Mercurial > repos > iuc > ampvis2_export_fasta

comparison test-data/generate.R @ 1:e10b5eebd415 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
author iuc
date Thu, 07 Apr 2022 14:04:02 +0000
parents 3c3c359d9b85
children
comparison
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0:3c3c359d9b85 1:e10b5eebd415
6 ape::write.tree(aalborgwwtps$tree, "AalborgWWTPs.nwk") 6 ape::write.tree(aalborgwwtps$tree, "AalborgWWTPs.nwk")
7 amp_export_fasta(aalborgwwtps, "AalborgWWTPs.fa", tax = F) 7 amp_export_fasta(aalborgwwtps, "AalborgWWTPs.fa", tax = F)
8 amp_export_otutable(aalborgwwtps, "AalborgWWTPs.otu") 8 amp_export_otutable(aalborgwwtps, "AalborgWWTPs.otu")
9 write.table(aalborgwwtps$tax, file = "AalborgWWTPs.tax", quote = F, sep = "\t", row.names = F) 9 write.table(aalborgwwtps$tax, file = "AalborgWWTPs.tax", quote = F, sep = "\t", row.names = F)
10 write.table(aalborgwwtps$metadata, file = "AalborgWWTPs.tsv", quote = F, sep = "\t") 10 write.table(aalborgwwtps$metadata, file = "AalborgWWTPs.tsv", quote = F, sep = "\t")
11
12 # construct data for merge_ampvis2
13 t <- amp_load(otutable = "AalborgWWTPs.otu.csv", metadata = "AalborgWWTPs.tsv", taxonomy = "AalborgWWTPs.tax.tsv", fasta = "AalborgWWTPs.fa", tree = "AalborgWWTPs.nwk")
14 d_2010 <- amp_subset_samples(t, Period %in% "2010")
15 # 60 samples and 109 OTUs have been filtered
16 # Before: 67 samples and 200 OTUs
17 # After: 7 samples and 91 OTUs
18 d_2011 <- amp_subset_samples(t, Period %in% "2011")
19 # 61 samples and 94 OTUs have been filtered
20 # Before: 67 samples and 200 OTUs
21 # After: 6 samples and 106 OTUs
22
23 saveRDS(d_2010, "AalborgWWTPs.2010.rds")
24 saveRDS(d_2011, "AalborgWWTPs.2011.rds")
25
26 # => merging should give 13 samples