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planemo upload for repository https://github.com/galaxyproject/tools-iuc/ commit abbc840d4383eee1f26abef04b1ce4df1e6e20a2
author iuc
date Fri, 06 Dec 2024 15:43:12 +0000
parents 3f7f3ef77c34
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3f7f3ef77c34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/ commit 960c1f69ec78943dfe72eff0a0992a2ce15d2555
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1 # test data explained
3f7f3ef77c34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/ commit 960c1f69ec78943dfe72eff0a0992a2ce15d2555
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3f7f3ef77c34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/ commit 960c1f69ec78943dfe72eff0a0992a2ce15d2555
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3 ## the tool will expect one file each with the corresponing endings in the DB folder
3f7f3ef77c34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/ commit 960c1f69ec78943dfe72eff0a0992a2ce15d2555
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3f7f3ef77c34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/ commit 960c1f69ec78943dfe72eff0a0992a2ce15d2555
iuc
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5 Trimmed version of:
3f7f3ef77c34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/ commit 960c1f69ec78943dfe72eff0a0992a2ce15d2555
iuc
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6 * OTU table (id for each taxon) (*.otu)
3f7f3ef77c34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/ commit 960c1f69ec78943dfe72eff0a0992a2ce15d2555
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7 * Ref. fasta DB (*.fasta)
3f7f3ef77c34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/ commit 960c1f69ec78943dfe72eff0a0992a2ce15d2555
iuc
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8 * Taxan assignemnt of each ref. DB sequence (*.txt)
3f7f3ef77c34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/ commit 960c1f69ec78943dfe72eff0a0992a2ce15d2555
iuc
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9 * clustering of the ref. sequences (starting with 0) corresponding to the ref. sequences (*.mscluster)
3f7f3ef77c34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/ commit 960c1f69ec78943dfe72eff0a0992a2ce15d2555
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3f7f3ef77c34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/ commit 960c1f69ec78943dfe72eff0a0992a2ce15d2555
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11 ## Command to get DBs
3f7f3ef77c34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/ commit 960c1f69ec78943dfe72eff0a0992a2ce15d2555
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3f7f3ef77c34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/ commit 960c1f69ec78943dfe72eff0a0992a2ce15d2555
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13 ```
3f7f3ef77c34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/ commit 960c1f69ec78943dfe72eff0a0992a2ce15d2555
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14 wget ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/pipeline-5.0/ref-dbs/silva_lsu-20200130.tar.gz
3f7f3ef77c34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/ commit 960c1f69ec78943dfe72eff0a0992a2ce15d2555
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15 mkdir temp
3f7f3ef77c34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/ commit 960c1f69ec78943dfe72eff0a0992a2ce15d2555
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16 tar xvzf silva_ssu-20200130.tar.gz -C temp
3f7f3ef77c34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/ commit 960c1f69ec78943dfe72eff0a0992a2ce15d2555
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17 mv temp/* silva_ssu-20200130
3f7f3ef77c34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/ commit 960c1f69ec78943dfe72eff0a0992a2ce15d2555
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18 ```