Mercurial > repos > erinija > dnp_fourier_transform

annotate dnp_fourier_transform.xml @ 0:0bd39cf9318b draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
author erinija
date Fri, 01 May 2020 12:09:01 +0000
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
0bd39cf9318b "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
1 <tool id="dnp_fourier_transform" name="Periodogram" version="0.1.0">
0bd39cf9318b "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
2 <requirements>
0bd39cf9318b "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
3 <requirement type="package" version="1.0">dnp-fourier</requirement>
0bd39cf9318b "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
4 </requirements>
0bd39cf9318b "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
5 <command detect_errors="exit_code" interpreter="sh"><![CDATA[
0bd39cf9318b "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
6 dnp-fourier-transform.sh "$input1" "$output1" "$input2" "$input3" "$input4"
0bd39cf9318b "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
7 ]]></command>
0bd39cf9318b "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
8 <inputs>
0bd39cf9318b "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
9 <param type="data" name="input1" format="tabular" label="Dinucleotide frequencies(no smoothing)"/>
0bd39cf9318b "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
10 <param name="input2" type="integer" value="2" label="Normalization type" />
0bd39cf9318b "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
11 <param name="input3" type="integer" value="3" label="Smoothing window size" />
0bd39cf9318b "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
12 <param name="input4" type="integer" value="4" label="Points to trim " />
0bd39cf9318b "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
13 </inputs>
0bd39cf9318b "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
14 <outputs>
0bd39cf9318b "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
15 <data name="output1" format="tabular" from_work_dir="fourier-output.tabular" />
0bd39cf9318b "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
16 </outputs>
0bd39cf9318b "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
17 <tests>
0bd39cf9318b "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
18 <test>
0bd39cf9318b "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
19 <param name="input1" value="fourier-input.tabular"/>
0bd39cf9318b "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
20 <param name="input2" value="2"/>
0bd39cf9318b "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
21 <param name="input3" value="3"/>
0bd39cf9318b "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
22 <param name="input4" value="4"/>
0bd39cf9318b "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
23 <output name="output1" file="fourier-output.tabular"/>
0bd39cf9318b "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
24 </test>
0bd39cf9318b "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
25 </tests>
0bd39cf9318b "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
26 <help><![CDATA[
0bd39cf9318b "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
27
0bd39cf9318b "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
28 Description::
0bd39cf9318b "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
29
0bd39cf9318b "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
30 This is a shell wrapper of the call to dnp-fourier which computes a periodogram
0bd39cf9318b "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
31 of a series given as a numerical column and it is called as follows
0bd39cf9318b "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
32 dnp-fourier -f input -o output -n {normalization 0|1|2} -l length_of_smoothing_window -t {type_of_output 1|2|3}
0bd39cf9318b "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
33
0bd39cf9318b "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
34 The parameters control a type of normalization and output:
0bd39cf9318b "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
35 Normalization
0bd39cf9318b "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
36 0 base normalization subtracts mean
0bd39cf9318b "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
37 1 linear normalization removes linear trand
0bd39cf9318b "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
38 2 quadratic normalization removes quadratic trend
0bd39cf9318b "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
39 Output type
0bd39cf9318b "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
40 1 normalization outputs normalized original series
0bd39cf9318b "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
41 2 smoothing outputs smoothed original series
0bd39cf9318b "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
42 3 Fourier transform outputs periofogram
0bd39cf9318b "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
43
0bd39cf9318b "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
44 Fourier transform has to be applied on symmetrized, nonsmoothed data, since it performs
0bd39cf9318b "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
45 smoothing internally. Dinucleotide frequency profiles usually have a quadratic gradient.
0bd39cf9318b "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
46 Therefore, a quadratic normalization is a default setting. Fourier transform is applied to every
0bd39cf9318b "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
47 column of the input table. In the output the first column contains period in base pairs.
0bd39cf9318b "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
48
0bd39cf9318b "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
49 Example::
0bd39cf9318b "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
50
0bd39cf9318b "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
51 Input tabular:
0bd39cf9318b "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
52
0bd39cf9318b "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
53 pos AA AC AG AT CA CC CG CT GA GC GG GT TA TC TG TT WW SS RR YY
0bd39cf9318b "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
54 -73 0.05664 0.0657 0.06966 0.03644 0.08026 0.09484 0.0362 0.09086 0.07084 0.04032 0.07318 0.06466 0.03862 0.06838 0.05722 0.05602 0.18772 0.24454 0.27032 0.3101
0bd39cf9318b "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
55 -72 0.0668 0.06476 0.0753 0.04282 0.07022 0.08034 0.03534 0.081 0.07222 0.03512 0.06774 0.0598 0.03934 0.07496 0.06628 0.06784 0.2168 0.21854 0.28206 0.30414
0bd39cf9318b "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
56 -71 0.063 0.0621 0.07668 0.04316 0.06926 0.07264 0.03316 0.07992 0.07546 0.03498 0.07306 0.06406 0.04182 0.07374 0.06874 0.06812 0.2161 0.21384 0.2882 0.29442
0bd39cf9318b "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
57 -70 0.0624 0.0643 0.07214 0.04424 0.0642 0.06998 0.03472 0.07718 0.0723 0.03982 0.07472 0.06818 0.04282 0.07674 0.06864 0.06754 0.217 0.21924 0.28156 0.29144
0bd39cf9318b "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
58 -69 0.0622 0.06456 0.074 0.0426 0.0661 0.07114 0.03414 0.08016 0.0703 0.03786 0.07118 0.06754 0.0421 0.07712 0.06988 0.06904 0.21594 0.21432 0.27768 0.29746
0bd39cf9318b "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
59 ...
0bd39cf9318b "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
60
0bd39cf9318b "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
61 Output tabular:
0bd39cf9318b "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
62
0bd39cf9318b "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
63 period AA AC AG AT CA CC CG CT GA GC GG GT RR SS TA TC TG TT WW YY
0bd39cf9318b "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
64 2.100000 0.055962 0.061351 0.059462 0.063974 0.060849 0.064279 0.061163 0.065880 0.065897 0.061155 0.063937 0.060605 0.055534 0.056766 0.064493 0.057985 0.061710 0.057163 0.062799 0.057165
0bd39cf9318b "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
65 2.200000 0.031410 0.027762 0.030298 0.030884 0.036627 0.031970 0.033761 0.030523 0.030757 0.033687 0.032216 0.036679 0.029025 0.036916 0.031027 0.030297 0.027772 0.031332 0.037597 0.029181
0bd39cf9318b "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
66 2.300000 0.024848 0.024942 0.026645 0.019923 0.020795 0.021051 0.021468 0.021097 0.023902 0.024067 0.023638 0.026876 0.024853 0.024313 0.027058 0.018547 0.019763 0.020160 0.022534 0.022048
0bd39cf9318b "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
67 2.400000 0.015580 0.017736 0.017503 0.017749 0.015925 0.017672 0.017981 0.017754 0.018037 0.017791 0.017940 0.019215 0.019337 0.017269 0.017458 0.017108 0.016969 0.019227 0.017725 0.017988
0bd39cf9318b "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
68 2.500000 0.013954 0.012568 0.013675 0.012484 0.014744 0.013639 0.012682 0.013358 0.013474 0.012607 0.013475 0.014589 0.013540 0.013804 0.012656 0.013723 0.012505 0.013873 0.014738 0.013618
0bd39cf9318b "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
69 ...
0bd39cf9318b "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
70
0bd39cf9318b "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
71
0bd39cf9318b "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
72 ]]></help>
0bd39cf9318b "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
73 <citations>
0bd39cf9318b "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
74 <citation type="bibtex">
0bd39cf9318b "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
75 @article{pranckeviciene2020nucleosome,
0bd39cf9318b "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
76 title={Nucleosome positioning sequence patterns as packing or regulatory. S1 Appendix},
0bd39cf9318b "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
77 author={Pranckeviciene, Erinija and Hosid, Sergey and Liang, Nathan and Ioshikhes, Ilya},
0bd39cf9318b "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
78 journal={PLoS computational biology},
0bd39cf9318b "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
79 volume={16},
0bd39cf9318b "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
80 number={1},
0bd39cf9318b "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
81 pages={e1007365},
0bd39cf9318b "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
82 year={2020},
0bd39cf9318b "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
83 publisher={Public Library of Science},
0bd39cf9318b "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
84 url = {https://doi.org/10.1371/journal.pcbi.1007365}
0bd39cf9318b "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
85 }</citation>
0bd39cf9318b "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
86 </citations>
0bd39cf9318b "planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
erinija
parents:
diff changeset
87 </tool>