Mercurial > repos > iuc > filter_tabular

annotate filter_tabular.xml @ 9:64a96306112e draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit daa9af57fe07ee83a45ddc9f855716f9d14a8e12"
author iuc
date Sat, 12 Sep 2020 01:19:57 +0000
parents b85c8fabaf77
children 499697bbd5a2
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9
64a96306112e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit daa9af57fe07ee83a45ddc9f855716f9d14a8e12"
iuc
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1 <tool id="filter_tabular" name="Filter Tabular" version="3.1.0">
0
c0c0226e1c9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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2 <description></description>
c0c0226e1c9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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3
c0c0226e1c9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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4 <macros>
c0c0226e1c9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
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5 <import>macros.xml</import>
c0c0226e1c9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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6 </macros>
8
b85c8fabaf77 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 1647065a8e6e8d8c98cd0d2194b695fb9425f541"
iuc
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7 <expand macro="requirements"/>
0
c0c0226e1c9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
iuc
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8 <command detect_errors="exit_code"><![CDATA[
c0c0226e1c9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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9 python '$__tool_directory__/filter_tabular.py'
c0c0226e1c9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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10 -i '$input'
c0c0226e1c9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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11 -j '$filter_json'
c0c0226e1c9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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12 -o '$output'
c0c0226e1c9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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13 ]]></command>
c0c0226e1c9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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14 <configfiles>
c0c0226e1c9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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15 <configfile name="filter_json">
c0c0226e1c9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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16 #import json
c0c0226e1c9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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17 @LINEFILTERS@
c0c0226e1c9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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18 #if $input_filters:
c0c0226e1c9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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19 #echo $json.dumps($input_filters)
c0c0226e1c9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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20 #end if
c0c0226e1c9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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21 </configfile>
c0c0226e1c9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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22 </configfiles>
c0c0226e1c9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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23 <inputs>
c0c0226e1c9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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24 <param name="input" type="data" format="tabular" label="Tabular Dataset to filter"/>
c0c0226e1c9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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25 <expand macro="macro_line_filters" />
c0c0226e1c9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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26 </inputs>
c0c0226e1c9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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27 <outputs>
c0c0226e1c9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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28 <data format="tabular" name="output" />
c0c0226e1c9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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29 </outputs>
c0c0226e1c9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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30 <tests>
c0c0226e1c9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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31 <test>
c0c0226e1c9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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32 <param name="input" ftype="tabular" value="pets.tsv"/>
c0c0226e1c9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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33 <repeat name="linefilters">
c0c0226e1c9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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34 <conditional name="filter">
c0c0226e1c9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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35 <param name="filter_type" value="regex"/>
c0c0226e1c9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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36 <param name="regex_pattern" value="^\d+"/>
c0c0226e1c9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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37 <param name="regex_action" value="include_find"/>
c0c0226e1c9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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38 </conditional>
c0c0226e1c9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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39 </repeat>
c0c0226e1c9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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40 <repeat name="linefilters">
c0c0226e1c9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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41 <conditional name="filter">
c0c0226e1c9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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42 <param name="filter_type" value="append_line_num"/>
c0c0226e1c9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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43 </conditional>
c0c0226e1c9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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44 </repeat>
c0c0226e1c9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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45 <repeat name="linefilters">
c0c0226e1c9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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46 <conditional name="filter">
c0c0226e1c9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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47 <param name="filter_type" value="select_columns"/>
c0c0226e1c9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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48 <param name="columns" value="7,2,3,4,1"/>
c0c0226e1c9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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49 </conditional>
c0c0226e1c9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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50 </repeat>
c0c0226e1c9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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51 <repeat name="linefilters">
c0c0226e1c9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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52 <conditional name="filter">
c0c0226e1c9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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53 <param name="filter_type" value="replace"/>
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54 <param name="column" value="c4"/>
c0c0226e1c9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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55 <param name="regex_pattern" value="(\d+)/(\d+)/(\d+)"/>
c0c0226e1c9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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56 <param name="regex_replace" value="19\3-\2-\1"/>
c0c0226e1c9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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57 </conditional>
c0c0226e1c9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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58 </repeat>
c0c0226e1c9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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59 <output name="output" file="filtered_people_results.tsv"/>
c0c0226e1c9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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60 </test>
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61 <test>
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62 <param name="input" ftype="tabular" value="pets.tsv"/>
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63 <repeat name="linefilters">
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64 <conditional name="filter">
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65 <param name="filter_type" value="comment"/>
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66 <param name="comment_char" value="35"/>
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67 </conditional>
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68 </repeat>
c0c0226e1c9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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69 <repeat name="linefilters">
c0c0226e1c9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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70 <conditional name="filter">
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71 <param name="filter_type" value="regex"/>
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72 <param name="regex_pattern" value="^\d+"/>
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73 <param name="regex_action" value="include_find"/>
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74 </conditional>
c0c0226e1c9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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75 </repeat>
c0c0226e1c9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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76 <repeat name="linefilters">
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77 <conditional name="filter">
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78 <param name="filter_type" value="append_line_num"/>
c0c0226e1c9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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79 </conditional>
c0c0226e1c9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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80 </repeat>
c0c0226e1c9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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81 <repeat name="linefilters">
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82 <conditional name="filter">
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83 <param name="filter_type" value="select_columns"/>
c0c0226e1c9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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84 <param name="columns" value="c7,c5,c6"/>
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85 </conditional>
c0c0226e1c9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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86 </repeat>
c0c0226e1c9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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87 <repeat name="linefilters">
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88 <conditional name="filter">
c0c0226e1c9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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89 <param name="filter_type" value="normalize"/>
c0c0226e1c9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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90 <param name="columns" value="c2,c3"/>
c0c0226e1c9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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91 <param name="separator" value=","/>
c0c0226e1c9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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92 </conditional>
c0c0226e1c9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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93 </repeat>
c0c0226e1c9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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94 <repeat name="linefilters">
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95 <conditional name="filter">
c0c0226e1c9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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96 <param name="filter_type" value="regex"/>
c0c0226e1c9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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97 <param name="regex_pattern" value="^\d+\t\t"/>
c0c0226e1c9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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98 <param name="regex_action" value="exclude_match"/>
c0c0226e1c9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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99 </conditional>
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100 </repeat>
c0c0226e1c9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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101 <output name="output" file="filtered_pets_results.tsv"/>
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102 </test>
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103
9
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104 <test>
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105 <param name="input" ftype="tabular" value="customers.tsv"/>
64a96306112e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit daa9af57fe07ee83a45ddc9f855716f9d14a8e12"
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106 <repeat name="linefilters">
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107 <conditional name="filter">
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108 <param name="filter_type" value="regex"/>
64a96306112e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit daa9af57fe07ee83a45ddc9f855716f9d14a8e12"
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109 <param name="regex_pattern" value="^\d+"/>
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110 <param name="regex_action" value="include_find"/>
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111 </conditional>
64a96306112e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit daa9af57fe07ee83a45ddc9f855716f9d14a8e12"
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112 </repeat>
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113 <repeat name="linefilters">
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114 <conditional name="filter">
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115 <param name="filter_type" value="replace"/>
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116 <param name="column" value="c4"/>
64a96306112e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit daa9af57fe07ee83a45ddc9f855716f9d14a8e12"
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117 <param name="regex_pattern" value=".*@(.*)"/>
64a96306112e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit daa9af57fe07ee83a45ddc9f855716f9d14a8e12"
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118 <param name="regex_replace" value="\1"/>
64a96306112e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit daa9af57fe07ee83a45ddc9f855716f9d14a8e12"
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119 <param name="add" value="after"/>
64a96306112e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit daa9af57fe07ee83a45ddc9f855716f9d14a8e12"
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120 </conditional>
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121 </repeat>
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122 <repeat name="linefilters">
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123 <conditional name="filter">
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124 <param name="filter_type" value="replace"/>
64a96306112e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit daa9af57fe07ee83a45ddc9f855716f9d14a8e12"
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125 <param name="column" value="c4"/>
64a96306112e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit daa9af57fe07ee83a45ddc9f855716f9d14a8e12"
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126 <param name="regex_pattern" value=".*(com|org|net)$"/>
64a96306112e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit daa9af57fe07ee83a45ddc9f855716f9d14a8e12"
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127 <param name="regex_replace" value="\1"/>
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128 <param name="add" value="append"/>
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129 </conditional>
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130 </repeat>
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131 <output name="output" file="filtered_customers_results.tsv"/>
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132 </test>
0
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133 </tests>
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134 <help><![CDATA[
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135 ==============
c0c0226e1c9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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136 Filter Tabular
c0c0226e1c9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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137 ==============
c0c0226e1c9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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138
c0c0226e1c9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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139 Filter a tabular dataset by applying line filters as it is being read.
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140 Multiple filters may be used with each filter using the result of the previous filter.
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141
c0c0226e1c9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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142 **Inputs**
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143
c0c0226e1c9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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144 A tabular dataset.
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145
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146
c0c0226e1c9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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147 **Outputs**
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148
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149 A filtered tabular dataset.
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150
c0c0226e1c9c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
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151
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152 @LINEFILTERS_HELP@
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153
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154 @LINEFILTERS_HELP_EXAMPLE@
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155
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156 ]]></help>
6
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157 <expand macro="citations" />
0
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158 </tool>