fastq_to_fasta_0.0.13.yaml

!mobyle/program
name: fastq_to_fasta
version: 0.0.13
title: FASTX Toolkit - FASTQ to FASTA
description: This tool converts FASTQ sequencing reads to FASTA sequences.
authors: Assaf Gordon, Cold Spring Harbor Laboratory
inputs: !mobyle/inputparagraph
    children:
    - !mobyle/inputprogramparameter
        prompt: fastqtofasta
        format: '"fastq_to_fasta"'
        argpos: 0
        name: fastxtoolkit_cmd
        command: false
        hidden: true
        type: !mobyle/stringtype {}
    - !mobyle/inputprogramparagraph
        prompt: Input
        name: Input
        argpos: 1
        children:
        - !mobyle/inputprogramparameter
            prompt: Input file format.
            format: (" " + str(value),"")[value == "fasta" or value =="fastq64"]
            simple: true
            mandatory: true
            name: fasta_or_fastq
            command: false
            type: !mobyle/stringtype
                default: -Q 33
                options:
                - {label: FASTQ (33), value: -Q 33}
                - {label: FASTQ (64), value: fastq64}
                - {label: FASTA, value: fasta}
        - !mobyle/inputprogramparameter
            prompt: 'FASTQ input file (-i):'
            format: '" -i " + str( value )'
            simple: true
            argpos: 9
            mandatory: true
            name: input_data
            command: false
            type: !mobyle/formattedtype
                data_terms: ['EDAM_data:2044']
    - !mobyle/inputprogramparagraph
        prompt: Options
        name: Options
        argpos: 3
        children:
        - !mobyle/inputprogramparameter
            prompt: Rename sequence identifiers to numbers?  (-n)
            format: ('',' -n ')[value]
            argpos: 5
            name: seq_identifies_to_numbers
            command: false
            type: !mobyle/booleantype {default: false}
        - !mobyle/inputprogramparameter
            prompt: Keep sequences with unknown (N) nucleotides? (-r)
            format: ("", " -r ")[value]
            argpos: 4
            name: keep_unknown_nucleotides
            command: false
            type: !mobyle/booleantype {default: false}
    - !mobyle/inputprogramparagraph
        prompt: Output
        name: Output
        argpos: 6
        children:
        - !mobyle/inputprogramparameter
            prompt: Compress output with GZIP? (-z)
            format: ('',' -z ')[value]
            simple: true
            argpos: 6
            name: compress_with_gzip
            command: false
            type: !mobyle/booleantype {default: false}
        - !mobyle/inputprogramparameter
            prompt: 'Enter experiment name (-o):'
            format: (" -o " + str(vdef) , " -o " + str(value))[value is not None]
            simple: true
            argpos: 10
            mandatory: true
            name: output_file
            command: false
            type: !mobyle/stringtype {default: output_data.fa}
outputs: !mobyle/outputparagraph
    children:
    - !mobyle/outputprogramparagraph
        prompt: Output
        name: Output
        argpos: 6
        children:
        - !mobyle/outputprogramparameter
            prompt: Sequence
            filenames: str(output_file)
            name: final_out
            type: !mobyle/formattedtype
                data_terms: ['EDAM_data:2044']
    - !mobyle/outputprogramparameter
        prompt: Standard output
        filenames: '"fastq_to_fasta.out"'
        name: stdout
        output_type: stdout
        type: !mobyle/formattedtype
            data_terms: ['EDAM_data:2048']
    - !mobyle/outputprogramparameter
        prompt: Standard error
        filenames: '"fastq_to_fasta.err"'
        name: stderr
        type: !mobyle/formattedtype
            data_terms: ['EDAM_data:2048']
operations: ['EDAM_operation:0561']
topics: ['EDAM_topic:0220']
env: {}