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1 <tool id="filter_tabular" name="Filter Tabular" version="5.0.0">
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2 <description></description>
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3
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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7
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8 <requirements>
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9 </requirements>
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10 <stdio>
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11 <exit_code range="1:" />
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12 </stdio>
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13 <command><![CDATA[
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14 python $__tool_directory__/filter_tabular.py
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15 -i '$input'
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16 -j '$filter_json'
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17 -o '$output'
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18 ]]></command>
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19 <configfiles>
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20 <configfile name="filter_json">
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21 #import json
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22 @LINEFILTERS@
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23 #if $input_filters:
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24 #echo $json.dumps($input_filters)
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25 #end if
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26 </configfile>
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27 </configfiles>
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28 <inputs>
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29 <param name="input" type="data" format="tabular" label="Tabular Dataset to filter"/>
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30 <expand macro="macro_line_filters" />
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31 </inputs>
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32 <outputs>
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33 <data format="tabular" name="output" />
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34 </outputs>
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35 <tests>
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36 <test>
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37 <param name="input" ftype="tabular" value="pets.tsv"/>
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38 <repeat name="linefilters">
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39 <param name="filter_type" value="comment"/>
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40 <param name="comment_char" value="35"/>
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41 </repeat>
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42 <repeat name="linefilters">
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43 <param name="filter_type" value="append_line_num"/>
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44 </repeat>
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45 <repeat name="linefilters">
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46 <param name="filter_type" value="select_columns"/>
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47 <param name="columns" value="7,2,3,4,1"/>
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48 </repeat>
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49 <repeat name="linefilters">
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50 <param name="filter_type" value="replace"/>
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51 <param name="column" value="c4"/>
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52 <param name="regex_pattern" value="(\d+)/(\d+)/(\d+)"/>
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53 <param name="regex_replace" value="19\3-\2-\1"/>
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54 </repeat>
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55 <output name="output" file="filtered_people_results.tsv"/>
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56 </test>
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57 <test>
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58 <param name="input" ftype="tabular" value="pets.tsv"/>
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59 <repeat name="linefilters">
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60 <param name="filter_type" value="comment"/>
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61 <param name="comment_char" value="35"/>
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62 </repeat>
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63 <repeat name="linefilters">
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64 <param name="filter_type" value="append_line_num"/>
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65 </repeat>
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66 <repeat name="linefilters">
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67 <param name="filter_type" value="select_columns"/>
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68 <param name="columns" value="c7,c5,c6"/>
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69 </repeat>
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70 <repeat name="linefilters">
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71 <param name="filter_type" value="normalize"/>
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72 <param name="columns" value="c2,c3"/>
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73 <param name="separator" value=","/>
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74 </repeat>
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75 <output name="output" file="filtered_pets_results.tsv"/>
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76 </test>
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77
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78 </tests>
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79 <help><![CDATA[
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80 ==============
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81 Filter Tabular
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82 ==============
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83
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84 Filter a tabular dataset by applying line filters as it is being read.
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85 Multiple filters may be used with each filter using the result of the previous filter.
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86
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87 **Inputs**
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88
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89 A tabular dataset.
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90
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91
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92 **Outputs**
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93
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94 A filtered tabular dataset.
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95
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96
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97 @LINEFILTERS_HELP@
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98
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99 @LINEFILTERS_HELP_EXAMPLE@
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100
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101 ]]></help>
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102 </tool>
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