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1 <tool id="column_join" name="Column Join" version="1.1.0">
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2 <description></description>
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3 <command interpreter="python">
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4 column_join.py
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5 --output=$output
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6 --input1=$input1
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7 --input2=$input2
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8 --hinge=$hinge
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9 --columns=$columns
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10 #if $fill_empty_columns.fill_empty_columns_switch == "fill_empty":
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11 --fill_options_file=$fill_options_file
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12 #end if
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13 #for $f in $file_chooser:
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14 ${f.input}
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15 #end for
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16 </command>
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17 <inputs>
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18 <param name="input1" type="data" format="tabular" label="Choose the first file for the join" />
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19 <param name="hinge" type="data_column" data_ref="input1" multiple="false" numerical="false" label="Use this column and columns to left the 'hinge' (matching data for each join)" help="All columns to left of selected column (plus selected column) will be used. Select 2 for pileup" />
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20 <param name="columns" type="data_column" data_ref="input1" multiple="true" numerical="false" label="Include these column" help="Multi-select list - hold the appropriate key while clicking to select multiple columns" />
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21 <conditional name="fill_empty_columns">
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22 <param name="fill_empty_columns_switch" type="select" label="Fill empty columns">
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23 <option value="no_fill" selected="True">No</option>
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24 <option value="fill_empty">Yes</option>
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25 </param>
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26 <when value="no_fill" />
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27 <when value="fill_empty">
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28 <conditional name="do_fill_empty_columns">
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29 <param name="column_fill_type" type="select" label="Fill Columns by">
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30 <option value="single_fill_value" selected="True">Single fill value</option>
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31 <option value="fill_value_by_column">Values by column</option>
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32 </param>
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33 <when value="single_fill_value">
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34 <param type="text" name="fill_value" label="Fill value" value="." />
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35 </when>
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36 <when value="fill_value_by_column">
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37 <repeat name="column_fill" title="Fill Column">
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38 <param name="column_number" label="Column" type="data_column" data_ref="input1" />
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39 <param type="text" name="fill_value" value="." />
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40 </repeat>
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41 </when>
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42 </conditional>
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43 </when>
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44 </conditional>
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45 <param name="input2" type="data" format="tabular" label="Choose the second file for the join" />
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46 <repeat name="file_chooser" title="Additional Input">
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47 <param name="input" label="Additional input file" type="data" format="tabular" />
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48 </repeat>
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49 </inputs>
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50 <configfiles>
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51 <configfile name="fill_options_file"><%
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52 import json
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53 %>
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54 #set $__fill_options = {}
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55 #if $fill_empty_columns['fill_empty_columns_switch'] == 'fill_empty':
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56 #if $fill_empty_columns['do_fill_empty_columns']['column_fill_type'] == 'single_fill_value':
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57 #set $__start_fill = $fill_empty_columns['do_fill_empty_columns']['fill_value'].value
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58 #else:
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59 #set $__start_fill = ""
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60 #end if
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61 #set $__fill_options['file1_columns'] = [ __start_fill for i in range( int( $input1.metadata.columns ) ) ]
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62 #if $fill_empty_columns['do_fill_empty_columns']['column_fill_type'] == 'fill_value_by_column':
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63 #for column_fill in $fill_empty_columns['do_fill_empty_columns']['column_fill']:
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64 #set $__fill_options['file1_columns'][ int( column_fill['column_number'].value ) - 1 ] = column_fill['fill_value'].value
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65 #end for
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66 #end if
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67 #end if
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68 ${json.dumps( __fill_options )}
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69 </configfile>
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70 </configfiles>
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71 <outputs>
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72 <data name="output" format="tabular" />
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73 </outputs>
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74 <tests>
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75 <test>
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76 <param name="input1" value="column_join_in1.pileup" ftype="pileup" />
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77 <param name="hinge" value="2" />
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78 <param name="columns" value="1,2,3,4,5,7" />
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79 <param name="fill_empty_columns_switch" value="fill_empty" />
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80 <param name="column_fill_type" value="single_fill_value" />
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81 <param name="fill_value" value="?" />
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82 <param name="input2" value="column_join_in2.pileup" ftype="pileup" />
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83 <param name="input" value="column_join_in3.pileup" ftype="pileup" />
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84 <output name="output" file="column_join_out1.pileup" ftype="tabular" />
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85 </test>
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86 <test>
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87 <param name="input1" value="column_join_in4.pileup" ftype="pileup" />
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88 <param name="hinge" value="2" />
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89 <param name="columns" value="1,2,3,4" />
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90 <param name="fill_empty_columns_switch" value="no_fill" />
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91 <param name="input2" value="column_join_in5.pileup" ftype="pileup" />
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92 <param name="input" value="column_join_in6.pileup" ftype="pileup" />
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93 <output name="output" file="column_join_out2.pileup" ftype="tabular" />
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94 </test>
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95 <!-- This test is failing for an unclear reason (the column values do not get
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96 passed into the script), but passes in the browser
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97 <test>
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98 <param name="input1" value="column_join_in7.pileup" ftype="tabular" />
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99 <param name="hinge" value="2" />
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100 <param name="columns" value="3,4,5" />
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101 <param name="fill_empty_columns_switch" value="fill_empty" />
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102 <param name="column_fill_type" value="fill_value_by_column" />
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103 <param name="column_number" value="5" />
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104 <param name="fill_value" value="X" />
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105 <param name="input2" value="column_join_in8.pileup" ftype="tabular" />
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106 <param name="input" value="column_join_in9.pileup" ftype="tabular" />
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107 <output name="output" file="column_join_out3.pileup" ftype="tabular" />
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108 </test>
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109 -->
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110 <test>
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111 <param name="input1" value="column_join_in10.pileup" ftype="pileup" />
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112 <param name="hinge" value="1" />
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113 <param name="columns" value="2,7" />
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114 <param name="fill_empty_columns_switch" value="no_fill" />
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115 <param name="input2" value="column_join_in11.pileup" ftype="pileup" />
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116 <param name="input" value="column_join_in12.pileup" ftype="pileup" />
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117 <output name="output" file="column_join_out4.pileup" ftype="tabular" />
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118 </test>
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119 <test>
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120 <!-- Test for handling missing column -->
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121 <param name="input1" value="column_join_in13.tabular" ftype="tabular" />
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122 <param name="hinge" value="1" />
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123 <param name="columns" value="5" />
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124 <param name="fill_empty_columns_switch" value="fill_empty" />
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125 <param name="column_fill_type" value="single_fill_value" />
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126 <param name="fill_value" value="0" />
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127 <param name="input2" value="column_join_in14.tabular" ftype="tabular" />
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128 <param name="input" value="column_join_in15.tabular" ftype="tabular" />
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129 <output name="output" file="column_join_out5.tabular" ftype="tabular" />
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130 </test>
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131 </tests>
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132 <help>
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133 **What it does**
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134
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135 This tool allows you to join several files with the same column structure into one file, removing certain columns if necessary. The user needs to select a 'hinge', which is the number of left-most columns to match on. They also need to select the columns to include in the join, which should include the hinge columns, too.
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136
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137 Note that the files are expected to have the same number of columns. If for some reason the join column is missing (this only applies to the last column(s)), the tool attempts to handle this situation by inserting an empty item (or the appropriate filler) for that column on that row. This could lead to the situation where a row has a hinge but entirely empty or filled columns, if the hinge exists in at least one file but every file that has it is missing the join column. Also, note that the tool does not distinguish between a file missing the hinge altogether and a file having the hinge but missing the column (in both cases the column would be empty or filled). There is an example of this below.
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138
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139 -----
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140
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141 **General Example**
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142
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143 Given the following files::
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144
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145 FILE 1
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146 chr2 1 T 6 .C..., I$$III
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147 chr2 2 G 6 ..N.., III@II
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148 chr2 3 C 7 ..C..., I$IIIII
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149 chr2 4 G 7 .G...., I#IIIII
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150 chr2 5 G 7 ...N.., IIII#BI
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151 chr2 6 A 7 ..T..., I$IDIII
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152 chr1 1 C 1 ^:. I
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153 chr1 2 G 2 .^:. $I
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154 chr1 3 A 2 .. I%
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155 chr1 4 C 2 .. I$
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156 chr1 5 T 3 ..^:. I#I
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157 chr1 6 G 3 ..^:, I#I
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158
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159 FILE 2
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160 chr1 3 T 1 ^:. I
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161 chr1 4 G 2 .^:. $I
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162 chr1 5 T 2 .. I%
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163 chr1 6 C 3 ..^:. III
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164 chr1 7 G 3 ..^:. I#I
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165 chr1 8 T 4 ...^:, I#II
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166 chr2 77 C 6 .G..., I$$III
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167 chr2 78 G 6 ..N.., III@II
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168 chr2 79 T 7 ..N..., I$IIIII
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169 chr2 80 C 7 .G...., I#IIIII
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170 chr2 81 G 7 ...A.., IIII#BI
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171 chr2 82 A 8 ...G..., I$IDIIII
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172 chr2 83 T 8 .A.....N IIIIIIII
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173 chr2 84 A 9 ......T. I$IIIIIII
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174
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175 FILE 3
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176 chr1 1 A 1 . I
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177 chr1 2 T 2 G. I$
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178 chr1 3 C 2 ., I@
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179 chr1 4 C 3 ..N III
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180 chr1 42 C 5 ...N^:. III@I
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181 chr1 43 C 5 .N..^:. IIIII
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182 chr1 44 T 5 .A.., IA@II
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183 chr1 45 A 6 .N...^:. IIIII$
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184 chr1 46 G 6 .GN..^:. I@IIII
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185 chr1 47 A 7 ....^:.., IIIII$I
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186 chr2 73 T 5 .N.., II$II
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187 chr2 74 A 5 ...., IIIII
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188 chr2 75 T 5 ...., IIIII
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189 chr2 76 T 5 ...., IIIII
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190 chr2 77 C 5 ...., IIIBI
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191 chr2 78 T 5 ...., IDIII
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192
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193 To join on columns 3 and 4 combining on columns 1 and 2, columns 1-4 should be selected for the 'Include these columns' option, and column 2 selected for the 'hinge'. With these settings, the following would be output::
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194
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195 chr1 1 C 1 A 1
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196 chr1 2 G 2 T 2
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197 chr1 3 A 2 T 1 C 2
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198 chr1 4 C 2 G 2 C 3
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199 chr1 5 T 3 T 2
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200 chr1 6 G 3 C 3
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201 chr1 7 G 3
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202 chr1 8 T 4
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203 chr1 42 C 5
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204 chr1 43 C 5
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205 chr1 44 T 5
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206 chr1 45 A 6
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207 chr1 46 G 6
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208 chr1 47 A 7
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209 chr2 1 T 6
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210 chr2 2 G 6
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211 chr2 3 C 7
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212 chr2 4 G 7
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213 chr2 5 G 7
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214 chr2 6 A 7
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215 chr2 73 T 5
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216 chr2 74 A 5
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217 chr2 75 T 5
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218 chr2 76 T 5
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219 chr2 77 C 6 C 5
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220 chr2 78 G 6 T 5
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221 chr2 79 T 7
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222 chr2 80 C 7
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223 chr2 81 G 7
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224 chr2 82 A 8
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225 chr2 83 T 8
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226 chr2 84 A 9
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227
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228 **Example with missing columns**
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229
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230 Given the following input files::
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231
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232 FILE 1
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233 1 A
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234 2 B b
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235 4 C c
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236 5 D
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237 6 E e
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238
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239 FILE 2
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240 1 M m
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241 2 N
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242 3 O o
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243 4 P p
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244 5 Q
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245 7 R r
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246
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247 if we join only column 3 using column 1 as the hinge and with a fill value of '0', this is what will be output::
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248
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249 1 0 m
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250 2 b 0
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251 3 0 o
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252 4 c p
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253 5 0 0
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254 6 e 0
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255 7 0 r
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256
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257 Row 5 appears in both files with the missing column, so it's got nothing but fill values in the output file.
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258
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259 </help>
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260 </tool>
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