Mercurial > repos > bgruening > join_files_on_column_fuzzy

annotate join_files_on_column_fuzzy.xml @ 2:f2068690addc draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit 73ccf407098f84351a1bd18438b80023d362b91f
author bgruening
date Fri, 13 Apr 2018 03:30:12 -0400
parents 8750c3125ec5
children 22ec3c1a20cd
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f2068690addc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit 73ccf407098f84351a1bd18438b80023d362b91f
bgruening
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1 <tool id="join_files_on_column_fuzzy" name="Join two files" version="1.0.1">
0
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2 <description>
64469e7ecf9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
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3 on column allowing a small difference
64469e7ecf9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
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4 </description>
64469e7ecf9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
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5 <requirements>
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8750c3125ec5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit b1763d10a1c39bc6651be891a993989c5a5617ff
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6 <requirement type="package" version="3.6">python</requirement>
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7 </requirements>
64469e7ecf9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
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8 <command>
64469e7ecf9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
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9 <![CDATA[
64469e7ecf9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
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10 python '$__tool_directory__/join_files_on_column_fuzzy.py'
64469e7ecf9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
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11 --f1 '$f1'
64469e7ecf9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
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12 --f2 '$f2'
64469e7ecf9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
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13 --c1 $c1
64469e7ecf9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
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14 --c2 $c2
64469e7ecf9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
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15 --outfile '$merged_file'
64469e7ecf9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
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16 $header
64469e7ecf9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
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17 $add_distance
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18 #if $merge_mode_select == 'closest':
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64469e7ecf9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
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19 --closest
1
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20 #end if:
8750c3125ec5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit b1763d10a1c39bc6651be891a993989c5a5617ff
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21 --distance $distance
8750c3125ec5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit b1763d10a1c39bc6651be891a993989c5a5617ff
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22 --unit $units
8750c3125ec5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit b1763d10a1c39bc6651be891a993989c5a5617ff
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23
0
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24 ]]>
64469e7ecf9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
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25 </command>
64469e7ecf9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
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26 <inputs>
1
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27 <param argument="--f1" type="data" optional="true" format="tabular" label="1st file"
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64469e7ecf9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
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28 help=""/>
64469e7ecf9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
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29 <param argument="--c1" type="data_column" data_ref="f1" label="Column to use from 1st file" help="The file needs to be sorted by this column, ascending."/>
64469e7ecf9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
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30 <param argument="--f2" type="data" optional="true" format="tabular" label="2nd file"
64469e7ecf9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
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31 help=""/>
64469e7ecf9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
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32 <param argument="--c2" type="data_column" data_ref="f2" label="Column to use from 2nd file" help="The file needs to be sorted by this column, ascending."/>
64469e7ecf9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
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33
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34 <param argument="--header" type="boolean" checked="false" truevalue="--header" falsevalue="" label="Does the input files contain a header line" />
64469e7ecf9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
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35 <param argument="--add_distance" type="boolean" checked="false" truevalue="--add_distance" falsevalue="" label="Add an addional column with the calculated distance." />
64469e7ecf9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
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36
1
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37 <param name="merge_mode_select" type="select" label="Choose the mode of merging.">
8750c3125ec5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit b1763d10a1c39bc6651be891a993989c5a5617ff
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38 <option value="closest" selected="True">Best match (in case of multiple best matches, only the first one is reported)</option>
8750c3125ec5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit b1763d10a1c39bc6651be891a993989c5a5617ff
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39 <option value="distance">Matching with a defined distance</option>
8750c3125ec5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit b1763d10a1c39bc6651be891a993989c5a5617ff
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40 </param>
8750c3125ec5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit b1763d10a1c39bc6651be891a993989c5a5617ff
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41 <param name="units" display="radio" type="select" value="ppm_value" label="Choose the metrics of your distance"
8750c3125ec5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit b1763d10a1c39bc6651be891a993989c5a5617ff
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42 help="ppm is useful for very small differences">
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43 <option value="absolute" selected="True">Absolute distance</option>
8750c3125ec5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit b1763d10a1c39bc6651be891a993989c5a5617ff
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44 <option value="ppm" >Distance in ppm</option>
8750c3125ec5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit b1763d10a1c39bc6651be891a993989c5a5617ff
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45 </param>
8750c3125ec5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit b1763d10a1c39bc6651be891a993989c5a5617ff
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46 <param name="distance" value="0.2" type="float" label="Allowed distance between the two values that will trigger a merge" help=""/>
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47 </inputs>
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48 <outputs>
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49 <data name="merged_file" format="tabular" />
64469e7ecf9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
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50 </outputs>
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51
64469e7ecf9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
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52 <tests>
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53 <test>
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54 <param name="f1" value="file1.tab" ftype="tabular"/>
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55 <param name="f2" value="file2.tab" ftype="tabular"/>
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56 <param name="c1" value="1"/>
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57 <param name="c2" value="1"/>
64469e7ecf9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
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58 <param name="merge_mode_select" value="distance"/>
64469e7ecf9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
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59 <param name="distance" value="0.1"/>
64469e7ecf9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
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60 <param name="units" value="absolute"/>
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61 <output name="merged_file" file="no_header_result1.tab" />
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62 </test>
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63 <test>
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64 <param name="f1" value="file1_header.tab" ftype="tabular"/>
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65 <param name="f2" value="file2_header.tab" ftype="tabular"/>
64469e7ecf9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
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66 <param name="c1" value="1"/>
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67 <param name="c2" value="1"/>
64469e7ecf9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
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68 <param name="merge_mode_select" value="distance"/>
64469e7ecf9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
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69 <param name="distance" value="0.2"/>
64469e7ecf9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
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70 <param name="units" value="absolute"/>
64469e7ecf9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
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71 <param name="header" value="true"/>
64469e7ecf9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
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72 <output name="merged_file" file="header_result2.tab" />
64469e7ecf9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
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73 </test>
64469e7ecf9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
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74 <test>
64469e7ecf9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
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75 <param name="f1" value="file1_header.tab" ftype="tabular"/>
64469e7ecf9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
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76 <param name="f2" value="file2_header.tab" ftype="tabular"/>
64469e7ecf9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
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77 <param name="c1" value="1"/>
64469e7ecf9f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
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78 <param name="c2" value="1"/>
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79 <param name="header" value="true"/>
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80 <param name="merge_mode_select" value="closest"/>
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81 <output name="merged_file" file="header_closest_result3.tab" />
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82 </test>
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83 <test>
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84 <param name="f1" value="file1_ppm.tab" ftype="tabular"/>
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85 <param name="f2" value="file2_ppm.tab" ftype="tabular"/>
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86 <param name="c1" value="1"/>
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87 <param name="c2" value="1"/>
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88 <param name="header" value="false"/>
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89 <param name="merge_mode_select" value="distance"/>
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90 <param name="distance" value="100"/>
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91 <param name="units" value="ppm"/>
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92 <output name="merged_file" file="no_header_ppm_result4.tab" />
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93 </test>
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94 <test>
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95 <param name="f1" value="file1_header.tab" ftype="tabular"/>
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96 <param name="f2" value="file2_header.tab" ftype="tabular"/>
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97 <param name="c1" value="1"/>
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98 <param name="c2" value="1"/>
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99 <param name="header" value="true"/>
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100 <param name="closest" value="true"/>
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101 <param name="add_distance" value="true"/>
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102 <output name="merged_file" file="header_closest_result5.tab" />
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103 </test>
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104 <test>
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105 <param name="f1" value="file1_ppm.tab" ftype="tabular"/>
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106 <param name="f2" value="file2_ppm.tab" ftype="tabular"/>
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107 <param name="c1" value="1"/>
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108 <param name="c2" value="1"/>
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109 <param name="header" value="false"/>
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110 <param name="merge_mode_select" value="distance"/>
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111 <param name="distance" value="100"/>
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112 <param name="units" value="ppm"/>
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113 <param name="add_distance" value="true"/>
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114 <output name="merged_file" file="no_header_ppm_result6.tab" />
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115 </test>
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116 </tests>
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117 <help>
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118 <![CDATA[
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119
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120 Join two files on a common column. It is possible to provide an allowed difference between both values (currently only numbers)
1
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121 as the absolute differece or as PPM.
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122
1
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123 Two modes are available:
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124
1
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125 1. In the **best match** mode only the rows are merged for the most similar (or identical) values. In case of multiple best matches, only the first one is reported.
0
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126
1
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127 2. The **Matching with a defined distance** option will offer you the possibility
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128 to provide a distance between the two values of the columns. Is the calculates distance smaller or equal than the given distance the columns will be joined. You can specify the allowed distance as an absolute distance or as PPM.
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129
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130
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131 ]]>
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132 </help>
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133 <citations>
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134 </citations>
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135 </tool>