process AMPIR { tag "$meta.id" label 'process_low' conda (params.enable_conda ? "conda-forge::r-ampir=1.1.0" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/r-ampir:1.1.0': 'quay.io/biocontainers/r-ampir:1.1.0' }" input: tuple val(meta), path(faa) val model val min_length val min_probability output: tuple val(meta), path("*.faa"), emit: amps_faa tuple val(meta), path("*.tsv"), emit: amps_tsv path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" min_length = ("${min_length}" == "[]") ? "": " min_len = as.integer(${min_length})," // Fall back to AMPir default value if none specified if ("$faa" == "${prefix}.faa") error "Input and output names are the same, set prefix in module configuration to disambiguate!" """ #!/usr/bin/env Rscript library(ampir) input_seqs <- read_faa('${faa}') prediction <- predict_amps(input_seqs,${min_length} model = '${model}') prediction <- prediction[which(prediction\$prob_AMP >= as.numeric(${min_probability})), ] output_seqs <- input_seqs[row.names(prediction), ] write.table(prediction, file = "${prefix}.tsv", row.names = FALSE, sep = "\t", quote = FALSE, dec = '.') df_to_faa(output_seqs, "${prefix}.faa") version_file_path <- "versions.yml" version_ampir <- paste(unlist(packageVersion("ampir")), collapse = ".") f <- file(version_file_path, "w") writeLines('"${task.process}":', f) writeLines(" ampir: ", f, sep = "") writeLines(version_ampir, f) close(f) """ }