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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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