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Add full user options for AMPir
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commit
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4 changed files with 22 additions and 13 deletions
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@ -9,8 +9,9 @@ process AMPIR {
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input:
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tuple val(meta), path(faa)
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val cut_off
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val model
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val min_length
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val min_probability
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output:
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tuple val(meta), path("*.faa"), emit: amps_faa
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@ -23,15 +24,17 @@ process AMPIR {
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script:
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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min_length = ("${min_length}" == "[]") ? "": " min_len = as.integer(${min_length})," // Fall back to AMPir default value if none specified
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"""
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#!/usr/bin/env Rscript
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library(ampir)
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protein_seqs <- read_faa('${faa}')
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prediction <- predict_amps(protein_seqs, model = '${model}')
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prediction <- protein_seqs[which(prediction\$prob_AMP >= as.integer(${cut_off})), ]
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df_to_faa(protein_seqs, "${prefix}.faa")
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write.table(prediction, file = "${prefix}.csv", row.names = FALSE, quote = FALSE, dec = '.')
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input_seqs <- read_faa('${faa}')
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prediction <- predict_amps(input_seqs,${min_length} model = '${model}')
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prediction <- prediction[which(prediction\$prob_AMP >= as.numeric(${min_probability})), ]
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output_seqs <- input_seqs[row.names(prediction), ]
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write.table(prediction, file = "${prefix}.csv", row.names = FALSE, sep = ";", quote = FALSE, dec = '.')
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df_to_faa(output_seqs, "${prefix}.faa")
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version_file_path <- "versions.yml"
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version_ampir <- paste(unlist(packageVersion("ampir")), collapse = ".")
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@ -25,9 +25,13 @@ input:
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pattern: "*.{faa,fasta}"
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- model:
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type: value
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description: Model for AMP prediction
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description: Built-in model for AMP prediction
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pattern: "{precursor,mature}"
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- cut_off:
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- min_length:
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type: value
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description: Minimum protein length for which predictions will be generated
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pattern: "[0-9]+"
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- min_probability:
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type: value
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description: Cut-off for AMP prediction
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pattern: "[0-9][0-9]"
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@ -10,9 +10,11 @@ workflow test_ampir {
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file(params.test_data['candidatus_portiera_aleyrodidarum']['genome']['proteome_fasta'], checkIfExists: true),
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]
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cut_off = "80"
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model = "precursor"
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AMPIR ( fasta, cut_off, model )
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min_length = []
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min_probability = "0.7"
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AMPIR ( fasta, model, min_length, min_probability )
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}
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@ -4,8 +4,8 @@
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- ampir
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files:
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- path: output/ampir/test.csv
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md5sum: 063fd8866f6a669457d7a49404fb449f
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md5sum: a3b3152373a8add3613ace8c71073e68
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- path: output/ampir/test.faa
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md5sum: e605d38752fd90261c924d51f7007189
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md5sum: 0435609144022c55ac196db053f0df89
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- path: output/ampir/versions.yml
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md5sum: 4a11d25b8a904a7ffb34ae88f6826888
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