Mercurial > repos > iuc > ampvis2_ordinate

annotate test-data/generate.R @ 0:f84ec808bee3 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
author iuc
date Mon, 04 Apr 2022 10:16:44 +0000
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children be1918c80d9f
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f84ec808bee3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
1 library(ampvis2)
f84ec808bee3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
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f84ec808bee3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
3 # subset taxa using 200 random OTUs
f84ec808bee3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
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4 aalborgwwtps <- amp_subset_taxa(AalborgWWTPs, tax_vector = sample(AalborgWWTPs$tax$OTU, 200))
f84ec808bee3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
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f84ec808bee3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
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6 ape::write.tree(aalborgwwtps$tree, "AalborgWWTPs.nwk")
f84ec808bee3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
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7 amp_export_fasta(aalborgwwtps, "AalborgWWTPs.fa", tax = F)
f84ec808bee3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
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8 amp_export_otutable(aalborgwwtps, "AalborgWWTPs.otu")
f84ec808bee3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
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9 write.table(aalborgwwtps$tax, file = "AalborgWWTPs.tax", quote = F, sep = "\t", row.names = F)
f84ec808bee3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
10 write.table(aalborgwwtps$metadata, file = "AalborgWWTPs.tsv", quote = F, sep = "\t")