cuffdiff_1.3.0.yaml

!mobyle/program
name: cuffdiff
version: 1.3.0
title: cuffdiff
description: Cuffdiff is part of Cufflinks. It finds significant changes in transcript
    expression, splicing, and promoter use.
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: '"cuffdiff"'
        argpos: 0
        name: cufflinks_cmd
        command: true
        hidden: true
        type: !mobyle/stringtype {}
    - !mobyle/inputprogramparagraph
        prompt: Input
        name: Input
        argpos: 999
        children:
        - !mobyle/inputprogramparameter
            comment: A transcript annotation file produced by cufflinks, cuffcompare,
                or other source.
            prompt: Transcripts
            format: '" " + str( value )'
            simple: true
            argpos: 30
            mandatory: true
            name: input_0
            command: false
            type: !mobyle/formattedtype
                data_terms: ['EDAM_data:2044']
        - !mobyle/inputprogramparameter
            prompt: Aligned RNA-Sequence reads in SAM/BAM format
            format: '" " + str(value)'
            simple: true
            argpos: 35
            mandatory: true
            name: input_align
            command: false
            type: !mobyle/formattedtype
                data_terms: ['EDAM_data:2044']
        - !mobyle/inputprogramparameter
            prompt: Aligned RNA-Sequence reads in SAM/BAM format (2)
            format: '" " + str(value)'
            simple: true
            argpos: 36
            mandatory: true
            name: input_align2
            command: false
            type: !mobyle/formattedtype
                data_terms: ['EDAM_data:2044']
    - !mobyle/inputprogramparagraph
        prompt: Options
        name: Options
        argpos: 3
        children:
        - !mobyle/inputprogramparameter
            prompt: Value of random number generator seed (--seed)
            format: ('', ' --seed ' + str(value))[value is not None and value != vdef]
            name: seed
            command: false
            type: !mobyle/integertype {default: 0}
        - !mobyle/inputprogramparameter
            comment: Instructs Cuffdiff to analyze the provided samples as a time
                series, rather than testing for differences between all pairs of samples.
                Samples should be provided in increasing time order at the command
                line (e.g first timepoint SAM, second timepoint SAM, etc.)
            prompt: Treat samples as a time-series (-T/--time-series)
            format: ('',' -T ')[value]
            name: time_series
            command: false
            type: !mobyle/booleantype {default: false}
        - !mobyle/inputprogramparameter
            comment: The minimum number of alignments in a locus that is needed to
                conduct significance testing on changes in that locus observed between
                samples. If no testing is performed, changes in the locus are deemed
                not signficant, and the locus' observed changes don't contribute to
                correction for multiple testing. The default is 10 fragment alignments.
            prompt: Minimum number of alignments in a locus for testing (-c/--min-alignment-count)
            format: ('', ' -c ' + str(value))[value is not None and value != vdef]
            name: min_alignment_count
            command: false
            type: !mobyle/integertype {default: 10}
        - !mobyle/inputprogramparameter
            comment: The allowed false discovery rate - the default is 0.05
            prompt: False discovery rate used in testing (--FDR)
            format: ('', ' --FDR ' + str(value))[value is not None and value != vdef]
            name: fdr
            command: false
            type: !mobyle/floattype {default: 0.05}
        - !mobyle/inputprogramparameter
            comment: Tells Cuffdiff to ignore all reads that could have come from
                transcripts in this GTF file. We recommend including any annotated
                rRNA, mitochondrial transcripts, and other abundant transcripts you
                wish to ignore in your analysis in this file. Due to variable efficiency
                of mRNA enrichment methods and rRNA depletion kits, masking these
                transcripts often improves the overall robustness of transcript abundance
                estimates.
            prompt: Ignore all alignment within transcripts in this file (-M/--mask-file)
            format: ('', ' -M ' + str(value))[value is not None]
            simple: true
            name: mask_file
            command: false
            type: !mobyle/formattedtype
                data_terms: ['EDAM_data:2044']
        - !mobyle/inputprogramparameter
            prompt: Use bias correction - reference fasta required (-b/--frag-bias-correct)
            format: ('', ' -b ' + str(value))[value is not None]
            name: frag_bias_correct
            command: false
            type: !mobyle/formattedtype
                data_terms: ['EDAM_data:2044']
        - !mobyle/inputprogramparameter
            comment: Tells Cufflinks to do an initial estimation procedure to more
                accurately weight reads mapping to multiple locations in the genome
            prompt: Use 'rescue method' for multi-reads [more accurate] (-u/--multi-read-correct)
            format: ('',' -u')[value]
            name: multi_read_correct
            command: false
            type: !mobyle/booleantype {default: false}
        - !mobyle/inputprogramparameter
            comment: With this option, Cufflinks normalizes by the upper quartile
                of the number of fragments mapping to individual loci instead of the
                total number of sequenced fragments. This can improve robustness of
                differential expression calls for less abundant genes and transcripts.
            prompt: Use upper-quartile normalization (-N/--upper-quartile-norm)
            format: ("", " -N")[value]
            name: upper_quartile_norm
            command: false
            type: !mobyle/booleantype {default: false}
        - !mobyle/inputprogramparameter
            comment: Specify a label for each sample, which will be included in various
                output files produced by Cuffdiff. This option should have a string
                of comma-delimited names corresponding to the names of the input files.
            prompt: Specify label for each sample (-L/--labels)
            format: ('', ' -L ' + str(value))[value is not None]
            name: label
            command: false
            type: !mobyle/stringtype {}
        - !mobyle/inputprogramparameter
            comment: Use this many threads to align reads - the default is 1
            prompt: Number of threads used during quantification (-p/--num-threads)
            format: ('', ' -p ' + str(value))[value is not None and value != vdef]
            name: num_threads
            command: false
            type: !mobyle/integertype {default: 1}
    - !mobyle/inputprogramparagraph
        prompt: Advanced Options
        name: AdvancedOptions
        children:
        - !mobyle/inputprogramparameter
            prompt: Library type (--library-type)
            format: ('', ' --library-type ' + str(value))[value is not None and value
                != vdef]
            name: library_type
            command: false
            type: !mobyle/stringtype
                default: fr-unstranded
                options:
                - {label: FF First Strand, value: ff-firststrand}
                - {label: FF Second Strand, value: ff-secondstrand}
                - {label: FF Unstranded, value: ff-unstranded}
                - {label: FR First Strand, value: fr-firststrand}
                - {label: FR Second Strand, value: fr-secondstrand}
                - {label: FR Unstranded, value: fr-unstranded}
                - {label: Transfrags, value: transfrags}
        - !mobyle/inputprogramparameter
            comment: 'This is the expected (mean) fragment length. The default is
                200bp. Note: Cufflinks now learns the fragment length mean for each
                SAM file, so using this option is no longer recommended with paired-end
                reads. It is recommended to enter values here if the input BAM file
                is small and using a paired-end alignment file.'
            prompt: Average fragment length [unpaired reads only] (-m/--frag-len-mean)
            format: ('', ' -m ' + str(value))[value is not None and value != vdef]
            name: frag_len_mean
            command: false
            type: !mobyle/integertype {default: 200}
        - !mobyle/inputprogramparameter
            comment: 'The standard deviation for the distribution on fragment lengths.
                The default is 80bp. Note: Cufflinks now learns the fragment length
                standard deviation for each SAM file, so using this option is no longer
                recommended with paired-end reads.'
            prompt: Fragment length standard deviation [unpaired reads only] (-s/--frag-len-std-dev)
            format: ('', ' -s ' + str(value))[value is not None and value != vdef]
            name: frag_len_std_dev
            command: false
            type: !mobyle/floattype {default: 80.0}
        - !mobyle/inputprogramparameter
            comment: 'Sets the number of importance samples generated for each locus
                during abundance estimation. Default: 1000'
            prompt: Number of importance samples for MAP restimation (--num-importance-samples)
            format: ('', ' --number-importance-samples ' + str(value))[value is not
                None and value != vdef]
            name: number_importance_samples
            command: false
            type: !mobyle/integertype {default: 1000}
        - !mobyle/inputprogramparameter
            prompt: Number of bootstrap replications (--num-bootstrap-samples)
            format: ('', ' --num-bootstrap-samples ' + str(value))[value is not None
                and value != vdef]
            name: num_bootstrap_samples
            command: false
            type: !mobyle/integertype {default: 20}
        - !mobyle/inputprogramparameter
            prompt: Fraction of fragments in each bootstrap sample (--bootstrap-fraction)
            format: ('', ' --bootstrap-fraction ' + str(value))[value is not None
                and value != vdef]
            name: bootstrap_fraction
            command: false
            type: !mobyle/floattype {default: 1.0}
        - !mobyle/inputprogramparameter
            comment: Sets the number of iterations allowed during maximum likelihood
                estimation of abundances. The default is 5000.
            prompt: Maximum iterations allowed for MLE calculation (--max-mle-iterations)
            format: ('', ' --max-mle-iterations ' + str(value))[value is not None
                and value != vdef]
            name: max_mle_iterations
            command: false
            type: !mobyle/integertype {default: 5000}
        - !mobyle/inputprogramparameter
            prompt: Count hits compatible with reference RNAs only (--compatible-hits-norm)
            format: ('',' --compatible-hits-norm')[value]
            name: compatible_hits_norm
            command: false
            type: !mobyle/booleantype {default: false}
        - !mobyle/inputprogramparameter
            comment: With this option, Cufflinks counts all fragments, including those
                not compatible with any reference transcript, towards the number of
                mapped fragments used in the FPKM denominator. This option can be
                combined with -N/--upper-quartile-norm. It is inactive by default.
            prompt: Count all hits for normalization (--total-hits-norm)
            format: ('',' --total-hits-norm')[value]
            name: total_hits_norm
            command: false
            type: !mobyle/booleantype {default: false}
        - !mobyle/inputprogramparameter
            comment: Use the Poisson fragment dispersion model instead of learning
                one in each condition
            prompt: Don't fit fragment counts for overdispersion? (--poisson-dispersion)
            format: ('',' --poisson-dispersion')[value]
            name: poisson_dispersion
            command: false
            type: !mobyle/booleantype {default: false}
        - !mobyle/inputprogramparameter
            comment: Cuffdiff will output a file for each condition (called <sample>_counts.txt)
                containing the fragment counts, fragment count variances, and fitted
                variance model
            prompt: Print count tables used to fit overdispersion (--emit-count-tables)
            format: ('',' --emit-count-tables')[value]
            name: emit_count_tables
            command: false
            type: !mobyle/booleantype {default: false}
        - !mobyle/inputprogramparameter
            prompt: Maximum fragments allowed in a bundle before skipping (--max-bundle-frags)
            format: ('', ' --max-bundle-frags ' + str(value))[value is not None and
                value != vdef]
            name: max_bundle_frags
            command: false
            type: !mobyle/integertype {default: 500000}
    - !mobyle/inputprogramparameter
        comment: Sets the name of the directory in which Cufflinks will write all
            of its output. The default is "./".
        prompt: Enter experiment name (-o)
        format: ''' -o ./'''
        name: output_dir
        command: false
        hidden: true
        type: !mobyle/stringtype {}
outputs: !mobyle/outputparagraph
    children:
    - !mobyle/outputprogramparameter
        prompt: FPKM tracking file 1
        filenames: '"*.count_tracking"'
        name: result_files
        type: !mobyle/formattedtype
            data_terms: ['EDAM_data:2048']
    - !mobyle/outputprogramparameter
        prompt: Standard output
        filenames: '"cuffdiff.out"'
        name: stdout
        output_type: stdout
        type: !mobyle/formattedtype
            data_terms: ['EDAM_data:2048']
    - !mobyle/outputprogramparameter
        prompt: Standard error
        filenames: '"cuffdiff.err"'
        name: stderr
        type: !mobyle/formattedtype
            data_terms: ['EDAM_data:2048']
operations: ['EDAM_operation:2495']
topics: ['EDAM_topic:0203']
env: {}