Mercurial > repos > iuc > gtdbtk_classify_wf

annotate gtdbtk_classify_wf.xml @ 1:dbf1798c0dcc draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gtdbtk commit 1dddd355fe97cb9d6bb37f93b98f3402184b4320
author iuc
date Thu, 16 Feb 2023 23:35:55 +0000
parents c4db8c4de66f
children 6501b5b33988
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c4db8c4de66f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gtdbtk commit 8487d2c73793be0afa5b34388b122e686ac8a094
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1 <tool id="gtdbtk_classify_wf" name="GTDB-Tk Classify genomes" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>by placement in GTDB reference tree</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <command detect_errors="exit_code"><![CDATA[
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8 #import re
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9
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10 mkdir input_dir &&
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11 mkdir output_dir &&
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12 mkdir output_tsv_dir &&
c4db8c4de66f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gtdbtk commit 8487d2c73793be0afa5b34388b122e686ac8a094
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13 mkdir output_newick_dir &&
c4db8c4de66f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gtdbtk commit 8487d2c73793be0afa5b34388b122e686ac8a094
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14 mkdir output_fasta_dir &&
c4db8c4de66f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gtdbtk commit 8487d2c73793be0afa5b34388b122e686ac8a094
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15 #for $i in $input:
c4db8c4de66f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gtdbtk commit 8487d2c73793be0afa5b34388b122e686ac8a094
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16 ## gtdbtk uses the file extension to determine the input format.
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17 #set ext = "." + $i.ext
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18 #set input_identifier = re.sub('[^\s\w\-]', '_', str($i.element_identifier)) + $ext
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19 ln -s '${i}' input_dir/'${input_identifier}' &&
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20 #end for
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21 export GTDBTK_DATA_PATH=$gtdbtk_db.fields.path &&
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22 gtdbtk classify_wf
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23 --genome_dir input_dir
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24 --extension '$ext'
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25 --out_dir output_dir
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26 --cpus \${GALAXY_SLOTS:-4}
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27 --min_perc_aa $advanced.min_perc_aa
c4db8c4de66f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gtdbtk commit 8487d2c73793be0afa5b34388b122e686ac8a094
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28 $advanced.force
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29 --min_af $advanced.min_af
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30
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31 ## Required unless mash_db is available:
dbf1798c0dcc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gtdbtk commit 1dddd355fe97cb9d6bb37f93b98f3402184b4320
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32 --skip_ani_screen
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33
0
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34 #if str($advanced.output_process_log) == 'yes':
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35 && cat output_dir/gtdbtk.warnings.log output_dir/gtdbtk.log > '$process_log'
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36 #end if
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37 ]]></command>
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38 <inputs>
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39 <param name="input" type="data" format="fasta,fasta.gz" multiple="true" label="Fasta (Genome) files"/>
1
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40 <param name="gtdbtk_db" type="select" label="GTDB-Tk database" help="This version of GTDB-Tk required GTDB version R207_v2. Please contact your service administrator if this version is not available to select.">
0
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41 <options from_data_table="gtdbtk_database">
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42 <validator type="no_options" message="No locally cached GTDB-Tk database is available"/>
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43 </options>
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44 </param>
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45 <section name="advanced" title="Advanced options">
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46 <param argument="--min_perc_aa" type="integer" min="0" max="100" value="10" label="Exclude genomes that do not have at least this percentage of AA in the MSA" help="Inclusive bound"/>
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47 <param argument="--force" type="boolean" truevalue="--force" falsevalue="" checked="false" label="Continue processing if an error occurs on a single genome?"/>
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48 <param argument="--min_af" type="float" min="0" max="1" value="0.65" label="Minimum alignment fraction to consider closest genome"/>
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49 <param name="output_process_log" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Output process log file?"/>
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50 </section>
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51 </inputs>
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52 <outputs>
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53 <data name="process_log" format="txt" label="${tool.name} on ${on_string} (process log)">
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54 <filter>advanced['output_process_log'] == 'yes'</filter>
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55 </data>
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56 <collection name="output_tsv" type="list" format="tsv" label="${tool.name} on ${on_string} (tsv)">
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57 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.tsv" ext="tsv" directory="output_dir"/>
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58 </collection>
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59 <collection name="output_newick" type="list" format="newick" label="${tool.name} on ${on_string} (newick)">
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60 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.tree" ext="newick" directory="output_dir"/>
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61 </collection>
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62 <collection name="output_fasta" type="list" format="fasta" label="${tool.name} on ${on_string} (fasta)">
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63 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.fasta" ext="fasta" directory="output_dir"/>
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64 </collection>
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65 </outputs>
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66 <tests>
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67 <!-- The commented test here is valid if we could store the GTDB-Tk database -->
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68 <!--
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69 <test expect_num_outputs="3">
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70 <param name="input" value="genome_1.fna.gz" ftype="fasta.gz"/>
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71 <param name="gtdbtk_db" value="gtdbtk202"/>
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72 <output_collection name="output_tsv" type="list" count="6">
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73 <element name="gtdbtk.ar122.filtered" ftype="tsv">
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74 <assert_contents>
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75 <has_size value="0"/>
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76 </assert_contents>
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77 </element>
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78 <element name="gtdbtk.ar122.markers_summary" ftype="tsv">
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79 <assert_contents>
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80 <has_text text="number_unique_genes"/>
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81 </assert_contents>
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82 </element>
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83 <element name="gtdbtk.ar122.summary" ftype="tsv">
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84 <assert_contents>
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85 <has_text text="genome_1_fna_gz"/>
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86 </assert_contents>
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87 </element>
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88 <element name="gtdbtk.bac120.markers_summary" ftype="tsv">
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89 <assert_contents>
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90 <has_text text="genome_1_fna_gz"/>
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91 </assert_contents>
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92 </element>
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93 <element name="gtdbtk.failed_genomes" ftype="tsv">
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94 <assert_contents>
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95 <has_size value="0"/>
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96 </assert_contents>
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97 </element>
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98 <element name="gtdbtk.translation_table_summary" ftype="tsv">
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99 <assert_contents>
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100 <has_text text="genome_1_fna_gz"/>
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101 </assert_contents>
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102 </element>
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103 </output_collection>
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104 <output_collection name="output_newick" type="list" count="1">
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105 <element name="gtdbtk.ar122.classify" ftype="newick">
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106 <assert_contents>
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107 <has_text text="GB_GCA_"/>
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108 </assert_contents>
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109 </element>
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110 </output_collection>
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111 <output_collection name="output_fasta" type="list" count="2">
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112 <element name="gtdbtk.ar122.msa" ftype="fasta">
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113 <assert_contents>
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114 <has_text text="GB_GCA_000008085"/>
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115 </assert_contents>
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116 </element>
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117 <element name="gtdbtk.ar122.user_msa" ftype="fasta">
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118 <assert_contents>
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119 <has_text text="genome_1_fna_gz"/>
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120 </assert_contents>
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121 </element>
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122 </output_collection>
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123 </test>
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124 -->
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125 <!-- GTDB-Tk databases are far too large to test currently -->
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126 <test expect_failure="true">
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127 <param name="input" value="genome_1.fna.gz" ftype="fasta.gz"/>
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128 <param name="gtdbtk_db" value="gtdbtk202"/>
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129 <assert_stderr>
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130 <has_text text="Fatal error: Exit code 1"/>
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131 </assert_stderr>
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132 </test>
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133 </tests>
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134 <help><![CDATA[
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135 **What it does**
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136
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137 GTDB-Tk is a software toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes
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138 based on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds or
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139 thousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can also
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140 be applied to isolate and single-cell genomes.
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141
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142 This tool accepts one or more fasta (genome) files and determines taxonomic classification of genomes by
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143 maximum-likelihood (ML) placement. The classification workflow consists of three steps: identify, align, and
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144 classify.
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145
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146 The identify step calls genes using Prodigal, and uses HMM models and the HMMER package to identify the 120 bacterial
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147 and 122 archaeal marker genes used for phylogenetic inference. Multiple sequence alignments (MSA) are obtained by
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148 aligning marker genes to their respective HMM model.
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149
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150 The align step concatenates the aligned marker genes and filters the concatenated MSA to approximately 5,000
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151 amino acids.
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152
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153 Finally, the classify step uses pplacer to find the maximum-likelihood placement of each genome in the GTDB-Tk
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154 reference tree. GTDB-Tk classifies each genome based on its placement in the reference tree, its relative evolutionary
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155 divergence, and/or average nucleotide identity (ANI) to reference genomes.
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156
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157 Results can be impacted by a lack of marker genes or contamination.
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158 ]]></help>
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159 <expand macro="citations"/>
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160 </tool>