Description

Convert a PretextView-curated AGP file and input assembly FASTA into a corrected AGP using agp-tpf-utils pretext-to-asm.

Input

Name
Description
Pattern

meta (map)

Groovy Map containing sample information e.g. [ id:'sample1' ]

mappedfasta (file)

Input assembly FASTA used for Pretext mapping

*.{fa,fna,fasta}

pretextagp (file)

AGP file exported from PretextView after manual curation

*.agp

Output

Name
Description
Pattern

correctedagp

meta (map)

Groovy Map containing sample information

${meta.id}_corrected*.agp (file)

Corrected AGP assembly coordinates after Pretext curation

${meta.id}_corrected*.agp

versions_agp_tpf_utils

${task.process} (string)

The process the versions were collected from

tola-agp-tpf-utils (string)

The tool name

1.3.4 (string)

The expression to obtain the version of the tool

Topics

Name
Description
Pattern

versions

${task.process} (string)

The process the versions were collected from

tola-agp-tpf-utils (string)

The tool name

1.3.4 (string)

The expression to obtain the version of the tool

Tools

agp-tpf-utils Documentation

Utilities for Tree of Life AGP and TPF assembly files. This module runs pretext-to-asm to remap a PretextView AGP onto the input assembly. Output filename uses task.ext.prefix (default meta.id), e.g. sample_corrected.hap1.1.primary.curated.agp when haplotype tags are present.

License: MIT
Authors