Mercurial > repos > iuc > checkm_analyze

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 97fbd010c5406d4980d64b320f25f4716aea2fc9
author iuc
date Tue, 17 Jun 2025 12:53:44 +0000
parents d5c2aa105c2e
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7ce554541b5c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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1 <tool id="checkm_analyze" name="CheckM analyze" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
7ce554541b5c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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2 <description>
7ce554541b5c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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3 Identify marker genes in bins and calculate genome statistics
7ce554541b5c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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4 </description>
7ce554541b5c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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5 <macros>
7ce554541b5c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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6 <import>macros.xml</import>
7ce554541b5c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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7 </macros>
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8 <expand macro="biotools"/>
7ce554541b5c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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9 <expand macro="requirements"/>
7ce554541b5c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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10 <expand macro="version"/>
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11 <command detect_errors="exit_code"><![CDATA[
7ce554541b5c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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12 @BIN_INPUTS@
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13
7ce554541b5c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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14 checkm analyze
7ce554541b5c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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15 '$marker_file'
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16 'bins'
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17 'output'
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18 $ali
7ce554541b5c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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19 $nt
7ce554541b5c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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20 $genes
7ce554541b5c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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21 --extension 'fasta'
7ce554541b5c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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22 --threads \${GALAXY_SLOTS:-1}
7ce554541b5c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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23 ]]></command>
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24 <inputs>
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25 <expand macro="bin_inputs" />
7ce554541b5c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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26 <expand macro="marker_file" />
7ce554541b5c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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27 <expand macro="analyze_params"/>
7ce554541b5c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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28 <param name="extra_outputs" type="select" multiple="true" optional="true" label="Extra outputs">
7ce554541b5c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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29 <expand macro="analyze_extra_output_options" />
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30 </param>
7ce554541b5c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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31 </inputs>
7ce554541b5c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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32 <outputs>
7ce554541b5c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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33 <collection name="hmmer_analyze" type="list" label="${tool.name} on ${on_string}: Marker gene HMM hits to each bin">
7ce554541b5c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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34 <discover_datasets pattern="(?P&lt;designation&gt;.*)/hmmer\.analyze\.txt" format="txt" directory="output/bins/" recurse="true" match_relative_path="true"/>
7ce554541b5c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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35 </collection>
7ce554541b5c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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36 <data name="bin_stats_analyze" format="tabular" from_work_dir="output/storage/bin_stats.analyze.tsv" label="${tool.name} on ${on_string}: Marker gene bin stats" />
7ce554541b5c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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37 <data name="checkm_hmm_info" format="zip" from_work_dir="output/storage/checkm_hmm_info.pkl.gz" label="${tool.name} on ${on_string}: Marker gene HMM info for each bin" />
7ce554541b5c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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38 <collection name="hmmer_analyze_ali" type="list" label="${tool.name} on ${on_string}: HMMER alignment file for each bin">
1
d5c2aa105c2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit a96defec82bfa9628fa821ffa6df5c68314a41d8
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39 <filter>ali and extra_outputs and 'hmmer_analyze_ali' in extra_outputs</filter>
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7ce554541b5c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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40 <discover_datasets pattern="(?P&lt;designation&gt;.*)/hmmer\.analyze\.ali\.txt" format="txt" directory="output/bins/" recurse="true" match_relative_path="true"/>
7ce554541b5c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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41 </collection>
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42 </outputs>
7ce554541b5c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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43 <tests>
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44 <test expect_num_outputs="3">
7ce554541b5c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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45 <conditional name="bins">
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46 <param name="select" value="collection"/>
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47 <param name="bins_coll">
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48 <collection type="list">
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49 <element name="637000110" ftype="fasta" value="637000110.fna"/>
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50 </collection>
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51 </param>
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52 </conditional>
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53 <param name="marker_file" ftype="tabular" value="lineage_marker_set"/>
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54 <param name="ali" value="false"/>
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55 <param name="nt" value="false"/>
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56 <param name="genes" value="false"/>
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57 <output_collection name="hmmer_analyze" count="1">
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58 <element name="637000110" ftype="txt">
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59 <assert_contents>
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60 <has_text text="target name"/>
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61 <has_text text="AC_000091_859"/>
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62 </assert_contents>
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63 </element>
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64 </output_collection>
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65 <output name="bin_stats_analyze" ftype="tabular">
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66 <assert_contents>
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67 <has_text text="637000110"/>
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68 <has_text text="GC"/>
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69 <has_text text="GC std"/>
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70 </assert_contents>
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71 </output>
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72 <output name="checkm_hmm_info" ftype="zip">
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73 <assert_contents>
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74 <has_size value="99600" delta="500"/>
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75 </assert_contents>
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76 </output>
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77 </test>
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78 <test expect_num_outputs="4">
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79 <conditional name="bins">
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80 <param name="select" value="collection"/>
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81 <param name="bins_coll">
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82 <collection type="list">
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83 <element name="637000110" ftype="fasta" value="637000110.fna"/>
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84 </collection>
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85 </param>
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86 </conditional>
7ce554541b5c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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87 <param name="marker_file" ftype="tabular" value="lineage_marker_set"/>
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88 <param name="ali" value="true"/>
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89 <param name="nt" value="true"/>
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90 <param name="genes" value="false"/>
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91 <param name="extra_outputs" value="hmmer_analyze_ali"/>
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92 <output_collection name="hmmer_analyze" count="1">
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93 <element name="637000110" ftype="txt">
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94 <assert_contents>
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95 <has_text text="target name"/>
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96 <has_text text="AC_000091_859"/>
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97 </assert_contents>
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98 </element>
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99 </output_collection>
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100 <output name="bin_stats_analyze" ftype="tabular">
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101 <assert_contents>
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102 <has_text text="637000110"/>
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103 <has_text text="GC"/>
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104 <has_text text="GC std"/>
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105 </assert_contents>
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106 </output>
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107 <output name="checkm_hmm_info" ftype="zip">
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108 <assert_contents>
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109 <has_size value="99600" delta="500"/>
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110 </assert_contents>
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111 </output>
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112 <output_collection name="hmmer_analyze_ali" count="1">
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113 <element name="637000110" ftype="txt">
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114 <assert_contents>
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115 <has_text text="hmmsearch"/>
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116 <has_text text="Query"/>
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117 <has_text text="ACCA"/>
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118 </assert_contents>
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119 </element>
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120 </output_collection>
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121 </test>
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122 </tests>
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123 <help><![CDATA[
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124 @HELP_HEADER@
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125
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126 This command identifies marker genes in bins and calculates genome statistics
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127 ]]></help>
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128 <expand macro="citations"/>
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129 </tool>