Mercurial > repos > xuebing > sharplabtool
diff tools/regVariation/delete_overlapping_indels.xml @ 0:9071e359b9a3
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author | xuebing |
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date | Fri, 09 Mar 2012 19:37:19 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/regVariation/delete_overlapping_indels.xml Fri Mar 09 19:37:19 2012 -0500 @@ -0,0 +1,66 @@ +<tool id="delete_overlapping_indels" name="Delete Overlapping Indels" version="1.0.0"> + <description>from a chromosome indels file</description> + + <command interpreter="perl"> + delete_overlapping_indels.pl $inputFile1 $inputIndelStartColumnNumber2 $inputIndelEndColumnNumber3 $outputFile1 + </command> + + <inputs> + <param format="tabular" name="inputFile1" type="data" label="Select indels file"/> + <param type="data_column" name="inputIndelStartColumnNumber2" data_ref="inputFile1" accept_default="true" label="Choose the indel start coordinate column number" /> + <param type="data_column" name="inputIndelEndColumnNumber3" data_ref="inputFile1" accept_default="true" label="Choose the the indel end coordinate column number" /> + </inputs> + + <outputs> + <data format="tabular" name="outputFile1"/> + </outputs> + + <tests> + <test> + <param name="inputFile1" value="indels1.tabular" /> + <param name="inputIndelStartColumnNumber2" value="5" /> + <param name="inputIndelEndColumnNumber3" value="6" /> + <output name="outputFile1" file="non_overlapping_indels1.tabular" /> + </test> + </tests> + + <help> + +.. class:: infomark + +**What it does** + +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. +It requires three inputs: + +- The first input is a TABULAR format file containing coordinates of indels in blocks extracted from multi-alignment. +- The second input is an integer number representing the number of the column where indel start coordinates are stored in the input file. +- The third input is an integer number representing the number of the column where indel end coordinates are stored in the input file. +- The output is a TABULAR format file containing all non-overlapping indels in the input file, and the first encountered indel of overlapping ones. + +Note: The number of the first column is 1. + + +**Example** + +Let us have the following insertions in the human genome. The start and end coordinates of insertions are on columns 5 and 6 respectively:: + + 3 hg18.chr22_insert 3 hg18.chr22 14508610 14508612 3924 - panTro2.chr2b 132518950 132518951 3910 + rheMac2.chr17 14311798 14311799 3896 + + 7 hg18.chr22_insert 13 hg18.chr22 14513678 14513690 348 - panTro2.chr2b 132517876 132517877 321 + rheMac2.chr17 14274462 14274463 337 + + 7 hg18.chr22_insert 6 hg18.chr22 14513688 14513699 348 - panTro2.chr2b 132517879 132517880 321 + rheMac2.chr17 14274465 14274466 337 + + 25 hg18.chr22_insert 9 hg18.chr22 14529501 14529509 385 - panTro2.chr22 14528775 14528776 376 - rheMac2.chr9 42869449 42869450 375 - + 36 hg18.chr22_insert 4 hg18.chr22 14566316 14566319 540 - panTro2.chr2b 132492077 132492078 533 + rheMac2.chr10 59230438 59230439 533 - + 40 hg18.chr22_insert 7 hg18.chr22 14508610 14508616 2337 - panTro2.chr2b 132487750 132487751 2313 + rheMac2.chr10 59128305 59128306 2332 + + 41 hg18.chr22_insert 4 hg18.chr22 14571556 14571559 2483 - panTro2.chr2b 132485878 132485879 2481 + rheMac2.chr10 59126094 59126095 2508 + + +By removing the overlapping indels which, we get:: + + 3 hg18.chr22_insert 3 hg18.chr22 14508610 14508612 3924 - panTro2.chr2b 132518950 132518951 3910 + rheMac2.chr17 14311798 14311799 3896 + + 7 hg18.chr22_insert 13 hg18.chr22 14513678 14513690 348 - panTro2.chr2b 132517876 132517877 321 + rheMac2.chr17 14274462 14274463 337 + + 25 hg18.chr22_insert 9 hg18.chr22 14529501 14529509 385 - panTro2.chr22 14528775 14528776 376 - rheMac2.chr9 42869449 42869450 375 - + 36 hg18.chr22_insert 4 hg18.chr22 14566316 14566319 540 - panTro2.chr2b 132492077 132492078 533 + rheMac2.chr10 59230438 59230439 533 - + 41 hg18.chr22_insert 4 hg18.chr22 14571556 14571559 2483 - panTro2.chr2b 132485878 132485879 2481 + rheMac2.chr10 59126094 59126095 2508 + + + </help> + +</tool> \ No newline at end of file