Mercurial > repos > rnateam > graphclust_fasta_to_gspan

annotate fasta2shrep_gspan.xml @ 1:358c52752305 draft

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author rnateam
date Sat, 21 Jan 2017 17:39:29 -0500
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1 <tool id="gspan" name="fasta_to_gspan" version="0.1">
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2 <requirements>
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3 <requirement type="package" version="0.1.7">graphclust-wrappers</requirement>
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4 <requirement type="package" version="2.1.6">rnashapes</requirement>
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5 </requirements>
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6 <stdio>
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7 <exit_code range="1:" />
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8 </stdio>
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9 <command>
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10 <![CDATA[
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12 'fasta2shrep_gspan.pl' --fasta '$dataFasta' $i_crop_unpaired_ends $i_abstr $i_stacks -t "3=0,5=80" -M $M -c $rel_energy_range -win $wins -shift $shift $u $seq_graph_t --group $group
b6e6830ff06b planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/GSPAN commit 21aaee40723b5341b4236edeb0e72995c2054053
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14 ]]>
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15 </command>
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16 <inputs>
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17 <param type="data" name="dataFasta" format="fasta" />
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18 <param name="i_stacks" truevalue="-stack" falsevalue="" checked="True" type="boolean" label="Add stacking information to graphs." help="-stack"/>
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19 <param name="i_abstr" truevalue="-abstr" falsevalue="" type="boolean" label="Add abstract structure graphs to the single shrep graph instances." help="-abstr"/>
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20 <param name="i_crop_unpaired_ends" truevalue="-cue" falsevalue="" type="boolean" label="Add abstract structure graphs to the single shrep graph instances." help="-cue"/>
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21 <param name="M" type="integer" value="5" size="7" label="Max number of shreps that should be taken per window." help="-M"/>
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22 <param name="rel_energy_range" type="integer" value="20" size="7" label=" Relative energy range, i.e. percentage (%) of MFE energy (RNAshapes)" help="-c"/>
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23 <param name="wins" type="text" value="40,150" size="20" label=" A list of window sizes to use" help="comma separated integers"/>
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24 <param name="shift" type="integer" value="30" size="7" label="The shift of the window, relative to the window size given inpercent." help="by default 30"/>
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25 <param name="u" truevalue="-u" falsevalue="" checked="True" type="boolean" label="Ignore unstable structures (RNAshapes)" help="-u"/>
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26 <param name="seq_graph_t" truevalue="--seq-graph-t" falsevalue="" checked="True" type="boolean" label="Add for each 't #' a graph which contains no structure" help="--seq-graph-t"/>
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27 <param name="group" type="integer" value="10000" size="7" label="Group size." help="by default 10000"/>
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28 </inputs>
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29 <outputs>
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30 <data name="gspan.zip" format="searchgui_archive" from_work_dir="GSPAN_Outputs/1.group.gspan.bz2" label="gspan zip" />
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31 </outputs>
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32 <tests>
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33 <test>
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34 <param name="dataFasta" value="data.fasta"/>
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35 <output name="gspan.zip" file="GSPAN_Outputs/1.group.gspan.bz2" />
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36 </test>
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37 </tests>
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38 <help>
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39 <![CDATA[
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40
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41 **What it does**
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43 For each fragment of input sequence we use RNAshapes to create a set of structures.
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44 The default parameters for example consider for each input fragment again a
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45 window of size 40nt and 150nt with a window shift of 30%. This allows to
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46 consider local structures as well as global structures for a fragment.
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47 From each such RNAshape window we take the top 5 shreps (suboptimal
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48 structures for the top 5 shapes) within 20% of the mfe energy of that window
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49 and convert them into graphs.
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50 As shape level (abstraction level) we use 3 for short sequences and 5 for
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51 sequences >= 80nt. Please see also RNAshapes documentation for all these
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52 terms.
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55 **Parameters**
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57 + **input** : Sequences in Fasta format.
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59 + **stack** : This adds an additional vertex (type P) for each pair of stacked base-pairs and four edges
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60 (type p) from each of the involved bases to the new vertex.
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62 + **abstr** : Add abstract structure graphs to the single shrep graph instances.
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64 + **cue** : Crop unpaired ends. If you give this flag, then the unpaired ends of each single structure are ignored. E.g. the structure
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65 ...(((...))).. becomes just (((...)))
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67 + **M** : Max number of shreps that should be taken per window.
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69 + **c** : Relative energy range, i.e. percentage (%) of MFE energy (RNAshapes) Use only one of -e and -c!
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71 + **wins** : A list of window sizes to use. If none are given (empty string ''), then the entire sequence is taken with no windows. Each window > 1 required!
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73 + **shift** : The shift of the window, relative to the window size given in percent. So you give which percent of the window size shall be
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74 used for the shift. Of course the shift is rounded down to the
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75 nearest whole number.
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76 Example 20 % of a window 150 would result in a step size of 30 nt.
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77 It is a relative parameter, as you can give different window sizes.
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78 If you do not give this parameter there is a default shift of 1 nt.
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79
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80 + **u** : Ignore unstable structures (RNAshapes). This option filters out closed structures with positive free energy.
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81
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82 + **seq-graph-t** : Add for each 't #' a graph which contains no structure
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83
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84 + **group** : Combine/group that number of input seqs into 1 gspan file output name is then '<INT>.group.gspan.bz2'
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85
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86 ]]>
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87 </help>
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88 <citations>
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89 <citation type="doi">10.1093/bioinformatics/bts224</citation>
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90 <citation type="bibtex">@article{jan:gie:2015,
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91 author={Janssen, Stefan and Giegerich, Robert},
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92 title={The RNA shapes studio},
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93 journal={Bioinformatics},
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94 year={2015},
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95 doi={10.1093/bioinformatics/btu649},
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96 url={http://bioinformatics.oxfordjournals.org/content/31/3/423.abstract}}</citation>
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97 </citations>
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98 </tool>