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annotate bwa.xml @ 18:48f306c57611 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
author iuc
date Fri, 24 Nov 2017 09:55:45 -0500
parents 051eba708f43
children 4f774c1e6049
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1 <?xml version="1.0"?>
18
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2 <tool id="bwa" name="Map with BWA" version="@VERSION@.3">
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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}
18
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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@">
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
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31 #if $use_rg:
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32 @set_rg_string@
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
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33 -r '$rg_string'
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34 #end if
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35 </token>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
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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>
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
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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."
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
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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."
48f306c57611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit c355891532cecaab6b3288a148a6b3bcb5973396
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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[
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81 @set_reference_fasta_filename@
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82
18
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83 ## setup vars for rg handling...
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84 @define_read_group_helpers@
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85 #if str( $input_type.input_type_selector ) == "paired":
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86 #set $rg_auto_name = $read_group_name_default($input_type.fastq_input1, $input_type.fastq_input2)
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87 #elif str( $input_type.input_type_selector ) in ["single_bam", "paired_bam"]:
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88 #set $rg_auto_name = $read_group_name_default($input_type.bam_input)
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89 #else
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90 #set $rg_auto_name = $read_group_name_default($input_type.fastq_input1)
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91 #end if
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92 @set_use_rg_var@
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93 @set_read_group_vars@
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94
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95 ## Begin bwa command line
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96
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97 ####### Fastq paired
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98
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99 #if str( $input_type.input_type_selector ) == "paired" or str( $input_type.input_type_selector ) == "paired_collection":
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100 bwa aln
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101 -t "\${GALAXY_SLOTS:-1}"
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102 @command_options@
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103 '$reference_fasta_filename'
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104 #if str( $input_type.input_type_selector ) == "paired_collection":
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105 '${input_type.fastq_input1.forward}'
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106 #else
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107 '${input_type.fastq_input1}'
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108 #end if
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109 > first.sai &&
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110
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111 bwa aln
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112 -t "\${GALAXY_SLOTS:-1}"
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113 @command_options@
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114 '${reference_fasta_filename}'
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115 #if str( $input_type.input_type_selector ) == "paired_collection":
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116 '${input_type.fastq_input1.reverse}'
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117 #else
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118 '${input_type.fastq_input2}'
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119 #end if
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120 > second.sai &&
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121
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122 bwa sampe
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123 #if str( $input_type.adv_pe_options.adv_pe_options_selector) == "True":
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124 -a ${$input_type.adv_pe_options.a}
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125 -o ${$input_type.adv_pe_options.o}
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126 -n ${$input_type.adv_pe_options.n}
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127 -N ${$input_type.adv_pe_options.N}
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128 #end if
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129 @read_group_options@
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130 #if str( $input_type.input_type_selector ) == "paired_collection":
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131 '${reference_fasta_filename}' first.sai second.sai '${input_type.fastq_input1.forward}' '${input_type.fastq_input1.reverse}'
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132 #else:
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133 '${reference_fasta_filename}' first.sai second.sai '${input_type.fastq_input1}' '${input_type.fastq_input2}'
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134 #end if
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135
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136 ## Fastq single
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137
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138 #elif str( $input_type.input_type_selector ) == "single":
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139 bwa aln
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140 -t "\${GALAXY_SLOTS:-1}"
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141
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142 @command_options@
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143
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144 '${reference_fasta_filename}'
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145 '${input_type.fastq_input1}'
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146 > first.sai &&
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147
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148 bwa samse
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149
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150 #if str( $input_type.adv_se_options.adv_se_options_selector) == "True":
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151 -n ${$input_type.adv_se_options.n}
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152 #end if
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153 @read_group_options@
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154 '${reference_fasta_filename}' first.sai '${input_type.fastq_input1}'
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155
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156 ####### BAM paired
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157
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158 #elif str( $input_type.input_type_selector ) == "paired_bam":
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159 bwa aln
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160 -t "\${GALAXY_SLOTS:-1}"
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161 -b
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162 -1
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163 @command_options@
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164 '${reference_fasta_filename}'
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165 '${input_type.bam_input}'
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166 > first.sai &&
2
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167
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168 bwa aln
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169 -t "\${GALAXY_SLOTS:-1}"
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170 -b
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171 -2
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172 @command_options@
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173 '${reference_fasta_filename}'
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174 '${input_type.bam_input}'
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175 > second.sai &&
2
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176
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177 bwa sampe
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178
18
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179 #if str( $input_type.adv_bam_pe_options.adv_pe_options_selector) == "True":
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180 -a ${$input_type.adv_bam_pe_options.a}
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181 -o ${$input_type.adv_bam_pe_options.o}
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182 -n ${$input_type.adv_bam_pe_options.n}
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183 -N ${$input_type.adv_bam_pe_options.N}
18
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184 #end if
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185 @read_group_options@
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186 '${reference_fasta_filename}' first.sai second.sai '${input_type.bam_input}' '${input_type.bam_input}'
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187
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188 ####### Fastq single ------------ to do next
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189
18
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190 #elif str( $input_type.input_type_selector ) == "single_bam":
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191 bwa aln
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192 -t "\${GALAXY_SLOTS:-1}"
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193 -b
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194 -0
2
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195
18
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196 @command_options@
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197
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198 '${reference_fasta_filename}'
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199 '${input_type.bam_input}'
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200 > first.sai &&
2
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201
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202 bwa samse
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203
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204 #if str( $input_type.adv_bam_se_options.adv_se_options_selector) == "True":
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205 -n ${$input_type.adv_bam_se_options.n}
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206 #end if
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207 @read_group_options@
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208 '${reference_fasta_filename}' first.sai '${input_type.bam_input}'
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209 #end if
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210
18
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211 | samtools sort -@\${GALAXY_SLOTS:-2} -O bam -o '$bam_output'
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212 ]]>
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213 </command>
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214
18
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215 <inputs>
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216 <expand macro="reference_source_conditional"/>
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217 <conditional name="input_type">
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218 <param name="input_type_selector" type="select" label="Select input type"
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219 help="Select between fastq and bam datasets and between paired and single end data">
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220 <option value="paired">Paired fastq</option>
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221 <option value="paired_collection">Paired fastq collection</option>
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222 <option value="single">Single fastq</option>
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223 <option value="paired_bam">Paired BAM</option>
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224 <option value="single_bam">Single BAM</option>
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225 </param>
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226 <when value="paired">
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227 <param name="fastq_input1" type="data" format="fastqsanger,fastqsanger.gz,fasta"
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228 label="Select first set of reads" help="Specify dataset with forward reads"/>
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229 <param name="fastq_input2" type="data" format="fastqsanger,fastqsanger.gz,fasta"
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230 label="Select second set of reads" help="Specify dataset with reverse reads"/>
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231 <conditional name="adv_pe_options">
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232 <expand macro="advanced_pe_options"/>
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233 </conditional>
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234 </when>
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235 <when value="paired_collection">
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236 <param name="fastq_input1" format="fastqsanger,fastqsanger.gz" type="data_collection" collection_type="paired" label="Select a paired collection"
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237 help="See help section for an explanation of dataset collections"/>
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238 <conditional name="adv_pe_options">
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239 <expand macro="advanced_pe_options"/>
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240 </conditional>
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241 </when>
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242 <when value="single">
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243 <param name="fastq_input1" type="data" format="fastqsanger,fastqsanger.gz,fasta"
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244 label="Select fastq dataset" help="Specify dataset with single reads"/>
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245 <conditional name="adv_se_options">
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246 <expand macro="advanced_se_options"/>
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247 </conditional>
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248 </when>
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249 <!-- 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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250 <when value="paired_bam">
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251 <param name="bam_input" type="data" format="bam" label="Select BAM dataset"
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252 help="Specify BAM dataset with paired reads"/>
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253 <conditional name="adv_bam_pe_options">
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254 <expand macro="advanced_pe_options"/>
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255 </conditional>
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256 </when>
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257 <when value="single_bam">
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258 <param name="bam_input" type="data" format="bam" label="Select BAM dataset"
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259 help="Specify BAM dataset with single reads"/>
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260 <conditional name="adv_bam_se_options">
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261 <expand macro="advanced_se_options"/>
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262 </conditional>
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263 </when>
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264 </conditional>
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265 <expand macro="read_group_conditional"/>
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266 <conditional name="analysis_type">
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267 <param name="analysis_type_selector" type="select" label="Select analysis mode">
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268 <option value="illumina">1.Simple Illumina mode</option>
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269 <option value="full">2.Full list of options</option>
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270 </param>
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271 <when value="illumina">
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272 <!-- do nothing -->
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273 </when>
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274 <when value="full">
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275 <param name="n" type="text" value="0.04"
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276 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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277 help="aln -n; default=0.04"/>
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278 <param name="o" type="integer" value="1" label="maximum number or gap openings"
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279 help="aln -o; default=1"/>
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280 <param name="e" type="integer" value="-1" label="maximum number of gap extensions"
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281 help="aln -e; -1 disables long gaps and invokes k-difference mode; default=-1"/>
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282 <param name="i" type="integer" value="5"
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283 label="do not put an indel within this many bp towards the ends" help="aln -i; default=5"/>
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284 <param name="d" type="integer" value="10" label="maximum occurrences for extending a long deletion"
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285 help="aln -d; default=10"/>
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286 <param name="l" type="integer" value="32" label="seed length" help="aln -l; default=32"/>
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287 <param name="k" type="integer" value="2" label="maximum differences in the seed"
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288 help="aln -k; default=2"/>
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289 <param name="m" type="integer" value="2000000" label="maximum entries in the queue"
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290 help="aln -m; default=2000000"/>
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291 <param name="M" type="integer" value="3" label="mismatch penalty" help="aln -M; default=3"/>
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292 <param name="O" type="integer" value="11" label="gap open penalty" help="aln -O; default=11"/>
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293 <param name="E" type="integer" value="4" label="gap extension penalty" help="aln -E; default=4"/>
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294 <param name="R" type="integer" value="30"
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295 label="stop searching when there are more than this value of equally best hits"
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296 help="aln -R; default=30"/>
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297 <param name="q" type="integer" value="0" label="quality threshold for read trimming down to 35bp"
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298 help="aln -q; default=0"/>
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299 <param name="B" type="integer" optional="True" label="length of barcode"
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300 help="aln -B; optional parameter"/>
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301 <param name="L" type="float" optional="True" label="log-scaled gap penalty for long deletions"
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302 help="aln -L; optional parameter"/>
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303 </when>
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304 </conditional>
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305 </inputs>
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306 <outputs>
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307 <data format="bam" name="bam_output" label="${tool.name} on ${on_string} (mapped reads in BAM format)">
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308 <expand macro="dbKeyActionsBwa"/>
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309 </data>
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310 </outputs>
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311 <tests>
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312 <test>
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313 <param name="reference_source_selector" value="history"/>
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314 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
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315 <param name="input_type_selector" value="single"/>
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316 <param name="fastq_input1" ftype="fasta" value="bwa-mem-fasta1.fa"/>
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317 <param name="analysis_type_selector" value="illumina"/>
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318 <output name="bam_output" ftype="bam" file="bwa-aln-test1-fasta.bam" lines_diff="2"/>
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319 </test>
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320 <test>
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321 <param name="reference_source_selector" value="history"/>
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322 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
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323 <param name="input_type_selector" value="paired"/>
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324 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/>
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325 <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
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326 <param name="analysis_type_selector" value="illumina"/>
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327 <output name="bam_output" ftype="bam" file="bwa-aln-test1.bam" lines_diff="2"/>
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328 </test>
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329 <test>
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330 <param name="reference_source_selector" value="history"/>
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331 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
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332 <param name="input_type_selector" value="paired"/>
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333 <param name="fastq_input1" ftype="fastqsanger.gz" value="bwa-mem-fastq1.fq.gz"/>
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334 <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
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335 <param name="analysis_type_selector" value="illumina"/>
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336 <output name="bam_output" ftype="bam" file="bwa-aln-test1.bam" lines_diff="2"/>
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337 </test>
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338 <test>
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339 <param name="reference_source_selector" value="history"/>
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340 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
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341 <param name="input_type_selector" value="paired_bam"/>
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342 <param name="bam_input" ftype="bam" value="bwa-aln-bam-input.bam"/>
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343 <param name="analysis_type_selector" value="illumina"/>
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344 <output name="bam_output" ftype="bam" file="bwa-aln-test2.bam" lines_diff="2"/>
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345 </test>
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346 <test>
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347 <param name="reference_source_selector" value="history"/>
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348 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
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349 <param name="input_type_selector" value="paired"/>
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350 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/>
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351 <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
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352 <param name="rg_selector" value="set"/>
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353 <param name="ID" value="rg1"/>
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354 <param name="PL" value="CAPILLARY"/>
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355 <param name="analysis_type_selector" value="illumina"/>
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356 <output name="bam_output" ftype="bam" file="bwa-aln-test3.bam" lines_diff="2"/>
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357 </test>
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358 </tests>
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359 <help><![CDATA[
0
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360 **What is does**
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361
18
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362 BWA is a software package for mapping low-divergent sequences against a large reference genome, such as the
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363 human genome. The bwa-aln algorithm is designed for Illumina sequence reads up to 100bp. For longer reads use
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364 the separate BWA-MEM Galaxy tool.
0
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365
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366 This Galaxy tool wraps bwa-aln, bwa-samse and -sampe modules of bwa read mapping tool:
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367
18
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368 - **bwa aln** - actual mapper placing reads onto the reference sequence
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369 - **bwa samse** - post-processor converting suffix array coordinates into genome coordinates in SAM format for
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370 single reads
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371 - **bam sampe** - post-processor for paired reads
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372
18
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373
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374 The Galaxy implementation takes fastq or BAM (unaligned BAM) datasets as input and produces output in BAM format,
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375 which can be further processed using various BAM utilities exiting in Galaxy (BAMTools, SAMTools, Picard).
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376
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377 -----
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378
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379 **Indices: Selecting reference genomes for BWA**
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380
18
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381 The Galaxy wrapper for BWA allows you to select between precomputed and user-defined indices for reference genomes
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382 using the **Will you select a reference genome from your history or use a built-in index?** select box.
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383
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384 This select box has two options:
4
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385
18
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386 1. **Use a built-in genome index** - when selected (this is default), Galaxy provides the user with **Select
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387 reference genome index** dropdown. Genomes listed in this dropdown have been pre-indexed with bwa index utility
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388 and are ready to be mapped against.
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389 2. **Use a genome from the history and build index** - when selected, Galaxy provides the user with **Select
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390 reference genome sequence** dropdown. This dropdown is populated by all FASTA formatted files listed in your
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391 current history. If your genome of interest is uploaded into history it will be shown there. Selecting a genome
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392 from this dropdown will cause Galaxy to first transparently index it using `bwa index` command, and then run
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393 mapping with `bwa aln`.
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394
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395
4
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396 If your genome of interest is not listed here you have two choices:
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397
18
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398 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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399 needs to be added
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400 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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401 and build index** option.
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402
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403
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404 @RG@
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405
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406 @info@
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407 ]]></help>
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408 <citations>
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409 <citation type="doi">10.1093/bioinformatics/btp324</citation>
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410 <citation type="doi">10.1093/bioinformatics/btp698</citation>
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411 </citations>
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412 </tool>