Mercurial > repos > erinija > dnp_subset_dinuc_profile

<tool id="dnp_subset_dinuc_profile" name="Dinucleotide frequencies" version="0.1.0">
    <requirements>
        <requirement type="package" version="1.0">dnp-diprofile</requirement>
    </requirements>
    <command detect_errors="exit_code" interpreter="sh"><![CDATA[
        dnp-subset-dinuc-profile.sh "$input1" "$input2" "$output1"
    ]]></command>
    <inputs>
        <param type="data" name="input1" format="fasta" label="From fasta" />
        <param type="text" name="input2"  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="diprofile-input.fasta"/>
            <param name="input2" value="AA AC AG AT CA CC CG CT GA GC GG GT TA TC TG TT"/>
            <output name="output1" file="diprofile-output.tabular"/>
        </test>
    </tests>
    <help><![CDATA[

Description::

   Compute positional profiles of dinucleotide frequency
   of occurrences on forward and its complementary
   sequences in a batch of aligned fasta sequences.
   Output columns are labeled by AA.f, AA.r ... where
   .f extension means forward and .r means complementary.

Example::

   Input fasta lines:
     >chr9:42475963-42476182
     CCAGGCAGACCCCATATTCAAGCTGCTGCCCCAGGGTGGTGTACAGATCTGGGGAGAAGAAGGATGA
     >chr9:42476175-42476394
     TCTGCACTCCAGCATGCCTGAGGAGAGGAGGGAATGCAGGATCCTAGTGGAAAGAGTACCAAGCTGG

   Output tabular:
     AA.f            AA.r            AC.f            AC.r   ...
     0.076000        0.059000        0.065000        0.078000 ...
     0.082000        0.060000        0.057000        0.076000 ...
     0.067000        0.075000        0.049000        0.071000 ...


    ]]></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 12:11:00 +0000
parents
children