Mercurial > repos > iuc > mummer_dnadiff

annotate dnadiff.xml @ 4:5561a1193611 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 026db7297e987c1b7ce7f5dd4f8746d1bd435538
author iuc
date Mon, 18 Mar 2024 12:40:51 +0000
parents c9685bc0407c
children
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c9685bc0407c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit bacb32814054404587451948b3a6682cf0d1a33a"
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1 <tool id="mummer_dnadiff" name="DNAdiff" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>Evaluate similarities/differences between two sequences</description>
deacc6b40cc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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3 <macros>
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4 <import>macros.xml</import>
deacc6b40cc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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5 </macros>
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c9685bc0407c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit bacb32814054404587451948b3a6682cf0d1a33a"
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6 <expand macro="bio_tools"/>
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deacc6b40cc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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7 <expand macro="requirements" />
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8 <command detect_errors="exit_code">
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9 <![CDATA[
deacc6b40cc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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10 ln -s $reference_sequence reference.fa &&
deacc6b40cc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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11 ln -s $query_sequence query.fa &&
deacc6b40cc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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12 dnadiff
deacc6b40cc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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13 'reference.fa' 'query.fa'
deacc6b40cc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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14
4
5561a1193611 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 026db7297e987c1b7ce7f5dd4f8746d1bd435538
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15 ]]>
0
deacc6b40cc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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16 </command>
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17 <inputs>
deacc6b40cc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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18 <param name="reference_sequence" type="data" format="fasta" label="Reference Sequence" help="FastA or multi-FastA" />
deacc6b40cc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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19 <param name="query_sequence" type="data" format="fasta" label="Query Sequence(s)" help="FastA or multi-FastA" />
deacc6b40cc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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20 <param name="report_only" type="select" label="Output only the general report file?" help="Select no to output all output files">
deacc6b40cc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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21 <option value="yes">YES</option>
deacc6b40cc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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22 <option value="no">NO</option>
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23 </param>
deacc6b40cc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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24 </inputs>
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25 <outputs>
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26 <data name="report" format="txt" from_work_dir="out.report" label="${tool.name} on ${on_string}: report" />
deacc6b40cc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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27 <data name="delta" format="tabular" from_work_dir="out.delta" label="${tool.name} on ${on_string}: delta">
deacc6b40cc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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28 <filter> report_only == 'no'</filter>
deacc6b40cc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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29 </data>
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30 <data name="delta1" format="tabular" from_work_dir="out.1delta" label="${tool.name} on ${on_string}: 1delta" >
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31 <filter> report_only == 'no' </filter>
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32 </data>
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33 <data name="mdelta" format="tabular" from_work_dir="out.mdelta" label="${tool.name} on ${on_string}: mdelta" >
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34 <filter> report_only == 'no' </filter>
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35 </data>
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36 <data name="coords1" format="tabular" from_work_dir="out.1coords" label="${tool.name} on ${on_string}: 1coords" >
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deacc6b40cc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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37 <filter> report_only == 'no' </filter>
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38 <actions>
deacc6b40cc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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39 <action name="column_names" type="metadata" default="[S1], [E1], [S2], [E2], [LEN 1], [LEN 2], [% IDY], [LEN R], [LEN Q], [COV R], [COV Q], [REF TAG], [QUERY TAG]" />
deacc6b40cc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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40 </actions>
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41 </data>
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42 <data name="mcoords" format="tabular" from_work_dir="out.mcoords" label="${tool.name} on ${on_string}: mcoords" >
deacc6b40cc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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43 <filter> report_only == 'no' </filter>
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44 <actions>
deacc6b40cc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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45 <action name="column_names" type="metadata" default="[S1], [E1], [S2], [E2], [LEN 1], [LEN 2], [% IDY], [LEN R], [LEN Q], [COV R], [COV Q], [REF TAG], [QUERY TAG]" />
deacc6b40cc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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46 </actions>
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47 </data>
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48 <data name="snps" format="tabular" from_work_dir="out.snps" label="${tool.name} on ${on_string}: snps" >
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49 <filter> report_only == 'no' </filter>
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50 <actions>
4
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51 <action name="column_names" type="metadata" default="[P1], [REF SUB], [QUERY SUB], [P2], [BUFF], [DIST], [LEN REF], [LEN QUERY], [REF FRAME], [QUERY FRAME], [REF TAG], [QUERY TAG]" />
0
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52 </actions>
deacc6b40cc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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53 </data>
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54 <data name="rdiff" format="tabular" from_work_dir="out.rdiff" label="${tool.name} on ${on_string}: rdiff" >
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55 <filter> report_only == 'no' </filter>
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56 <actions>
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57 <action name="column_names" type="metadata" default="Seq ID, Feature Type, Feature Start, Feature End, Feature Length" />
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58 </actions>
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59 </data>
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60 <data name="qdiff" format="tabular" from_work_dir="out.qdiff" label="${tool.name} on ${on_string}: qdiff" >
deacc6b40cc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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61 <filter> report_only == 'no' </filter>
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62 <actions>
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63 <action name="column_names" type="metadata" default="Seq ID, Feature Type, Feature Start, Feature End, Feature Length" />
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64 </actions>
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65 </data>
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66 </outputs>
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67 <tests>
4
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68 <test expect_num_outputs="9">
0
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69 <param name="reference_sequence" ftype="fasta" value="human_aqp3.fasta" />
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70 <param name="query_sequence" ftype="fasta" value="mouse_aqp3.fasta"/>
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71 <param name="report_only" value="no" />
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72 <output name="report" ftype="txt" compare="diff" sort="true" lines_diff="2" value="report.txt"/>
deacc6b40cc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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73 <output name="delta" ftype="tabular" compare="diff" lines_diff="2" value="delta.txt"/>
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74 <output name="delta1" ftype="tabular" compare="diff" lines_diff="2" value="1delta.txt"/>
0
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75 <output name="mdelta" ftype="tabular" compare="diff" lines_diff="2" value="mdelta.txt"/>
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c9685bc0407c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit bacb32814054404587451948b3a6682cf0d1a33a"
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76 <output name="coords1" ftype="tabular" compare="diff" value="1coords.txt"/>
0
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77 <output name="mcoords" ftype="tabular" compare="diff" value="mcoords.txt"/>
deacc6b40cc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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78 <output name="snps" ftype="tabular" compare="diff" value="snps.txt"/>
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79 <output name="rdiff" ftype="tabular" compare="diff" value="rdiff.txt"/>
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80 <output name="qdiff" ftype="tabular" compare="diff" value="qdiff.txt"/>
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81 </test>
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82 </tests>
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83 <help><![CDATA[
deacc6b40cc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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84 This script is a wrapper around nucmer that builds an alignment using default parameters, and runs many of nucmer's helper scripts to process the output and report alignment statistics, SNPs, breakpoints, etc. It is designed for evaluating the sequence and structural similarity of two highly similar sequence sets. E.g. comparing two different assemblies of the same organism, or comparing two strains of the same species.
deacc6b40cc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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85
deacc6b40cc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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86 **Output files:**
deacc6b40cc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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87 * report: Summary of alignments, differences and SNPs
deacc6b40cc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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88 * delta: Standard nucmer alignment output
deacc6b40cc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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89 * 1delta: 1-to-1 alignment from delta-filter -1
deacc6b40cc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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90 * mdelta: M-to-M alignment from delta-filter -m
deacc6b40cc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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91 * 1coords: 1-to-1 coordinates from show-coords -THrcl .1delta
deacc6b40cc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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92 * mcoords: M-to-M coordinates from show-coords -THrcl .mdelta
deacc6b40cc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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93 * snps: SNPs from show-snps -rlTHC .1delta
deacc6b40cc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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94 * rdiff: Classified ref breakpoints from show-diff -rH .mdelta
deacc6b40cc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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95 * qdiff: Classified qry breakpoints from show-diff -qH .mdelta
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96 ]]></help>
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97 <expand macro="citation" />
deacc6b40cc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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98 </tool>