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"planemo upload commit 4846fbc43d4c7437de1ce996392fd13a71abd9c7"
author erinija
date Tue, 07 Sep 2021 15:03:57 +0000
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1 <tool id="dnp_mapping" name="Mapping nucleosome position" version="0.1.0">
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2 <requirements>
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3 <requirement type="package" version="1.0">dnp-mapping</requirement>
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4 </requirements>
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5 <command detect_errors="exit_code" interpreter="bash"><![CDATA[
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6 dnp-mapping.sh '$input1' '$input2' '$input3' '$input4' '$output1' '$output2'
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7 ]]></command>
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8 <inputs>
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9 <param type="data" name="input1" format="tabular" label="Tabular fasta" />
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10 <param type="data" name="input2" format="tabular" label="Patterns matrix" />
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11 <param name="input3" type="integer" value="0" label="Trim from start of sequences" />
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12 <param name="input4" type="integer" value="400" label="Sequence length" />
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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 <data name="output2" format="tabular" />
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17 </outputs>
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18 <tests>
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19 <test>
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20 <param name="input1" value="601"/>
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21 <param name="input2" value="class1_mtr"/>
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22 <param name="input3" value="0"/>
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23 <param name="input4" value="400"/>
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24 <output name="output1" file="cf"/>
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25 <output name="output2" file="pos"/>
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26 </test>
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27 </tests>
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28 <help><![CDATA[
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29
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30 Description::
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31
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32
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33 Maps nucleosome position in sequence given a pattern
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34 of dinucleotide frequencies along the sequence by
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35 computing a correlation between the sequence and the pattern.
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36
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37 Pattern matrix should contain a header line identifying
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38 dinucleotides of which the pattern is. Trim from start
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39 number tells how many positions to trim from the start
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40 of the sequence (default 0). Sequence length is how many
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41 positions in sequence to retain after trimming
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42 (default the rest of the sequence).
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43
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44
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45 Example::
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46
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47 Input tabular fasta:
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48 Widom601Seq CGGGATCCTAATGACCAAGGAAAGCATGATTCTTCA...
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49
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50 Input pattern matrix file:
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51 YY CC
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52 0.285353 0.056062
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53 0.281269 0.055327
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54 0.280065 0.054823
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55
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56
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57 Output tabular position file:
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58 Widom601Seq test-data/class6_mtr 153 0.140767
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59
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60 ]]></help>
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61 <citations>
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62 <citation type="bibtex">
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63 @article{ioshikhes2011,
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64 title={Variety of genomic DNA patterns for nucleosome positioning},
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65 author={Ioshikhes, Ilya and Hosid, Sergey and Pugh Franklin},
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66 journal={Genome Research},
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67 volume={21},
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68 number={11},
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69 pages={1863-1871},
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70 year={2011},
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71 publisher={CSH Press},
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72 url = {https://genome.cshlp.org/content/21/11/1863.full}
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73 }</citation>
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74 </citations>
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75 </tool>