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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
author bgruening
date Wed, 30 Jan 2019 04:12:32 -0500
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1 <tool id="rnaz_randomize_aln" name="RNAz Randomize Aln" version="2.1">
2 <requirements>
3 <requirement type="package" version="2.1">rnaz</requirement>
4 </requirements>
5 <command detect_errors="exit_code"><![CDATA[
6 rnazRandomizeAln.pl
7 --window $window
8 --slide $slide
9 --level $level
10 '$input'
11 > '$output'
12 ]]></command>
13 <inputs>
14 <param type="data" name="input" format="text" />
15 <param argument="--window" name="window" type="integer" value="120" label="Window size, default 120" />
16 <param argument="--slide" name="slide" type="integer" value="120" label="Window step size, default 120" />
17 <param argument="--level" name="level" type="integer" value="2" label="Level of coarse graining" />
18 </inputs>
19 <outputs>
20 <data name="output" format="data"/>
21 </outputs>
22 <tests>
23 <test>
24 <param name="input" value="randomize.aln"/>
25 <output name="output" file="notsorandom.aln"/>
26 </test>
27 </tests>
28 <help><![CDATA[
29 Usage:
30 rnazRandomizeAln.pl [options] [file]
31
32 Options:
33 -w N, --window=N
34 -s N, --slide=N
35 Long alignment blocks should be shuffled locally in order to
36 maintain local characteristics of the alignment. Therefore
37 alignments can be shuffled in windows. You can specify here the
38 size of a window and the offset. Defaults are window=120 and
39 slide=120, i.e. the alignments are shuffled in non-overlapping
40 windows of 120 columns.
41
42 -l N, --level=N
43 The shuffling algorithm tries to mantain local conservation
44 patterns, i.e. it shuffles only columns of the same degree of
45 conservation. This becomes limiting if you have many sequences
46 in your alignment. Therfore you can choose the level of coarse
47 graining with this option.
48
49 To decide which columns have the same degree of conservation,
50 the mean pairwise identity (MPI) of each column is calculated
51 and finally only columns of the same value are shuffled. You can
52 adjust the rounding of the MPI and thus the coarse graining
53 level with this option. If you have two columns with say 0.52
54 and 0.48 MPI you get:
55
56 level 0: 1 and 0
57
58 level 1: 50 and 50
59
60 level 2: 52 and 48
61
62 So on level 0 you only have conserved (MPI > 0.5) and
63 non-conserved (MPI < 0.5) columns while on level 2 you need
64 almost exactly the same MPI to shuffle two columns.
65
66 Default value is 2.
67
68
69 ]]></help>
70
71 <citations>
72 <citation type="doi">10.1142/9789814295291_0009</citation>
73 </citations>
74
75 </tool>