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1 <tool id="tp_multijoin'_tool" name="Multi-Join" version="@BASE_VERSION@.0">
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2 <description>(combine multiple files)</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements">
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7 <requirement type="package" version="5.18.1">perl</requirement>
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8 <requirement type="package" version="1.0">text_processing_perl_packages</requirement>
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9 </expand>
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10 <command interpreter="perl">
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11 <![CDATA[
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12 multijoin
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13 --key '$key_column'
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14 --values '$value_columns'
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15 --filler '$filler'
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16 $ignore_dups
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17 $output_header
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18 $input_header
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19 $first_file
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20 #for $file in $files:
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21 '$file'
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22 #end for
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23 > '$outfile'
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24 ]]>
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25 </command>
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26 <inputs>
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27 <param name="first_file" type="data" format="txt" label="File to join"/>
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28 <param name="files" multiple="True" type="data" format="txt" label="add additional file" />
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29
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30 <param name="key_column" label="Common key column" type="integer"
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31 value="1" help="Usually gene-ID or other common value" />
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2
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32
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33 <param name="value_columns" label="Column with values to preserve"
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34 type="data_column" data_ref="first_file" accept_default="true" multiple="True" display="checkboxes"/>
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35
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36 <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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37 <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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38 <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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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 </inputs>
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47 <outputs>
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48 <data name="outfile" format="first_file" metadata_source="first_file" />
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49 </outputs>
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50 <tests>
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51 <test>
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52 <param name="first_file" value="multijoin1.txt" />
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53 <param name="files" value="multijoin2.txt,multijoin3.txt" />
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54 <param name="key_column" value="4" />
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55 <param name="value_columns" value="c7,c8,c9" />
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56 <param name="output_header" value="True" />
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57 <output name="outfile" file="multijoin_result1.txt" />
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58 </test>
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59 </tests>
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60 <help>
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61 <![CDATA[
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62 **What it does**
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63
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64 This tool joins multiple tabular files based on a common key column.
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65
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66 -----
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67
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68 **Example**
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69
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70 To join three files, based on the 4th column, and keeping the 7th,8th,9th columns:
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71
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72 **First file (AAA)**::
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73
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74 chr4 888449 890171 FBtr0308778 0 + 266 1527 1722
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75 chr4 972167 979017 FBtr0310651 0 - 3944 6428 6850
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76 chr4 972186 979017 FBtr0089229 0 - 3944 6428 6831
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77 chr4 972186 979017 FBtr0089231 0 - 3944 6428 6831
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78 chr4 972186 979017 FBtr0089233 0 - 3944 6428 6831
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79 chr4 995793 996435 FBtr0111046 0 + 7 166 642
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80 chr4 995793 997931 FBtr0111044 0 + 28 683 2138
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81 chr4 995793 997931 FBtr0111045 0 + 28 683 2138
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82 chr4 1034029 1047719 FBtr0089223 0 - 5293 13394 13690
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83 ...
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84
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85
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86 **Second File (BBB)**::
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87
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88 chr4 90286 134453 FBtr0309803 0 + 657 29084 44167
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89 chr4 251355 266499 FBtr0089116 0 + 56 1296 15144
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90 chr4 252050 266506 FBtr0308086 0 + 56 1296 14456
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91 chr4 252050 266506 FBtr0308087 0 + 56 1296 14456
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92 chr4 252053 266528 FBtr0300796 0 + 56 1296 14475
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93 chr4 252053 266528 FBtr0300800 0 + 56 1296 14475
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94 chr4 252055 266528 FBtr0300798 0 + 56 1296 14473
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95 chr4 252055 266528 FBtr0300799 0 + 56 1296 14473
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96 chr4 252541 266528 FBtr0300797 0 + 56 1296 13987
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97 ...
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98
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99 **Third file (CCC)**::
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100
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101 chr4 972167 979017 FBtr0310651 0 - 9927 6738 6850
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102 chr4 972186 979017 FBtr0089229 0 - 9927 6738 6831
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103 chr4 972186 979017 FBtr0089231 0 - 9927 6738 6831
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104 chr4 972186 979017 FBtr0089233 0 - 9927 6738 6831
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105 chr4 995793 996435 FBtr0111046 0 + 5 304 642
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106 chr4 995793 997931 FBtr0111044 0 + 17 714 2138
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107 chr4 995793 997931 FBtr0111045 0 + 17 714 2138
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108 chr4 1034029 1047719 FBtr0089223 0 - 17646 13536 13690
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109 ...
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110
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111
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112 **Joining** the files, using **key column 4**, **value columns 7,8,9** and a **header line**, will return::
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113
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114 key AAA__V7 AAA__V8 AAA__V9 BBB__V7 BBB__V8 BBB__V9 CCC__V7 CCC__V8 CCC__V9
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115 FBtr0089116 0 0 0 56 1296 15144 0 0 0
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116 FBtr0089223 5293 13394 13690 0 0 0 17646 13536 13690
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117 FBtr0089229 3944 6428 6831 0 0 0 9927 6738 6831
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118 FBtr0089231 3944 6428 6831 0 0 0 9927 6738 6831
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119 FBtr0089233 3944 6428 6831 0 0 0 9927 6738 6831
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120 FBtr0111044 28 683 2138 0 0 0 17 714 2138
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121 FBtr0111045 28 683 2138 0 0 0 17 714 2138
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122 FBtr0111046 7 166 642 0 0 0 5 304 642
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123 FBtr0300796 0 0 0 56 1296 14475 0 0 0
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124 ...
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125
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126 .. class:: infomark
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127
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128 Input files need not be sorted.
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129
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130 @REFERENCES@
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131 ]]>
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132 </help>
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133 </tool>
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