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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 <command detect_errors="exit_code"><![CDATA[
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11 python '$__tool_directory__/filter_tabular.py'
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12 -i '$input'
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13 -j '$filter_json'
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14 -o '$output'
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15 ]]></command>
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16 <configfiles>
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17 <configfile name="filter_json">
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18 #import json
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19 @LINEFILTERS@
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20 #if $input_filters:
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21 #echo $json.dumps($input_filters)
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22 #end if
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23 </configfile>
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24 </configfiles>
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25 <inputs>
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26 <param name="input" type="data" format="tabular" label="Tabular Dataset to filter"/>
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27 <expand macro="macro_line_filters" />
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28 </inputs>
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29 <outputs>
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30 <data format="tabular" name="output" />
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31 </outputs>
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32 <tests>
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33 <test>
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34 <param name="input" ftype="tabular" value="pets.tsv"/>
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35 <repeat name="linefilters">
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36 <conditional name="filter">
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37 <param name="filter_type" value="regex"/>
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38 <param name="regex_pattern" value="^\d+"/>
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39 <param name="regex_action" value="include_find"/>
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40 </conditional>
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20
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41 </repeat>
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42 <repeat name="linefilters">
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21
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43 <conditional name="filter">
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44 <param name="filter_type" value="append_line_num"/>
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45 </conditional>
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20
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46 </repeat>
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47 <repeat name="linefilters">
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48 <conditional name="filter">
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49 <param name="filter_type" value="select_columns"/>
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50 <param name="columns" value="7,2,3,4,1"/>
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51 </conditional>
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52 </repeat>
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53 <repeat name="linefilters">
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21
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54 <conditional name="filter">
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55 <param name="filter_type" value="replace"/>
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56 <param name="column" value="c4"/>
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57 <param name="regex_pattern" value="(\d+)/(\d+)/(\d+)"/>
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58 <param name="regex_replace" value="19\3-\2-\1"/>
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59 </conditional>
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20
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60 </repeat>
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61 <output name="output" file="filtered_people_results.tsv"/>
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62 </test>
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63 <test>
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64 <param name="input" ftype="tabular" value="pets.tsv"/>
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65 <repeat name="linefilters">
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66 <conditional name="filter">
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67 <param name="filter_type" value="comment"/>
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68 <param name="comment_char" value="35"/>
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69 </conditional>
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70 </repeat>
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71 <repeat name="linefilters">
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72 <conditional name="filter">
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73 <param name="filter_type" value="regex"/>
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74 <param name="regex_pattern" value="^\d+"/>
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75 <param name="regex_action" value="include_find"/>
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76 </conditional>
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77 </repeat>
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78 <repeat name="linefilters">
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79 <conditional name="filter">
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80 <param name="filter_type" value="append_line_num"/>
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81 </conditional>
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82 </repeat>
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83 <repeat name="linefilters">
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84 <conditional name="filter">
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85 <param name="filter_type" value="select_columns"/>
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86 <param name="columns" value="c7,c5,c6"/>
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87 </conditional>
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88 </repeat>
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89 <repeat name="linefilters">
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90 <conditional name="filter">
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91 <param name="filter_type" value="normalize"/>
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92 <param name="columns" value="c2,c3"/>
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93 <param name="separator" value=","/>
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94 </conditional>
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95 </repeat>
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96 <repeat name="linefilters">
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97 <conditional name="filter">
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98 <param name="filter_type" value="regex"/>
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99 <param name="regex_pattern" value="^\d+\t\t"/>
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100 <param name="regex_action" value="exclude_match"/>
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101 </conditional>
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102 </repeat>
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103 <output name="output" file="filtered_pets_results.tsv"/>
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104 </test>
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105
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106 </tests>
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107 <help><![CDATA[
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108 ==============
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109 Filter Tabular
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110 ==============
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111
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112 Filter a tabular dataset by applying line filters as it is being read.
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113 Multiple filters may be used with each filter using the result of the previous filter.
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114
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115 **Inputs**
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116
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117 A tabular dataset.
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118
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119
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120 **Outputs**
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121
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122 A filtered tabular dataset.
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123
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124
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125 @LINEFILTERS_HELP@
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126
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127 @LINEFILTERS_HELP_EXAMPLE@
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128
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129 ]]></help>
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130 </tool>
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