Mercurial > repos > bgruening > join_files_on_column_fuzzy
annotate join_files_on_column_fuzzy.xml @ 0:64469e7ecf9f draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
author | bgruening |
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date | Sun, 26 Nov 2017 16:13:51 -0500 |
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children | 8750c3125ec5 |
rev | line source |
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0
64469e7ecf9f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
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1 <tool id="join_files_on_column_fuzzy" name="Join two files" version="1.0.0"> |
64469e7ecf9f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
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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
bgruening
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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
bgruening
parents:
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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
bgruening
parents:
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5 <requirements> |
64469e7ecf9f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
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6 <requirement type="package" version="3.6">python</requirement> |
64469e7ecf9f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
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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
bgruening
parents:
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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
bgruening
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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
bgruening
parents:
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10 python '$__tool_directory__/join_files_on_column_fuzzy.py' |
64469e7ecf9f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
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11 --f1 '$f1' |
64469e7ecf9f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
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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
bgruening
parents:
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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
bgruening
parents:
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14 --c2 $c2 |
64469e7ecf9f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
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15 --outfile '$merged_file' |
64469e7ecf9f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
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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
bgruening
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17 $add_distance |
64469e7ecf9f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
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18 #if $merge_mode.merge_mode_select == 'closest': |
64469e7ecf9f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
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19 --closest |
64469e7ecf9f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
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20 #else: |
64469e7ecf9f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
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21 --distance $merge_mode.distance |
64469e7ecf9f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
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22 --unit $merge_mode.units |
64469e7ecf9f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
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23 #end if |
64469e7ecf9f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
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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
bgruening
parents:
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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
bgruening
parents:
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26 <inputs> |
64469e7ecf9f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
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27 <param argument="--f1" type="data" optional="true" format="tabular" label="1st file" |
64469e7ecf9f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
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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
bgruening
parents:
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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
bgruening
parents:
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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
bgruening
parents:
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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
bgruening
parents:
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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
bgruening
parents:
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33 |
64469e7ecf9f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
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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
bgruening
parents:
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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
bgruening
parents:
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36 |
64469e7ecf9f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
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37 <conditional name="merge_mode"> |
64469e7ecf9f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
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38 <param name="merge_mode_select" type="select" label="Choose the mode of merging."> |
64469e7ecf9f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
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39 <option value="closest" selected="True">Best match (in case of multiple best matches, only the first one is reported)</option> |
64469e7ecf9f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
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40 <option value="distance">Matching with a defined distance</option> |
64469e7ecf9f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
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41 </param> |
64469e7ecf9f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
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42 <when value="closest"/> |
64469e7ecf9f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
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43 <when value="distance"> |
64469e7ecf9f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
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44 <param name="units" display="radio" type="select" value="ppm_value" label="Choose the metrics of your distance" |
64469e7ecf9f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
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45 help="ppm is useful for very small differences"> |
64469e7ecf9f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
parents:
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46 <option value="absolute" selected="True">Absolute distance</option> |
64469e7ecf9f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
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47 <option value="ppm" >Distance in ppm</option> |
64469e7ecf9f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
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48 </param> |
64469e7ecf9f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
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49 <param name="distance" value="0.2" type="float" label="Allowed distance between the two values that will trigger a merge" help=""/> |
64469e7ecf9f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
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50 </when> |
64469e7ecf9f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
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51 </conditional> |
64469e7ecf9f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
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52 </inputs> |
64469e7ecf9f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
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53 <outputs> |
64469e7ecf9f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
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54 <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
bgruening
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55 </outputs> |
64469e7ecf9f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
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56 |
64469e7ecf9f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
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57 <tests> |
64469e7ecf9f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
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58 <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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59 <param name="f1" value="file1.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
bgruening
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60 <param name="f2" value="file2.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
bgruening
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61 <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
bgruening
parents:
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62 <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
bgruening
parents:
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63 <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
bgruening
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64 <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
bgruening
parents:
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65 <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
bgruening
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66 <output name="merged_file" file="no_header_result1.tab" /> |
64469e7ecf9f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
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67 </test> |
64469e7ecf9f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
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68 <test> |
64469e7ecf9f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy commit fd2bc86108994c9eda731b305ca6a8c71554cfaa
bgruening
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69 <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
bgruening
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70 <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
bgruening
parents:
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71 <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
bgruening
parents:
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72 <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
bgruening
parents:
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73 <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
bgruening
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74 <param name="distance" value="0.2"/> |
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75 <param name="units" value="absolute"/> |
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76 <param name="header" value="true"/> |
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77 <output name="merged_file" file="header_result2.tab" /> |
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78 </test> |
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79 <test> |
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80 <param name="f1" value="file1_header.tab" ftype="tabular"/> |
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81 <param name="f2" value="file2_header.tab" ftype="tabular"/> |
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82 <param name="c1" value="1"/> |
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83 <param name="c2" value="1"/> |
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84 <param name="header" value="true"/> |
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85 <param name="closest" value="true"/> |
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86 <output name="merged_file" file="header_closest_result3.tab" /> |
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87 </test> |
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88 <test> |
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89 <param name="f1" value="file1_ppm.tab" ftype="tabular"/> |
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90 <param name="f2" value="file2_ppm.tab" ftype="tabular"/> |
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91 <param name="c1" value="1"/> |
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92 <param name="c2" value="1"/> |
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93 <param name="header" value="false"/> |
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94 <param name="merge_mode_select" value="distance"/> |
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95 <param name="distance" value="100"/> |
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96 <param name="units" value="ppm"/> |
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97 <output name="merged_file" file="no_header_ppm_result4.tab" /> |
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98 </test> |
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99 <test> |
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100 <param name="f1" value="file1_header.tab" ftype="tabular"/> |
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101 <param name="f2" value="file2_header.tab" ftype="tabular"/> |
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102 <param name="c1" value="1"/> |
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103 <param name="c2" value="1"/> |
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104 <param name="header" value="true"/> |
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105 <param name="closest" value="true"/> |
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106 <param name="add_distance" value="true"/> |
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107 <output name="merged_file" file="header_closest_result5.tab" /> |
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108 </test> |
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109 <test> |
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110 <param name="f1" value="file1_ppm.tab" ftype="tabular"/> |
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111 <param name="f2" value="file2_ppm.tab" ftype="tabular"/> |
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112 <param name="c1" value="1"/> |
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113 <param name="c2" value="1"/> |
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114 <param name="header" value="false"/> |
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115 <param name="merge_mode_select" value="distance"/> |
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116 <param name="distance" value="100"/> |
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117 <param name="units" value="ppm"/> |
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118 <param name="add_distance" value="true"/> |
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119 <output name="merged_file" file="no_header_ppm_result6.tab" /> |
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120 </test> |
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121 </tests> |
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122 <help> |
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123 <![CDATA[ |
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124 |
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125 Join two files on a common column. It is possible to provide an allowed difference between both values (currently only numbers) |
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126 as the absolute differece or as PPM. |
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127 |
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128 Two modes are available: |
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129 |
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130 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. |
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131 |
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132 1. The **Matching with a defined distance** option will offer you the possibility |
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133 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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134 |
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135 |
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136 ]]> |
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137 </help> |
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138 <citations> |
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139 </citations> |
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140 </tool> |
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141 |