Mercurial > repos > erinija > dnp_compute_composite

<tool id="dnp_compute_composite" name="Composite profiles" version="0.1.0">
    <requirements>
    </requirements>
    <command detect_errors="exit_code" interpreter="sh"><![CDATA[
        dnp-compute-composite.sh "$input1" "$output1"
    ]]></command>
    <inputs>
        <param type="data" name="input1" format="tabular" />
    </inputs>
    <outputs>
        <data name="output1" format="tabular" />
    </outputs>
    <tests>
        <test>
            <param name="input1" value="compute-composite-input.tabular"/>
            <output name="output1" file="compute-composite-output.tabular"/>
        </test>
    </tests>
    <help><![CDATA[

Description::

   Composite dinucleotides weak/weak WW (A or T) , strong/strong SS (G or C), purine/purine RR (A or G),
   and pyrimidine/pyrimidine YY (C or T) are generalized dinucleotode frequency patterns in nucleosome sequences.
   Given a tabular innput file with all 16 dinucleotides the composite patterns are computed as follows
   WW=AA+AT+TA+TT, SS=CC+CG+GC+GG, RR=AG+GA+AA+GG, YY=CC+TT+CT+TC and their columns are added to the original table.

Examples::

   Input tabular:

   pos    AA      AC      AG      AT      ...
   -73    0.08616 0.08034 0.07146 0.05934 ...
   -72    0.11976 0.04966 0.03412 0.07274 ...
   -71    0.07202 0.08882 0.18912 0.0462  ...
   ...

   Output columns of computed composites added, tabular:

   ...   WW      SS      RR
   ...   0.27644 0.1614  0.29494
   ...   0.36788 0.1091  0.29428
   ...   0.21406 0.12566 0.34432
   ...


    ]]></help>
    <citations>
        <citation type="bibtex">
@article{pranckeviciene2020nucleosome,
  title={Nucleosome positioning sequence patterns as packing or regulatory. S1 Appendix},
  author={Pranckeviciene, Erinija and Hosid, Sergey and Liang, Nathan and Ioshikhes, Ilya},
  journal={PLoS computational biology},
  volume={16},
  number={1},
  pages={e1007365},
  year={2020},
  publisher={Public Library of Science},
  url = {https://doi.org/10.1371/journal.pcbi.1007365}
}</citation>
    </citations>
</tool>
author	erinija
date	Fri, 01 May 2020 12:12:16 +0000
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