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<tool id="dnp_correlation_between_profiles" name="Correlations" version="0.1.0">
    <requirements>
        <requirement type="package" version="1.0">dnp-corrprofile</requirement>
    </requirements>
    <command detect_errors="exit_code" interpreter="sh"><![CDATA[
        dnp-correlation-between-profiles.sh "$input1" "$input2" "$input3" "$output1" 
    ]]></command>
    <inputs>
        <param type="data" name="input1" format="tabular" label="Dinucleotide frequency profiles" />
        <param name="input2" type="integer" value="146" label="Sliding window size" />
        <param name="input3" type="text" value="AA AC AG AT CA CC CG CT GA GC GG GT TA TC TG TT" label="Dinucleotides" />
    </inputs>
    <outputs>
        <data name="output1" format="tabular" />
    </outputs>
    <tests>
        <test>
            <param name="input1" value="seq25000.di.freq.profiles"/>
            <param name="input2" value="146"/>
            <param name="input3" value="AA AC AG AT CA CC CG CT GA GC GG GT TA TC TG TT"/>
            <output name="output1" file="seq25000.di.corr.profiles"/>
        </test>
    </tests>
    <help><![CDATA[
        
Description::

   A highest symmetry between dinucleotide frequency of occurrence 
   profiles on forward and complementary sequences can be determined by
   a maximum positive Pearson correlation coefficient computed along
   each position of the profile within a sliding window. A size of 
   a sliding window equals a length of a nucleosome (146bp).

   Input file contains columns of dinucleotide frequencies named
   by *.f and *.r corresponding to forward and complementary profile.
   
   Output contains columns of correlation coefficients in which each row
   corresponds to a position of the frequency profile. A first column (0) 
   is average of all correlations. A maximum correlation value and position
   of each dinucleotide are printed to a standard output.

Example::

   
   Input tabular:
      AA.f      AA.r      AC.f      AC.r      AG.f      AG.r
      0.076320  0.067920  0.057800  0.078120  0.081600   0.061960
      0.072540  0.069520  0.041800  0.079820  0.076300   0.055190
      ...       ...       ...       ...       ...        ...

   Output tabular:
      0        AA        AC       AG
      0.042205 0.0882716 0.030175 0.126967 
      ...      ...       ...      ...


    ]]></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>