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<tool id="dnp_smooth" name="Smooth" version="0.1.0">
    <requirements>
        <requirement type="package" version="1.0">dnp-fourier</requirement>
    </requirements>
    <command detect_errors="exit_code" interpreter="sh"><![CDATA[
        dnp-smooth.sh "$input1" "$input2" "$input3" "$output1"
    ]]></command>
    <inputs>

        <param type="data" name="input1" format="tabular" label="Dinucleotide frequency profiles"/>
        <param name="input2" type="integer" value="3" label="Smoothing window size" />
        <param name="input3" type="integer" value="4" label="Number of points to trim from both sides" />

    </inputs>
    <outputs>
        <data name="output1" format="tabular" />
    </outputs>
    <tests>
        <test>
            <param name="input1" value="smoothing-input.tabular"/>
            <param name="input2" value="3"/>
            <param name="input3" value="4"/>
            <output name="output1" file="smoothed-output.tabular"/>
        </test>
    </tests>
    <help><![CDATA[
        

Description::

   Applies smoothing on dinucleotide profiles. Smoothing reduces noise and enhances
   representation of the dinucleotide frequency  profiles. Smoothing is performed by
   moving average with chosen window size (optimal winsize=3). 

   Smoothing script is based on a shell wrapper of the call to dnp-fourier tool which computes a periodogram
   of a series given as a numerical column parameters as follows:
   dnp-fourier -f input -o output  -n {normalization 0|1|2}  -l length_of_smoothing_window -t {type_of_output 1|2|3}

   The parameters control a type of normalization and output:
   Normalization
       0 base normalization  subtracts mean
       1 linear normalization removes linear trand 
       2 quadratic normalization removes quadratic trend
   Output  type
       1 normalization outputs normalized original series
       2 smoothing outputs smoothed original series
       3 Fourier transform outputs periofogram

Example::

    Input tabular:

    pos AA      AC      AG      AT      CA      CC      CG      CT      GA      GC      GG      GT      TA      TC      TG      TT      WW      SS      RR      YY
    -73 0.05664 0.0657  0.06966 0.03644 0.08026 0.09484 0.0362  0.09086 0.07084 0.04032 0.07318 0.06466 0.03862 0.06838 0.05722 0.05602 0.18772 0.24454 0.27032 0.3101
    -72 0.0668  0.06476 0.0753  0.04282 0.07022 0.08034 0.03534 0.081   0.07222 0.03512 0.06774 0.0598  0.03934 0.07496 0.06628 0.06784 0.2168  0.21854 0.28206 0.30414
    -71 0.063   0.0621  0.07668 0.04316 0.06926 0.07264 0.03316 0.07992 0.07546 0.03498 0.07306 0.06406 0.04182 0.07374 0.06874 0.06812 0.2161  0.21384 0.2882  0.29442
    -70 0.0624  0.0643  0.07214 0.04424 0.0642  0.06998 0.03472 0.07718 0.0723  0.03982 0.07472 0.06818 0.04282 0.07674 0.06864 0.06754 0.217   0.21924 0.28156 0.29144
    -69 0.0622  0.06456 0.074   0.0426  0.0661  0.07114 0.03414 0.08016 0.0703  0.03786 0.07118 0.06754 0.0421  0.07712 0.06988 0.06904 0.21594 0.21432 0.27768 0.29746
    ...

    Output is an original input table but smoothed by moving average with given window size, tabular.


    ]]></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>