modules/gappa_examineheattree

colours a phylogeny with placement densities

phylogenyphylogenetic placementheattreevisualisation

https://github.com/nf-core/modules/[...]/modules/nf-core/gappa/examineheattree

Description

colours a phylogeny with placement densities

Input

name:type

description

pattern

`meta`
`:map`

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

`jplace`
`:file`

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

*.{jplace,jplace.gz}

Output

name:type

description

pattern

`newick`

`meta`
`:map`

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

`*.newick`
`:file`

phylogenetic tree file in newick format

*.newick

`nexus`

`meta`
`:map`

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

`*.nexus`
`:file`

coloured phylogenetic tree file in nexus format

*.nexus

`phyloxml`

`meta`
`:map`

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

`*.phyloxml`
`:file`

coloured phylogenetic tree file in phyloxml format

*.phyloxml

`svg`

`meta`
`:map`

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

`*.svg`
`:file`

coloured phylogenetic tree file in svg format

*.svg

`colours`

`meta`
`:map`

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

`*.colours.txt`
`:file`

colours used in plot

*.colours.txt

`log`

`meta`
`:map`

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

`*.log`
`:file`

log file from the run

*.log

`versions_gappa`

`${task.process}`
`:string`

The name of the process

`gappa`
`:string`

The name of the tool

`gappa --version 2>&1 | sed 's/v//'`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

`${task.process}`
`:string`

The name of the process

`gappa`
`:string`

The name of the tool

`gappa --version 2>&1 | sed 's/v//'`
`:eval`

The expression to obtain the version of the tool

Tools

gappa
GPL v3

Genesis Applications for Phylogenetic Placement Analysis

github.com/lczech/gappa github.com/lczech/gappa/wiki https://github.com/lczech/gappa 10.1093/bioinformatics/btaa070

modules/gappa_examineheattree

Description

Input

`meta`
`:map`

`jplace`
`:file`

Output

`newick`

`meta`
`:map`

`*.newick`
`:file`

`nexus`

`meta`
`:map`

`*.nexus`
`:file`

`phyloxml`

`meta`
`:map`

`*.phyloxml`
`:file`

`svg`

`meta`
`:map`

`*.svg`
`:file`

`colours`

`meta`
`:map`

`*.colours.txt`
`:file`

`log`

`meta`
`:map`

`*.log`
`:file`

`versions_gappa`

`${task.process}`
`:string`

`gappa`
`:string`

`gappa --version 2>&1 | sed 's/v//'`
`:eval`

Topics

`versions`

`${task.process}`
`:string`

`gappa`
`:string`

`gappa --version 2>&1 | sed 's/v//'`
`:eval`

Tools

gappa
GPL v3

included in

maintainer

get in touch

modules/gappa_examineheattree

Description

Input

meta:map

jplace:file

Output

newick

meta:map

*.newick:file

nexus

meta:map

*.nexus:file

phyloxml

meta:map

*.phyloxml:file

svg

meta:map

*.svg:file

colours

meta:map

*.colours.txt:file

log

meta:map

*.log:file

versions_gappa

${task.process}:string

gappa:string

gappa --version 2>&1 | sed 's/v//':eval

Topics

versions

${task.process}:string

gappa:string

gappa --version 2>&1 | sed 's/v//':eval

Tools

gappa GPL v3

included in

maintainer

get in touch

`meta`
`:map`

`jplace`
`:file`

`newick`

`meta`
`:map`

`*.newick`
`:file`

`nexus`

`meta`
`:map`

`*.nexus`
`:file`

`phyloxml`

`meta`
`:map`

`*.phyloxml`
`:file`

`svg`

`meta`
`:map`

`*.svg`
`:file`

`colours`

`meta`
`:map`

`*.colours.txt`
`:file`

`log`

`meta`
`:map`

`*.log`
`:file`

`versions_gappa`

`${task.process}`
`:string`

`gappa`
`:string`

`gappa --version 2>&1 | sed 's/v//'`
`:eval`

`versions`

`${task.process}`
`:string`

`gappa`
`:string`

`gappa --version 2>&1 | sed 's/v//'`
`:eval`

gappa
GPL v3