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annotate bwa-mem.xml @ 26:2477830927ec draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit 6e9628b1d92fdb358b79959ad54a456cfa46fa33
author iuc
date Fri, 17 May 2024 21:09:07 +0000
parents e188dc7a68e6
children
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1 <?xml version="1.0"?>
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2 <tool id="bwa_mem" name="Map with BWA-MEM" version="@TOOL_VERSION@" profile="22.05">
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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>
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6 <import>bwa_macros.xml</import>
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7 </macros>
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8 <expand macro="bio_tools"/>
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9 <expand macro="requirements"/>
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10 <expand macro="stdio"/>
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11 <command><![CDATA[
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12 @pipefail@
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13 @set_reference_fasta_filename@
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14
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15 ## Begin BWA-MEM command line
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16
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17 bwa mem
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64f11cf59c6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit 055c6c3de6c9e0f219f5792f6580244815c1cd31"
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64f11cf59c6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit 055c6c3de6c9e0f219f5792f6580244815c1cd31"
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19 #if str( $output_sort ) == "unsorted":
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20 -t 1
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21 #else
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22 -t "\${GALAXY_SLOTS:-1}"
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23 #end if
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24 ## Verbosity is set to 1 (errors only)
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25 -v 1
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26
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27 #if str( $fastq_input.fastq_input_selector ) == "paired_iv":
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28 ## For interleaved fastq files set -p option
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
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29 -p
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30 ## check that insert statistics is used
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
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31 #if str( $fastq_input.iset_stats ):
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32 -I '${fastq_input.iset_stats}'
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33 #end if
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34 #end if
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35
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36 #if str( $analysis_type.analysis_type_selector ) not in ["illumina", "full"]:
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
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37 -x '$analysis_type.analysis_type_selector'
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38 #elif str( $analysis_type.analysis_type_selector ) == "full":
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39 ## Algorithmic options
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40 #if str( $analysis_type.algorithmic_options.algorithmic_options_selector ) == "set":
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41 -k '${analysis_type.algorithmic_options.k}'
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
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42 -w '${analysis_type.algorithmic_options.w}'
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
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43 -d '${analysis_type.algorithmic_options.d}'
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44 -r '${analysis_type.algorithmic_options.r}'
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
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45 -y '${analysis_type.algorithmic_options.y}'
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46 -c '${analysis_type.algorithmic_options.c}'
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47 -D '${analysis_type.algorithmic_options.D}'
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48 -W '${analysis_type.algorithmic_options.W}'
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49 -m '${analysis_type.algorithmic_options.m}'
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50 ${analysis_type.algorithmic_options.S}
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51 ${analysis_type.algorithmic_options.P}
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52 ${analysis_type.algorithmic_options.e}
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53 #end if
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54
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55 ## Scoring options
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56 #if str( $analysis_type.scoring_options.scoring_options_selector ) == "set":
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57 -A '${analysis_type.scoring_options.A}'
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58 -B '${analysis_type.scoring_options.B}'
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59 -O '${analysis_type.scoring_options.O}'
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60 -E '${analysis_type.scoring_options.E}'
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61 -L '${analysis_type.scoring_options.L}'
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62 -U '${analysis_type.scoring_options.U}'
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63 #end if
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64
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65 ## IO options
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66 #if str( $analysis_type.io_options.io_options_selector ) == "set":
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67 -T '${analysis_type.io_options.T}'
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68 -h '${analysis_type.io_options.h}'
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69 ${analysis_type.io_options.a}
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70 ${analysis_type.io_options.C}
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71 ${analysis_type.io_options.V}
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72 ${analysis_type.io_options.Y}
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73 ${analysis_type.io_options.M}
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74 ${analysis_type.io_options.five}
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75 ${analysis_type.io_options.q}
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76 #end if
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77
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78 #end if
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79
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80 ## Handle read group options...
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81 @define_read_group_helpers@
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82 #if str( $fastq_input.fastq_input_selector ) == "paired":
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83 #set $rg_auto_name = $read_group_name_default($fastq_input.fastq_input1, $fastq_input.fastq_input2)
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84 #else:
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85 #set $rg_auto_name = $read_group_name_default($fastq_input.fastq_input1)
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86 #end if
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87 @set_use_rg_var@
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88 @set_read_group_vars@
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89 #if $use_rg
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90 @set_rg_string@
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91 -R '$rg_string'
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92 #end if
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93
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94 #if str( $fastq_input.fastq_input_selector ) == "paired":
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95 ## check that insert statistics is used
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96 #if str( $fastq_input.iset_stats ):
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97 -I '${fastq_input.iset_stats}'
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98 #end if
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99
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100 '${reference_fasta_filename}'
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101 '${fastq_input.fastq_input1}'
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102 '${fastq_input.fastq_input2}'
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103 #elif str( $fastq_input.fastq_input_selector ) == "paired_collection":
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104 ## check that insert statistics is used
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105 #if str( $fastq_input.iset_stats ):
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106 -I '${fastq_input.iset_stats}'
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107 #end if
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108
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109 '${reference_fasta_filename}'
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110 '${fastq_input.fastq_input1.forward}'
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111 '${fastq_input.fastq_input1.reverse}'
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112 #else:
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113 '${reference_fasta_filename}'
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114 '${fastq_input.fastq_input1}'
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115 #end if
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116
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117 #if str( $output_sort ) == "coordinate":
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118 | samtools sort -@\${GALAXY_SLOTS:-2} -T "\${TMPDIR:-.}" -O bam -o '$bam_output'
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119 #elif str( $output_sort ) == "name":
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120 | samtools sort -n -@\${GALAXY_SLOTS:-2} -T "\${TMPDIR:-.}" -O bam -o '$bam_output'
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121 #else
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122 | samtools view -@ \${GALAXY_SLOTS:-2} -bS - -o '$bam_output'
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123 #end if
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124
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125
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126 ]]></command>
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127
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128 <inputs>
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129 <expand macro="reference_source_conditional" />
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130 <conditional name="fastq_input">
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131 <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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132 <option value="paired">Paired</option>
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133 <option value="single">Single</option>
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134 <option value="paired_collection">Paired Collection</option>
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135 <option value="paired_iv">Paired Interleaved</option>
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136 </param>
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137 <when value="paired">
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138 <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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139 <param name="fastq_input2" type="data" format="fastqsanger,fastqsanger.gz,fasta" label="Select second set of reads" help="Specify dataset with reverse reads"/>
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140 <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.">
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141 <sanitizer invalid_char="">
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142 <valid initial="string.digits"><add value=","/> </valid>
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143 </sanitizer>
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144 </param>
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145 </when>
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146 <when value="single">
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147 <param name="fastq_input1" type="data" format="fastqsanger,fastqsanger.gz,fasta" label="Select fastq dataset" help="Specify dataset with single reads"/>
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148 </when>
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149 <when value="paired_collection">
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150 <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"/>
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151 <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.">
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152 <sanitizer invalid_char="">
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153 <valid initial="string.digits"><add value=","/> </valid>
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154 </sanitizer>
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155 </param>
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156 </when>
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157 <when value="paired_iv">
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158 <param name="fastq_input1" type="data" format="fastqsanger,fastqsanger.gz,fasta" label="Select fastq dataset" help="Specify dataset with interleaved reads"/>
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159 <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.">
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160 <sanitizer invalid_char="">
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161 <valid initial="string.digits"><add value=","/> </valid>
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162 </sanitizer>
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163 </param>
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164 </when>
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165 </conditional>
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166
18
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167 <expand macro="read_group_conditional" />
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168
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169 <conditional name="analysis_type">
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170 <param name="analysis_type_selector" type="select" label="Select analysis mode" help="Please note that minimap2 is recommended over BWA as the aligner for long-read or contig data, for which it outperforms BWA in speed and typically in accuracy (see tool help below).">
18
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171 <option value="illumina">1.Simple Illumina mode</option>
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172 <option value="pacbio">2.PacBio mode (-x pacbio)</option>
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173 <option value="ont2d">3.Nanopore 2D-reads mode (-x ont2d)</option>
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174 <option value="intractg">4.Intra-species contigs mode (-x intractg)</option>
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175 <option value="full">5.Full list of options</option>
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176 </param>
18
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177 <when value="illumina">
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178 <!-- do nothing -->
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179 </when>
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180 <when value="pacbio">
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181 <!-- do nothing. all magic happens within <command> tag -->
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182 </when>
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183 <when value="ont2d">
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184 <!-- do nothing. all magic happens within <command> tag -->
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185 </when>
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186 <when value="intractg">
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187 <!-- do nothing. all magic happens within <command> tag -->
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188 </when>
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189 <when value="full">
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190 <conditional name="algorithmic_options">
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191 <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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192 <option value="set">Set</option>
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193 <option value="do_not_set" selected="True">Do not set</option>
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194 </param>
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195 <when value="set">
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196 <param name="k" type="integer" value="19" label="Minimum seed length" help="-k; default=19"/>
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197 <param name="w" type="integer" value="100" label="Band width for banded alignment" help="-w; default=100"/>
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198 <param name="d" type="integer" value="100" label="Off-diagonal X-dropoff" help="-d; default=100"/>
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199 <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" />
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200 <param name="y" type="integer" value="20" label="Seed occurrence for the 3rd round seeding" help="-y; default=20" />
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201 <param name="c" type="integer" value="500" label="Skip seeds with more than that many occurrences" help="-c; default=500"/>
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202 <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"/>
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203 <param name="W" type="integer" value="0" label="Discard a chain if seeded bases shorter than THIS VALUE" help="-W; default=0"/>
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204 <param name="m" type="integer" value="50" label="Perform at most this many rounds of mate rescues for each read" help="-m; default=50"/>
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205 <param name="S" type="boolean" truevalue="-S" falsevalue="" label="Skip mate rescue" help="-S"/>
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206 <param name="P" type="boolean" truevalue="-P" falsevalue="" label="Skip pairing; mate rescue performed unless -S also in use" help="-P"/>
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207 <param name="e" type="boolean" truevalue="-e" falsevalue="" label="Discard full-length exact matches" help="-e"/>
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208 </when>
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209 <when value="do_not_set">
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210 <!-- do nothing -->
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211 </when>
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212 </conditional>
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213
18
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214 <conditional name="scoring_options">
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215 <param name="scoring_options_selector" type="select" label="Set scoring options?" help="Sets -A, -B, -O, -E, -L, and -U options.">
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216 <option value="set">Set</option>
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217 <option value="do_not_set" selected="True">Do not set</option>
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218 </param>
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219 <when value="set">
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220 <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"/>
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221 <param name="B" type="integer" value="4" label="Penalty for a mismatch" help="-B; default=4"/>
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222 <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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223 <sanitizer invalid_char="">
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224 <valid initial="string.digits"><add value=","/> </valid>
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225 </sanitizer>
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226 </param>
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227 <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">
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228 <sanitizer invalid_char="">
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229 <valid initial="string.digits"><add value=","/> </valid>
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230 </sanitizer>
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231 </param>
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232 <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">
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233 <sanitizer invalid_char="">
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234 <valid initial="string.digits"><add value=","/> </valid>
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235 </sanitizer>
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236 </param>
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237 <param name="U" type="integer" value="17" label="Penalty for an unpaired read pair" help="-U; default=17"/>
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238 </when>
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239 <when value="do_not_set">
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240 <!-- do nothing -->
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241 </when>
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242 </conditional>
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243
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244 <conditional name="io_options">
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245 <param name="io_options_selector" type="select" label="Set input/output options" help="Sets -T, -h, -a, -C, -V, -Y, and -M options.">
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246 <option value="set">Set</option>
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247 <option value="do_not_set" selected="True">Do not set</option>
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248 </param>
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249 <when value="set">
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250 <param name="five" argument="-5" type="boolean" truevalue="-5" falsevalue="" label="For split alignment, take alignment with smallest coordinate as primary" help="Useful for HiC data"/>
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251 <param argument="-q" type="boolean" truevalue="-q" falsevalue="" label="Don't lower MAPQ for split alignment" help="By default the MAPQ score of a supplementary alignment will be lowered to the primary alignment score."/>
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252 <param name="T" type="integer" value="30" label="Minimum score to output" help="-T; default=30"/>
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253 <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" />
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254 <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"/>
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255 <param name="C" type="boolean" truevalue="-C" falsevalue="" label="Append FASTA/FASTQ comment to BAM output" help="-C"/>
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256 <param name="V" type="boolean" truevalue="-V" falsevalue="" label="Output the reference FASTA header in the XR tag" help="-C"/>
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257 <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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258 <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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259 </when>
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260 <when value="do_not_set">
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261 <!-- do nothing -->
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262 </when>
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263 </conditional>
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264 </when>
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265 </conditional>
24
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266 <param name="output_sort" type="select" label="BAM sorting mode" help="The 'Not sorted' option can extend the run time of the tool significantly (cause it requires running on only a single thread).">
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267 <option value="coordinate" selected="True">Sort by chromosomal coordinates</option>
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268 <option value="name">Sort by read names (i.e., the QNAME field) </option>
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269 <option value="unsorted">Not sorted (sorted as input)</option>
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270 </param>
18
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271 </inputs>
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272
18
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273 <outputs>
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274 <data format="bam" name="bam_output" label="${tool.name} on ${on_string} (mapped reads in BAM format)">
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275 <expand macro="dbKeyActionsBwaMem" />
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276 <change_format>
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277 <when input="output_sort" value="name" format="qname_sorted.bam" />
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278 <when input="output_sort" value="unsorted" format="qname_input_sorted.bam" />
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279 </change_format>
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280 </data>
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281 </outputs>
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282 <tests>
26
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283 <!-- `samtools sort` in the new update adds PG lines to the output so the lines_diff is changed from "2" to "4" -->
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284 <test expect_num_outputs="1">
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285 <param name="reference_source_selector" value="history" />
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286 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
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287 <param name="fastq_input_selector" value="paired"/>
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288 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/>
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289 <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
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290 <param name="analysis_type_selector" value="illumina"/>
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291 <output name="bam_output" ftype="bam" file="bwa-mem-test1.bam" lines_diff="4" />
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292 </test>
26
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293 <test expect_num_outputs="1">
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294 <param name="reference_source_selector" value="history" />
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295 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
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296 <param name="fastq_input_selector" value="single"/>
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297 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fasta1.fa"/>
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298 <param name="analysis_type_selector" value="illumina"/>
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299 <output name="bam_output" ftype="bam" file="bwa-mem-test1-fasta.bam" lines_diff="4" />
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300 </test>
26
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301 <test expect_num_outputs="1">
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302 <param name="reference_source_selector" value="history" />
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303 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
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304 <param name="fastq_input_selector" value="paired"/>
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305 <param name="fastq_input1" ftype="fastqsanger.gz" value="bwa-mem-fastq1.fq.gz"/>
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306 <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
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307 <param name="analysis_type_selector" value="illumina"/>
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308 <output name="bam_output" ftype="bam" file="bwa-mem-test1.bam" lines_diff="4" />
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309 </test>
26
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310 <test expect_num_outputs="1">
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311 <param name="reference_source_selector" value="history" />
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312 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
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313 <param name="index_a" value="is"/>
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314 <param name="fastq_input_selector" value="paired"/>
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315 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/>
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316 <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
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317 <param name="rg_selector" value="set"/>
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318 <param name="ID" value="rg1"/>
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319 <param name="PL" value="CAPILLARY"/>
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320 <param name="LB" value="AARDVARK-1" />
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321 <param name="analysis_type_selector" value="illumina"/>
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322 <output name="bam_output" ftype="bam" file="bwa-mem-test2.bam" lines_diff="4" />
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323 </test>
26
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324 <test expect_num_outputs="1">
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325 <param name="reference_source_selector" value="history" />
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326 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
64f11cf59c6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit 055c6c3de6c9e0f219f5792f6580244815c1cd31"
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327 <param name="fastq_input_selector" value="paired"/>
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328 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/>
64f11cf59c6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit 055c6c3de6c9e0f219f5792f6580244815c1cd31"
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329 <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
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330 <param name="analysis_type_selector" value="illumina"/>
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331 <param name="output_sort" value="unsorted"/>
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332 <output name="bam_output" ftype="qname_input_sorted.bam" file="bwa-mem-test3.bam" lines_diff="4" />
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333 </test>
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334 <test expect_num_outputs="1">
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335 <param name="reference_source_selector" value="history" />
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336 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
64f11cf59c6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit 055c6c3de6c9e0f219f5792f6580244815c1cd31"
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337 <param name="fastq_input_selector" value="paired"/>
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338 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/>
64f11cf59c6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit 055c6c3de6c9e0f219f5792f6580244815c1cd31"
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339 <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
64f11cf59c6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit 055c6c3de6c9e0f219f5792f6580244815c1cd31"
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340 <param name="analysis_type_selector" value="illumina"/>
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341 <param name="output_sort" value="name"/>
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342 <output name="bam_output" ftype="qname_sorted.bam" file="bwa-mem-test4.bam" lines_diff="4" />
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343 </test>
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344 <test expect_num_outputs="1">
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345 <param name="reference_source_selector" value="history" />
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346 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
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diff changeset
347 <conditional name="fastq_input">
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348 <param name="fastq_input_selector" value="paired_collection"/>
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349 <param name="fastq_input1">
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diff changeset
350 <collection type="paired">
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351 <element name="forward" value="bwa-mem-fastq1.fq" />
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352 <element name="reverse" value="bwa-mem-fastq2.fq" />
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353 </collection>
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354 </param>
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355 </conditional>
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diff changeset
356 <conditional name="analysis_type">
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357 <param name="analysis_type_selector" value="illumina"/>
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358 </conditional>
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359 <param name="output_sort" value="name"/>
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360 <output name="bam_output" ftype="qname_sorted.bam" file="bwa-mem-test4.bam" lines_diff="4" />
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361 </test>
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362 </tests>
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363 <help><![CDATA[
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364
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365 **What it does**
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366
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367 This Galaxy tool wraps the bwa-mem module of the BWA_ read mapping tool. For more details about the different modules of the BWA package see the `BWA manual`_.
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368
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369 The Galaxy implementation takes fastq files as input and produces output in BAM format, which can be further processed using various BAM utilities existing in Galaxy (BAMTools, SAMTools, Picard).
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370
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371 From http://arxiv.org/abs/1303.3997:
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372
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373 BWA-MEM is an alignment algorithm for aligning sequence reads or long query sequences against a large reference genome such as human.
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374 It automatically chooses between local and end-to-end alignments, supports paired-end reads and performs chimeric alignment.
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375 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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376
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377 -----
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378
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379 @ref_genomes@
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380
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381 -----
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382
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383 **Analysis modes**
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384
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385 The tool supports different preconfigured analysis modes optimized for different types of input data. Alternatively, it allows you to take full control over all available options.
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386
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387 The preconfigured modes are:
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388
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389 1. *Simple Illumina mode*
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390
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391 This corresponds to the simplest possible and standard bwa mem application in which it aligns single or paired-end data to a reference using default parameters. It is equivalent to the following command: bwa mem <reference index> <fastq dataset1> [fastq dataset2]
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392 2. *PacBio mode*
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393
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394 This mode is adjusted specifically for mapping of long PacBio subreads. It is running bwa mame with the `-x pacbio` option.
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395 3. *Nanopore 2D-reads mode*
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396
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397 This mode is running bwa mem with the `-x ont2d` option.
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398 4. *Intra-sepcies contigs mode*
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399
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400 This mode is running bwa mem with the `-x intractg` option.
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401
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402 .. class:: infomark
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403
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404 Please note: minimap2_ is recommended over and outperforms BWA-MEM for most types of input data except for Illumina short reads. For Illumina short-read mapping you may also consider using `BWA-MEM2`_, which is about twice as fast as BWA-MEM.
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405
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406 -----
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407
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408 **Bam sorting mode**
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409
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410 The generated bam files can be sorted according to three criteria: coordinates, names and input order.
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411
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412 In coordinate sorted mode the reads are sorted by coordinates. It means that the reads from the beginning of the first chromosome are first in the file.
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413
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414 When sorted by read name, the file is sorted by the reference ID (i.e., the QNAME field).
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415
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416 Finally, the *No sorted (sorted as input)* option yield a BAM file in which the records are sorted in an order corresponding to the order of the reads in the original input file. This option requires using a single thread to perform the conversion from SAM to BAM format, so the runtime is extended.
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417
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418
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419 @RG@
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420
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421 @links@
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422 .. _minimap2: https://github.com/lh3/minimap2
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423 .. _`BWA-MEM2`: https://github.com/bwa-mem2/bwa-mem2
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424 ]]></help>
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425 <citations>
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426 <citation type="doi">10.1093/bioinformatics/btp324</citation>
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427 <citation type="doi">10.1093/bioinformatics/btp698</citation>
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428 <citation type="bibtex">@misc{1303.3997,
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429 Author = {Heng Li},
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430 Title = {Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM},
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431 Year = {2013},
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432 Eprint = {arXiv:1303.3997},
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433 url = {http://arxiv.org/abs/1303.3997},
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434 }</citation>
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435 </citations>
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436 </tool>