Mercurial > repos > iuc > presto_parseheaders

annotate presto_parseheaders.xml @ 0:90315cb06d06 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
author iuc
date Wed, 30 May 2018 15:36:08 -0400
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children 55e95d8104f2
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90315cb06d06 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
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1 <tool id="presto_parseheaders" name="pRESTO ParseHeaders" version="@PRESTO_VERSION@">
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2 <description>Manage annotations in FASTQ headers.</description>
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3
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4 <macros>
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5 <import>presto_macros.xml</import>
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6 </macros>
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7
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8 <expand macro="requirements"/>
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9
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10 <version_command>ParseHeaders.py --version</version_command>
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11 <command detect_errors="exit_code"><![CDATA[
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12 ln -s '$fastq_in' in.fastq &&
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13 ParseHeaders.py $cc.command
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14 -s in.fastq
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15
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16 #if $varExists('cc.f')
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17 -f $cc.f
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18 #end if
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19 #if $varExists('cc.u')
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20 -u $cc.u
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21 #end if
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22 #if $varExists('cc.act')
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23 --act $cc.act
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24 #end if
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25 #if $varExists('cc.k')
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26 -k $cc.k
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27 #end if
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28
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29 --outdir=.
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30 --outname=tmp &&
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31 mv ./tmp_*header* '$output'
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32 ]]></command>
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33
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34 <inputs>
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35 <param name="fastq_in" type="data" format="fastq" label="Input FASTQ file"/>
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36
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37 <conditional name="cc">
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38 <param name="command" type="select" label="Command">
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39 <option value="add">Add field/value pairs to header annotations (add)</option>
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40 <option value="collapse">Collapse header annotations with multiple entries (collapse)</option>
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41 <option value="copy">Copy header annotation fields (copy)</option>
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42 <option value="delete">Delete fields from header annotations (delete)</option>
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43 <option value="expand">Expand annotation fields with multiple values (expand)</option>
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44 <option value="rename">Rename header annotation fields (rename)</option>
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45 <option value="table">Write sequence headers to a table (table)</option>
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46 </param>
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47 <when value="add">
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48 <param argument="-f" type="text" value="" label="Field(s)" help="Space-separated list of field names to add.">
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49 <expand macro="text-regex-validator"/>
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50 </param>
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51 <param argument="-u" type="text" value="" label="Value(s)" help="Space-separated list of values, one per field.">
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52 <expand macro="text-regex-validator"/>
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53 </param>
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54 </when>
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55 <when value="collapse">
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56 <param argument="-f" type="text" value="" label="Field(s)" help="Space-separated list of field names to collapse values within.">
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57 <expand macro="text-regex-validator"/>
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58 </param>
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59 <param argument="--act" type="text" value="" label="Action(s)" help="Space-separated list of actions, one per field [min,max,sum,first,last,set,cat].">
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60 <expand macro="text-regex-validator"/>
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61 </param>
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62 </when>
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63 <when value="copy">
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64 <param argument="-f" type="text" value="" label="Source Field(s)" help="Space-separated list of field names to copy.">
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65 <expand macro="text-regex-validator"/>
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66 </param>
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67 <param argument="-k" type="text" value="" label="Target Field(s)" help="Space-separated list of target field names, one per source field.">
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68 <expand macro="text-regex-validator"/>
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69 </param>
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70 <param argument="--act" type="text" value="" label="Action(s)" help="Space-separated list of actions, one per target field [min,max,sum,first,last,set,cat].">
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71 <expand macro="text-regex-validator"/>
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72 </param>
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73 </when>
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74 <when value="delete">
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75 <param argument="-f" type="text" value="" label="Field(s)" help="Space-separated list of field names to delete.">
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76 <expand macro="text-regex-validator"/>
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77 </param>
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78 </when>
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79 <when value="expand">
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80 <param argument="-f" type="text" value="" label="Field(s)" help="Space-separated list of field names to expand.">
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81 <expand macro="text-regex-validator"/>
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82 </param>
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83 </when>
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84 <when value="rename">
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85 <param argument="-f" type="text" value="" label="Source Field(s)" help="Space-separated list of field names to rename.">
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86 <expand macro="text-regex-validator"/>
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87 </param>
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88 <param argument="-k" type="text" value="" label="Target Field(s)" help="Space-separated list of new field names.">
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89 <expand macro="text-regex-validator"/>
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90 </param>
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91 <param argument="--act" type="text" value="" label="Action(s)" help="Space-separated list of actions, one per new field [min,max,sum,first,last,set,cat].">
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92 <expand macro="text-regex-validator"/>
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93 </param>
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94 </when>
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95 <when value="table">
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96 <param argument="-f" type="text" value="" label="Field(s)" help="Space-separated list of field names to report on.">
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97 <expand macro="text-regex-validator"/>
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98 </param>
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99 </when>
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100 </conditional>
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101 </inputs>
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102
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103 <outputs>
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104 <data name="output" format="fastq">
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105 <change_format>
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106 <when input="command" value="table" format="tsv"/>
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107 </change_format>
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108 </data>
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109 </outputs>
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110
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111 <tests>
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112 <test>
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113 <param name="command" value="add"/>
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114 <param name="fastq_in" value="presto_parseheaders_test_in.fastq"/>
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115 <param name="f" value="FOO BAR"/>
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116 <param name="u" value="hello world"/>
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117 <output name="output" file="presto_parseheaders_test_add_out.fastq" sort="true"/>
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118 </test>
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119
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120 <test>
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121 <param name="command" value="collapse"/>
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122 <param name="fastq_in" value="presto_parseheaders_test_in.fastq"/>
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123 <param name="f" value="CONSCOUNT"/>
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124 <param name="act" value="sum"/>
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125 <output name="output" file="presto_parseheaders_test_collapse_out.fastq" sort="true"/>
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126 </test>
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127
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128 <test>
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129 <param name="command" value="copy"/>
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130 <param name="fastq_in" value="presto_parseheaders_test_in.fastq"/>
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131 <param name="f" value="PRCONS"/>
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132 <param name="k" value="PRIMER"/>
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133 <param name="act" value="set"/>
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134 <output name="output" file="presto_parseheaders_test_copy_out.fastq" sort="true"/>
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135 </test>
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136
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137 <test>
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138 <param name="command" value="delete"/>
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139 <param name="fastq_in" value="presto_parseheaders_test_in.fastq"/>
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140 <param name="f" value="CONSCOUNT SEQORIENT"/>
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141 <output name="output" file="presto_parseheaders_test_delete_out.fastq" sort="true"/>
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142 </test>
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143
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144 <test>
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145 <param name="command" value="expand"/>
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146 <param name="fastq_in" value="presto_parseheaders_test_in.fastq"/>
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147 <param name="f" value="CONSCOUNT"/>
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148 <output name="output" file="presto_parseheaders_test_expand_out.fastq" sort="true"/>
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149 </test>
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150
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151 <test>
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152 <param name="command" value="rename"/>
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153 <param name="fastq_in" value="presto_parseheaders_test_in.fastq"/>
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154 <param name="f" value="PRCONS"/>
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155 <param name="k" value="PRIMER"/>
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156 <param name="act" value="set"/>
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157 <output name="output" file="presto_parseheaders_test_rename_out.fastq" sort="true"/>
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158 </test>
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159
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160 <test>
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161 <param name="command" value="table"/>
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162 <param name="fastq_in" value="presto_parseheaders_test_in.fastq"/>
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163 <param name="f" value="PRCONS PRIMER"/>
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164 <output name="output" file="presto_parseheaders_test_table_out.tsv" sort="true"/>
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165 </test>
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166 </tests>
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167
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168 <help><![CDATA[
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169 Adds, removes, renames and otherwise transforms annotations in FASTQ headers.
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170
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171 See the `pRESTO online help <@PRESTO_URL_BASE@/ParseHeaders.html>`_ for more information.
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172
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173 @HELP_NOTE@
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174 ]]></help>
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175 <expand macro="citations" />
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176 </tool>