/tools/genetrack/genetrack_indexer.xml
https://bitbucket.org/cistrome/cistrome-harvard/ · XML · 64 lines · 37 code · 21 blank · 6 comment · 0 complexity · ed373ab148854b2c1c114af03ea2ce66 MD5 · raw file
- <tool id="bed2genetrack" name="GeneTrack indexer" version="1.0.1">
-
- <description>on a BED file</description>
- <command interpreter="python">
- genetrack_indexer.py -i $input -o $output -s $shift -v 0 -f BED -x
- </command>
-
- <inputs>
-
- <param format="bed6" name="input" type="data" help="Input data">
- <label>Select input bed file</label>
- </param>
-
- <param name="shift" size="4" type="integer" value="0" help="distance in basepairs">
- <label>Shift at 5' end</label>
- </param>
- <!-- this parameter is currently not used, may not be feasible to use it
- <param name="coverage" type="select" label="Full coverage">
- <option value="no">NO</option>
- <option value="yes">YES</option>
- </param>
- -->
-
- </inputs>
- <outputs>
- <data format="genetrack" name="output" />
- </outputs>
-
- <help>
- **Help**
- This tool will create a visualization of the bed file that is selected.
- **Parameters**
- - **Shift at 5' end** should be used when the location of interest is at a fixed distance from
- the 5' end for **all sequenced fragments**!
-
- For example if the sequenced sample consists
- mono-nucleosomal DNA (146bp) we should expect that
- each nucleosome midpoint is located at 73 bp from the 5' end of the fragment.
- Therefore we would enter 73 as the shift parameter. Once corrected the reads
- on each strand will coincide and indicate the actual midpoints
- of the nucleosomes.
-
- When shifting the averaging process in GeneTrack is able correct for longer or shorter
- than expected fragment sizes as long as the errors are reasonably random.
- See http://genetrack.bx.psu.edu/ for more information on GeneTrack.
- ------
- **Citation**
- For the underlying tool, please cite `Albert I, Wachi S, Jiang C, Pugh BF. GeneTrack--a genomic data processing and visualization framework. Bioinformatics. 2008 May 15;24(10):1305-6. <http://www.ncbi.nlm.nih.gov/pubmed/18388141>`_
- If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*
- </help>
- </tool>