[2] | 1 | <tool id="bed2genetrack" name="GeneTrack indexer" version="1.0.1"> |
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| 2 | |
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| 3 | <description>on a BED file</description> |
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| 4 | |
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| 5 | <command interpreter="python"> |
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| 6 | genetrack_indexer.py -i $input -o $output -s $shift -v 0 -f BED -x |
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| 7 | </command> |
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| 8 | |
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| 9 | <inputs> |
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| 10 | |
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| 11 | <param format="bed6" name="input" type="data" help="Input data"> |
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| 12 | <label>Select input bed file</label> |
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| 13 | </param> |
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| 14 | |
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| 15 | <param name="shift" size="4" type="integer" value="0" help="distance in basepairs"> |
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| 16 | <label>Shift at 5' end</label> |
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| 17 | </param> |
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| 18 | |
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| 19 | <!-- this parameter is currently not used, may not be feasible to use it |
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| 20 | <param name="coverage" type="select" label="Full coverage"> |
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| 21 | <option value="no">NO</option> |
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| 22 | <option value="yes">YES</option> |
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| 23 | </param> |
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| 24 | --> |
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| 25 | |
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| 26 | </inputs> |
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| 27 | |
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| 28 | <outputs> |
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| 29 | <data format="genetrack" name="output" /> |
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| 30 | </outputs> |
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| 31 | |
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| 32 | <help> |
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| 33 | **Help** |
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| 34 | |
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| 35 | This tool will create a visualization of the bed file that is selected. |
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| 36 | |
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| 37 | **Parameters** |
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| 38 | |
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| 39 | - **Shift at 5' end** should be used when the location of interest is at a fixed distance from |
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| 40 | the 5' end for **all sequenced fragments**! |
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| 41 | |
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| 42 | For example if the sequenced sample consists |
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| 43 | mono-nucleosomal DNA (146bp) we should expect that |
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| 44 | each nucleosome midpoint is located at 73 bp from the 5' end of the fragment. |
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| 45 | Therefore we would enter 73 as the shift parameter. Once corrected the reads |
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| 46 | on each strand will coincide and indicate the actual midpoints |
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| 47 | of the nucleosomes. |
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| 48 | |
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| 49 | When shifting the averaging process in GeneTrack is able correct for longer or shorter |
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| 50 | than expected fragment sizes as long as the errors are reasonably random. |
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| 51 | |
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| 52 | </help> |
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| 53 | |
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| 54 | </tool> |
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