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planemo upload commit 7f3c6fb6db52daedaa0c59d6ca7f39710778f242-dirty
author jpayne
date Mon, 11 Aug 2025 15:46:24 +0000
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1 <tool id="csp2-screen" name="CSP2 (Screening Mode)" version="0.9.7.7">
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2 <description>Screen query assemblies against reference assemblies</description>
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3 <requirements>
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4 <!-- <requirement type="package" version="24.10.1">nextflow</requirement>
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5 <requirement type="package" version="1.5.8">micromamba</requirement> -->
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6 <container type="docker">cfsanbiostatistics/csp2:v.0.9.7.7-galaxy</container>
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7 </requirements>
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8 <version_command>nextflow -version</version_command>
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9 <command detect_errors="exit_code"><![CDATA[
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10 mkdir -p queries references .nextflow
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11 #set readext=""
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12 #set renamedref=$source.reference.element_identifier.replace(": ", ".").replace(" ", "_")
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13 #for $reads in $coll
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14 && ln -sf '${reads}' 'queries/${reads.element_identifier.replace(": ", ".").replace(" ", "_")}.fasta'
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15 #end for
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16 && ln -sf '$source.reference' 'references/${renamedref}.fasta'
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17 && echo "*** Files in queries directory: ***"
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18 && ls -lah queries/
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19 && nextflow run
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20 /app/CSP2.nf -c $__tool_directory__/nextflow.config -profile standard
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21 --runmode screen
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22 --fasta queries
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23 --ref_fasta 'references/${renamedref}.fasta'
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24 --min_cov $opt.min_cov
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25 --min_iden $opt.min_iden
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26 --min_len $opt.min_len
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27 --ref_edge $opt.ref_edge
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28 --query_edge $opt.query_edge
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29 --dwin $opt.dwin
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30 --wsnps $opt.wsnps
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31 --out CSP2_Screen_Output
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32 --quiet
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33 && echo "*** Files in output directory: ***"
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34 && ls -lahR CSP2_Screen_Output
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35 && tail -n +2 CSP2_Screen_Output/Isolate_Data.tsv > ${isolate_data}
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36 && tail -n +2 CSP2_Screen_Output/Raw_MUMmer_Summary.tsv > ${raw_mummer}
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37 && tail -n +2 CSP2_Screen_Output/Screening_Results.tsv > ${screening_results}
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38 && echo "*** Nextflow log follows: ***"
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39 && cat .nextflow.log
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40 ]]>
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41 </command>
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42 <inputs>
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43 <conditional name="source">
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44 <param name="source_select" type="select" label="Use a curated GalaxyTrakr reference or a reference from your history">
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45 <option value="curated">Use a GalaxyTrakr reference</option>
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46 <option value="history">Use a reference from your history</option>
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47 </param>
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48 <when value="curated">
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49 <param name="reference" type="select" label="Select reference fasta">
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50 <options from_data_table="all_fasta">
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51 <filter type="sort_by" column="2"/>
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52 <validator type="no_options" message="No assemblies are available for the selected input dataset"/>
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53 </options>
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54 </param>
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55 </when>
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56 <when value="history">
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57 <param type="data" name="reference" format="fasta" label="Select reference FASTA"/>
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58 </when>
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59 </conditional>
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60 <!-- <conditional name="query">
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61 <param name="query_select" type="select" label="Screen a list of paired-end reads or a list of assemblies">
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62 <option value="reads">Screen a list of paired reads</option>
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63 <option value="assemblies">Screen a list of assemblies</option>
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64 </param>
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65 <when value="reads">
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66 <param label="Paired reads" name="coll" type="data_collection" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" collection_type="list:paired" />
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67 </when>
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68 <when value="assemblies"> -->
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69 <param label="Assemblies" name="coll" type="data_collection" format="fasta" collection_type="list" />
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70 <!-- </when> -->
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71 <!-- </conditional> -->
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72 <section name="opt" title="Advanced options...">
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73 <param argument="--min_cov" name="min_cov" type="float" value="85" label="Minimum reference genome coverage to proceed with distance estimation" />
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74 <param argument="--min_eden" name="min_iden" type="float" value="99" label="Minimum alignment percent identity to detect SNPs" />
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75 <param argument="--min_len" name="min_len" type="integer" value="500" label="Minimum alignment length to detect SNPs" />
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76 <param argument="--ref_edge" name="ref_edge" type="integer" value="150" label="Prune SNPs within this many bases of reference contig edge" />
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77 <param argument="--query_edge" name="query_edge" type="integer" value="150" label="Prune SNPs within this many bases of query contig edge" />
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78 <param argument="--dwin" name="dwin" type="text" value="1000,125,15" label="Comma-separated set of window sizes for SNP density filtration (Set to 0 to disable density filtration)" />
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79 <param argument="--wsnips" name="wsnps" type="text" value="3,2,1" label="Comma-separated list of maximum SNP counts per density window" />
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80 </section>
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81 </inputs>
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82 <outputs>
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83 <data name="raw_mummer" format="tabular" label="Raw MUMmer Output">
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84 <actions>
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85 <action name="column_names" type="metadata" default="SNPDiffs_File,Query_ID,Query_Assembly,Query_Contig_Count,Query_Assembly_Bases,Query_N50,Query_N90,Query_L50,Query_L90,Query_SHA256,Reference_ID,Reference_Assembly,Reference_Contig_Count,Reference_Assembly_Bases,Reference_N50,Reference_N90,Reference_L50,Reference_L90,Reference_SHA256,SNPs,Reference_Percent_Aligned,Query_Percent_Aligned,Median_Percent_Identity,Median_Alignment_Length,Kmer_Similarity,Shared_Kmers,Reference_Unique_Kmers,Query_Unique_Kmers,Reference_Breakpoints,Query_Breakpoints,Reference_Relocations,Query_Relocations,Reference_Translocations,Query_Translocations,Reference_Inversions,Query_Inversions,Reference_Insertions,Query_Insertions,Reference_Tandem,Query_Tandem,Indels,Invalid,gSNPs,gIndels" />
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86 </actions>
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87 </data>
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88 <data name="isolate_data" format="tabular" label="Isolate Data">
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89 <actions>
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90 <action name="column_names" type="metadata" default="Isolate_ID,Isolate_Type,Assembly_Path,Contig_Count,Assembly_Bases,N50,N90,L50,L90,SHA256" />
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91 </actions>
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92 </data>
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93 <data name="screening_results" format="tabular" label="Screening Results">
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94 <actions>
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95 <action name="column_names" type="metadata" default="Query_ID,Reference_ID,Screen_Category,CSP2_Screen_SNPs,Query_Percent_Aligned,Reference_Percent_Aligned,Query_Contigs,Query_Bases,Reference_Contigs,Reference_Bases,Raw_SNPs,Purged_Length,Purged_Identity,Purged_LengthIdentity,Purged_Invalid,Purged_Indel,Purged_Duplicate,Purged_Het,Purged_Density,Filtered_Query_Edge,Filtered_Ref_Edge,Filtered_Both_Edge,Kmer_Similarity,Shared_Kmers,Query_Unique_Kmers,Reference_Unique_Kmers,MUMmer_gSNPs,MUMmer_gIndels" />
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96 </actions>
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97 </data>
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98 <!-- <data name="nextflow_log" format="txt" label="Nextflow Log" from_work_dir="Nextflow_Log.txt" /> -->
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99 </outputs>
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100 <tests>
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101 <test>
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102 <param name="source_select" value="history" />
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103 <param name="reference" value="assemblies/Sample_A.fasta" ftype="fasta" />
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104 <!-- <param name="query_select" value="assemblies" /> -->
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105 <param name="coll">
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106 <collection type="list">
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107 <!-- <element name="Sample_A" value="assemblies/Sample_A.fasta" /> -->
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108 <element name="Sample_B" value="assemblies/Sample_B.fasta" />
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109 <element name="Sample_C" value="assemblies/Sample_C.fasta" />
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110 <element name="Sample_D" value="assemblies/Sample_D.fasta" />
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111 <element name="Sample_E" value="assemblies/Sample_E.fasta" />
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112 <element name="Sample_F" value="assemblies/Sample_F.fasta" />
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113 <element name="Sample_G" value="assemblies/Sample_G.fasta" />
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114 <element name="Sample_H" value="assemblies/Sample_H.fasta" />
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115 <element name="Sample_I" value="assemblies/Sample_I.fasta" />
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116 <element name="Sample_J" value="assemblies/Sample_J.fasta" />
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117 <element name="Sample_K" value="assemblies/Sample_K.fasta" />
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118 <element name="Sample_L" value="assemblies/Sample_L.fasta" />
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119 <element name="Sample_M" value="assemblies/Sample_M.fasta" />
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120 <element name="Sample_N" value="assemblies/Sample_N.fasta" />
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121 <element name="Sample_O" value="assemblies/Sample_O.fasta" />
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122 </collection>
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123 </param>
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124
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125 <output name="screening_results" value="Screening_Results.tsv" />
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126 <output name="isolate_data" value="Isolate_Data.tsv" />
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127 </test>
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128 <!-- <test>
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129 <param name="source_select" value="history" />
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130 <param name="reference" value="assemblies/Sample_A.fasta" ftype="fasta" />
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131 <param name="query_select" value="reads" />
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132 <param name="coll">
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133 <collection type="list:paired">
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134 <element name="Sample_A" >
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135 <collection type="paired">
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136 <element name="forward" value="reads/Week_42_Reads_1.fq.gz" ftype="fastqsanger.gz" />
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137 <element name="reverse" value="reads/Week_42_Reads_2.fq.gz" ftype="fastqsanger.gz" />
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138 </collection>
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139 </element>
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140 </collection>
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141 </param>
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142 <output name="screening_results" value="Screening_Results.tsv" />
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143 <output name="isolate_data" value="Isolate_Data.tsv" />
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144 </test> -->
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145 </tests>
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146 <help>
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147 This tool takes query assemblies and reference assemblies and calculates the pairwise distance between each query/reference combination. If no reference is provided, all queries are compared to all other queries.
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148 </help>
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149 <citations>
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150 <citation type="doi">10.XXXX/placeholder.doi</citation>
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151 <citation type="bibtex">@article{example2024,title={CFSAN SNP Pipeline 2 (CSP2): a pipeline for fast and accurate SNP distance estimation from bacterial genome assemblies.},author={Doe, John and Smith, Jane},journal={Submitted},year={2024}}
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152 </citation>
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153 </citations>
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154 </tool>