annotate bwa-mem.xml @ 4:774491f4a074 draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 33c17fa6a2d8c15972d93031b2ca4182cdf31439
author devteam
date Thu, 01 Jun 2017 11:38:11 -0400
parents 0bde88ff668c
children b59a6178a6e0
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1 <?xml version="1.0"?>
4
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2 <tool id="bwa_mem" name="Map with BWA-MEM" version="@VERSION@.2">
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3 <description>- map medium and long reads (&gt; 100 bp) against reference genome</description>
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4 <macros>
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5 <import>read_group_macros.xml</import>
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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6 <import>bwa_macros.xml</import>
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7 </macros>
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8 <expand macro="requirements" />
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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9 <expand macro="stdio" />
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10 <command>
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11 <![CDATA[
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12 @set_reference_fasta_filename@
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c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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14 ## Begin BWA-MEM command line
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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16 bwa mem
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17 -t "\${GALAXY_SLOTS:-1}"
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18 -v 1 ## Verbosity is set to 1 (errors only)
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19
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20 #if str( $fastq_input.fastq_input_selector ) == "paired_iv": ## For interleaved fastq files set -p option
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21 -p
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22 #if str( $fastq_input.iset_stats ): ## check that insert statistics is used
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23 -I "${fastq_input.iset_stats}"
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24 #end if
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25 #end if
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26
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27 #if str( $analysis_type.analysis_type_selector ) == "pacbio":
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28 -x pacbio
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29 #elif str( $analysis_type.analysis_type_selector ) == "ont2d":
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30 -x ont2d
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31 #elif str( $analysis_type.analysis_type_selector ) == "intractg":
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32 -x intractg
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33 #elif str( $analysis_type.analysis_type_selector ) == "full":
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34 #if str( $analysis_type.algorithmic_options.algorithmic_options_selector ) == "set": ## Algorithmic options
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35 -k "${analysis_type.algorithmic_options.k}"
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36 -w "${analysis_type.algorithmic_options.w}"
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37 -d "${analysis_type.algorithmic_options.d}"
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38 -r "${analysis_type.algorithmic_options.r}"
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39 -y "${analysis_type.algorithmic_options.y}"
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40 -c "${analysis_type.algorithmic_options.c}"
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41 -D "${analysis_type.algorithmic_options.D}"
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42 -W "${analysis_type.algorithmic_options.W}"
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43 -m "${analysis_type.algorithmic_options.m}"
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44 ${analysis_type.algorithmic_options.S}
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45 ${analysis_type.algorithmic_options.P}
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46 ${analysis_type.algorithmic_options.e}
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47 #end if
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48
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49 #if str( $analysis_type.scoring_options.scoring_options_selector ) == "set": ## Scoring options
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50 -A "${analysis_type.scoring_options.A}"
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51 -B "${analysis_type.scoring_options.B}"
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52 -O "${analysis_type.scoring_options.O}"
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53 -E "${analysis_type.scoring_options.E}"
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54 -L "${analysis_type.scoring_options.L}"
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55 -U "${analysis_type.scoring_options.U}"
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56 #end if
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57
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58 #if str( $analysis_type.io_options.io_options_selector ) == "set": ## IO options
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59 -T "${analysis_type.io_options.T}"
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60 -h "${analysis_type.io_options.h}"
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61 ${analysis_type.io_options.a}
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62 ${analysis_type.io_options.C}
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63 ${analysis_type.io_options.V}
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64 ${analysis_type.io_options.Y}
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65 ${analysis_type.io_options.M}
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66 #end if
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67
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68 #end if
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69
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70 ## Handle read group options...
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71 @define_read_group_helpers@
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72 #if str( $fastq_input.fastq_input_selector ) == "paired":
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73 #set $rg_auto_name = $read_group_name_default($fastq_input.fastq_input1, $fastq_input.fastq_input2)
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74 #else:
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75 #set $rg_auto_name = $read_group_name_default($fastq_input.fastq_input1)
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76 #end if
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77 @set_use_rg_var@
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78 @set_read_group_vars@
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79 #if $use_rg
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80 @set_rg_string@
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81 -R '$rg_string'
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82 #end if
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83
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84 #if str( $fastq_input.fastq_input_selector ) == "paired":
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85 #if str( $fastq_input.iset_stats ): ## check that insert statistics is used
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86 -I "${fastq_input.iset_stats}"
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87 #end if
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88
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89 "${reference_fasta_filename}"
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90 "${fastq_input.fastq_input1}" "${fastq_input.fastq_input2}"
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91 #elif str( $fastq_input.fastq_input_selector ) == "paired_collection":
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92 #if str( $fastq_input.iset_stats ): ## check that insert statistics is used
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93 -I "${fastq_input.iset_stats}"
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94 #end if
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95
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96 "${reference_fasta_filename}"
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97 "${fastq_input.fastq_input1.forward}" "${fastq_input.fastq_input1.reverse}"
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98 #else:
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99 "${reference_fasta_filename}"
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100 "${fastq_input.fastq_input1}"
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101 #end if
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102
2
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103 | samtools sort -O bam -o '$bam_output'
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104 ]]>
0
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105 </command>
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106
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107 <inputs>
2
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108 <expand macro="reference_source_conditional" />
0
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109 <conditional name="fastq_input">
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110 <param name="fastq_input_selector" type="select" label="Single or Paired-end reads" help="Select between paired and single end data">
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111 <option value="paired">Paired</option>
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112 <option value="single">Single</option>
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113 <option value="paired_collection">Paired Collection</option>
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114 <option value="paired_iv">Paired Interleaved</option>
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115 </param>
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116 <when value="paired">
4
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117 <param name="fastq_input1" type="data" format="fastqsanger,fastqsanger.gz,fasta" label="Select first set of reads" help="Specify dataset with forward reads"/>
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118 <param name="fastq_input2" type="data" format="fastqsanger,fastqsanger.gz,fasta" label="Select second set of reads" help="Specify dataset with reverse reads"/>
0
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119 <param name="iset_stats" type="text" optional="True" label="Enter mean, standard deviation, max, and min for insert lengths." help="-I; This parameter is only used for paired reads. Only mean is required while sd, max, and min will be inferred. Examples: both &quot;250&quot; and &quot;250,25&quot; will work while &quot;250,,10&quot; will not. See below for details.">
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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120 <sanitizer invalid_char="">
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121 <valid initial="string.digits"><add value=","/> </valid>
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122 </sanitizer>
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123 </param>
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124 </when>
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125 <when value="single">
4
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126 <param name="fastq_input1" type="data" format="fastqsanger,fastqsanger.gz,fasta" label="Select fastq dataset" help="Specify dataset with single reads"/>
0
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127 </when>
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128 <when value="paired_collection">
4
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129 <param name="fastq_input1" format="fastqsanger,fastqsanger.gz,fasta" type="data_collection" collection_type="paired" label="Select a paired collection" help="See help section for an explanation of dataset collections"/>
0
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130 <param name="iset_stats" type="text" optional="True" label="Enter mean, standard deviation, max, and min for insert lengths." help="-I; This parameter is only used for paired reads. Only mean is required while sd, max, and min will be inferred. Examples: both &quot;250&quot; and &quot;250,25&quot; will work while &quot;250,,10&quot; will not. See below for details.">
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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131 <sanitizer invalid_char="">
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132 <valid initial="string.digits"><add value=","/> </valid>
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133 </sanitizer>
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134 </param>
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135 </when>
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136 <when value="paired_iv">
4
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137 <param name="fastq_input1" type="data" format="fastqsanger,fastqsanger.gz,fasta" label="Select fastq dataset" help="Specify dataset with interleaved reads"/>
0
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138 <param name="iset_stats" type="text" optional="True" label="Enter mean, standard deviation, max, and min for insert lengths." help="-I; This parameter is only used for paired reads. Only mean is required while sd, max, and min will be inferred. Examples: both &quot;250&quot; and &quot;250,25&quot; will work while &quot;250,,10&quot; will not. See below for details.">
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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139 <sanitizer invalid_char="">
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140 <valid initial="string.digits"><add value=","/> </valid>
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141 </sanitizer>
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142 </param>
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143 </when>
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144 </conditional>
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145
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146 <expand macro="read_group_conditional" />
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147
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148 <conditional name="analysis_type">
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149 <param name="analysis_type_selector" type="select" label="Select analysis mode">
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150 <option value="illumina">1.Simple Illumina mode</option>
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151 <option value="pacbio">2.PacBio mode (-x pacbio)</option>
2
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152 <option value="ont2d">3.Nanopore 2D-reads mode (-x ont2d)</option>
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153 <option value="intractg">4.Intra-species contigs mode (-x intractg)</option>
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154 <option value="full">5.Full list of options</option>
0
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155 </param>
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156 <when value="illumina">
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157 <!-- do nothing -->
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158 </when>
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159 <when value="pacbio">
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160 <!-- do nothing. all magic happens within <command> tag -->
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161 </when>
2
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162 <when value="ont2d">
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163 <!-- do nothing. all magic happens within <command> tag -->
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164 </when>
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165 <when value="intractg">
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166 <!-- do nothing. all magic happens within <command> tag -->
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167 </when>
0
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168 <when value="full">
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169 <conditional name="algorithmic_options">
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170 <param name="algorithmic_options_selector" type="select" label="Set algorithmic options?" help="Sets -k, -w, -d, -r, -y, -c, -D, -W, -m, -S, -P, and -e options.">
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171 <option value="set">Set</option>
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172 <option value="do_not_set" selected="True">Do not set</option>
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173 </param>
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174 <when value="set">
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175 <param name="k" type="integer" value="19" label="Minimum seed length" help="-k; default=19"/>
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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176 <param name="w" type="integer" value="100" label="Band width for banded alignment" help="-w; default=100"/>
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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177 <param name="d" type="integer" value="100" label="Off-diagonal X-dropoff" help="-d; default=100"/>
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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178 <param name="r" type="float" value="1.5" label="Look for internal seeds inside a seed longer than -k * THIS VALUE" help="-r; default=1.5; This is a key heuristic parameter for tuning the performance. Larger value yields fewer seeds, which leads to faster alignment speed but lower accuracy" />
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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179 <param name="y" type="integer" value="20" label="Seed occurrence for the 3rd round seeding" help="-y; default=20" />
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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180 <param name="c" type="integer" value="500" label="Skip seeds with more than that many occurrences" help="-c; default=500"/>
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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181 <param name="D" type="float" value="0.5" label="Drop chains shorter than this fraction of the longest overlapping chain" help="-D; default=0.5"/>
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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182 <param name="W" type="integer" value="0" label="Discard a chain if seeded bases shorter than THIS VALUE" help="-W; default=0"/>
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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183 <param name="m" type="integer" value="50" label="Perform at most this many rounds of mate rescues for each read" help="-m; default=50"/>
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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184 <param name="S" type="boolean" truevalue="-S" falsevalue="" label="Skip mate rescue" help="-S"/>
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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185 <param name="P" type="boolean" truevalue="-P" falsevalue="" label="Skip pairing; mate rescue performed unless -S also in use" help="-P"/>
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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186 <param name="e" type="boolean" truevalue="-e" falsevalue="" label="Discard full-length exact matches" help="-e"/>
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187 </when>
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188 <when value="do_not_set">
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189 <!-- do nothing -->
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190 </when>
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191 </conditional>
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192
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193 <conditional name="scoring_options">
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194 <param name="scoring_options_selector" type="select" label="Set scoring options?" help="Sets -A, -B, -O, -E, -L, and -U options.">
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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195 <option value="set">Set</option>
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196 <option value="do_not_set" selected="True">Do not set</option>
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197 </param>
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198 <when value="set">
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199 <param name="A" type="integer" value="1" label="Score for a sequence match" help="-A; scales options -T, -d, -B, -O, -E, -L, and -U unless overridden; default=1"/>
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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200 <param name="B" type="integer" value="4" label="Penalty for a mismatch" help="-B; default=4"/>
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201 <param name="O" type="text" value="6,6" label="Gap open penalties for deletions and insertions" help="-O; default=6,6">
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202 <sanitizer invalid_char="">
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203 <valid initial="string.digits"><add value=","/> </valid>
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204 </sanitizer>
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205 </param>
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206 <param name="E" type="text" value="1,1" label="Gap extension penalties; a gap of size k cost &#39;-O + -E*k&#39;. If two numbers are specified, the first is the penalty of extending a deletion and the second for extending an insertion" help="-E; default=1,1">
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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207 <sanitizer invalid_char="">
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208 <valid initial="string.digits"><add value=","/> </valid>
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209 </sanitizer>
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210 </param>
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211 <param name="L" type="text" value="5,5" label="Penalties for 5&#39;-end and 3&#39;-end clipping" help="-L; default=5,5; When performing Smith-Waterman extension, BWA-MEM keeps track of the best score reaching the end of query. If this score is larger than the best Smith-Waterman score minus the clipping penalty, clipping will not be applied. Note that in this case, the SAM AS tag reports the best Smith-Waterman score; clipping penalty is not deduced">
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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212 <sanitizer invalid_char="">
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213 <valid initial="string.digits"><add value=","/> </valid>
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214 </sanitizer>
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215 </param>
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216 <param name="U" type="integer" value="17" label="Penalty for an unpaired read pair" help="-U; default=17"/>
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217 </when>
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218 <when value="do_not_set">
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219 <!-- do nothing -->
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220 </when>
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221 </conditional>
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222
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223 <conditional name="io_options">
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224 <param name="io_options_selector" type="select" label="Set input/output options" help="Sets -T, -h, -a, -C, -V, -Y, and -M options.">
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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225 <option value="set">Set</option>
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226 <option value="do_not_set" selected="True">Do not set</option>
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227 </param>
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228 <when value="set">
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229 <param name="T" type="integer" value="30" label="Minimum score to output" help="-T; default=30"/>
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230 <param name="h" type="integer" value="5" label="If there are less than THIS VALUE hits with score &gt;80% of the max score, output them all in the XA tag" help="-h; default=5" />
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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231 <param name="a" type="boolean" truevalue="-a" falsevalue="" label="Output all alignments for single-ends or unpaired paired-ends" help="-a; These alignments will be flagged as secondary alignments"/>
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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232 <param name="C" type="boolean" truevalue="-C" falsevalue="" label="Append FASTA/FASTQ comment to BAM output" help="-C"/>
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233 <param name="V" type="boolean" truevalue="-V" falsevalue="" label="Output the reference FASTA header in the XR tag" help="-C"/>
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234 <param name="Y" type="boolean" truevalue="-Y" falsevalue="" label="Use soft clipping for supplementary alignments" help="-Y; By default, BWA-MEM uses soft clipping for the primary alignment and hard clipping for supplementary alignments" />
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235 <param name="M" type="boolean" truevalue="-M" falsevalue="" label="Mark shorter split hits of a chimeric alignment in the FLAG field as 'secondary alignment' instead of 'supplementary alignment'" help="-M; For Picard&lt;1.96 compatibility" />
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236 </when>
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237 <when value="do_not_set">
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238 <!-- do nothing -->
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239 </when>
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240 </conditional>
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241 </when>
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242 </conditional>
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243 </inputs>
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244
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245 <outputs>
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246 <data format="bam" name="bam_output" label="${tool.name} on ${on_string} (mapped reads in BAM format)">
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247 <expand macro="dbKeyActionsBwaMem" />
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248 </data>
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249 </outputs>
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250
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251 <tests>
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252 <test>
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253 <param name="reference_source_selector" value="history" />
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254 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
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255 <param name="fastq_input_selector" value="paired"/>
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256 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/>
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257 <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
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258 <param name="analysis_type_selector" value="illumina"/>
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259 <output name="bam_output" ftype="bam" file="bwa-mem-test1.bam" lines_diff="2" />
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260 </test>
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261 <test>
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262 <param name="reference_source_selector" value="history" />
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263 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
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264 <param name="fastq_input_selector" value="single"/>
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265 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fasta1.fa"/>
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266 <param name="analysis_type_selector" value="illumina"/>
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267 <output name="bam_output" ftype="bam" file="bwa-mem-test1-fasta.bam" lines_diff="2" />
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268 </test>
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269 <test>
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270 <param name="reference_source_selector" value="history" />
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271 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
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272 <param name="fastq_input_selector" value="paired"/>
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273 <param name="fastq_input1" ftype="fastqsanger.gz" value="bwa-mem-fastq1.fq.gz"/>
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274 <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
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275 <param name="analysis_type_selector" value="illumina"/>
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276 <output name="bam_output" ftype="bam" file="bwa-mem-test1.bam" lines_diff="2" />
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277 </test>
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278 <test>
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279 <param name="reference_source_selector" value="history" />
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280 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
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281 <param name="index_a" value="is"/>
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282 <param name="fastq_input_selector" value="paired"/>
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283 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/>
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284 <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
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285 <param name="rg_selector" value="set"/>
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286 <param name="ID" value="rg1"/>
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287 <param name="PL" value="CAPILLARY"/>
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288 <param name="LB" value="AARDVARK-1" />
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289 <param name="analysis_type_selector" value="illumina"/>
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290 <output name="bam_output" ftype="bam" file="bwa-mem-test2.bam" lines_diff="2" />
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291 </test>
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292 </tests>
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293 <help>
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294 **What is does**
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295
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296 From http://arxiv.org/abs/1303.3997:
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297
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298 BWA-MEM is a new alignment algorithm for aligning sequence reads or long query sequences against a large reference genome such as human.
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299 It automatically chooses between local and end-to-end alignments, supports paired-end reads and performs chimeric alignment.
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300 The algorithm is robust to sequencing errors and applicable to a wide range of sequence lengths from 70bp to a few megabases.
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301 For mapping 100bp sequences, BWA-MEM shows better performance than several state-of-art read aligners to date.
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302
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303 It is best suited for mapping long (>70 nt) reads against large reference genomes.
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304
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305 This Galaxy tool wraps bwa-mem module of bwa read mapping tool. Galaxy implementation takes fastq files as input and produces output in BAM (not SAM) format, which can be further processed using various BAM utilities exiting in Galaxy (BAMTools, SAMTools, Picard).
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306
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307 -----
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308
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309 **Indices: Selecting reference genomes for BWA**
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310
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311 Galaxy wrapper for BWA allows you select between precomputed and user-defined indices for reference genomes using **Will you select a reference genome from your history or use a built-in index?** flag. This flag has two options:
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312
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313 1. **Use a built-in genome index** - when selected (this is default), Galaxy provides the user with **Select reference genome index** dropdown. Genomes listed in this dropdown have been pre-indexed with bwa index utility and are ready to be mapped against.
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314 2. **Use a genome from the history and build index** - when selected, Galaxy provides the user with **Select reference genome sequence** dropdown. This dropdown is populated by all FASTA formatted files listed in your current history. If your genome of interest is uploaded into history it will be shown there. Selecting a genome from this dropdown will cause Galaxy to first transparently index it using `bwa index` command, and then run mapping with `bwa mem`.
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315
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316 If your genome of interest is not listed here you have two choices:
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317
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318 1. Contact galaxy team using **Help->Support** link at the top of the interface and let us know that an index needs to be added
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319 2. Upload your genome of interest as a FASTA file to Galaxy history and selected **Use a genome from the history and build index** option.
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320
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321 -----
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322
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323 **Galaxy-specific option**
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324
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325 Galaxy allows four levels of control over bwa-mem options provided by **Select analysis mode** menu option. These are:
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326
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327 1. *Simple Illumina mode*: The simplest possible bwa mem application in which it alignes single or paired-end data to reference using default parameters. It is equivalent to the following command: bwa mem &lt;reference index&gt; &lt;fastq dataset1&gt; [fastq dataset2]
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328 2. *PacBio mode*: The mode adjusted specifically for mapping of long PacBio subreads. Equivalent to the following command: bwa mem -k17 -W40 -r10 -A1 -B1 -O1 -E1 -L0 &lt;reference index&gt; &lt;PacBio dataset in fastq format&gt;
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329 3. *Full list of options*: Allows access to all options through Galaxy interface.
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330
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331 ------
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332
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333 **BWA MEM options**
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334
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335 Each Galaxy parameter widget corresponds to command line flags listed below:
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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336
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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337 Algorithm options::
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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338
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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339 -k INT minimum seed length [19]
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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340 -w INT band width for banded alignment [100]
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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341 -d INT off-diagonal X-dropoff [100]
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342 -r FLOAT look for internal seeds inside a seed longer than {-k} * FLOAT [1.5]
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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343 -y INT find MEMs longer than {-k} * {-r} with size less than INT [0]
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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344 -c INT skip seeds with more than INT occurrences [500]
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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345 -D FLOAT drop chains shorter than FLOAT fraction of the longest overlapping chain [0.50]
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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346 -W INT discard a chain if seeded bases shorter than INT [0]
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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347 -m INT perform at most INT rounds of mate rescues for each read [50]
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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348 -S skip mate rescue
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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349 -P skip pairing; mate rescue performed unless -S also in use
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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350 -e discard full-length exact matches
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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351
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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352 Scoring options::
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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353
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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354 -A INT score for a sequence match, which scales options -TdBOELU unless overridden [1]
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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355 -B INT penalty for a mismatch [4]
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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356 -O INT[,INT] gap open penalties for deletions and insertions [6,6]
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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357 -E INT[,INT] gap extension penalty; a gap of size k cost '{-O} + {-E}*k' [1,1]
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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358 -L INT[,INT] penalty for 5'- and 3'-end clipping [5,5]
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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359 -U INT penalty for an unpaired read pair [17]
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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360
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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361 Input/output options::
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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362
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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363 -p first query file consists of interleaved paired-end sequences
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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364 -R STR read group header line such as '@RG\tID:foo\tSM:bar' [null]
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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365
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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366 -v INT verbose level: 1=error, 2=warning, 3=message, 4+=debugging [3]
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367 -T INT minimum score to output [30]
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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368 -h INT if there are &lt;INT hits with score &gt;80% of the max score, output all in XA [5]
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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369 -a output all alignments for SE or unpaired PE
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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370 -C append FASTA/FASTQ comment to SAM output
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371 -V output the reference FASTA header in the XR tag
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372 -Y use soft clipping for supplementary alignments
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373 -M mark shorter split hits as secondary
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374
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375 -I FLOAT[,FLOAT[,INT[,INT]]]
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376 specify the mean, standard deviation (10% of the mean if absent), max
c9c78719ef26 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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377 (4 sigma from the mean if absent) and min of the insert size distribution.
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378 FR orientation only. [inferred]
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379
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380 @dataset_collections@
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381
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382 @RG@
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383
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384 @info@
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385 </help>
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386 <citations>
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387 <citation type="doi">10.1093/bioinformatics/btp324</citation>
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388 <citation type="doi">10.1093/bioinformatics/btp698</citation>
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389 <citation type="bibtex">@misc{1303.3997,
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390 Author = {Heng Li},
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391 Title = {Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM},
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392 Year = {2013},
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393 Eprint = {arXiv:1303.3997},
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394 url = {http://arxiv.org/abs/1303.3997},
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395 }</citation>
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396 </citations>
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397 </tool>