modules/bftools_showinf

Extract OME xml data from OME-tif

metadataome-tifome-tiffimagingbioinformatics tools

https://github.com/nf-core/modules/[...]/modules/nf-core/bftools/showinf

Description

Extract OME xml data from OME-tif

Input

name:type

description

pattern

`meta`
`:map`

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

`image`
`:file`

Path to image file containing OME metadata

Output

name:type

description

pattern

`xml`

`meta`
`:map`

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

`*.xml`
`:file`

XML with OME tag metadata

`versions`

`versions.yml`
`:file`

File containing software versions

versions.yml

Tools

bftools
GNU General Public License v2.0

Suite of tools to handle several imaging protocols.

openmicroscopy.org/bio-formats bio-formats.readthedocs.io/en/stable/users https://github.com/ome/bioformats 10.1083/jcb.201004104

modules/bftools_showinf

Description

Input

`meta`
`:map`

`image`
`:file`

Output

`xml`

`meta`
`:map`

`*.xml`
`:file`

`versions`

`versions.yml`
`:file`

Tools

bftools
GNU General Public License v2.0

included in

maintainer

get in touch

modules/bftools_showinf

Description

Input

meta:map

image:file

Output

xml

meta:map

*.xml:file

versions

versions.yml:file

Tools

bftools GNU General Public License v2.0

included in

maintainer

get in touch

`meta`
`:map`

`image`
`:file`

`xml`

`meta`
`:map`

`*.xml`
`:file`

`versions`

`versions.yml`
`:file`

bftools
GNU General Public License v2.0