Mercurial > repos > xuebing > sharplabtool
comparison tools/regVariation/delete_overlapping_indels.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="delete_overlapping_indels" name="Delete Overlapping Indels" version="1.0.0"> | |
| 2 <description>from a chromosome indels file</description> | |
| 3 | |
| 4 <command interpreter="perl"> | |
| 5 delete_overlapping_indels.pl $inputFile1 $inputIndelStartColumnNumber2 $inputIndelEndColumnNumber3 $outputFile1 | |
| 6 </command> | |
| 7 | |
| 8 <inputs> | |
| 9 <param format="tabular" name="inputFile1" type="data" label="Select indels file"/> | |
| 10 <param type="data_column" name="inputIndelStartColumnNumber2" data_ref="inputFile1" accept_default="true" label="Choose the indel start coordinate column number" /> | |
| 11 <param type="data_column" name="inputIndelEndColumnNumber3" data_ref="inputFile1" accept_default="true" label="Choose the the indel end coordinate column number" /> | |
| 12 </inputs> | |
| 13 | |
| 14 <outputs> | |
| 15 <data format="tabular" name="outputFile1"/> | |
| 16 </outputs> | |
| 17 | |
| 18 <tests> | |
| 19 <test> | |
| 20 <param name="inputFile1" value="indels1.tabular" /> | |
| 21 <param name="inputIndelStartColumnNumber2" value="5" /> | |
| 22 <param name="inputIndelEndColumnNumber3" value="6" /> | |
| 23 <output name="outputFile1" file="non_overlapping_indels1.tabular" /> | |
| 24 </test> | |
| 25 </tests> | |
| 26 | |
| 27 <help> | |
| 28 | |
| 29 .. class:: infomark | |
| 30 | |
| 31 **What it does** | |
| 32 | |
| 33 This program detects overlapping indels in a chromosome and keeps all non-overlapping indels. As for overlapping indels, the first encountered one is kept and all others are removed. | |
| 34 It requires three inputs: | |
| 35 | |
| 36 - The first input is a TABULAR format file containing coordinates of indels in blocks extracted from multi-alignment. | |
| 37 - The second input is an integer number representing the number of the column where indel start coordinates are stored in the input file. | |
| 38 - The third input is an integer number representing the number of the column where indel end coordinates are stored in the input file. | |
| 39 - The output is a TABULAR format file containing all non-overlapping indels in the input file, and the first encountered indel of overlapping ones. | |
| 40 | |
| 41 Note: The number of the first column is 1. | |
| 42 | |
| 43 | |
| 44 **Example** | |
| 45 | |
| 46 Let us have the following insertions in the human genome. The start and end coordinates of insertions are on columns 5 and 6 respectively:: | |
| 47 | |
| 48 3 hg18.chr22_insert 3 hg18.chr22 14508610 14508612 3924 - panTro2.chr2b 132518950 132518951 3910 + rheMac2.chr17 14311798 14311799 3896 + | |
| 49 7 hg18.chr22_insert 13 hg18.chr22 14513678 14513690 348 - panTro2.chr2b 132517876 132517877 321 + rheMac2.chr17 14274462 14274463 337 + | |
| 50 7 hg18.chr22_insert 6 hg18.chr22 14513688 14513699 348 - panTro2.chr2b 132517879 132517880 321 + rheMac2.chr17 14274465 14274466 337 + | |
| 51 25 hg18.chr22_insert 9 hg18.chr22 14529501 14529509 385 - panTro2.chr22 14528775 14528776 376 - rheMac2.chr9 42869449 42869450 375 - | |
| 52 36 hg18.chr22_insert 4 hg18.chr22 14566316 14566319 540 - panTro2.chr2b 132492077 132492078 533 + rheMac2.chr10 59230438 59230439 533 - | |
| 53 40 hg18.chr22_insert 7 hg18.chr22 14508610 14508616 2337 - panTro2.chr2b 132487750 132487751 2313 + rheMac2.chr10 59128305 59128306 2332 + | |
| 54 41 hg18.chr22_insert 4 hg18.chr22 14571556 14571559 2483 - panTro2.chr2b 132485878 132485879 2481 + rheMac2.chr10 59126094 59126095 2508 + | |
| 55 | |
| 56 By removing the overlapping indels which, we get:: | |
| 57 | |
| 58 3 hg18.chr22_insert 3 hg18.chr22 14508610 14508612 3924 - panTro2.chr2b 132518950 132518951 3910 + rheMac2.chr17 14311798 14311799 3896 + | |
| 59 7 hg18.chr22_insert 13 hg18.chr22 14513678 14513690 348 - panTro2.chr2b 132517876 132517877 321 + rheMac2.chr17 14274462 14274463 337 + | |
| 60 25 hg18.chr22_insert 9 hg18.chr22 14529501 14529509 385 - panTro2.chr22 14528775 14528776 376 - rheMac2.chr9 42869449 42869450 375 - | |
| 61 36 hg18.chr22_insert 4 hg18.chr22 14566316 14566319 540 - panTro2.chr2b 132492077 132492078 533 + rheMac2.chr10 59230438 59230439 533 - | |
| 62 41 hg18.chr22_insert 4 hg18.chr22 14571556 14571559 2483 - panTro2.chr2b 132485878 132485879 2481 + rheMac2.chr10 59126094 59126095 2508 + | |
| 63 | |
| 64 </help> | |
| 65 | |
| 66 </tool> |