bigorf_extract_1.0.yaml

!mobyle/program
name: bigorf_extract
version: '1.0'
title: bigorf_extract
description: extract sequences with the largest ORF from a sequence translated with
    EMBOSS transseq and checktrans
authors: E. Deveaud
inputs: !mobyle/inputparagraph
    children:
    - !mobyle/inputprogramparameter
        comment: This is where you should enter the list of candidate ORFs for each
            gene
        prompt: Protein sequences to filter
        format: '" " + value'
        simple: true
        argpos: 2
        name: protein_sequences
        command: false
        type: !mobyle/formattedtype
            format_terms: ['EDAM_format:2200']
            data_terms: ['EDAM_data:2976']
    - !mobyle/inputprogramparameter
        comment: Number of characters that should be stripped. Default value is 4
            because transseq adds 2 characters (_[frame index]) and checktrans another
            2 (_[candidate index])
        prompt: Integer
        format: '" -s %d" % value'
        argpos: 1
        name: characters_to_strip
        command: false
        type: !mobyle/integertype {default: 4}
outputs: !mobyle/outputparagraph
    children:
    - !mobyle/outputprogramparameter
        prompt: Sequence
        filenames: '"bigorf_extract.out"'
        name: protein_sequence_out
        output_type: stdout
        type: !mobyle/formattedtype
            format_terms: ['EDAM_format:2200']
            data_terms: ['EDAM_data:2976']
    - !mobyle/outputprogramparameter
        prompt: Standard error
        filenames: '"bigorf_extract.err"'
        name: stderr
        type: !mobyle/formattedtype
            data_terms: ['EDAM_data:2048']
operations: ['EDAM_operation:0436']
topics: ['EDAM_topic:0108']
command: bigorf_extract.py
env: {}