Mercurial > repos > bgruening > graphclust_preprocessing
annotate preprocessing.xml @ 0:7ba39ab6f48d draft default tip
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
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| date | Thu, 15 Dec 2016 18:18:10 -0500 | 
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7ba39ab6f48d
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
 bgruening parents: diff
changeset | 1 <tool id="preproc" name="Preprocessing" version="0.1"> | 
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7ba39ab6f48d
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
 bgruening parents: diff
changeset | 2 <requirements> | 
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7ba39ab6f48d
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
 bgruening parents: diff
changeset | 3 <requirement type="package" version="0.1">graphclust-wrappers</requirement> | 
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7ba39ab6f48d
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
 bgruening parents: diff
changeset | 4 </requirements> | 
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7ba39ab6f48d
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
 bgruening parents: diff
changeset | 5 <stdio> | 
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7ba39ab6f48d
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
 bgruening parents: diff
changeset | 6 <exit_code range="1:" /> | 
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7ba39ab6f48d
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
 bgruening parents: diff
changeset | 7 </stdio> | 
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7ba39ab6f48d
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
 bgruening parents: diff
changeset | 8 <command> | 
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7ba39ab6f48d
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
 bgruening parents: diff
changeset | 9 <![CDATA[ | 
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7ba39ab6f48d
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
 bgruening parents: diff
changeset | 10 | 
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7ba39ab6f48d
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
 bgruening parents: diff
changeset | 11 'preprocessing.pl' | 
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7ba39ab6f48d
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
 bgruening parents: diff
changeset | 12 '$fastaFile' $max_length $in_winShift $min_seq_length | 
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7ba39ab6f48d
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
 bgruening parents: diff
changeset | 13 | 
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7ba39ab6f48d
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
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changeset | 14 ]]> | 
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7ba39ab6f48d
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
 bgruening parents: diff
changeset | 15 </command> | 
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7ba39ab6f48d
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
 bgruening parents: diff
changeset | 16 <inputs> | 
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7ba39ab6f48d
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
 bgruening parents: diff
changeset | 17 <param type="data" name="fastaFile" format="fasta" /> | 
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7ba39ab6f48d
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
 bgruening parents: diff
changeset | 18 <param name="max_length" type="integer" value="10000" size="5" label="window size"/> | 
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7ba39ab6f48d
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
 bgruening parents: diff
changeset | 19 <param name="in_winShift" type="integer" value="100" size="5" label="window shift in percent"/> | 
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7ba39ab6f48d
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
 bgruening parents: diff
changeset | 20 <param name="min_seq_length" type="integer" value="5" size="5" label="minimum sequence length"/> | 
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7ba39ab6f48d
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
 bgruening parents: diff
changeset | 21 </inputs> | 
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7ba39ab6f48d
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
 bgruening parents: diff
changeset | 22 | 
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7ba39ab6f48d
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
 bgruening parents: diff
changeset | 23 <outputs> | 
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7ba39ab6f48d
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
 bgruening parents: diff
changeset | 24 <data name="data.fasta" format="fasta" from_work_dir="FASTA/data.fasta" label="data.fasta"/> | 
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7ba39ab6f48d
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
 bgruening parents: diff
changeset | 25 <data name="data.map" format="txt" from_work_dir="FASTA/data.map" label="data.map"/> | 
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7ba39ab6f48d
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
 bgruening parents: diff
changeset | 26 <data name="data.names" format="txt" from_work_dir="FASTA/data.names" label="data.names"/> | 
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7ba39ab6f48d
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
 bgruening parents: diff
changeset | 27 <data name="data.fasta.scan" format="fasta" from_work_dir="FASTA/data.fasta.scan" label="data.fasta.scan"/> | 
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7ba39ab6f48d
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
 bgruening parents: diff
changeset | 28 <data name="FASTA" format="zip" from_work_dir="FASTA.zip" label="FASTA.ZIP"/> | 
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7ba39ab6f48d
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
 bgruening parents: diff
changeset | 29 </outputs> | 
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7ba39ab6f48d
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
 bgruening parents: diff
changeset | 30 | 
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7ba39ab6f48d
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
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changeset | 31 | 
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7ba39ab6f48d
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
 bgruening parents: diff
changeset | 32 <tests> | 
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7ba39ab6f48d
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
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changeset | 33 <test> | 
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7ba39ab6f48d
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
 bgruening parents: diff
changeset | 34 <param name="fastaFile" value="input.fa"/> | 
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7ba39ab6f48d
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
 bgruening parents: diff
changeset | 35 <param name="max_length" value="10000"/> | 
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7ba39ab6f48d
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
 bgruening parents: diff
changeset | 36 <param name="in_winShift" value="100"/> | 
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7ba39ab6f48d
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
 bgruening parents: diff
changeset | 37 <param name="min_seq_length" value="5"/> | 
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7ba39ab6f48d
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
 bgruening parents: diff
changeset | 38 <output name="data.fasta" file="FASTA/data.fasta"/> | 
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7ba39ab6f48d
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
 bgruening parents: diff
changeset | 39 <output name="data.map" file="FASTA/data.map" /> | 
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7ba39ab6f48d
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
 bgruening parents: diff
changeset | 40 <output name="data.names" file="FASTA/data.names"/> | 
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7ba39ab6f48d
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
 bgruening parents: diff
changeset | 41 <output name="data.fasta.scan" file="FASTA/data.fasta.scan" /> | 
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7ba39ab6f48d
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
 bgruening parents: diff
changeset | 42 </test> | 
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7ba39ab6f48d
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
 bgruening parents: diff
changeset | 43 </tests> | 
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7ba39ab6f48d
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
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changeset | 44 | 
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7ba39ab6f48d
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
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changeset | 45 <help> | 
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7ba39ab6f48d
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
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changeset | 46 <![CDATA[ | 
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7ba39ab6f48d
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
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changeset | 47 | 
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7ba39ab6f48d
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
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changeset | 48 **What it does** | 
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7ba39ab6f48d
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
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changeset | 49 | 
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
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changeset | 50 The tool takes as an input file of sequences in Fasta format and creates the final input for GraphCLust based on given parameters. | 
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
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changeset | 51 | 
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7ba39ab6f48d
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
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changeset | 52 **Parameters** | 
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7ba39ab6f48d
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
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changeset | 53 | 
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7ba39ab6f48d
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
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changeset | 54 + **window size** : All input sequences are splitted into fragments of this length. | 
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7ba39ab6f48d
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
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changeset | 55 The shift of the sliding window can be defined via option *window shift in percent*. | 
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7ba39ab6f48d
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
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changeset | 56 This paramter reflects the expected length of signals to be found. | 
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7ba39ab6f48d
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
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changeset | 57 Slightly larger windows are usually ok. Too small windows can disturb existing signals. | 
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
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changeset | 58 | 
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7ba39ab6f48d
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
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changeset | 59 | 
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
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changeset | 60 | 
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
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changeset | 61 | 
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7ba39ab6f48d
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
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changeset | 62 + **window shift in percent** : Relative window size in % for window shift during input preprocessing. | 
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7ba39ab6f48d
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
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changeset | 63 Please note that a small shift results in much more fragments for clustering. The benefit is that RNA | 
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
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changeset | 64 motifs/structures are not destroyed by arbitrary split points. Smaller | 
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7ba39ab6f48d
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
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changeset | 65 shifts usually increase the cluster quality. Too small shifts (<20) are not | 
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
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changeset | 66 recommended as a dense center is "polluted" by overlapping fragments and | 
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
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changeset | 67 no other occurences in the dataset can be found. | 
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
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changeset | 68 | 
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
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changeset | 69 | 
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
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changeset | 70 | 
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
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changeset | 71 | 
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
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changeset | 72 | 
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
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changeset | 73 + **minimum sequence length** : Minimal length of input sequences. | 
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
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changeset | 74 Every input sequence below that length is ignored completely during clustering. | 
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
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changeset | 75 | 
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
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changeset | 76 | 
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
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changeset | 77 ]]></help> | 
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
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changeset | 78 | 
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
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changeset | 79 | 
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
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changeset | 80 <citations> | 
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
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changeset | 81 <citation type="doi">10.1093/bioinformatics/bts224</citation> | 
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7ba39ab6f48d
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
 bgruening parents: diff
changeset | 82 </citations> | 
| 
7ba39ab6f48d
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
 bgruening parents: diff
changeset | 83 | 
| 
7ba39ab6f48d
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
 bgruening parents: diff
changeset | 84 | 
| 
7ba39ab6f48d
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit f447414150c19865e904d3914a68e2479fadddce
 bgruening parents: diff
changeset | 85 </tool> | 
