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"planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
author erinija
date Fri, 01 May 2020 12:07:46 +0000
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1 <tool id="dnp_binary_strings" name="Binary strings from fasta" version="0.1.0">
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2 <requirements>
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3 <requirement type="package" version="1.0">dnp-binstrings</requirement>
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4 </requirements>
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5 <command detect_errors="exit_code" interpreter="sh"><![CDATA[
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6 dnp-binary-strings.sh '$input1' '$input2' '$output1'
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7 ]]></command>
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8 <inputs>
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9 <param type="data" name="input1" format="fasta" label="From fasta" />
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10 <param name="input2" type="text" value="AA AC" label="Dinucleotides" />
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11 </inputs>
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12 <outputs>
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13 <data name="output1" format="tabular" />
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14 </outputs>
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15 <tests>
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16 <test>
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17 <param name="input1" value="seq4.fasta"/>
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18 <param name="input2" value="AA AC"/>
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19 <output name="output1" file="seq4.tabular"/>
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20 </test>
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21 </tests>
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22 <help><![CDATA[
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23
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24 Description::
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25
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26
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27 Convert fasta sequences to a binary sequence of 01
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28 in which ones indicate a presence of a given
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29 dinucleotide at that position.
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30
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31 Each input fasta sequence has a corresponding output
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32 row with tab separated columns- binary string, dinucleotide,
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33 original fasta string, number of the dinucleotide occurrences
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34
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35
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36 Example::
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37
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38 Input fasta:
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39 chr9:42475963-42476182
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40 CCAGGCAGACCCCATA
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41
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42 Output tabular:
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43 100000000111000 CC chr9:42475963-42476182 CCAGGCAGACCCCATA 4
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44
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45
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46 ]]></help>
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47 <citations>
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48 <citation type="bibtex">
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49 @article{pranckeviciene2020nucleosome,
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50 title={Nucleosome positioning sequence patterns as packing or regulatory. S1 Appendix},
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51 author={Pranckeviciene, Erinija and Hosid, Sergey and Liang, Nathan and Ioshikhes, Ilya},
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52 journal={PLoS computational biology},
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53 volume={16},
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54 number={1},
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55 pages={e1007365},
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56 year={2020},
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57 publisher={Public Library of Science},
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58 url = {https://doi.org/10.1371/journal.pcbi.1007365}
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59 }</citation>
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60 </citations>
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61 </tool>