Mercurial > repos > bgruening > rnaz_randomize_aln

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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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5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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1 <tool id="rnaz_randomize_aln" name="RNAz Randomize Aln" version="2.1">
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2 <requirements>
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3 <requirement type="package" version="2.1">rnaz</requirement>
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4 </requirements>
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5 <command detect_errors="exit_code"><![CDATA[
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6 rnazRandomizeAln.pl
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7 --window $window
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8 --slide $slide
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9 --level $level
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10 '$input'
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11 > '$output'
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12 ]]></command>
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13 <inputs>
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14 <param type="data" name="input" format="text" />
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15 <param argument="--window" name="window" type="integer" value="120" label="Window size, default 120" />
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16 <param argument="--slide" name="slide" type="integer" value="120" label="Window step size, default 120" />
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17 <param argument="--level" name="level" type="integer" value="2" label="Level of coarse graining" />
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18 </inputs>
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19 <outputs>
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20 <data name="output" format="data"/>
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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21 </outputs>
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22 <tests>
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23 <test>
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24 <param name="input" value="randomize.aln"/>
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25 <output name="output" file="notsorandom.aln"/>
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26 </test>
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27 </tests>
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28 <help><![CDATA[
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29 Usage:
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30 rnazRandomizeAln.pl [options] [file]
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31
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32 Options:
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33 -w N, --window=N
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34 -s N, --slide=N
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35 Long alignment blocks should be shuffled locally in order to
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36 maintain local characteristics of the alignment. Therefore
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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37 alignments can be shuffled in windows. You can specify here the
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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38 size of a window and the offset. Defaults are window=120 and
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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39 slide=120, i.e. the alignments are shuffled in non-overlapping
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40 windows of 120 columns.
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41
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42 -l N, --level=N
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43 The shuffling algorithm tries to mantain local conservation
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44 patterns, i.e. it shuffles only columns of the same degree of
5d006d19f70a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
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45 conservation. This becomes limiting if you have many sequences
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46 in your alignment. Therfore you can choose the level of coarse
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47 graining with this option.
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48
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49 To decide which columns have the same degree of conservation,
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50 the mean pairwise identity (MPI) of each column is calculated
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51 and finally only columns of the same value are shuffled. You can
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52 adjust the rounding of the MPI and thus the coarse graining
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53 level with this option. If you have two columns with say 0.52
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54 and 0.48 MPI you get:
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55
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56 level 0: 1 and 0
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57
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58 level 1: 50 and 50
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59
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60 level 2: 52 and 48
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61
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62 So on level 0 you only have conserved (MPI > 0.5) and
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63 non-conserved (MPI < 0.5) columns while on level 2 you need
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64 almost exactly the same MPI to shuffle two columns.
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65
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66 Default value is 2.
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67
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68
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69 ]]></help>
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70
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71 <citations>
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72 <citation type="doi">10.1142/9789814295291_0009</citation>
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73 </citations>
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74
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75 </tool>