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1 <tool id="comp1" name="Compare two Datasets" version="1.0.2">
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2 <description>to find common or distinct rows</description>
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3 <command interpreter="python">joinWrapper.py $input1 $input2 $field1 $field2 $mode $out_file1</command>
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4 <inputs>
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5 <param format="tabular" name="input1" type="data" label="Compare"/>
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6 <param name="field1" label="Using column" type="data_column" data_ref="input1">
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7 <validator type="no_options" message="Invalid column choice. Please try again after editing metadata of your input dataset by clicking on the pencil icon next to it."/>
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8 </param>
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9 <param format="tabular" name="input2" type="data" label="against" />
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10 <param name="field2" label="and column" type="data_column" data_ref="input2">
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11 <validator type="no_options" message="Invalid column choice. Please try again after editing metadata of your input dataset by clicking on the pencil icon next to it."/>
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12 </param>
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13 <param name="mode" type="select" label="To find" help="See examples below for explanation of these options">
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14 <option value="N">Matching rows of 1st dataset</option>
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15 <option value="V">Non Matching rows of 1st dataset</option>
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16 </param>
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17 </inputs>
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18 <outputs>
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19 <data format="input" name="out_file1" metadata_source="input1" />
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20 </outputs>
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21 <tests>
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22 <test>
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23 <param name="input1" value="1.bed"/>
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24 <param name="input2" value="2.bed"/>
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25 <param name="field1" value="2"/>
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26 <param name="field2" value="2"/>
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27 <param name="mode" value="N"/>
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28 <output name="out_file1" file="fs-compare.dat"/>
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29 </test>
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30 <!--test case with duplicated key values-->
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31 <test>
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32 <param name="input1" value="1.bed"/>
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33 <param name="input2" value="3.bed"/>
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34 <param name="field1" value="1"/>
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35 <param name="field2" value="1"/>
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36 <param name="mode" value="V"/>
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37 <output name="out_file1" file="fs-compare-2.dat"/>
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38 </test>
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39 </tests>
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40 <help>
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41
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42 .. class:: infomark
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43
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44 **TIP:** If your data is not TAB delimited, use *Text Manipulation->Convert*
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45
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46 -----
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47
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48 **Syntax**
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49
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50 This tool finds lines in one dataset that HAVE or DO NOT HAVE a common field with another dataset.
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51
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52 -----
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53
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54 **Example**
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55
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56 If this is **First dataset**::
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57
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58 chr1 10 20 geneA
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59 chr1 50 80 geneB
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60 chr5 10 40 geneL
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61
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62 and this is **Second dataset**::
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63
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64 geneA tumor-suppressor
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65 geneB Foxp2
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66 geneC Gnas1
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67 geneE INK4a
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68
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69 Finding lines of the **First dataset** whose 4th column matches the 1st column of the **Second dataset** yields::
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70
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71 chr1 10 20 geneA
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72 chr1 50 80 geneB
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73
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74 Conversely, using option **Non Matching rows of First dataset** on the same fields will yield::
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75
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76 chr5 10 40 geneL
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77
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78 </help>
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79 </tool>
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