view dnp_select_range.xml @ 0:c0c35d9cd215 draft default tip

"planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"

<tool id="dnp_select_range" name="Select interval" version="0.1.0">
    <requirements>
    </requirements>
    <command detect_errors="exit_code" interpreter="sh"><![CDATA[
        dnp-select-range.sh "$input1" "$input2" "$input3" "$input4" "$output1" 
    ]]></command>
    <inputs>

       <param type="data" name="input1" format="tabular" label="Table of profiles"/>
        <param name="input2" type="integer" value="20"    label="Start position" />
        <param name="input3" type="integer" value="146"  label="Size of selection" />
        <param name="input4" 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="select-range-input.tabular"/>
            <param name="input2" value="20"/>
            <param name="input3" value="146"/>
            <param name="input4" value="AA AC AG AT CA CC CG CT GA GC GG GT TA TC TG TT"/>
            <output name="output1" file="select-range-output.tabular"/>
        </test>
    </tests>
    <help><![CDATA[
        
Description::

   Selects rows from input table within a given range and adds a column with positional information.
   An example below shows a selection starting from row=20.

Example::

   Input tabular:

   AA.f	        AA.r	        AC.f	        AC.r	        AG.f	        AG.r	        AT.f	        AT.r       ...
   0.0763         0.067920	0.057800	0.078120	0.081600	0.061960	0.055600	0.044080
   0.077160	0.073760	0.056000	0.072160	0.079400	0.060720	0.055960	0.047040
   0.083320	0.071200	0.053840	0.080760	0.084560	0.064880	0.050440	0.048720
   0.077960	0.068200	0.056040	0.075520	0.080120	0.061680	0.053160	0.047400
   0.078200	0.069120	0.056880	0.074000	0.084360	0.060840	0.053520	0.046280
   ... 

   Output tabular:

   pos	AA.f	        AC.f	        AG.f	        AT.f	        CA.f	        CC.f	        CG.f	        CT.f     ...
   20	0.100200	0.084720	0.077200	0.072480	0.066160	0.044160	0.004560	0.060720
   21	0.172440	0.024800	0.002080	0.101240	0.131840	0.007200	0.000320	0.095920
   22	0.077160	0.096240	0.314320	0.047360	0.012040	0.028560	0.011840	0.013680
   ...


    ]]></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>