Mercurial > repos > rnateam > graphclust_preprocessing
annotate preprocessing.xml @ 0:a0f4b85dc739 draft
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
| author | rnateam |
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| date | Fri, 16 Dec 2016 07:33:19 -0500 |
| parents | |
| children | 35d2fb6f3647 |
| rev | line source |
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a0f4b85dc739
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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1 <tool id="preproc" name="Preprocessing" version="0.1"> |
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a0f4b85dc739
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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parents:
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2 <requirements> |
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a0f4b85dc739
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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3 <requirement type="package" version="0.1">graphclust-wrappers</requirement> |
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a0f4b85dc739
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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parents:
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4 </requirements> |
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a0f4b85dc739
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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5 <stdio> |
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a0f4b85dc739
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
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6 <exit_code range="1:" /> |
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a0f4b85dc739
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
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7 </stdio> |
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a0f4b85dc739
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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8 <command> |
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a0f4b85dc739
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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9 <![CDATA[ |
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a0f4b85dc739
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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10 |
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a0f4b85dc739
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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11 'preprocessing.pl' |
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a0f4b85dc739
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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12 '$fastaFile' $max_length $in_winShift $min_seq_length |
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a0f4b85dc739
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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13 |
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a0f4b85dc739
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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14 ]]> |
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a0f4b85dc739
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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15 </command> |
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a0f4b85dc739
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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16 <inputs> |
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a0f4b85dc739
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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parents:
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17 <param type="data" name="fastaFile" format="fasta" /> |
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a0f4b85dc739
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
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18 <param name="max_length" type="integer" value="10000" size="5" label="window size"/> |
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a0f4b85dc739
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
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19 <param name="in_winShift" type="integer" value="100" size="5" label="window shift in percent"/> |
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a0f4b85dc739
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
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changeset
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20 <param name="min_seq_length" type="integer" value="5" size="5" label="minimum sequence length"/> |
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a0f4b85dc739
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
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21 </inputs> |
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a0f4b85dc739
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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22 |
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a0f4b85dc739
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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23 <outputs> |
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a0f4b85dc739
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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24 <data name="data.fasta" format="fasta" from_work_dir="FASTA/data.fasta" label="data.fasta"/> |
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a0f4b85dc739
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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parents:
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25 <data name="data.map" format="txt" from_work_dir="FASTA/data.map" label="data.map"/> |
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a0f4b85dc739
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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26 <data name="data.names" format="txt" from_work_dir="FASTA/data.names" label="data.names"/> |
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a0f4b85dc739
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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27 <data name="data.fasta.scan" format="fasta" from_work_dir="FASTA/data.fasta.scan" label="data.fasta.scan"/> |
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a0f4b85dc739
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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parents:
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28 <data name="FASTA" format="zip" from_work_dir="FASTA.zip" label="FASTA.ZIP"/> |
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a0f4b85dc739
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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29 </outputs> |
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a0f4b85dc739
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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30 |
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a0f4b85dc739
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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31 |
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a0f4b85dc739
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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32 <tests> |
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a0f4b85dc739
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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33 <test> |
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a0f4b85dc739
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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34 <param name="fastaFile" value="input.fa"/> |
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a0f4b85dc739
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
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35 <param name="max_length" value="10000"/> |
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a0f4b85dc739
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
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36 <param name="in_winShift" value="100"/> |
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a0f4b85dc739
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
rnateam
parents:
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37 <param name="min_seq_length" value="5"/> |
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a0f4b85dc739
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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38 <output name="data.fasta" file="FASTA/data.fasta"/> |
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a0f4b85dc739
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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parents:
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39 <output name="data.map" file="FASTA/data.map" /> |
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a0f4b85dc739
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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40 <output name="data.names" file="FASTA/data.names"/> |
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a0f4b85dc739
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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41 <output name="data.fasta.scan" file="FASTA/data.fasta.scan" /> |
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a0f4b85dc739
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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42 </test> |
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a0f4b85dc739
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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43 </tests> |
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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44 |
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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45 <help> |
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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46 <![CDATA[ |
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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47 |
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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48 **What it does** |
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a0f4b85dc739
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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49 |
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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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 21aaee40723b5341b4236edeb0e72995c2054053
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51 |
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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52 **Parameters** |
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a0f4b85dc739
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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53 |
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a0f4b85dc739
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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54 + **window size** : All input sequences are splitted into fragments of this length. |
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a0f4b85dc739
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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55 The shift of the sliding window can be defined via option *window shift in percent*. |
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a0f4b85dc739
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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56 This paramter reflects the expected length of signals to be found. |
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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57 Slightly larger windows are usually ok. Too small windows can disturb existing signals. |
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a0f4b85dc739
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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58 |
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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59 |
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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60 |
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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61 |
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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62 + **window shift in percent** : Relative window size in % for window shift during input preprocessing. |
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a0f4b85dc739
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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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 21aaee40723b5341b4236edeb0e72995c2054053
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64 motifs/structures are not destroyed by arbitrary split points. Smaller |
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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65 shifts usually increase the cluster quality. Too small shifts (<20) are not |
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a0f4b85dc739
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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66 recommended as a dense center is "polluted" by overlapping fragments and |
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a0f4b85dc739
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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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 21aaee40723b5341b4236edeb0e72995c2054053
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68 |
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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69 |
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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70 |
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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71 |
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72 |
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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73 + **minimum sequence length** : Minimal length of input sequences. |
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a0f4b85dc739
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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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 21aaee40723b5341b4236edeb0e72995c2054053
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75 |
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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76 |
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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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77 ]]></help> |
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a0f4b85dc739
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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78 |
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a0f4b85dc739
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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79 |
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a0f4b85dc739
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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80 <citations> |
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a0f4b85dc739
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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81 <citation type="doi">10.1093/bioinformatics/bts224</citation> |
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a0f4b85dc739
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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82 </citations> |
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a0f4b85dc739
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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83 |
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a0f4b85dc739
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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84 |
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a0f4b85dc739
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust commit 21aaee40723b5341b4236edeb0e72995c2054053
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85 </tool> |