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annotate lasttrain.xml @ 0:7f7e48d3b85d draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
author iuc
date Wed, 17 Jun 2020 10:20:20 +0000
parents
children 036d64816c8b
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7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
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1 <tool id="last_train" name="LAST-train" version="@LAST_CONDA_VERSION@+galaxy0" profile="18.01">
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
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2
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
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3 <description>finds the rates (probabilities) of insertion, deletion, and substitutions between two sets of sequences.</description>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
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4
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
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5 <macros>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
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6 <import>macros_last.xml</import>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
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7 </macros>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
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8
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
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9 <requirements>
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10 <requirement type="package" version="@LAST_CONDA_VERSION@">last</requirement>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
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11 </requirements>
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
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12
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
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13 <command detect_errors="exit_code"><![CDATA[
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
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14 #if $db_opts.db_opts_input == 'lastdb'
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
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15 ln -s '$db_opts.lastdatabase.extra_files_path' './db_files' &&
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
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16 #end if
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17
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
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18 last-train
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19
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
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20 -Q $init_options.Q
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21
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
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22 -r $init_options.r
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23 -q $init_options.q
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24
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
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25 -a $init_options.cost_opt.a
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26 -b $init_options.cost_opt.b
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
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27 -A $init_options.cost_opt.A
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28 -B $init_options.cost_opt.B
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29
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
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30 -D $last_train_opt.align_opt.D
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
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31 -E $last_train_opt.align_opt.E
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
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32 -s $last_train_opt.align_opt.s
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
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33 -S $last_train_opt.align_opt.S
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
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34 -T $last_train_opt.align_opt.T
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35 -m $last_train_opt.align_opt.m
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
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36 -k $last_train_opt.align_opt.k
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37 -X $last_train_opt.align_opt.X
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
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38
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
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39 -P \${GALAXY_SLOTS:-1}
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
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40
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
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41 #if $db_opts.db_opts_input == 'db'
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
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42 '${"' '".join(str($db_opts.database.fields.path).split(","))}'
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
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43 #else if $db_opts.db_opts_input == 'lastdb'
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
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44 'db_files/lastdb'
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45 #end if
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46
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
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47 '$query_fasta'
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48
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
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49 >'$outfile'
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50
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
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51 ]]></command>
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52
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
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53 <inputs>
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54 <expand macro="input_db" />
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55 <param name="query_fasta" type="data" format="FASTA" label="Queries input files" />
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
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56 <conditional name="init_options">
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57 <param argument="-Q" type="select" multiple="false" label="Input format">
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58 <option value="0" selected="true">Fasta or fastq-ignore</option>
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59 <option value="1">Fastq-sanger</option>
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60 </param>
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61 <when value="0">
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62 <param argument="-r" type="integer" value="5" label="Match score"/>
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63 <param argument="-q" type="integer" value="5" label="Mismatch cost"/>
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64 <expand macro="cost_macro" a="15" b="3"/>
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65 </when>
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66 <when value="1">
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67 <param argument="-r" type="integer" value="6" label="Match score"/>
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68 <param argument="-q" type="integer" value="18" label="Mismatch cost"/>
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69 <expand macro="cost_macro" a="21" b="9"/>
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70 </when>
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71 </conditional>
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72
7f7e48d3b85d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit eee0dd5282b34bcfbfd79381be8474e8fcf2dbb8"
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73 <section name="last_train_opt" title="Last-train options" expanded="false">
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74 <!-- Training options missing -->
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75 <section name="align_opt" title="Alignment options" expanded="true">
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76 <param argument="-D" type="integer" value="1000000" label="Query letters per random alignment"/>
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77 <param argument="-E" type="integer" value="10" label="Maximum expected alignments per square giga"/>
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78 <param argument="-s" type="select" multiple="false" label="Query strand to use">
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79 <option value="0">Reverse</option>
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80 <option value="1" selected="true">Forward</option>
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81 <option value="2">Both</option>
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82 </param>
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83 <param argument="-S" type="select" multiple="false" label="Score matrix applies to forward strand of:">
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84 <option value="0">Reference</option>
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85 <option value="1" selected="true">Query</option>
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86 </param>
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87 <!--<param name="gapless_align" argument="-C" type="integer" value="" label="Omit gapless alignments in COUNT others with > score-per-length"/>-->
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88 <param argument="-T" type="select" multiple="false" label="Type of alignment:">
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89 <option value="0" selected="true">Local</option>
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90 <option value="1">Overlap</option>
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91 </param>
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92 <param argument="-m" type="integer" value="10" label="Maximum initial matches per query position"/>
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93 <param argument="-k" type="integer" value="1" label="Use initial matches starting at every STEP-th position in each query"/>
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94 <param argument="-X" type="select" multiple="false" label="N/X is ambiguous in:">
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95 <option value="0" selected="true">Neither sequence</option>
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96 <option value="1">Reference</option>
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97 <option value="2">Query</option>
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98 <option value="3">Both</option>
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99 </param>
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100 </section>
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101 </section>
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102 </inputs>
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103
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104 <outputs>
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105 <data name="outfile" format="txt" label="LAST train from ${on_string}" />
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106 </outputs>
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107
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108 <tests>
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109 <test>
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110 <conditional name="db_opts">
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111 <param name="db_opts_input" value="db"/>
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112 <param name="database" value="humdb"/>
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113 </conditional>
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114 <param name="query_fasta" value="fuguMito.fa"/>
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115 <output name="outfile" file="last_train.txt" ftype="txt" lines_diff="22"/>
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116 </test>
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117 </tests>
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118
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119 <help>@LAST_HELP@</help>
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120 <citations><expand macro="citations"/></citations>
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121 </tool>