Mercurial > repos > iuc > data_manager_mapseq
annotate readme.md @ 1:4cd97cc67061 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/ commit 373300c0508fc239fa6d1c8a0351fa9cbb9c0426
author | iuc |
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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
iuc
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2 |
dbf2735e8480
planemo upload for repository https://github.com/galaxyproject/tools-iuc/ commit 66e797aaa79b92c282a8127260cdfd5702207e35
iuc
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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
iuc
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4 |
dbf2735e8480
planemo upload for repository https://github.com/galaxyproject/tools-iuc/ commit 66e797aaa79b92c282a8127260cdfd5702207e35
iuc
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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
iuc
parents:
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10 |
dbf2735e8480
planemo upload for repository https://github.com/galaxyproject/tools-iuc/ commit 66e797aaa79b92c282a8127260cdfd5702207e35
iuc
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11 ## Command to get DBs |
dbf2735e8480
planemo upload for repository https://github.com/galaxyproject/tools-iuc/ commit 66e797aaa79b92c282a8127260cdfd5702207e35
iuc
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12 |
dbf2735e8480
planemo upload for repository https://github.com/galaxyproject/tools-iuc/ commit 66e797aaa79b92c282a8127260cdfd5702207e35
iuc
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13 ``` |
dbf2735e8480
planemo upload for repository https://github.com/galaxyproject/tools-iuc/ commit 66e797aaa79b92c282a8127260cdfd5702207e35
iuc
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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
iuc
parents:
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15 mkdir temp |
dbf2735e8480
planemo upload for repository https://github.com/galaxyproject/tools-iuc/ commit 66e797aaa79b92c282a8127260cdfd5702207e35
iuc
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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
iuc
parents:
diff
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17 mv temp/* silva_ssu-20200130 |
dbf2735e8480
planemo upload for repository https://github.com/galaxyproject/tools-iuc/ commit 66e797aaa79b92c282a8127260cdfd5702207e35
iuc
parents:
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18 ``` |