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planemo upload for repository https://github.com/galaxyproject/tools-iuc/ commit 373300c0508fc239fa6d1c8a0351fa9cbb9c0426
author iuc
date Sat, 23 Mar 2024 07:20:14 +0000
parents dbf2735e8480
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dbf2735e8480 planemo upload for repository https://github.com/galaxyproject/tools-iuc/ commit 66e797aaa79b92c282a8127260cdfd5702207e35
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1 # test data explained
dbf2735e8480 planemo upload for repository https://github.com/galaxyproject/tools-iuc/ commit 66e797aaa79b92c282a8127260cdfd5702207e35
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dbf2735e8480 planemo upload for repository https://github.com/galaxyproject/tools-iuc/ commit 66e797aaa79b92c282a8127260cdfd5702207e35
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3 ## the tool will expect one file each with the corresponing endings in the DB folder
dbf2735e8480 planemo upload for repository https://github.com/galaxyproject/tools-iuc/ commit 66e797aaa79b92c282a8127260cdfd5702207e35
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dbf2735e8480 planemo upload for repository https://github.com/galaxyproject/tools-iuc/ commit 66e797aaa79b92c282a8127260cdfd5702207e35
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5 Trimmed version of:
dbf2735e8480 planemo upload for repository https://github.com/galaxyproject/tools-iuc/ commit 66e797aaa79b92c282a8127260cdfd5702207e35
iuc
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6 * OTU table (id for each taxon) (*.otu)
dbf2735e8480 planemo upload for repository https://github.com/galaxyproject/tools-iuc/ commit 66e797aaa79b92c282a8127260cdfd5702207e35
iuc
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7 * Ref. fasta DB (*.fasta)
dbf2735e8480 planemo upload for repository https://github.com/galaxyproject/tools-iuc/ commit 66e797aaa79b92c282a8127260cdfd5702207e35
iuc
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8 * Taxan assignemnt of each ref. DB sequence (*.txt)
dbf2735e8480 planemo upload for repository https://github.com/galaxyproject/tools-iuc/ commit 66e797aaa79b92c282a8127260cdfd5702207e35
iuc
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9 * clustering of the ref. sequences (starting with 0) corresponding to the ref. sequences (*.mscluster)
dbf2735e8480 planemo upload for repository https://github.com/galaxyproject/tools-iuc/ commit 66e797aaa79b92c282a8127260cdfd5702207e35
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dbf2735e8480 planemo upload for repository https://github.com/galaxyproject/tools-iuc/ commit 66e797aaa79b92c282a8127260cdfd5702207e35
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11 ## Command to get DBs
dbf2735e8480 planemo upload for repository https://github.com/galaxyproject/tools-iuc/ commit 66e797aaa79b92c282a8127260cdfd5702207e35
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dbf2735e8480 planemo upload for repository https://github.com/galaxyproject/tools-iuc/ commit 66e797aaa79b92c282a8127260cdfd5702207e35
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13 ```
dbf2735e8480 planemo upload for repository https://github.com/galaxyproject/tools-iuc/ commit 66e797aaa79b92c282a8127260cdfd5702207e35
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14 wget ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/pipeline-5.0/ref-dbs/silva_lsu-20200130.tar.gz
dbf2735e8480 planemo upload for repository https://github.com/galaxyproject/tools-iuc/ commit 66e797aaa79b92c282a8127260cdfd5702207e35
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15 mkdir temp
dbf2735e8480 planemo upload for repository https://github.com/galaxyproject/tools-iuc/ commit 66e797aaa79b92c282a8127260cdfd5702207e35
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16 tar xvzf silva_ssu-20200130.tar.gz -C temp
dbf2735e8480 planemo upload for repository https://github.com/galaxyproject/tools-iuc/ commit 66e797aaa79b92c282a8127260cdfd5702207e35
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17 mv temp/* silva_ssu-20200130
dbf2735e8480 planemo upload for repository https://github.com/galaxyproject/tools-iuc/ commit 66e797aaa79b92c282a8127260cdfd5702207e35
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18 ```