Mercurial > repos > erinija > dnp_select_range

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"planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
author erinija
date Fri, 01 May 2020 12:07:01 +0000
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1 <tool id="dnp_select_range" name="Select interval" version="0.1.0">
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2 <requirements>
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3 </requirements>
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4 <command detect_errors="exit_code" interpreter="sh"><![CDATA[
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5 dnp-select-range.sh "$input1" "$input2" "$input3" "$input4" "$output1"
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6 ]]></command>
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7 <inputs>
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8
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9 <param type="data" name="input1" format="tabular" label="Table of profiles"/>
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10 <param name="input2" type="integer" value="20" label="Start position" />
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11 <param name="input3" type="integer" value="146" label="Size of selection" />
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12 <param name="input4" type="text" value="AA AC AG AT CA CC CG CT GA GC GG GT TA TC TG TT" label="Dinucleotides" />
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13 </inputs>
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14 <outputs>
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15 <data name="output1" format="tabular" />
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16 </outputs>
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17 <tests>
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18 <test>
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19 <param name="input1" value="select-range-input.tabular"/>
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20 <param name="input2" value="20"/>
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21 <param name="input3" value="146"/>
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22 <param name="input4" value="AA AC AG AT CA CC CG CT GA GC GG GT TA TC TG TT"/>
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23 <output name="output1" file="select-range-output.tabular"/>
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24 </test>
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25 </tests>
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26 <help><![CDATA[
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27
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28 Description::
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29
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30 Selects rows from input table within a given range and adds a column with positional information.
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31 An example below shows a selection starting from row=20.
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32
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33 Example::
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34
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35 Input tabular:
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36
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37 AA.f AA.r AC.f AC.r AG.f AG.r AT.f AT.r ...
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38 0.0763 0.067920 0.057800 0.078120 0.081600 0.061960 0.055600 0.044080
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39 0.077160 0.073760 0.056000 0.072160 0.079400 0.060720 0.055960 0.047040
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40 0.083320 0.071200 0.053840 0.080760 0.084560 0.064880 0.050440 0.048720
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41 0.077960 0.068200 0.056040 0.075520 0.080120 0.061680 0.053160 0.047400
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42 0.078200 0.069120 0.056880 0.074000 0.084360 0.060840 0.053520 0.046280
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43 ...
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44
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45 Output tabular:
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46
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47 pos AA.f AC.f AG.f AT.f CA.f CC.f CG.f CT.f ...
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48 20 0.100200 0.084720 0.077200 0.072480 0.066160 0.044160 0.004560 0.060720
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49 21 0.172440 0.024800 0.002080 0.101240 0.131840 0.007200 0.000320 0.095920
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50 22 0.077160 0.096240 0.314320 0.047360 0.012040 0.028560 0.011840 0.013680
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51 ...
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52
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53
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54 ]]></help>
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55 <citations>
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56 <citation type="bibtex">
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57 @article{pranckeviciene2020nucleosome,
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58 title={Nucleosome positioning sequence patterns as packing or regulatory. S1 Appendix},
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59 author={Pranckeviciene, Erinija and Hosid, Sergey and Liang, Nathan and Ioshikhes, Ilya},
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60 journal={PLoS computational biology},
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61 volume={16},
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62 number={1},
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63 pages={e1007365},
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64 year={2020},
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65 publisher={Public Library of Science},
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66 url = {https://doi.org/10.1371/journal.pcbi.1007365}
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67 }</citation>
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68 </citations>
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69 </tool>