]
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
907 -5 INT High-quality trim. Trim INT bases from the high-quality (left) end of each
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
908 read before alignment. [0]
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
909 -3 INT Low-quality trim. Trim INT bases from the low-quality (right) end of each
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
910 read before alignment. [0]
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
911 -n INT Mismatch seed. Maximum number of mismatches permitted in the seed (defined
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
912 with seed length option). Can be 0, 1, 2, or 3. [2]
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
913 -e INT Mismatch quality. Maximum permitted total of quality values at mismatched
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
914 read positions. Bowtie rounds quality values to the nearest 10 and saturates
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
915 at 30. [70]
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
916 -l INT Seed length. The number of bases on the high-quality end of the read to
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
917 which the -n ceiling applies. Must be at least 5. [28]
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
918 --nomaqround Suppress Maq rounding. Values are internally rounded to the nearest 10 and
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
919 saturate at 30. This options turns off that rounding. [off]
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
920 -v INT Maq- or SOAP-like alignment policy. This option turns off the default
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
921 Maq-like alignment policy in favor of a SOAP-like one. End-to-end alignments
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
922 with at most INT mismatches. [off]
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
923 -I INT Minimum insert. The minimum insert size for valid paired-end alignments.
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
924 Does checking on untrimmed reads if -5 or -3 is used. [0]
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
925 -X INT Maximum insert. The maximum insert size for valid paired-end alignments.
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
926 Does checking on untrimmed reads if -5 or -3 is used. [250]
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
927 --fr Mate orientation. The upstream/downstream mate orientations for a valid
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
928 paired-end alignment against the forward reference strand. [--fr]
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
929 --rf Mate orientation. [off]
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
930 --ff Mate orientation. [off]
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
931 --pairtries INT Maximum alignment attempts for paired-end data. [100]
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
932 --nofw No forward aligning. Choosing this option means that Bowtie will not attempt
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
933 to align against the forward reference strand. [off]
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
934 --norc No reverse-complement aligning. Setting this will mean that Bowtie will not
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
935 attempt to align against the reverse-complement reference strand. [off]
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
936 --un FILENAME Write all reads that could not be aligned to file [off]
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
937 --max FILENAME Write all reads with a number of valid alignments exceeding the limit
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
938 set with the -m option to file [off]
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
939 --maxbts INT Maximum backtracks. The maximum number of backtracks permitted when aligning
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
940 a read in -n 2 or -n 3 mode. [125 without --best] [800 with --best]
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
941 -y Try hard. Try as hard as possible to find valid alignments when they exist,
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
942 including paired-end alignments. [off]
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
943 --chunkmbs INT Thread memory. The number of megabytes of memory a given thread is given to
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
944 store path descriptors in --best mode. [32]
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
945 -k INT Valid alignments. The number of valid alignments per read or pair. [off]
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jackcurragh
parents:
diff changeset
946 -a All valid alignments. Choosing this means that all valid alignments per read
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
947 or pair will be reported. [off]
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
948 -m INT Suppress alignments. Suppress all alignments for a particular read or pair
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
949 if more than INT reportable alignments exist for it. [no limit]
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
950 --best Best mode. Make Bowtie guarantee that reported singleton alignments are
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
951 "best" in terms of stratum (the number of mismatches) and quality values at
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
952 mismatched position. [off]
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
953 --strata Best strata. When running in best mode, report alignments that fall into the
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
954 best stratum if there are ones falling into more than one. [off]
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
955 -o INT Offrate override. Override the offrate of the index with INT. Some row
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
956 markings are discarded when index read into memory. INT must be greater than
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
957 the value used to build the index (default: 5). [off]
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
958 --seed INT Random seed. Use INT as the seed for the pseudo-random number generator. [off]
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
959 --snpphred INT Use INT as the SNP penalty for decoding colorspace alignments. True ratio of
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jackcurragh
parents:
diff changeset
960 SNPs per base in the subject genome. [see --snpfrac]
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jackcurragh
parents:
diff changeset
961 --snpfrac DEC Use DEC as the estimated ratio of SNPs per base when decoding colorspace
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
962 alignments. [0.001]
1b109d213a42 Uploaded
jackcurragh
parents:
diff changeset
963 --col-keepends Keep the extreme-end nucleotides and qualities when decoding colorspace
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jackcurragh
parents:
diff changeset
964 alignments. [off]
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jackcurragh
parents:
diff changeset
965
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jackcurragh
parents:
diff changeset
966 </help>
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jackcurragh
parents:
diff changeset
967 <citations>
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jackcurragh
parents:
diff changeset
968 <citation type="doi">10.1186/gb-2009-10-3-r25</citation>
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jackcurragh
parents:
diff changeset
969 </citations>
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jackcurragh
parents:
diff changeset
970 </tool>