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1 <tool id="cshl_easyjoin" name="Join" version="0.1.1">
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2 <description>two files</description>
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3 <command interpreter="perl">easyjoin $jointype
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4 -t ' '
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5 $header
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6 -e '$empty_string_filler'
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7 -o auto
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8 $ignore_case
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9 -1 "$column1"
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10 -2 "$column2"
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11 "$input1" "$input2"
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12 > '$output'
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13 </command>
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14
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15 <inputs>
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16 <param format="txt" name="input1" type="data" label="1st file" />
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17 <param name="column1" label="Column to use from 1st file" type="data_column" data_ref="input1" accept_default="true" />
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18
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19 <param format="txt" name="input2" type="data" label="2nd File" />
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20 <param name="column2" label="Column to use from 2nd file" type="data_column" data_ref="input2" accept_default="true" />
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21
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22 <param name="jointype" type="select" label="Output lines appearing in">
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23 <option value=" ">BOTH 1st & 2nd file.</option>
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24 <option value="-v 1">1st but not in 2nd file. [-v 1]</option>
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25 <option value="-v 2">2nd but not in 1st file. [-v 2]</option>
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26 <option value="-a 1">both 1st & 2nd file, plus unpairable lines from 1st file. [-a 1]</option>
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27 <option value="-a 2">both 1st & 2nd file, plus unpairable lines from 2st file. [-a 2]</option>
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28 <option value="-a 1 -a 2">All Lines [-a 1 -a 2]</option>
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29 <option value="-v 1 -v 2">All unpairable lines [-v 1 -v 2]</option>
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30 </param>
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31
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32 <param name="header" type="boolean" checked="false" truevalue="--header" falsevalue="" label="First line is a header line" help="Use if first line contains column headers. It will not be sorted." />
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33
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34 <param name="ignore_case" type="boolean" checked="false" truevalue="-i" falsevalue="" label="Ignore case" help="Sort and Join key column values regardless of upper/lower case letters." />
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35
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36 <param name="empty_string_filler" type="text" size="20" value="0" label="Value to put in unpaired (empty) fields">
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37 <sanitizer>
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38 <valid initial="string.printable">
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39 <remove value="'"/>
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40 </valid>
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41 </sanitizer>
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42 </param>
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43
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44 </inputs>
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45 <outputs>
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46 <data name="output" format="input" metadata_source="input1"
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47 />
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48 </outputs>
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49
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50 <help>
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51 **What it does**
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52
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53 This tool joins two tabular files based on a common key column.
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54
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55 -----
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56
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57 **Example**
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58
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59 **First file**::
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60
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61 Fruit Color
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62 Apple red
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63 Banana yellow
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64 Orange orange
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65 Melon green
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66
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67 **Second File**::
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68
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69 Fruit Price
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70 Orange 7
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71 Avocado 8
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72 Apple 4
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73 Banana 3
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74
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75 **Joining** both files, using **key column 1** and a **header line**, will return::
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76
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77 Fruit Color Price
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78 Apple red 4
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79 Avocado . 8
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80 Banana yellow 3
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81 Melon green .
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82 Orange orange 7
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83
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84 # Input files need not be sorted.
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85 # The header line (**Fruit Color Price**) was joined and kept as first line.
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86 # Missing values ( Avocado's color, missing from the first file ) are replaced with a period character.
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87
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88 -----
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89
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90 *easyjoin* was written by A. Gordon
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91
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92 </help>
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93 </tool>
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