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<tool id="dnp_fourier_transform" name="Periodogram" version="0.1.0">
    <requirements>
        <requirement type="package" version="1.0">dnp-fourier</requirement>
    </requirements>
    <command detect_errors="exit_code" interpreter="sh"><![CDATA[
        dnp-fourier-transform.sh "$input1" "$output1" "$input2" "$input3" "$input4"
    ]]></command>
    <inputs>
      <param type="data" name="input1" format="tabular" label="Dinucleotide frequencies(no smoothing)"/>
      <param name="input2" type="integer" value="2" label="Normalization type" />
      <param name="input3" type="integer" value="3" label="Smoothing window size" />
      <param name="input4" type="integer" value="4" label="Points to trim " />
    </inputs>
    <outputs>
        <data name="output1" format="tabular" from_work_dir="fourier-output.tabular" />
    </outputs>
    <tests>
        <test>
            <param name="input1" value="fourier-input.tabular"/>
            <param name="input2" value="2"/>
            <param name="input3" value="3"/>
            <param name="input4" value="4"/>
            <output name="output1" file="fourier-output.tabular"/>
        </test>
    </tests>
    <help><![CDATA[
        
Description::

    This is a shell wrapper of the call to dnp-fourier which computes a periodogram 
    of a series given as a numerical column and it is called 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

     Fourier transform has to be applied on symmetrized, nonsmoothed data, since it performs
     smoothing internally.  Dinucleotide frequency profiles usually have a quadratic gradient.
     Therefore, a quadratic normalization is a default setting. Fourier transform is applied to every 
     column of the input table. In the output the first column contains period in base pairs.

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 tabular:

    period	AA	AC	AG	AT	CA	CC	CG	CT	GA	GC	GG	GT	RR	SS	TA	TC	TG	TT	WW	YY
    2.100000	0.055962	0.061351	0.059462	0.063974	0.060849	0.064279	0.061163	0.065880	0.065897	0.061155	0.063937	0.060605	0.055534	0.056766	0.064493	0.057985	0.061710	0.057163	0.062799	0.057165
    2.200000	0.031410	0.027762	0.030298	0.030884	0.036627	0.031970	0.033761	0.030523	0.030757	0.033687	0.032216	0.036679	0.029025	0.036916	0.031027	0.030297	0.027772	0.031332	0.037597	0.029181 
    2.300000	0.024848	0.024942	0.026645	0.019923	0.020795	0.021051	0.021468	0.021097	0.023902	0.024067	0.023638	0.026876	0.024853	0.024313	0.027058	0.018547	0.019763	0.020160	0.022534	0.022048
    2.400000	0.015580	0.017736	0.017503	0.017749	0.015925	0.017672	0.017981	0.017754	0.018037	0.017791	0.017940	0.019215	0.019337	0.017269	0.017458	0.017108	0.016969	0.019227	0.017725	0.017988
    2.500000	0.013954	0.012568	0.013675	0.012484	0.014744	0.013639	0.012682	0.013358	0.013474	0.012607	0.013475	0.014589	0.013540	0.013804	0.012656	0.013723	0.012505	0.013873	0.014738	0.013618
    ...


    ]]></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>