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annotate bwa.xml @ 23:3fe632431b68 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit 777181bd04849dab271ee2cc95e45c182947d308"
author iuc
date Tue, 19 May 2020 11:29:11 -0400
parents 8d2a528a9513
children e188dc7a68e6
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1 <?xml version="1.0"?>
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2 <tool id="bwa" name="Map with BWA" version="@VERSION@.4">
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3 <description>- map short reads (&lt; 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 <token name="@command_options@">
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8 #if str( $analysis_type.analysis_type_selector ) == "full":
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9 -n ${analysis_type.n}
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10 -o ${analysis_type.o}
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11 -e ${analysis_type.e}
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12 -i ${analysis_type.i}
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13 -d ${analysis_type.d}
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14 -l ${analysis_type.l}
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15 -k ${analysis_type.k}
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16 -m ${analysis_type.m}
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17 -M ${analysis_type.M}
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18 -O ${analysis_type.O}
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19 -E ${analysis_type.E}
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20 -R ${analysis_type.R}
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21 -q ${analysis_type.q}
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22 #if str( $analysis_type.B ):
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23 -B ${analysis_type.B}
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24 #end if
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25 #if str( $analysis_type.L ):
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26 -L ${analysis_type.L}
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27 #end if
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28 #end if
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29 </token>
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30 <token name="@read_group_options@">
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31 #if $use_rg:
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32 @set_rg_string@
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33 -r '$rg_string'
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34 #end if
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35 </token>
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36 <xml name="advanced_pe_options">
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
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37 <param name="adv_pe_options_selector" type="select" label="Set advanced paired end options?"
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38 help="Provides additional controls">
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39 <option value="set">Set</option>
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40 <option value="do_not_set" selected="True">Do not set</option>
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41 </param>
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42 <when value="set">
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43 <param name="a" type="integer" value="500"
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44 label="Maximum insert size for a read pair to be considered being mapped properly."
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45 help="sampe -a; This option is only used when there are not enough good alignment to infer the distribution of insert sizes; default=500"/>
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46 <param name="o" type="integer" value="100000"
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47 label="Maximum occurrences of a read for pairing. A read with more occurrences will be treated as a single-end read."
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48 help="sampe -o; Reducing this parameter helps faster pairing; default=100000"/>
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49 <param name="n" type="integer" value="3"
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50 label="Maximum number of alignments to output in the XA tag for reads paired properly."
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51 help="sampe -n; If a read has more than this many hits, the XA tag will not be written; default=3"/>
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52 <param name="N" type="integer" value="10"
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53 label="Maximum number of alignments to output in the XA tag for disconcordant read pairs (excluding singletons)."
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54 help="sampe -N; If a read has more than this many hits, the XA tag will not be written; default=10"/>
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55 <param name="c" type="float" value="0.00005" label="Prior of chimeric rate (lower bound)"
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56 help="sampe -c"/>
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57 </when>
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58 <when value="do_not_set">
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59 <!-- do nothing -->
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60 </when>
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61 </xml>
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62 <xml name="advanced_se_options">
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63 <param name="adv_se_options_selector" type="select" label="Set advanced single end options?"
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64 help="Provides additional controls">
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65 <option value="set">Set</option>
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66 <option value="do_not_set" selected="True">Do not set</option>
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67 </param>
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68 <when value="set">
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69 <param name="n" type="integer" value="3" label="Maximum number of alignments to output in the XA tag."
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70 help="-n; If a read has more than this many hits, the XA tag will not be written; default=3"/>
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71 </when>
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72 <when value="do_not_set">
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73 <!-- do nothing -->
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74 </when>
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75 </xml>
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76 </macros>
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77 <expand macro="requirements"/>
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78 <expand macro="stdio"/>
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79 <command>
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80 <![CDATA[
21
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81 @pipefail@
18
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82 @set_reference_fasta_filename@
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83
18
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84 ## setup vars for rg handling...
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85 @define_read_group_helpers@
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86 #if str( $input_type.input_type_selector ) == "paired":
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87 #set $rg_auto_name = $read_group_name_default($input_type.fastq_input1, $input_type.fastq_input2)
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88 #elif str( $input_type.input_type_selector ) in ["single_bam", "paired_bam"]:
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89 #set $rg_auto_name = $read_group_name_default($input_type.bam_input)
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90 #else
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91 #set $rg_auto_name = $read_group_name_default($input_type.fastq_input1)
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92 #end if
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93 @set_use_rg_var@
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94 @set_read_group_vars@
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95
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96 ## Begin bwa command line
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97
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98 ####### Fastq paired
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99
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100 #if str( $input_type.input_type_selector ) == "paired" or str( $input_type.input_type_selector ) == "paired_collection":
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101 bwa aln
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102 -t "\${GALAXY_SLOTS:-1}"
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103 @command_options@
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104 '$reference_fasta_filename'
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105 #if str( $input_type.input_type_selector ) == "paired_collection":
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106 '${input_type.fastq_input1.forward}'
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107 #else
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108 '${input_type.fastq_input1}'
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109 #end if
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110 > first.sai &&
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111
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112 bwa aln
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113 -t "\${GALAXY_SLOTS:-1}"
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114 @command_options@
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115 '${reference_fasta_filename}'
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116 #if str( $input_type.input_type_selector ) == "paired_collection":
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117 '${input_type.fastq_input1.reverse}'
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118 #else
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119 '${input_type.fastq_input2}'
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120 #end if
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121 > second.sai &&
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122
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123 bwa sampe
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124 #if str( $input_type.adv_pe_options.adv_pe_options_selector) == "True":
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125 -a ${$input_type.adv_pe_options.a}
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126 -o ${$input_type.adv_pe_options.o}
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127 -n ${$input_type.adv_pe_options.n}
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128 -N ${$input_type.adv_pe_options.N}
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129 #end if
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130 @read_group_options@
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131 #if str( $input_type.input_type_selector ) == "paired_collection":
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132 '${reference_fasta_filename}' first.sai second.sai '${input_type.fastq_input1.forward}' '${input_type.fastq_input1.reverse}'
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133 #else:
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134 '${reference_fasta_filename}' first.sai second.sai '${input_type.fastq_input1}' '${input_type.fastq_input2}'
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135 #end if
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136
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137 ## Fastq single
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138
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139 #elif str( $input_type.input_type_selector ) == "single":
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140 bwa aln
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141 -t "\${GALAXY_SLOTS:-1}"
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142
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143 @command_options@
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144
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145 '${reference_fasta_filename}'
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146 '${input_type.fastq_input1}'
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147 > first.sai &&
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148
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149 bwa samse
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150
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151 #if str( $input_type.adv_se_options.adv_se_options_selector) == "True":
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152 -n ${$input_type.adv_se_options.n}
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153 #end if
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154 @read_group_options@
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155 '${reference_fasta_filename}' first.sai '${input_type.fastq_input1}'
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156
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157 ####### BAM paired
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158
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159 #elif str( $input_type.input_type_selector ) == "paired_bam":
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160 bwa aln
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161 -t "\${GALAXY_SLOTS:-1}"
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162 -b
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163 -1
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164 @command_options@
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165 '${reference_fasta_filename}'
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166 '${input_type.bam_input}'
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167 > first.sai &&
2
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168
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169 bwa aln
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170 -t "\${GALAXY_SLOTS:-1}"
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171 -b
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172 -2
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173 @command_options@
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174 '${reference_fasta_filename}'
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175 '${input_type.bam_input}'
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176 > second.sai &&
2
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177
18
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178 bwa sampe
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179
18
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180 #if str( $input_type.adv_bam_pe_options.adv_pe_options_selector) == "True":
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181 -a ${$input_type.adv_bam_pe_options.a}
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182 -o ${$input_type.adv_bam_pe_options.o}
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183 -n ${$input_type.adv_bam_pe_options.n}
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184 -N ${$input_type.adv_bam_pe_options.N}
18
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185 #end if
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186 @read_group_options@
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187 '${reference_fasta_filename}' first.sai second.sai '${input_type.bam_input}' '${input_type.bam_input}'
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188
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189 ####### Fastq single ------------ to do next
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190
18
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191 #elif str( $input_type.input_type_selector ) == "single_bam":
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192 bwa aln
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193 -t "\${GALAXY_SLOTS:-1}"
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194 -b
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195 -0
2
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196
18
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197 @command_options@
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198
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199 '${reference_fasta_filename}'
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200 '${input_type.bam_input}'
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201 > first.sai &&
2
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202
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203 bwa samse
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204
18
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205 #if str( $input_type.adv_bam_se_options.adv_se_options_selector) == "True":
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206 -n ${$input_type.adv_bam_se_options.n}
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207 #end if
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208 @read_group_options@
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209 '${reference_fasta_filename}' first.sai '${input_type.bam_input}'
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210 #end if
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211
23
3fe632431b68 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit 777181bd04849dab271ee2cc95e45c182947d308"
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212 | samtools sort -@\${GALAXY_SLOTS:-2} -T "\${TMPDIR:-.}" -O bam -o '$bam_output'
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213 ]]>
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214 </command>
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215
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216 <inputs>
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217 <expand macro="reference_source_conditional"/>
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218 <conditional name="input_type">
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219 <param name="input_type_selector" type="select" label="Select input type"
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220 help="Select between fastq and bam datasets and between paired and single end data">
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221 <option value="paired">Paired fastq</option>
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222 <option value="paired_collection">Paired fastq collection</option>
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223 <option value="single">Single fastq</option>
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224 <option value="paired_bam">Paired BAM</option>
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225 <option value="single_bam">Single BAM</option>
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226 </param>
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227 <when value="paired">
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228 <param name="fastq_input1" type="data" format="fastqsanger,fastqsanger.gz,fasta"
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229 label="Select first set of reads" help="Specify dataset with forward reads"/>
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230 <param name="fastq_input2" type="data" format="fastqsanger,fastqsanger.gz,fasta"
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231 label="Select second set of reads" help="Specify dataset with reverse reads"/>
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232 <conditional name="adv_pe_options">
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233 <expand macro="advanced_pe_options"/>
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234 </conditional>
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235 </when>
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236 <when value="paired_collection">
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237 <param name="fastq_input1" format="fastqsanger,fastqsanger.gz" type="data_collection" collection_type="paired" label="Select a paired collection"
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238 help="See help section for an explanation of dataset collections"/>
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239 <conditional name="adv_pe_options">
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240 <expand macro="advanced_pe_options"/>
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241 </conditional>
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242 </when>
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243 <when value="single">
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244 <param name="fastq_input1" type="data" format="fastqsanger,fastqsanger.gz,fasta"
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245 label="Select fastq dataset" help="Specify dataset with single reads"/>
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246 <conditional name="adv_se_options">
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247 <expand macro="advanced_se_options"/>
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248 </conditional>
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249 </when>
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250 <!-- the difference between single and paired bams is in the <command> tag portion and realated to -0, -1, and -2 options -->
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251 <when value="paired_bam">
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252 <param name="bam_input" type="data" format="bam" label="Select BAM dataset"
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253 help="Specify BAM dataset with paired reads"/>
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254 <conditional name="adv_bam_pe_options">
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255 <expand macro="advanced_pe_options"/>
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256 </conditional>
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257 </when>
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258 <when value="single_bam">
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259 <param name="bam_input" type="data" format="bam" label="Select BAM dataset"
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260 help="Specify BAM dataset with single reads"/>
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261 <conditional name="adv_bam_se_options">
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262 <expand macro="advanced_se_options"/>
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263 </conditional>
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264 </when>
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265 </conditional>
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266 <expand macro="read_group_conditional"/>
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267 <conditional name="analysis_type">
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268 <param name="analysis_type_selector" type="select" label="Select analysis mode">
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269 <option value="illumina">1.Simple Illumina mode</option>
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270 <option value="full">2.Full list of options</option>
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271 </param>
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272 <when value="illumina">
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273 <!-- do nothing -->
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274 </when>
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275 <when value="full">
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276 <param name="n" type="text" value="0.04"
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277 label="maximum edit distance if the value is integer, or the fraction of missing alignments given 2% uniform base error rate if float. In the latter case, the maximum edit distance is automatically chosen for different read lengths."
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278 help="aln -n; default=0.04"/>
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279 <param name="o" type="integer" value="1" label="maximum number or gap openings"
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280 help="aln -o; default=1"/>
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281 <param name="e" type="integer" value="-1" label="maximum number of gap extensions"
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282 help="aln -e; -1 disables long gaps and invokes k-difference mode; default=-1"/>
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283 <param name="i" type="integer" value="5"
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284 label="do not put an indel within this many bp towards the ends" help="aln -i; default=5"/>
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285 <param name="d" type="integer" value="10" label="maximum occurrences for extending a long deletion"
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286 help="aln -d; default=10"/>
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287 <param name="l" type="integer" value="32" label="seed length" help="aln -l; default=32"/>
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288 <param name="k" type="integer" value="2" label="maximum differences in the seed"
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289 help="aln -k; default=2"/>
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290 <param name="m" type="integer" value="2000000" label="maximum entries in the queue"
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291 help="aln -m; default=2000000"/>
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292 <param name="M" type="integer" value="3" label="mismatch penalty" help="aln -M; default=3"/>
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293 <param name="O" type="integer" value="11" label="gap open penalty" help="aln -O; default=11"/>
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294 <param name="E" type="integer" value="4" label="gap extension penalty" help="aln -E; default=4"/>
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295 <param name="R" type="integer" value="30"
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296 label="stop searching when there are more than this value of equally best hits"
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297 help="aln -R; default=30"/>
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298 <param name="q" type="integer" value="0" label="quality threshold for read trimming down to 35bp"
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299 help="aln -q; default=0"/>
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300 <param name="B" type="integer" optional="True" label="length of barcode"
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301 help="aln -B; optional parameter"/>
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302 <param name="L" type="float" optional="True" label="log-scaled gap penalty for long deletions"
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303 help="aln -L; optional parameter"/>
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304 </when>
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305 </conditional>
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306 </inputs>
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307 <outputs>
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308 <data format="bam" name="bam_output" label="${tool.name} on ${on_string} (mapped reads in BAM format)">
20
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309 <expand macro="dbKeyActionsBwaMem"/>
18
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310 </data>
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311 </outputs>
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312 <tests>
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313 <test>
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314 <param name="reference_source_selector" value="history"/>
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315 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
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316 <param name="input_type_selector" value="single"/>
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317 <param name="fastq_input1" ftype="fasta" value="bwa-mem-fasta1.fa"/>
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318 <param name="analysis_type_selector" value="illumina"/>
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319 <output name="bam_output" ftype="bam" file="bwa-aln-test1-fasta.bam" lines_diff="2"/>
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320 </test>
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321 <test>
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322 <param name="reference_source_selector" value="history"/>
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323 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
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324 <param name="input_type_selector" value="paired"/>
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325 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/>
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326 <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
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327 <param name="analysis_type_selector" value="illumina"/>
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328 <output name="bam_output" ftype="bam" file="bwa-aln-test1.bam" lines_diff="2"/>
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329 </test>
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330 <test>
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331 <param name="reference_source_selector" value="history"/>
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332 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
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333 <param name="input_type_selector" value="paired"/>
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334 <param name="fastq_input1" ftype="fastqsanger.gz" value="bwa-mem-fastq1.fq.gz"/>
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335 <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
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336 <param name="analysis_type_selector" value="illumina"/>
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337 <output name="bam_output" ftype="bam" file="bwa-aln-test1.bam" lines_diff="2"/>
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338 </test>
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339 <test>
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340 <param name="reference_source_selector" value="history"/>
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341 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
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342 <param name="input_type_selector" value="paired_bam"/>
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343 <param name="bam_input" ftype="bam" value="bwa-aln-bam-input.bam"/>
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344 <param name="analysis_type_selector" value="illumina"/>
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345 <output name="bam_output" ftype="bam" file="bwa-aln-test2.bam" lines_diff="2"/>
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346 </test>
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347 <test>
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348 <param name="reference_source_selector" value="history"/>
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349 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
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350 <param name="input_type_selector" value="paired"/>
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351 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/>
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352 <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
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353 <param name="rg_selector" value="set"/>
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354 <param name="ID" value="rg1"/>
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355 <param name="PL" value="CAPILLARY"/>
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356 <param name="analysis_type_selector" value="illumina"/>
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357 <output name="bam_output" ftype="bam" file="bwa-aln-test3.bam" lines_diff="2"/>
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358 </test>
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359 </tests>
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360 <help><![CDATA[
0
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361 **What is does**
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362
18
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363 BWA is a software package for mapping low-divergent sequences against a large reference genome, such as the
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364 human genome. The bwa-aln algorithm is designed for Illumina sequence reads up to 100bp. For longer reads use
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365 the separate BWA-MEM Galaxy tool.
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366
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367 This Galaxy tool wraps bwa-aln, bwa-samse and -sampe modules of bwa read mapping tool:
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368
18
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369 - **bwa aln** - actual mapper placing reads onto the reference sequence
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370 - **bwa samse** - post-processor converting suffix array coordinates into genome coordinates in SAM format for
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371 single reads
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372 - **bam sampe** - post-processor for paired reads
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373
18
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374
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375 The Galaxy implementation takes fastq or BAM (unaligned BAM) datasets as input and produces output in BAM format,
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376 which can be further processed using various BAM utilities exiting in Galaxy (BAMTools, SAMTools, Picard).
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377
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378 -----
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379
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380 **Indices: Selecting reference genomes for BWA**
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381
18
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382 The Galaxy wrapper for BWA allows you to select between precomputed and user-defined indices for reference genomes
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383 using the **Will you select a reference genome from your history or use a built-in index?** select box.
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384
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385 This select box has two options:
4
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386
18
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387 1. **Use a built-in genome index** - when selected (this is default), Galaxy provides the user with **Select
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388 reference genome index** dropdown. Genomes listed in this dropdown have been pre-indexed with bwa index utility
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389 and are ready to be mapped against.
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390 2. **Use a genome from the history and build index** - when selected, Galaxy provides the user with **Select
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
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391 reference genome sequence** dropdown. This dropdown is populated by all FASTA formatted files listed in your
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392 current history. If your genome of interest is uploaded into history it will be shown there. Selecting a genome
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393 from this dropdown will cause Galaxy to first transparently index it using `bwa index` command, and then run
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
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394 mapping with `bwa aln`.
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395
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396
4
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397 If your genome of interest is not listed here you have two choices:
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398
18
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399 1. Contact galaxy team using **Help->Support** link at the top of the interface and let us know that an index
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400 needs to be added
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
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401 2. Upload your genome of interest as a FASTA file to Galaxy history and selected **Use a genome from the history
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402 and build index** option.
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403
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404
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405 @RG@
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406
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407 @info@
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408 ]]></help>
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409 <citations>
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410 <citation type="doi">10.1093/bioinformatics/btp324</citation>
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411 <citation type="doi">10.1093/bioinformatics/btp698</citation>
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412 </citations>
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413 </tool>