annotate bowtie2_macros.xml @ 26:09b2cdb7ace5 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 41371d219eaafc811eadf7646a7f0ecf002e4239"
author iuc
date Tue, 12 Jan 2021 16:58:26 +0000
parents 17062a0decb7
children a6d65b0c67af
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1 <macros>
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09b2cdb7ace5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 41371d219eaafc811eadf7646a7f0ecf002e4239"
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2 <token name="@TOOL_VERSION@">2.4.2</token>
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3 <!-- Import this at the top of your command block and then
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4 define rg_auto_name. -->
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5 <token name="@define_read_group_helpers@">
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6 #def identifier_or_name($input1)
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7 #if hasattr($input1, 'element_identifier')
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8 #return $input1.element_identifier
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9 #else
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10 #return $input1.name.rstrip('.gz').rstrip('.fastq').rstrip('.fq').rstrip('.bz2')
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11 #end if
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12 #end def
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14 #def clean(name)
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15 #import re
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16 #set $name_clean = re.sub('[^\w\-_\.]', '_', $name)
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17 #return $name_clean
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18 #end def
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20 #def read_group_name_default($input1, $input2=None)
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21 #if $input2 is None
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22 #return $clean($identifier_or_name($input1))
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23 #else
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24 #import itertools
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25 #set $input_name1 = $clean($identifier_or_name($input1))
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26 #set $input_name2 = $clean($identifier_or_name($input2))
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27 #set $common_prefix = ''.join([c[0] for c in itertools.takewhile(lambda x: all(x[0] == y for y in x), itertools.izip(*[$input_name1, $input_name2]))])
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28 #if len($common_prefix) > 3
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29 #return $common_prefix
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30 #else
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31 #return $input_name1
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32 #end if
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33 #end if
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34 #end def
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36 #def format_read_group(prefix, value, quote='', arg='')
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37 #if $value
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38 #return $arg + $quote + $prefix + $value + $quote
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39 #else
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40 #return ''
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41 #end if
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42 #end def
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44 #def rg_param(name)
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45 #if $varExists("rg")
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46 #return $rg.get($name, None)
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47 #else
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48 #return $getVar($name, None)
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49 #end if
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50 #end def
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51
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52 #set $use_rg = True
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53 </token>
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54 <!-- preconditions use_rg and rg_auto_name have been
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55 defined.
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56 -->
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57 <token name="@set_read_group_vars@">
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58 #if $use_rg
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59 #if $rg_param('read_group_id_conditional') is None
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60 #set $rg_id = $rg_auto_name
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61 #elif $rg_param('read_group_id_conditional').do_auto_name
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62 #set $rg_id = $rg_auto_name
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63 #else
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64 #set $rg_id = str($rg_param('read_group_id_conditional').ID)
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65 #end if
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66
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67 #if $rg_param('read_group_sm_conditional') is None
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68 #set $rg_sm = ''
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69 #elif $rg_param('read_group_sm_conditional').do_auto_name
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70 #set $rg_sm = $rg_auto_name
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71 #else
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72 #set $rg_sm = str($rg_param('read_group_sm_conditional').SM)
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73 #end if
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74
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75 #if $rg_param('PL')
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76 #set $rg_pl = str($rg_param('PL'))
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77 #else
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78 #set $rg_pl = ''
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79 #end if
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80
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81 #if $rg_param('read_group_lb_conditional') is None
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82 #set $rg_lb = ''
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83 #elif $rg_param('read_group_lb_conditional').do_auto_name
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84 #set $rg_lb = $rg_auto_name
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85 #else
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86 #set $rg_lb = str($rg_param('read_group_lb_conditional').LB)
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87 #end if
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88
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89 #if $rg_param('CN')
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90 #set $rg_cn = str($rg_param('CN'))
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91 #else
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92 #set $rg_cn = ''
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93 #end if
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94
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95 #if $rg_param("DS")
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96 #set $rg_ds = str($rg_param("DS"))
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97 #else
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98 #set $rg_ds = ''
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99 #end if
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100
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101 #if $rg_param("DT")
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102 #set $rg_dt = str($rg_param("DT"))
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103 #else
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104 #set $rg_dt = ''
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105 #end if
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106
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107 #if $rg_param("FO")
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108 #set $rg_fo = str($rg_param("FO"))
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109 #else
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110 #set $rg_fo = ''
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111 #end if
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112
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113 #if $rg_param("KS")
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114 #set $rg_ks = str($rg_param("KS"))
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115 #else
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116 #set $rg_ks = ''
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117 #end if
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118
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119 #if $rg_param("PG")
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120 #set $rg_pg = str($rg_param("PG"))
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121 #else
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122 #set $rg_pg = ''
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123 #end if
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124
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125 #if $rg_param("PI") != None
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126 #set $rg_pi = str($rg_param("PI"))
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127 #else
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128 #set $rg_pi = ''
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129 #end if
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130
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131 #if $rg_param("PU")
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132 #set $rg_pu = str($rg_param("PU"))
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133 #else
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134 #set $rg_pu = ''
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135 #end if
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136 #end if
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137 </token>
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138 <token name="@set_use_rg_var@">
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139 #set $use_rg = str($rg.rg_selector) != "do_not_set"
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140 </token>
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141 <xml name="read_group_auto_name_conditional">
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142 <param name="do_auto_name" type="boolean" label="Auto-assign" help="Use dataset name or collection information to automatically assign this value" checked="false" />
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143 <when value="true">
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144 </when>
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145 <when value="false">
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146 <yield />
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147 </when>
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148 </xml>
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149 <xml name="read_group_id_param">
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150 <param name="ID" type="text" value="" label="Read group identifier (ID)" help="This value must be unique among multiple samples in your experiment" optional="false">
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151 <validator type="empty_field" />
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152 </param>
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153 </xml>
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154 <xml name="read_group_id_conditional">
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155 <conditional name="read_group_id_conditional">
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156 <expand macro="read_group_auto_name_conditional">
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157 <expand macro="read_group_id_param" />
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158 </expand>
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159 </conditional>
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160 </xml>
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161 <xml name="read_group_sm_param">
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162 <param name="SM" type="text" value="" label="Read group sample name (SM)" help="This value should be descriptive. Use pool name where a pool is being sequenced" />
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163 </xml>
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164 <xml name="read_group_sm_conditional">
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165 <conditional name="read_group_sm_conditional">
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166 <expand macro="read_group_auto_name_conditional">
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167 <expand macro="read_group_sm_param" />
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168 </expand>
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169 </conditional>
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170 </xml>
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171 <!-- Above SM param is optional (for SAM/BAM spec, this is required
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172 as per Picard.
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173 -->
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174 <xml name="read_group_sm_param_required">
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175 <param name="SM" type="text" value="" label="Read group sample name (SM)" optional="false" help="This value should be descriptive. Use pool name where a pool is being sequenced">
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176 <validator type="empty_field" />
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177 </param>
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178 </xml>
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179 <xml name="read_group_sm_required_conditional">
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180 <conditional name="read_group_sm_conditional">
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181 <expand macro="read_group_auto_name_conditional">
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182 <expand macro="read_group_sm_param" />
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183 </expand>
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184 </conditional>
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185 </xml>
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186 <xml name="read_group_pl_param">
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187 <param name="PL" type="select" label="Platform/technology used to produce the reads (PL)">
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188 <option value="CAPILLARY">CAPILLARY</option>
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189 <option value="LS454">LS454</option>
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190 <option selected="True" value="ILLUMINA">ILLUMINA</option>
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191 <option value="SOLID">SOLID</option>
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192 <option value="HELICOS">HELICOS</option>
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193 <option value="IONTORRENT">IONTORRENT</option>
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194 <option value="PACBIO">PACBIO</option>
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195 </param>
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196 </xml>
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197 <xml name="read_group_lb_param">
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198 <param name="LB" type="text" label="Library name (LB)" optional="true" />
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199 </xml>
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200 <xml name="read_group_lb_conditional">
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201 <conditional name="read_group_lb_conditional">
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202 <expand macro="read_group_auto_name_conditional">
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203 <expand macro="read_group_lb_param" />
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204 </expand>
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205 </conditional>
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206 </xml>
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207 <xml name="read_group_lb_required_param">
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208 <param name="LB" type="text" label="Library name (LB)" optional="false">
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209 <validator type="empty_field" />
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210 </param>
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211 </xml>
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212 <xml name="read_group_lb_required_conditional">
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213 <conditional name="read_group_lb_conditional">
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214 <expand macro="read_group_auto_name_conditional">
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215 <expand macro="read_group_lb_required_param" />
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216 </expand>
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217 </conditional>
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218 </xml>
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219 <xml name="read_group_cn_param">
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220 <param name="CN" type="text" label="Sequencing center that produced the read (CN)" />
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221 </xml>
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222 <xml name="read_group_ds_param">
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223 <param name="DS" type="text" label="Description (DS)" />
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224 </xml>
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225 <xml name="read_group_dt_param">
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226 <param name="DT" type="text" label="Date that run was produced (DT)" help="ISO8601 format date or date/time, like YYYY-MM-DD" />
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227 </xml>
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228 <xml name="read_group_fo_param">
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229 <param name="FO" type="text" optional="true" label="Flow order (FO)" help="The array of nucleotide bases that correspond to the nucleotides used for each flow of each read. Multi-base flows are encoded in IUPAC format, and non-nucleotide flows by various other characters. Format: /\*|[ACMGRSVTWYHKDBN]+/">
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230 <validator type="regex" message="Invalid flow order">\*|[ACMGRSVTWYHKDBN]+$</validator>
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231 </param>
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232 </xml>
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233 <xml name="read_group_ks_param">
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234 <param name="KS" type="text" label="The array of nucleotide bases that correspond to the key sequence of each read (KS)" />
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235 </xml>
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236 <xml name="read_group_pg_param">
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237 <param name="PG" type="text" label="Programs used for processing the read group (PG)" />
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238 </xml>
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239 <xml name="read_group_pi_param">
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240 <param name="PI" type="integer" optional="true" label="Predicted median insert size (PI)" />
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241 </xml>
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242 <xml name="read_group_pu_param">
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243 <param name="PU" type="text" label="Platform unit (PU)" help="Unique identifier (e.g. flowcell-barcode.lane for Illumina or slide for SOLiD)" optional="True" />
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244 </xml>
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245 <xml name="read_group_pu_required_param">
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246 <param name="PU" type="text" label="Platform unit (PU)" help="Unique identifier (e.g. flowcell-barcode.lane for Illumina or slide for SOLiD)" optional="False" />
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247 </xml>
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248 <!-- Only ID is required - all groups available -->
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249 <xml name="read_group_inputs_spec">
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250 <expand macro="read_group_id_conditional" />
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251 <expand macro="read_group_sm_conditional" />
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252 <expand macro="read_group_pl_param" />
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253 <expand macro="read_group_lb_conditional" />
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254 <expand macro="read_group_cn_param" />
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255 <expand macro="read_group_ds_param" />
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256 <expand macro="read_group_dt_param" />
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257 <expand macro="read_group_fo_param" />
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258 <expand macro="read_group_ks_param" />
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259 <expand macro="read_group_pg_param" />
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260 <expand macro="read_group_pi_param" />
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261 <expand macro="read_group_pu_param" />
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262 </xml>
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263 <!-- ID, SM, LB, PU, PL all required - not ks, pg, or fo params. -->
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264 <xml name="read_group_inputs_picard">
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265 <expand macro="read_group_id_conditional" />
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266 <expand macro="read_group_sm_required_conditional" />
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267 <expand macro="read_group_lb_required_conditional" />
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268 <expand macro="read_group_pl_param" />
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269 <expand macro="read_group_pu_required_param" />
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270 <expand macro="read_group_cn_param" />
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271 <expand macro="read_group_ds_param" />
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272 <expand macro="read_group_pi_param" />
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273 <expand macro="read_group_dt_param" />
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274 </xml>
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275 <xml name="read_group_conditional">
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276 <conditional name="rg">
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277 <param name="rg_selector" type="select" label="Set read groups information?" help="Specifying read group information can greatly simplify your downstream analyses by allowing combining multiple datasets.">
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278 <option value="set">Set read groups (SAM/BAM specification)</option>
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279 <option value="set_picard">Set read groups (Picard style)</option>
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280 <option value="set_id_auto">Automatically assign ID using name of history item(s)</option>
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281 <option value="do_not_set" selected="True">Do not set</option>
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282 </param>
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283 <when value="set_picard">
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284 <expand macro="read_group_inputs_picard" />
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285 </when>
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286 <when value="set">
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287 <expand macro="read_group_inputs_spec" />
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288 </when>
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289 <when value="set_id_auto">
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290 </when>
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291 <when value="do_not_set">
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292 </when>
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293 </conditional>
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294 </xml>
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295 <xml name="paired_end_options">
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296 <conditional name="paired_options">
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297 <param name="paired_options_selector" type="select" label="Do you want to set paired-end options?" help="See &quot;Alignment Options&quot; section of Help below for information">
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298 <option value="no" selected="True">No</option>
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299 <option value="yes">Yes</option>
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300 </param>
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301 <when value="yes">
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302 <param argument="-I" type="integer" value="0" min="0" label="Set the minimum fragment length for valid paired-end alignments"
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303 help="E.g. if `-I 60` is specified and a paired-end alignment consists of two 20-bp alignments in the appropriate orientation with a 20-bp gap between them, that alignment is considered valid (as long as `-X` is also satisfied). A 19-bp gap would not be valid in that case. If trimming options `-3` or `-5` are also used, the `-I` constraint is applied with respect to the untrimmed mates. The larger the difference between `-I` and `-X`, the slower Bowtie 2 will run. This is because larger differences bewteen `-I` and `-X` require that Bowtie 2 scan a larger window to determine if a concordant alignment exists. For typical fragment length ranges (200 to 400 nucleotides), Bowtie 2 is very efficient. Default=0"/>
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304 <param argument="-X" type="integer" value="500" min="0" label="Set the maximum fragment length for valid paired-end alignments"
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305 help="E.g. if `-X 100` is specified and a paired-end alignment consists of two 20-bp alignments in the proper orientation with a 60-bp gap between them, that alignment is considered valid (as long as `-I` is also satisfied). A 61-bp gap would not be valid in that case. If trimming options `-3` or `-5` are also used, the `-X` constraint is applied with respect to the untrimmed mates, not the trimmed mates; Default=500"/>
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306 <param name="fr_rf_ff" type="select" display="radio" label="Select the upstream/downstream mate orientations for a valid paired-end alignment against the forward reference strand"
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307 help="--fr, --rf, or --ff; E.g., if `--fr` is specified and there is a candidate paired-end alignment where mate 1 appears upstream of the reverse complement of mate 2 and the fragment length constraints (`-I` and `-X`) are met, that alignment is valid. Also, if mate 2 appears upstream of the reverse complement of mate 1 and all other constraints are met, that too is valid. `--rf` likewise requires that an upstream mate1 be reverse-complemented and a downstream mate2 be forward-oriented. `--ff` requires both an upstream mate 1 and a downstream mate 2 to be forward-oriented; Default=--fr (appropriate for Illumina's Paired-end Sequencing Assay)">
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308 <option value="--fr" selected="True">--fr</option>
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309 <option value="--rf">--rf</option>
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310 <option value="--ff">--ff</option>
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311 </param>
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312 <param argument="--no-mixed" name="no_mixed" type="boolean" truevalue="--no-mixed" falsevalue="" checked="False" label="Disable no-mixed behavior" help="--no-mixed; By default, when `bowtie2` cannot find a concordant or discordant alignment for a pair, it then tries to find alignments for the individual mates; default=False"/>
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313 <param argument="--no-discordant" name="no_discordant" type="boolean" truevalue="--no-discordant" falsevalue="" checked="False" label="Disable no-discordant behavior" help="--no-discordant; By default, `bowtie2` looks for discordant alignments if it cannot find any concordant alignments. A discordant alignment is an alignment where both mates align uniquely, but that does not satisfy the paired-end constraints (`--fr`/`--rf`/`--ff`, `-I`, `-X`); default=False"/>
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314 <param argument="--dovetail" name="dovetail" type="boolean" truevalue="--dovetail" falsevalue="" checked="False" label="Allow mate dovetailing" help="--dovetail; If the mates `dovetail`, that is if one mate alignment extends past the beginning of the other such that the wrong mate begins upstream, consider that to be concordant. Default=False"/>
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315 <param argument="--no-contain" name="no_contain" type="boolean" truevalue="--no-contain" falsevalue="" checked="False" label="Disallow one mate alignment to contain another" help="--no-contain; If one mate alignment contains the other, consider that to be non-concordant. Default=False"/>
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316 <param argument="--no-overlap" name="no_overlap" type="boolean" truevalue="--no-overlap" falsevalue="" checked="False" label="Disallow mate alignments to overlap" help="--no-overlap; If one mate alignment overlaps the other at all, consider that to be non-concordant. Default=False"/>
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317 </when>
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318 <when value="no">
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319 <!-- do nothing -->
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320 </when>
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321 </conditional>
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322 </xml>
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323 <xml name="align_unalign">
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324 <param name="unaligned_file" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write unaligned reads (in fastq format) to separate file(s)" help="--un/--un-conc (possibly with -gz or -bz2); This triggers --un parameter for single reads and --un-conc for paired reads" />
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325 <param name="aligned_file" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write aligned reads (in fastq format) to separate file(s)" help="--al/--al-conc (possibly with -gz or -bz2); This triggers --al parameter for single reads and --al-conc for paired reads" />
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326 </xml>
23
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327 <xml name="dbKeyActions">
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328 <conditional name="reference_genome.source">
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329 <when value="indexed">
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330 <action type="metadata" name="dbkey">
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331 <option type="from_data_table" name="bowtie2_indexes" column="1">
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332 <filter type="param_value" ref="reference_genome.index" column="0"/>
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333 </option>
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334 </action>
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335 </when>
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336 <when value="history">
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337 <action type="metadata" name="dbkey">
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338 <option type="from_param" name="reference_genome.own_file" param_attribute="dbkey" />
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339 </action>
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340 </when>
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341 </conditional>
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342 </xml>
15
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343 </macros>