Mercurial > repos > xuebing > sharplabtool
comparison tools/filters/compare.xml @ 0:9071e359b9a3
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| author | xuebing |
|---|---|
| date | Fri, 09 Mar 2012 19:37:19 -0500 |
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| -1:000000000000 | 0:9071e359b9a3 |
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| 1 <tool id="comp1" name="Compare two Datasets" version="1.0.2"> | |
| 2 <description>to find common or distinct rows</description> | |
| 3 <command interpreter="python">joinWrapper.py $input1 $input2 $field1 $field2 $mode $out_file1</command> | |
| 4 <inputs> | |
| 5 <param format="tabular" name="input1" type="data" label="Compare"/> | |
| 6 <param name="field1" label="Using column" type="data_column" data_ref="input1"> | |
| 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."/> | |
| 8 </param> | |
| 9 <param format="tabular" name="input2" type="data" label="against" /> | |
| 10 <param name="field2" label="and column" type="data_column" data_ref="input2"> | |
| 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."/> | |
| 12 </param> | |
| 13 <param name="mode" type="select" label="To find" help="See examples below for explanation of these options"> | |
| 14 <option value="N">Matching rows of 1st dataset</option> | |
| 15 <option value="V">Non Matching rows of 1st dataset</option> | |
| 16 </param> | |
| 17 </inputs> | |
| 18 <outputs> | |
| 19 <data format="input" name="out_file1" metadata_source="input1" /> | |
| 20 </outputs> | |
| 21 <tests> | |
| 22 <test> | |
| 23 <param name="input1" value="1.bed"/> | |
| 24 <param name="input2" value="2.bed"/> | |
| 25 <param name="field1" value="2"/> | |
| 26 <param name="field2" value="2"/> | |
| 27 <param name="mode" value="N"/> | |
| 28 <output name="out_file1" file="fs-compare.dat"/> | |
| 29 </test> | |
| 30 <!--test case with duplicated key values--> | |
| 31 <test> | |
| 32 <param name="input1" value="1.bed"/> | |
| 33 <param name="input2" value="3.bed"/> | |
| 34 <param name="field1" value="1"/> | |
| 35 <param name="field2" value="1"/> | |
| 36 <param name="mode" value="V"/> | |
| 37 <output name="out_file1" file="fs-compare-2.dat"/> | |
| 38 </test> | |
| 39 </tests> | |
| 40 <help> | |
| 41 | |
| 42 .. class:: infomark | |
| 43 | |
| 44 **TIP:** If your data is not TAB delimited, use *Text Manipulation->Convert* | |
| 45 | |
| 46 ----- | |
| 47 | |
| 48 **Syntax** | |
| 49 | |
| 50 This tool finds lines in one dataset that HAVE or DO NOT HAVE a common field with another dataset. | |
| 51 | |
| 52 ----- | |
| 53 | |
| 54 **Example** | |
| 55 | |
| 56 If this is **First dataset**:: | |
| 57 | |
| 58 chr1 10 20 geneA | |
| 59 chr1 50 80 geneB | |
| 60 chr5 10 40 geneL | |
| 61 | |
| 62 and this is **Second dataset**:: | |
| 63 | |
| 64 geneA tumor-suppressor | |
| 65 geneB Foxp2 | |
| 66 geneC Gnas1 | |
| 67 geneE INK4a | |
| 68 | |
| 69 Finding lines of the **First dataset** whose 4th column matches the 1st column of the **Second dataset** yields:: | |
| 70 | |
| 71 chr1 10 20 geneA | |
| 72 chr1 50 80 geneB | |
| 73 | |
| 74 Conversely, using option **Non Matching rows of First dataset** on the same fields will yield:: | |
| 75 | |
| 76 chr5 10 40 geneL | |
| 77 | |
| 78 </help> | |
| 79 </tool> |