cuffmerge_1.3.0.yaml

!mobyle/program
name: cuffmerge
version: 1.3.0
title: Cuffmerge
description: Cuffmerge takes two or more Cufflinks GTF files and merges them into
    a single unified transcript catalog.  Optionally, you can provide the script with
    a reference GTF, and the script will use it to attach gene names and other metadata
    to the merged catalog.
authors: Trapnell C., Williams B.A., Pertea G., Mortazavi A.M., Kwan G., van Baren
    M.J., Salzberg S.L., Wold B. & Pachter L.
inputs: !mobyle/inputparagraph
    children:
    - !mobyle/inputprogramparameter
        prompt: Initial command
        format: '"cuffmerge"'
        argpos: 1
        name: cufflinks_cmd
        command: true
        hidden: true
        type: !mobyle/stringtype {}
    - !mobyle/inputprogramparagraph
        prompt: Input
        name: Input
        children:
        - !mobyle/inputprogramparameter {comment: 'Provide the GTF files that you
                want in the text file "manifest", which lists the GTF files that you''d
                like to merge together into a single GTF file.', prompt: GTF manifest
                file, format: '" echo -e "+"\\\\n".join(value) + " > manifest.txt
                && "', simple: true, argpos: 0, mandatory: true, name: assembly_GTF_list,
            command: false}
        - !mobyle/inputprogramparameter
            prompt: Add manifest
            format: '" manifest.txt"'
            argpos: 50
            name: manifest_file
            command: false
            hidden: true
            type: !mobyle/stringtype {}
    - !mobyle/inputprogramparagraph
        prompt: Options
        name: Options
        argpos: 3
        children:
        - !mobyle/inputprogramparameter
            comment: An optional "reference" annotation GTF.
            prompt: Use Reference Annotation(-g/--ref-gtf)
            format: (""," -g " + str(value))[value is not None and value != "upload"]
            simple: true
            name: use_reference_annotation
            command: false
            type: !mobyle/stringtype
                default: 'null'
                options:
                - {label: Choose a genome annotation, value: 'null'}
        - !mobyle/inputprogramparameter
            comment: Genomic DNA sequences for the reference.
            prompt: Upload reference annotation
            format: (""," -g " + str(value))[value is not None]
            simple: true
            name: annotation_data
            precond: {use_reference_annotation: upload}
            command: false
            type: !mobyle/formattedtype
                data_terms: ['EDAM_data:2044']
        - !mobyle/inputprogramparameter
            comment: Use sequence data for some optional classification functions
            prompt: Use Sequence Data
            format: (""," -s " + str(value))[value is not None and value != "upload"]
            simple: true
            name: use_sequence_data
            command: false
            type: !mobyle/stringtype
                default: 'null'
                options:
                - {label: Choose a genome, value: 'null'}
        - !mobyle/inputprogramparameter
            comment: Genomic DNA sequences for the reference. Upload zip file if you
                are referencing multiple files
            prompt: Upload reference sequences
            format: (""," -s " + str(value))[value is not None]
            simple: true
            name: sequence_data
            precond: {use_sequence_data: upload}
            command: false
            type: !mobyle/formattedtype
                data_terms: ['EDAM_data:2044']
        - !mobyle/inputprogramparameter
            comment: 'Discard isoforms with abundance below this. Range: 0-1.0'
            prompt: Minimum isoform fraction
            format: ('', ' --min-isoform-fraction ' + str(value))[value is not None
                and value != vdef]
            name: min_frac
            command: false
            type: !mobyle/floattype {default: 0.05}
        - !mobyle/inputprogramparameter
            comment: Use this many threads to merge assemblies. - the default is 1
            prompt: Number of threads used during merge assemblies (-p/--num-threads)
            format: '" -p 5"'
            name: num_threads
            command: false
            hidden: true
            type: !mobyle/integertype {}
    - !mobyle/inputprogramparameter
        comment: 'Sets the Directory where merged assembly will be written  [ default:
            ./merged_asm  ]'
        prompt: Enter experiment name (-o)
        format: '" -o ./"'
        name: output_dir
        command: false
        hidden: true
        type: !mobyle/stringtype {}
outputs: !mobyle/outputparagraph
    children:
    - !mobyle/outputprogramparameter
        prompt: out GTF
        filenames: '"merged.gtf"'
        name: out_file
        type: !mobyle/formattedtype
            data_terms: ['EDAM_data:2044']
    - !mobyle/outputprogramparameter
        prompt: Standard output
        filenames: '"cuffmerge.out"'
        name: stdout
        output_type: stdout
        type: !mobyle/formattedtype
            data_terms: ['EDAM_data:2048']
    - !mobyle/outputprogramparameter
        prompt: Standard error
        filenames: '"cuffmerge.err"'
        name: stderr
        type: !mobyle/formattedtype
            data_terms: ['EDAM_data:2048']
env: {}