Description

Merges the pqueries of several jplace files, placed on a common reference tree, into a single jplace file

Input

name:type
description
pattern

meta

:map

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

jplace

:file

Two or more jplace files output from phylogenetic placement, e.g. EPA-NG, gzipped or not. All of them must reference the same tree; gappa aborts with “Input jplace files have differing reference trees.” if they do not.

*.{jplace,jplace.gz}

Output

name:type
description
pattern

jplace

meta

:map

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

*.merge.jplace*

:file

Single jplace file holding the pqueries of every input file. Gzipped when --compress is passed via task.ext.args.

*.merge.jplace{,.gz}

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

maintainer
Github user erikrikarddaniel
get in touch
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