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1 <tool id="cshl_multijoin" name="Multi-Join" version="0.1.1">
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2 <description>(combine multiple files)</description>
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3 <command interpreter="perl">multijoin
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4 --key '$key_column'
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5 --values '$value_columns'
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6 --filler '$filler'
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7 $ignore_dups
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8 $output_header
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9 $input_header
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10 #for $file in $files
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11 '$file.filename'
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12 #end for
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13 > '$output'
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14 </command>
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15
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16 <inputs>
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17 <repeat name="files" title="file to join">
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18 <param name="filename" label="Add file" type="data" format="txt" />
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19 </repeat>
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20
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21 <param name="key_column" label="Common key column" type="integer"
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22 value="1" help="Usually gene-ID or other common value" />
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23
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24 <param name="value_columns" label="Column with values to join" type="text"
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25 value="2,3,4" help="Enter comma-separated list of columns, e.g. 3,6,8">
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26 <sanitizer>
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27 <valid initial="string.printable">
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28 <remove value="'"/>
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29 </valid>
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30 </sanitizer>
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31 </param>
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32
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33 <param name="output_header" type="boolean" checked="false" truevalue="--out-header" falsevalue="" label="Add header line to the output file" help="" />
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34
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35 <param name="input_header" type="boolean" checked="false" truevalue="--in-header" falsevalue="" label="Input files contain a header line (as first line)" help="" />
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36
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37 <param name="ignore_dups" type="boolean" checked="false" truevalue="--ignore-dups" falsevalue="" label="Ignore duplicated keys" help="If not set, duplicated keys in the same file will cause an error." />
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38
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39 <param name="filler" type="text" size="20" value="0" label="Value to put in unpaired (empty) fields">
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40 <sanitizer>
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41 <valid initial="string.printable">
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42 <remove value="'"/>
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43 </valid>
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44 </sanitizer>
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45 </param>
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46
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47 </inputs>
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48 <outputs>
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49 <data name="output" format="input" metadata_source="input1" />
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50 </outputs>
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51
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52 <help>
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53 **What it does**
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54
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55 This tool joins multiple tabular files based on a common key column.
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56
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57 -----
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58
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59 **Example**
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60
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61 To join three files, based on the 4th column, and keeping the 7th,8th,9th columns:
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62
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63 **First file (AAA)**::
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64
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65 chr4 888449 890171 FBtr0308778 0 + 266 1527 1722
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66 chr4 972167 979017 FBtr0310651 0 - 3944 6428 6850
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67 chr4 972186 979017 FBtr0089229 0 - 3944 6428 6831
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68 chr4 972186 979017 FBtr0089231 0 - 3944 6428 6831
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69 chr4 972186 979017 FBtr0089233 0 - 3944 6428 6831
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70 chr4 995793 996435 FBtr0111046 0 + 7 166 642
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71 chr4 995793 997931 FBtr0111044 0 + 28 683 2138
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72 chr4 995793 997931 FBtr0111045 0 + 28 683 2138
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73 chr4 1034029 1047719 FBtr0089223 0 - 5293 13394 13690
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74 ...
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75
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76
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77 **Second File (BBB)**::
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78
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79 chr4 90286 134453 FBtr0309803 0 + 657 29084 44167
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80 chr4 251355 266499 FBtr0089116 0 + 56 1296 15144
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81 chr4 252050 266506 FBtr0308086 0 + 56 1296 14456
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82 chr4 252050 266506 FBtr0308087 0 + 56 1296 14456
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83 chr4 252053 266528 FBtr0300796 0 + 56 1296 14475
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84 chr4 252053 266528 FBtr0300800 0 + 56 1296 14475
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85 chr4 252055 266528 FBtr0300798 0 + 56 1296 14473
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86 chr4 252055 266528 FBtr0300799 0 + 56 1296 14473
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87 chr4 252541 266528 FBtr0300797 0 + 56 1296 13987
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88 ...
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89
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90 **Third file (CCC)**::
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91
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92 chr4 972167 979017 FBtr0310651 0 - 9927 6738 6850
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93 chr4 972186 979017 FBtr0089229 0 - 9927 6738 6831
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94 chr4 972186 979017 FBtr0089231 0 - 9927 6738 6831
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95 chr4 972186 979017 FBtr0089233 0 - 9927 6738 6831
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96 chr4 995793 996435 FBtr0111046 0 + 5 304 642
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97 chr4 995793 997931 FBtr0111044 0 + 17 714 2138
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98 chr4 995793 997931 FBtr0111045 0 + 17 714 2138
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99 chr4 1034029 1047719 FBtr0089223 0 - 17646 13536 13690
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100 ...
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101
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102
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103 **Joining** the files, using **key column 4**, **value columns 7,8,9** and a **header line**, will return::
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104
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105 key AAA__V7 AAA__V8 AAA__V9 BBB__V7 BBB__V8 BBB__V9 CCC__V7 CCC__V8 CCC__V9
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106 FBtr0089116 0 0 0 56 1296 15144 0 0 0
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107 FBtr0089223 5293 13394 13690 0 0 0 17646 13536 13690
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108 FBtr0089229 3944 6428 6831 0 0 0 9927 6738 6831
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109 FBtr0089231 3944 6428 6831 0 0 0 9927 6738 6831
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110 FBtr0089233 3944 6428 6831 0 0 0 9927 6738 6831
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111 FBtr0111044 28 683 2138 0 0 0 17 714 2138
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112 FBtr0111045 28 683 2138 0 0 0 17 714 2138
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113 FBtr0111046 7 166 642 0 0 0 5 304 642
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114 FBtr0300796 0 0 0 56 1296 14475 0 0 0
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115 ...
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116
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117
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118 # Input files need not be sorted.
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119
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120 -----
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121
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122 *multijoin* was written by A. Gordon (gordon at cshl dot edu)
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123
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124 </help>
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125 </tool>
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