[2] | 1 | <tool id="rgLDIndep1" name="LD Independent:"> |
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| 2 | <code file="rgLDIndep_code.py"/> |
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| 3 | |
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| 4 | <description>filter high LD pairs - decrease redundancy</description> |
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| 5 | |
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| 6 | <command interpreter="python"> |
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| 7 | rgLDIndep.py '$input_file.extra_files_path' '$input_file.metadata.base_name' '$title1' '$mind' |
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| 8 | '$geno' '$hwe' '$maf' '$mef' '$mei' '$out_file1' |
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| 9 | '$out_file1.files_path' '$window' '$step' '$r2' |
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| 10 | </command> |
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| 11 | |
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| 12 | <inputs> |
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| 13 | <param name="input_file" type="data" label="RGenetics genotype data from your current history" |
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| 14 | size="80" format="pbed" /> |
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| 15 | <param name="title1" type="text" size="80" label="Descriptive title for cleaned genotype file" value="LD_Independent"/> |
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| 16 | <param name="r2" type="float" value = "0.1" |
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| 17 | label="r2 threshold: Select only pairs at or below this r^2 threshold (eg 0.1)" |
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| 18 | help="LD threshold defining LD independent markers" /> |
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| 19 | <param name="window" type="integer" value = "40" label="Window: Window size to limit LD pairwise" |
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| 20 | help = "Bigger is better but time taken blows up exponentially as the window grows!" /> |
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| 21 | <param name="step" type="integer" value = "30" label="Step: Move window this far and recompute" |
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| 22 | help = "Smaller is better but of course, time increases..." /> |
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| 23 | <param name="geno" type="float" label="Maximum Missing Fraction: Markers" value="1.0" /> |
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| 24 | <param name="mind" type="float" value="1.0" label="Maximum Missing Fraction: Subjects"/> |
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| 25 | <param name="mef" type="float" label="Maximum Mendel Error Rate: Family" value="1.0"/> |
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| 26 | <param name="mei" type="float" label="Maximum Mendel Error Rate: Marker" value="1.0"/> |
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| 27 | <param name="hwe" type="float" value="0.0" label="Smallest HWE p value (set to 0 for all)" /> |
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| 28 | <param name="maf" type="float" value="0.0" |
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| 29 | label="Smallest Allowable Minor Allele Frequency (set to 0.0 for all)"/> |
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| 30 | |
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| 31 | </inputs> |
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| 32 | |
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| 33 | <outputs> |
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| 34 | <data format="pbed" name="out_file1" metadata_source="input_file" /> |
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| 35 | </outputs> |
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| 36 | <tests> |
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| 37 | <test> |
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| 38 | |
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| 39 | <param name='input_file' value='tinywga' ftype='pbed' > |
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| 40 | <metadata name='base_name' value='tinywga' /> |
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| 41 | <composite_data value='tinywga.bim' /> |
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| 42 | <composite_data value='tinywga.bed' /> |
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| 43 | <composite_data value='tinywga.fam' /> |
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| 44 | <edit_attributes type='name' value='tinywga' /> |
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| 45 | </param> |
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| 46 | <param name='title1' value='rgLDIndeptest1' /> |
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| 47 | <param name="mind" value="1" /> |
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| 48 | <param name="geno" value="1" /> |
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| 49 | <param name="hwe" value="0" /> |
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| 50 | <param name="maf" value="0" /> |
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| 51 | <param name="mef" value="1" /> |
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| 52 | <param name="mei" value="1" /> |
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| 53 | <param name="window" value="10000" /> |
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| 54 | <param name="step" value="5000" /> |
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| 55 | <param name="r2" value="0.1" /> |
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| 56 | <output name='out_file1' file='rgtestouts/rgLDIndep/rgLDIndeptest1.pbed' ftype='pbed' compare="diff" lines_diff='7'> |
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| 57 | <extra_files type="file" name='rgLDIndeptest1.bim' value="rgtestouts/rgLDIndep/rgLDIndeptest1.bim" compare="sim_size" delta="1000"/> |
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| 58 | <extra_files type="file" name='rgLDIndeptest1.fam' value="rgtestouts/rgLDIndep/rgLDIndeptest1.fam" compare="diff" /> |
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| 59 | <extra_files type="file" name='rgLDIndeptest1.bed' value="rgtestouts/rgLDIndep/rgLDIndeptest1.bed" compare="sim_size" delta = "1000" /> |
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| 60 | </output> |
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| 61 | </test> |
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| 62 | </tests> |
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| 63 | <help> |
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| 64 | |
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| 65 | .. class:: infomark |
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| 66 | |
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| 67 | **Attribution** |
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| 68 | |
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| 69 | This tool relies on Plink from Shaun Purcell. For full documentation, please see his web site |
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| 70 | at http://pngu.mgh.harvard.edu/~purcell/plink/ where there is excellent documentation describing |
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| 71 | the parameters you can set here. |
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| 72 | |
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| 73 | Rgenetics merely exposes them, wrapping Plink so you can use it in Galaxy. |
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| 74 | |
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| 75 | **Summary** |
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| 76 | |
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| 77 | In addition to filtering some marker and sample quality measures, |
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| 78 | this tool reduces the amount of overlapping information, by removing |
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| 79 | most of the duplicate information contained in linkage disequilibrium. This is |
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| 80 | a lossy process and for some methods, signal may be lost. However, this makes |
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| 81 | the dataset far more compact (eg 10% of the original storage size) while still |
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| 82 | being highly informative and less biased for some (note NOT all!) statistical methods. |
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| 83 | This is the Clean tool with additional data reduction via Plink LD pruning. |
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| 84 | Use the Clean tool if you don't want LD pruning - which you don't for most statistical testing. |
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| 85 | For ancestry and relatedness, you may well want LD pruned data as it has |
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| 86 | some specific desirable properties. |
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| 87 | |
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| 88 | **LD** |
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| 89 | |
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| 90 | Pairwise Linkage disequilibrium (LD) measures the extent to which the genotype at one locus |
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| 91 | predicts the state of another locus at the level of an entire population. |
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| 92 | When population LD between a pair of markers is high, |
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| 93 | knowing an individual's genotype at one locus allows confident prediction of the genotype at the other. |
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| 94 | In other words, high LD means information redundancy between markers. For some |
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| 95 | purposes, removing some of this redundancy can improve the performance of some analyses. |
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| 96 | Executing this tool will create a new genotype dataset in your current history containing |
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| 97 | LD independent markers - most of the genetic information is retained but without as much redundancy. |
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| 98 | |
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| 99 | Set a pairwise LD threshold (eg r^2 = 0.2) and the (smaller) resulting dataset will have no |
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| 100 | pairs of marker with r^2 greater than 0.2. Additional filters are available to remove markers |
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| 101 | below a specific minor allele frequency, or above a specific level of missingness, |
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| 102 | and to remove subjects using similar criteria. Subjects and markers for family data can be |
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| 103 | filtered by proportions of Mendelian errors in observed transmission. |
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| 104 | |
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| 105 | ----- |
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| 106 | |
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| 107 | **Syntax** |
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| 108 | |
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| 109 | - **Genotype data** is the input pedfile chosen from available library files |
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| 110 | - **New name** is the name to use for the filtered output file |
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| 111 | - **Missfrac threshold: subjects** is the threshold for missingness by subject. Subjects with more than this fraction missing will be excluded from the import |
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| 112 | - **Missfrac threshold: markers** is the threshold for missingness by marker. Markers with more than this fraction missing will be excluded from the import |
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| 113 | - **MaxMendel Individuals** Mendel error fraction above which to exclude subjects with more than the specified fraction of mendelian errors in transmission (for family data only) |
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| 114 | - **MaxMendel Families** Mendel error fraction above which to exclude families with more than the specified fraction of mendelian errors in transmission (for family data only) |
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| 115 | - **HWE** is the threshold for HWE test p values below which the marker will not be imported. Set this to -1 and all markers will be imported regardless of HWE p value |
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| 116 | - **MAF** is the threshold for minor allele frequency - SNPs with lower MAF will be excluded |
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| 117 | - **r^2** is the pairwise LD threshold as r^2. Lower -> less marker redundancy -> fewer markers |
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| 118 | - **Window** is the window width for LD threshold. Bigger -> slower -> more complete |
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| 119 | - **Skip** is the distance to move the window along the genome. Should be window or less. |
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| 120 | |
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| 121 | ----- |
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| 122 | |
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| 123 | **Disclaimer** |
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| 124 | |
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| 125 | This tool relies on Plink from Shaun Purcell. For full documentation, please see his web site |
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| 126 | at http://pngu.mgh.harvard.edu/~purcell/plink/ where thereis excellent documentation describing |
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| 127 | the parameters you can set here. Rgenetics merely exposes them, and wraps Plink so you can use it in Galaxy. |
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| 128 | |
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| 129 | This tool is designed to create genotype data files with more or less LD independent sets of markers. These |
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| 130 | reduced genotype data files are particularly useful for purposes such as evaluating |
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| 131 | ancestry (eg eigenstrat) or relatedness (eg rgGRR) |
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| 132 | |
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| 133 | LD pruning decreases redundancy among the genotype data by removing one of each pair of markers |
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| 134 | in strong LD (above the r^2 threshold) over successive genomic windows (the Window parameter), |
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| 135 | skipping (the Skip parameter bases between windows. The defaults should produce useable outputs. |
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| 136 | |
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| 137 | This might be more efficient for rgGRR and |
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| 138 | eigenstrat...The core quote is |
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| 139 | |
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| 140 | "This generates the same output files as the first version; |
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| 141 | the only difference is that a simple pairwise threshold is used. |
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| 142 | The first two parameters (50 and 5) are the same as above (window size and step); |
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| 143 | the third parameter represents the r^2 threshold. |
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| 144 | Note: this represents the pairwise SNP-SNP metric now, not the |
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| 145 | multiple correlation coefficient; also note, this is based on the |
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| 146 | genotypic correlation, i.e. it does not involve phasing. |
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| 147 | " |
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| 148 | |
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| 149 | ----- |
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| 150 | |
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| 151 | |
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| 152 | |
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| 153 | This Galaxy tool was written by Ross Lazarus for the Rgenetics project |
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| 154 | It uses Plink for most calculations - for full Plink attribution, source code and documentation, |
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| 155 | please see http://pngu.mgh.harvard.edu/~purcell/plink/ plus some custom python code |
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| 156 | |
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| 157 | </help> |
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| 158 | </tool> |
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