/tools/regVariation/delete_overlapping_indels.xml
https://bitbucket.org/cistrome/cistrome-harvard/ · XML · 66 lines · 48 code · 18 blank · 0 comment · 0 complexity · 9dea0c35c519da38cc87617afb5ca2f1 MD5 · raw file
- <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>