Description

A tool to parse and summarise results from antimicrobial peptides tools and present functional classification.

Input

name:type
description
pattern

meta:map

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

amp_input:list

The path to the directory containing the results for the AMP tools for each sample processed or a list of files corresponding to each file generated by AMP tools.

[*amptool.tsv, *amptool.tsv]

faa_input:file

The path to the file corresponding to the respective protein fasta files with ‘.faa’ extension. File names have to contain the corresponding sample name, i.e. sample_1.faa

*.faa

opt_amp_db:directory

The path to the folder containing the fasta and tsv database files.

*/

Output

name:type
description
pattern

sample_dir

meta:map

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

${meta.id}/:directory

The output directory that contains the summary output and related alignment files for one sample.

/*

txt

meta:map

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

${meta.id}/*diamond_matches.txt:file

An alignment file containing the results from the DIAMOND alignment step done on all AMP hits.

/*/*_diamond_matches.txt

csv

meta:map

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

${meta.id}/*ampcombi.csv:file

A file containing the summary report of all predicted AMP hits from all AMP tools given as input and the corresponding taxonomic and functional classification from the alignment step.

/*/*_ampcombi.csv

faa

meta:map

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

${meta.id}/*amp.faa:file

A fasta file containing the amino acid sequences of all predicted AMP hits.

/*/*_amp.faa

summary_csv

meta:map

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

AMPcombi_summary.csv:file

A file that concatenates all samples ampcombi summaries. This is activated with --complete_summary true.

AMPcombi_summary.csv

summary_html

meta:map

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

AMPcombi_summary.html:file

A file that concatenates all samples ampcombi summaries. This is activated with --complete_summary true.

AMPcombi_summary.html

log

meta:map

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

*.log:file

A log file that captures the standard output ina log file. Can be activated by --log.

*.log

results_db

meta:map

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

amp_ref_database/:directory

If the AMP reference database is not provided by the user using the flag `—amp_database’, by default the DRAMP database will be downloaded, filtered and stored in this folder.

/amp_ref_database

results_db_dmnd

meta:map

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

amp_ref_database/*.dmnd:file

AMP reference database converted to DIAMOND database format.

/amp_ref_database/*.dmnd

results_db_fasta

meta:map

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

amp_ref_database/*.clean.fasta:file

AMP reference database fasta file, cleaned of diamond-incompatible characters.

/amp_ref_database/*.clean.fasta

results_db_tsv

meta:map

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

amp_ref_database/*.tsv:file

AMP reference database in tsv-format with two columns containing header and sequence.

/amp_ref_database/*.tsv

versions

versions.yml:file

File containing software versions

versions.yml

Tools

ampcombi
MIT

This tool parses the results of amp prediction tools into a single table and aligns the hits against a reference database of antimicrobial peptides for functional classifications.

github.com/Darcy220606/AMPcombi https://github.com/Darcy220606/AMPcombi/tree/dev
Github user darcy220606
Github user louperelo
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