Mercurial > repos > artbio > gsc_center_scale

annotate center_scale.xml @ 1:a96cc346819c draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_center_scale commit 7865eb7eb9d862e9967fe519d28df705d973fbaf
author artbio
date Fri, 12 Jul 2019 11:44:50 -0400
parents bcbd7179d8ec
children 163befe5f05b
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a96cc346819c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_center_scale commit 7865eb7eb9d862e9967fe519d28df705d973fbaf
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1 <tool id="center_scale" name="Center or scale (standardize) data" version="0.9.5">
0
bcbd7179d8ec planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_center_scale commit b839b440f0760ff9cd75969d418432702947a669
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2 <description></description>
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3 <requirements>
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4 <requirement type="package" version="1.6.0">r-optparse</requirement>
bcbd7179d8ec planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_center_scale commit b839b440f0760ff9cd75969d418432702947a669
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5 </requirements>
bcbd7179d8ec planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_center_scale commit b839b440f0760ff9cd75969d418432702947a669
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6 <stdio>
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7 <exit_code range="1:" level="fatal" description="Tool exception" />
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8 </stdio>
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9 <command detect_errors="exit_code"><![CDATA[
bcbd7179d8ec planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_center_scale commit b839b440f0760ff9cd75969d418432702947a669
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10 Rscript $__tool_directory__/center_scale.R
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11 --data '$input'
bcbd7179d8ec planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_center_scale commit b839b440f0760ff9cd75969d418432702947a669
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12 --center '$center'
bcbd7179d8ec planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_center_scale commit b839b440f0760ff9cd75969d418432702947a669
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13 --scale '$scale'
bcbd7179d8ec planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_center_scale commit b839b440f0760ff9cd75969d418432702947a669
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14 #if $factor.factor_options == 'TRUE':
bcbd7179d8ec planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_center_scale commit b839b440f0760ff9cd75969d418432702947a669
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15 --factor '$file'
bcbd7179d8ec planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_center_scale commit b839b440f0760ff9cd75969d418432702947a669
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16 #end if
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17 --output '$output'
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18 ]]></command>
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19 <inputs>
bcbd7179d8ec planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_center_scale commit b839b440f0760ff9cd75969d418432702947a669
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20 <param name="input" type="data" format="tabular" label="Input file with values to transform"
bcbd7179d8ec planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_center_scale commit b839b440f0760ff9cd75969d418432702947a669
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21 help="Must be tabular separated with columns and row names, variables in rows, observations in columns" />
bcbd7179d8ec planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_center_scale commit b839b440f0760ff9cd75969d418432702947a669
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22 <param name="center" type="select" label="Center data to mean">
bcbd7179d8ec planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_center_scale commit b839b440f0760ff9cd75969d418432702947a669
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23 <option value="TRUE" selected="true">Yes</option>
bcbd7179d8ec planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_center_scale commit b839b440f0760ff9cd75969d418432702947a669
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24 <option value="FALSE">No</option>
bcbd7179d8ec planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_center_scale commit b839b440f0760ff9cd75969d418432702947a669
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25 </param>
bcbd7179d8ec planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_center_scale commit b839b440f0760ff9cd75969d418432702947a669
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26 <param name="scale" type="select" label="Scale data to standard deviation">
bcbd7179d8ec planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_center_scale commit b839b440f0760ff9cd75969d418432702947a669
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27 <option value="TRUE" selected="true">Yes</option>
bcbd7179d8ec planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_center_scale commit b839b440f0760ff9cd75969d418432702947a669
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28 <option value="FALSE">No</option>
bcbd7179d8ec planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_center_scale commit b839b440f0760ff9cd75969d418432702947a669
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29 </param>
bcbd7179d8ec planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_center_scale commit b839b440f0760ff9cd75969d418432702947a669
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30 <conditional name="factor">
bcbd7179d8ec planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_center_scale commit b839b440f0760ff9cd75969d418432702947a669
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31 <param name="factor_options" type="select" label="group data by factor ?">
bcbd7179d8ec planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_center_scale commit b839b440f0760ff9cd75969d418432702947a669
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32 <option value="TRUE">Yes</option>
bcbd7179d8ec planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_center_scale commit b839b440f0760ff9cd75969d418432702947a669
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33 <option value="FALSE" selected="true">No</option>
bcbd7179d8ec planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_center_scale commit b839b440f0760ff9cd75969d418432702947a669
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34 </param>
bcbd7179d8ec planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_center_scale commit b839b440f0760ff9cd75969d418432702947a669
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35 <when value="TRUE">
bcbd7179d8ec planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_center_scale commit b839b440f0760ff9cd75969d418432702947a669
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36 <param name="file" type="data" format="tabular" label="Grouping map"
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37 help="A two-column observation|factor_level table that assigns group ids to observations" />
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38 </when>
bcbd7179d8ec planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_center_scale commit b839b440f0760ff9cd75969d418432702947a669
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39 <when value="FALSE">
bcbd7179d8ec planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_center_scale commit b839b440f0760ff9cd75969d418432702947a669
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40 </when>
bcbd7179d8ec planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_center_scale commit b839b440f0760ff9cd75969d418432702947a669
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41 </conditional>
bcbd7179d8ec planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_center_scale commit b839b440f0760ff9cd75969d418432702947a669
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42 </inputs>
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43 <outputs>
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44 <data name="output" format="tabular" label="scale ${on_string}" />
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45 </outputs>
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46 <tests>
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47 <test>
1
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48 <param name="input" value="fulldata.tsv" ftype="tabular"/>
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49 <param name="scale" value="TRUE"/>
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50 <param name="center" value="TRUE"/>
0
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51 <output name="output" file="full_standardize.tab" ftype="tabular"/>
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52 </test>
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53 <test>
1
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54 <param name="input" value="fulldata.tsv" ftype="tabular"/>
0
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55 <param name="scale" value="FALSE"/>
1
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56 <param name="center" value="TRUE"/>
0
bcbd7179d8ec planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_center_scale commit b839b440f0760ff9cd75969d418432702947a669
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57 <output name="output" file="full_center.tab" ftype="tabular"/>
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58 </test>
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59 <test>
1
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60 <param name="input" value="fulldata.tsv" ftype="tabular"/>
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61 <param name="scale" value="TRUE"/>
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62 <param name="center" value="FALSE"/>
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63 <output name="output" file="full_scale.tab" ftype="tabular"/>
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64 </test>
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65 <test>
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66 <param name="input" value="fulldata.tsv" ftype="tabular" />
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67 <param name="scale" value="TRUE"/>
a96cc346819c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_center_scale commit 7865eb7eb9d862e9967fe519d28df705d973fbaf
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68 <param name="center" value="TRUE"/>
0
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69 <param name="factor_options" value="TRUE" />
1
a96cc346819c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_center_scale commit 7865eb7eb9d862e9967fe519d28df705d973fbaf
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70 <param name="file" value="fulldata.map.tsv" ftype="tabular" />
0
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71 <output name="output" file="group_standardize.tab" ftype="tabular"/>
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72 </test>
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73 <test>
1
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74 <param name="input" value="fulldata.tsv" ftype="tabular" />
0
bcbd7179d8ec planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_center_scale commit b839b440f0760ff9cd75969d418432702947a669
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75 <param name="scale" value="FALSE"/>
1
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76 <param name="center" value="TRUE"/>
0
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77 <param name="factor_options" value="TRUE" />
1
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78 <param name="file" value="fulldata.map.tsv" ftype="tabular" />
0
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79 <output name="output" file="group_center.tab" ftype="tabular"/>
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80 </test>
1
a96cc346819c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_center_scale commit 7865eb7eb9d862e9967fe519d28df705d973fbaf
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81 <test>
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82 <param name="input" value="fulldata.tsv" ftype="tabular" />
a96cc346819c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_center_scale commit 7865eb7eb9d862e9967fe519d28df705d973fbaf
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83 <param name="scale" value="TRUE"/>
a96cc346819c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_center_scale commit 7865eb7eb9d862e9967fe519d28df705d973fbaf
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84 <param name="center" value="FALSE"/>
a96cc346819c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_center_scale commit 7865eb7eb9d862e9967fe519d28df705d973fbaf
artbio
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85 <param name="factor_options" value="TRUE" />
a96cc346819c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_center_scale commit 7865eb7eb9d862e9967fe519d28df705d973fbaf
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86 <param name="file" value="fulldata.map.tsv" ftype="tabular" />
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87 <output name="output" file="group_scale.tab" ftype="tabular"/>
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88 </test>
0
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89 </tests>
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90 <help>
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91
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92 **What it does**
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93
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94 The tool perform various normalization operations on a data table, including mean centering,
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95 standard deviation rescaling, or both (standardization).
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96
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97 In addition, these operations can be performed on subsets of observations, is the user provides
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98 a two-column table that maps observations to groups (factor levels).
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99
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100 **Inputs**
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101
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102 A data table with observations (samples, library sequencings) in columns (library names
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103 are column names) and variables (genes) in rows (gene names are row names).
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104
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105 Optionally, a two-column table may be used to map observations to a factor level. In this
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106 case, normalization operations will be performed by group having same level.
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107
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108 **Outputs**
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109
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110 A table with same numbers of columns and rows as input table, and transformed values.
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111
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112 </help>
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113 <citations>
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114 <citation type="bibtex">
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115 @Manual{,
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116 title = {R: A Language and Environment for Statistical Computing},
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117 author = {{R Core Team}},
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118 organization = {R Foundation for Statistical Computing},
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119 address = {Vienna, Austria},
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120 year = {2014},
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121 url = {http://www.R-project.org/},
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122 }
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123 </citation>
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124 </citations>
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125 </tool>