Mercurial > repos > iuc > binning_refiner

annotate binning_refiner.xml @ 0:f350d182f786 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
author iuc
date Fri, 18 Feb 2022 13:12:43 +0000
parents
children 1c8d0916f97f
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0
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
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1 <tool id="bin_refiner" name="Binning refiner" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
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2 <description>refines metagenome bins</description>
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
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3 <macros>
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
iuc
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4 <import>macros.xml</import>
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
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5 </macros>
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
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6 <expand macro="requirements"/>
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
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7 <command detect_errors="exit_code"><![CDATA[
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8 #import re
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
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9
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
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10 ## Binning refiner prepends the -p param value
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
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11 ## (which we set to be the string 'refined' in
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
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12 ## the command line) to a hard-coded string (i.e.,
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
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13 ## '_Binning_refiner_outputs') to set the base
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
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14 ## output directory.
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
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15
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
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16 ## Binning_refiner requires 2 levels of directories
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
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17 ## for the input bins.
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
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18 mkdir -p input_bin_dir/bins &&
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
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19 #for $f in $input_bins:
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
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20 #set identifier = re.sub('[^\s\w\-]', '_', str($f.element_identifier))
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
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21 #set file_name = $identifier + '.' + $f.ext
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
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22 ## Binning_refiner doesn't handle gzipped files.
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
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23 #if $f.ext.endswith(".gz")
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
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24 gunzip -c '${f}' > 'input_bin_dir/bins/${file_name}' &&
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
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25 #else:
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
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26 ln -s '${f}' 'input_bin_dir/bins/${file_name}' &&
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27 #end if
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28 #end for
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29
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
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30 Binning_refiner
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31 -i input_bin_dir
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
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32 -p 'refined'
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33 && mv 'refined_Binning_refiner_outputs/refined_contigs.txt' '$output_refined_contigs'
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34 && mv 'refined_Binning_refiner_outputs/refined_sources_and_length.txt' '$output_sources_and_length'
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
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35 ]]></command>
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36 <inputs>
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
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37 <param name="input_bins" format="fasta,fasta.gz" type="data" multiple="true" label="Binned fasta files"/>
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
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38 <param argument="-m" type="integer" value="512" label="Minimum size (Kbp) of refined bin" help="Bins smaller than this will be eliminated"/>
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
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39 </inputs>
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
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40 <outputs>
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
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41 <collection name="output_refined_bins" type="list" label="${tool.name} on ${on_string}: (refined bins)">
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42 <discover_datasets pattern="(?P&lt;designation&gt;.*)\.fasta" format="fasta" directory="refined_Binning_refiner_outputs/refined_refined_bins"/>
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43 </collection>
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44 <data name="output_refined_contigs" format="tabular" label="${tool.name} on ${on_string} (refined contigs)"/>
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45 <data name="output_sources_and_length" format="tabular" label="${tool.name} on ${on_string} (sources and length)"/>
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46 </outputs>
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47 <tests>
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48 <test expect_num_outputs="3">
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49 <param name="input_bins" value="MetaBAT_17.fa.gz,MetaBAT_18.fa.gz,MetaBAT_19.fa.gz,MetaBAT_20.fa.gz,MetaBAT_21.fa.gz,MetaBAT_22.fa.gz,MetaBAT_23.fa.gz,Concoct_1.fa.gz,Concoct_3.fa.gz,Concoct_8.fa.gz" ftype="fasta.gz"/>
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50 <output_collection name="output_refined_bins" type="list" count="7">
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51 <element name="refined_1" ftype="fasta">
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52 <assert_contents>
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53 <has_size value="1320640"/>
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54 <has_text text=">scaffold_2064"/>
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55 <has_n_lines n="21765"/>
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56 </assert_contents>
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57 </element>
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58 <element name="refined_2" ftype="fasta">
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59 <assert_contents>
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60 <has_size value="941488"/>
f350d182f786 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/ commit 591fef692e8efeb65c5214e6512aeaaf66201b26"
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61 <has_text text=">scaffold_1301"/>
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62 <has_n_lines n="15461"/>
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63 </assert_contents>
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64 </element>
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65 <element name="refined_3" ftype="fasta">
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66 <assert_contents>
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67 <has_size value="883642"/>
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68 <has_text text=">scaffold_262"/>
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69 <has_n_lines n="14495"/>
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70 </assert_contents>
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71 </element>
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72 <element name="refined_4" ftype="fasta">
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73 <assert_contents>
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74 <has_size value="758509"/>
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75 <has_text text=">scaffold_923"/>
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76 <has_n_lines n="12484"/>
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77 </assert_contents>
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78 </element>
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79 <element name="refined_5" ftype="fasta">
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80 <assert_contents>
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81 <has_size value="722197"/>
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82 <has_text text=">scaffold_232"/>
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83 <has_n_lines n="11849"/>
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84 </assert_contents>
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85 </element>
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86 <element name="refined_6" ftype="fasta">
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87 <assert_contents>
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88 <has_size value="637342"/>
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89 <has_text text=">scaffold_259"/>
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90 <has_n_lines n="10460"/>
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91 </assert_contents>
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92 </element>
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93 <element name="refined_7" ftype="fasta">
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94 <assert_contents>
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95 <has_size value="560996"/>
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96 <has_text text=">scaffold_1510"/>
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97 <has_n_lines n="9219"/>
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98 </assert_contents>
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99 </element>
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100 </output_collection>
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101 <output name="output_refined_contigs" file="output_refined_contigs.tabular" ftype="tabular"/>
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102 <output name="output_sources_and_length" file="output_sources_and_length.tabular" ftype="tabular"/>
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103 </test>
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104 </tests>
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105 <help><![CDATA[
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106 **What it does**
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107
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108 Reconciles the outputs of different binning programs with the aim to improve the quality of genome bins,
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109 especially with respect to contamination levels.
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110
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111 The tool accepts one or more fasta datasets (i.e., bins) that were produced by metagenome binning tools
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112 (CONCOCT MaxBin2, MetaBAT2 and others).
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113
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114 All refined bins larger than the specified "Minimum size (Kbp) of refined bin" will be output as a dataset
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115 collection of fasta files. Additional outputs include a tabular dataset containing the id of the contigs
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116 in each refined bin (refined contigs) and another tabular dataset containing the size of each refined bin
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117 and the origin of its contigs (sources and length).
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118
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119 **More information**
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120
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121 https://github.com/songweizhi/Binning_refiner
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122
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123 ]]></help>
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124 <expand macro="citations"/>
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125 </tool>