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