Description

assigns taxonomy to query sequences in phylogenetic placement output

Input

name:type
description
pattern

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘test’ ]

jplace{:bash}

:file

jplace file output from phylogenetic placement, e.g. EPA-NG, gzipped or not

*.{jplace,jplace.gz}

taxonomy{:bash}

:file

taxonomy file

Output

name:type
description
pattern

examineassign{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘test’ ]

./.{:bash}

:directory

Execution directory

profile{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘test’ ]

*profile.tsv{:bash}

:file

profile tsv file

*profile.tsv

labelled_tree{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘test’ ]

*labelled_tree.newick{:bash}

:file

labelled tree in newick format

*labelled_tree.newick

per_query{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘test’ ]

*per_query.tsv{:bash}

:file

per query taxonomy assignments in tsv format

*per_query.tsv

krona{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘test’ ]

*krona.profile{:bash}

:file

krona profile file

*krona.profile

sativa{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘test’ ]

*sativa.tsv{:bash}

:file

sativa output file

*sativa.tsv

versions{:bash}

versions.yml{:bash}

:file

File containing software versions

versions.yml

Tools

included in
ampliseqphyloplace
maintainer
Github user erikrikarddaniel
get in touch
Ask a question on Slack Open an issue on GitHub