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<tool id="dnp_mapping" name="Mapping nucleosome position" version="0.1.0">
    <requirements>
        <requirement type="package" version="1.0">dnp-mapping</requirement>
    </requirements>
    <command detect_errors="exit_code" interpreter="bash"><![CDATA[
        dnp-mapping.sh '$input1' '$input2' '$input3' '$input4' '$output1' '$output2'
    ]]></command>
    <inputs>
      <param type="data" name="input1" format="tabular" label="Tabular fasta" />
      <param type="data" name="input2" format="tabular" label="Patterns matrix" />
      <param name="input3" type="integer" value="0" label="Trim from start of sequences" />
      <param name="input4" type="integer" value="400" label="Sequence length" />
    </inputs>
    <outputs>
        <data name="output1" format="tabular" />
        <data name="output2" format="tabular" />
    </outputs>
    <tests>
        <test>
            <param name="input1" value="601"/>
            <param name="input2" value="class1_mtr"/>
            <param name="input3" value="0"/>
            <param name="input4" value="400"/>
            <output name="output1" file="cf"/>
            <output name="output2" file="pos"/>
        </test>
    </tests>
    <help><![CDATA[

Description::


   Maps nucleosome position in sequence given a pattern 
   of dinucleotide frequencies along the sequence by 
   computing a correlation between the sequence and the pattern.

   Pattern matrix should contain a header line identifying 
   dinucleotides of which the pattern is. Trim from start
   number tells how many positions to trim from the start 
   of the sequence (default 0). Sequence length is how many 
   positions in sequence to retain after trimming 
   (default the rest of the sequence).   


Example::

   Input tabular fasta:
	Widom601Seq     CGGGATCCTAATGACCAAGGAAAGCATGATTCTTCA...

   Input pattern matrix file:
      	YY CC
	0.285353 0.056062
	0.281269 0.055327
	0.280065 0.054823
      
   
   Output tabular position file:
	Widom601Seq     test-data/class6_mtr    153 0.140767

    ]]></help>
    <citations>
        <citation type="bibtex">
@article{ioshikhes2011,
  title={Variety of genomic DNA patterns for nucleosome positioning},
  author={Ioshikhes, Ilya  and Hosid, Sergey and Pugh Franklin},
  journal={Genome Research},
  volume={21},
  number={11},
  pages={1863-1871},
  year={2011},
  publisher={CSH Press},
  url = {https://genome.cshlp.org/content/21/11/1863.full}
}</citation>
    </citations>
</tool>