Mercurial > repos > erinija > dnp_correlation_between_profiles
comparison dnp_correlation_between_profiles.xml @ 0:b45de206654d draft default tip
"planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
author | erinija |
---|---|
date | Fri, 01 May 2020 12:08:23 +0000 |
parents | |
children |
comparison
equal
deleted
inserted
replaced
-1:000000000000 | 0:b45de206654d |
---|---|
1 <tool id="dnp_correlation_between_profiles" name="Correlations" version="0.1.0"> | |
2 <requirements> | |
3 <requirement type="package" version="1.0">dnp-corrprofile</requirement> | |
4 </requirements> | |
5 <command detect_errors="exit_code" interpreter="sh"><![CDATA[ | |
6 dnp-correlation-between-profiles.sh "$input1" "$input2" "$input3" "$output1" | |
7 ]]></command> | |
8 <inputs> | |
9 <param type="data" name="input1" format="tabular" label="Dinucleotide frequency profiles" /> | |
10 <param name="input2" type="integer" value="146" label="Sliding window size" /> | |
11 <param name="input3" type="text" value="AA AC AG AT CA CC CG CT GA GC GG GT TA TC TG TT" label="Dinucleotides" /> | |
12 </inputs> | |
13 <outputs> | |
14 <data name="output1" format="tabular" /> | |
15 </outputs> | |
16 <tests> | |
17 <test> | |
18 <param name="input1" value="seq25000.di.freq.profiles"/> | |
19 <param name="input2" value="146"/> | |
20 <param name="input3" value="AA AC AG AT CA CC CG CT GA GC GG GT TA TC TG TT"/> | |
21 <output name="output1" file="seq25000.di.corr.profiles"/> | |
22 </test> | |
23 </tests> | |
24 <help><![CDATA[ | |
25 | |
26 Description:: | |
27 | |
28 A highest symmetry between dinucleotide frequency of occurrence | |
29 profiles on forward and complementary sequences can be determined by | |
30 a maximum positive Pearson correlation coefficient computed along | |
31 each position of the profile within a sliding window. A size of | |
32 a sliding window equals a length of a nucleosome (146bp). | |
33 | |
34 Input file contains columns of dinucleotide frequencies named | |
35 by *.f and *.r corresponding to forward and complementary profile. | |
36 | |
37 Output contains columns of correlation coefficients in which each row | |
38 corresponds to a position of the frequency profile. A first column (0) | |
39 is average of all correlations. A maximum correlation value and position | |
40 of each dinucleotide are printed to a standard output. | |
41 | |
42 Example:: | |
43 | |
44 | |
45 Input tabular: | |
46 AA.f AA.r AC.f AC.r AG.f AG.r | |
47 0.076320 0.067920 0.057800 0.078120 0.081600 0.061960 | |
48 0.072540 0.069520 0.041800 0.079820 0.076300 0.055190 | |
49 ... ... ... ... ... ... | |
50 | |
51 Output tabular: | |
52 0 AA AC AG | |
53 0.042205 0.0882716 0.030175 0.126967 | |
54 ... ... ... ... | |
55 | |
56 | |
57 ]]></help> | |
58 <citations> | |
59 <citation type="bibtex"> | |
60 @article{pranckeviciene2020nucleosome, | |
61 title={Nucleosome positioning sequence patterns as packing or regulatory. S1 Appendix}, | |
62 author={Pranckeviciene, Erinija and Hosid, Sergey and Liang, Nathan and Ioshikhes, Ilya}, | |
63 journal={PLoS computational biology}, | |
64 volume={16}, | |
65 number={1}, | |
66 pages={e1007365}, | |
67 year={2020}, | |
68 publisher={Public Library of Science}, | |
69 url = {https://doi.org/10.1371/journal.pcbi.1007365} | |
70 }</citation> | |
71 </citations> | |
72 </tool> |