cufflinks_1.3.0.yaml

!mobyle/program
name: cufflinks
version: 1.3.0
title: Cufflinks
description: Cufflinks assembles transcripts, estimates their abundances, and tests
    for differential expression and regulation in RNA-Sequence samples. It accepts
    aligned RNA-Sequence reads and assembles the alignments into a parsimonious set
    of transcripts. Cufflinks then estimates the relative abundances of these transcripts
    based on how many reads support each one.
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/inputprogramparagraph
        prompt: Input
        name: Input
        argpos: 999
        children:
        - !mobyle/inputprogramparameter
            comment: Supply the SAM/BAM format file. you can use the accepted.bam
                file from tophat
            prompt: 'Aligned reads file (BAM/SAM format):'
            format: '" " + str( value )'
            simple: true
            argpos: 40
            mandatory: true
            name: input_align
            command: false
            type: !mobyle/formattedtype
                data_terms: ['EDAM_data:2044']
    - !mobyle/inputprogramparagraph
        prompt: Options
        name: Options
        argpos: 3
        children:
        - !mobyle/inputprogramparameter
            prompt: Number of threads to run
            format: ''' -p 5'''
            name: num_threads
            command: false
            hidden: true
            type: !mobyle/integertype {}
        - !mobyle/inputprogramparameter
            comment: Tells Cufflinks to use the supplied reference annotation (a GFF
                file) to estimate isoform expression. It will not assemble novel transcripts,
                and the program will ignore alignments not structurally compatible
                with any reference transcript.
            prompt: Quantitate against reference transcript annotations (-G/--GTF)
                <reference_annotation.(gtf/gff)>
            format: ("", " -G " + str(value)) [value is not None]
            name: gtf_annotation
            command: false
            type: !mobyle/formattedtype
                data_terms: ['EDAM_data:2044']
        - !mobyle/inputprogramparameter
            comment: Tells Cufflinks to use the supplied reference annotation (GFF)
                to guide RABT assembly. Reference transcripts will be tiled with faux-reads
                to provide additional information in assembly. Output will include
                all reference transcripts as well as any novel genes and isoforms
                that are assembled.
            prompt: Use reference transcript annotation to guide assembly (-g/--GTF-guide)
            format: ("", " -g " + str(value)) [value is not None]
            name: guide_reference_annotation
            command: false
            type: !mobyle/formattedtype
                data_terms: ['EDAM_data:2044']
        - !mobyle/inputprogramparameter
            comment: Tells Cufflinks to ignore all reads that could have come from
                transcripts in this GTF file. We recommend including any annotated
                rRNA, mitochondrial transcripts 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]
            name: mask_file
            command: false
            type: !mobyle/formattedtype
                data_terms: ['EDAM_data:2044']
        - !mobyle/inputprogramparameter
            comment: Providing Cufflinks with a multifasta file via this option instructs
                it to run our new bias detection and correction algorithm which can
                significantly improve accuracy of transcript abundance estimates.
            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: "In cases where Cufflinks cannot determine the platform and protocol\
                \ used to generate input reads, you can supply this information manually,\
                \ which will allow Cufflinks to infer source strand information with\
                \ certain protocols. The available options are listed below. For paired-end\
                \ data, we currently only support protocols where reads are point\
                \ towards each other. 1) fr-unstranded (default, e.g. Standard Illumina):\
                \ Reads from the left-most end of the fragment (in transcript coordinates)\
                \ map to the transcript strand, and the right-most end maps to the\
                \ opposite strand.  2) fr-firststrand (e.g. dUTP, NSR, NNSR): Same\
                \ as above except we enforce the rule that the right-most end of the\
                \ fragment (in transcript coordinates) is the first sequenced (or\
                \ only sequenced for single-end reads). Equivalently, it is assumed\
                \ that only the strand generated during first strand synthesis is\
                \ sequenced. 3) fr-secondstrand\t(e.g. Directional Illumina (Ligation),\
                \ Standard SOLiD): Same as above except we enforce the rule that the\
                \ left-most end of the fragment (in transcript coordinates) is the\
                \ first sequenced (or only sequenced for single-end reads). Equivalently,\
                \ it is assumed that only the strand generated during second strand\
                \ synthesis is sequenced."
            prompt: Library used for input reads (--library-type)
            format: ("", " --library-type " + str(value)) [value is not None]
            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/inputprogramparagraph
        prompt: Abundance Estimation Options
        name: EstimationOptions
        children:
        - !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 std 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/integertype {default: 80}
        - !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: ("", " -option_quartile_norm")[value]
            argpos: 7
            name: upper_quartile_norm
            command: false
            type: !mobyle/booleantype {default: false}
        - !mobyle/inputprogramparameter
            comment: 'Sets the number of iterations allowed during maximum likelihood
                estimation of abundances. Default: 5,000'
            prompt: Maximum iterations allowed for MLE calculation (--max-mle-iterations)
            format: ("", " --max-mle-iterations " + str(value)) [value is not None]
            name: max_mle_iterations
            command: false
            type: !mobyle/integertype {default: 5000}
        - !mobyle/inputprogramparameter
            prompt: Number of importance samples for MAP estimation (--num-importance-samples)
            format: ('', ' --num-importance-samples ' + str(value))[value is not None
                and value != vdef]
            name: num_importance_samples
            command: false
            type: !mobyle/integertype {default: 1000}
        - !mobyle/inputprogramparameter
            comment: With this option, Cufflinks counts only those fragments compatible
                with some reference transcript towards the number of mapped hits used
                in the FPKM denominator. This option can be combined with -N/--upper-quartile-norm.
                It is inactive by default, and can only be used in combination with
                --GTF. Use with either RABT or ab initio assembly is not supported.
            prompt: Count hits compatible with reference RNAs only (--compatible-hits-norm)
            format: ("", " --compatible-hits-norm")[value]
            name: compatible_hits_norm
            precond:
                gtf_annotation: {'#ne': None}
            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 hits used in the FPKM denominator. This option can be combined
                with -N/--upper-quartile-norm. It is active 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/inputprogramparagraph
        prompt: Assembly Options
        name: AssemblyOptions
        children:
        - !mobyle/inputprogramparameter
            comment: Cufflinks will report transfrags in GTF format, with a prefix
                given by this option. The default prefix is "CUFF".
            prompt: Assembled transcripts have this iD prefix (-L/--label)
            format: ("", " -L " + str(value)) [value is not None and value != vdef]
            name: label
            command: false
            type: !mobyle/stringtype {default: CUFF}
        - !mobyle/inputprogramparameter
            comment: After calculating isoform abundance for a gene, Cufflinks filters
                out transcripts that it believes are very low abundance, because isoforms
                expressed at extremely low levels often cannot reliably be assembled,
                and may even be artifacts of incompletely spliced precursors of processed
                transcripts. This parameter is also used to filter out introns that
                have far fewer spliced alignments supporting them. The default is
                0.1, or 10% of the most abundant isoform (the major isoform) of the
                gene.
            prompt: Suppress transcripts below this abundance level (-F/--min-isoform-fraction,
                <0.0-1.0>)
            format: ("" , " -F "+str(value) )[value is not None and value != vdef]
            argpos: 5
            name: max_isoform_frac
            command: false
            type: !mobyle/floattype {default: 0.1}
            ctrls:
            -   message: requires a float value between 0.0 and 1.0
                test:
                    '#and':
                    -   value: {'#gte': '0.0'}
                    -   value: {'#lte': '1.0'}
        - !mobyle/inputprogramparameter
            comment: Some RNA-Seq protocols produce a significant amount of reads
                that originate from incompletely spliced transcripts, and these reads
                can confound the assembly of fully spliced mRNAs. Cufflinks uses this
                parameter to filter out alignments that lie within the intronic intervals
                implied by the spliced alignments. The minimum depth of coverage in
                the intronic region covered by the alignment is divided by the number
                of spliced reads, and if the result is lower than this parameter value,
                the intronic alignments are ignored. The default is 15%.
            prompt: Suppress intra-intronic transcripts below this level (-j/--pre-mrna-fraction,
                <0.0-1.0>)
            format: ("" , " -j "+str(value) )[value is not None and value != vdef]
            argpos: 6
            name: opt_pre_mrna_frac
            command: false
            type: !mobyle/floattype {default: 0.15}
            ctrls:
            -   message: requires a float value between 0.0 and 1.0
                test:
                    '#and':
                    -   value: {'#gte': '0.0'}
                    -   value: {'#lte': '1.0'}
        - !mobyle/inputprogramparameter
            comment: The maximum intron length. Cufflinks will not report transcripts
                with introns longer than this, and will ignore SAM alignments with
                REF_SKIP CIGAR operations longer than this. The default is 300,000.
            prompt: Ignore alignments with gaps longer than this (-I/--max-intron-length)
            format: ("" , " -I "+str(value) )[value is not None and value != vdef]
            argpos: 4
            name: option_max_intron
            command: false
            type: !mobyle/integertype {default: 300000}
        - !mobyle/inputprogramparameter
            comment: 'The alpha value for the binomial test used during false positive
                spliced alignment filtration. Default: 0.001'
            prompt: Alpha for junction binomial test filter (-a/--junc-alpha, <0.0-1.0>
            format: ("", " -a " + str(value)) [value is not None and value != vdef]
            name: junc_alpha
            command: false
            type: !mobyle/floattype {default: 0.001}
            ctrls:
            -   message: requires a float value between 0.0 and 1.0
                test:
                    '#and':
                    -   value: {'#gte': '0.0'}
                    -   value: {'#lte': '1.0'}
        - !mobyle/inputprogramparameter
            comment: 'Spliced reads with less than this percent of their length on
                each side of the junction are considered suspicious and are candidates
                for filtering prior to assembly. Default: 0.09.'
            prompt: Percent read overhang taken as suspiciously small (-A/--small-anchor-fraction,
                <0.0-1.0>)
            format: ("", " -A " + str(value)) [value is not None and value != vdef]
            name: small_anchor_fraction
            command: false
            type: !mobyle/floattype {default: 0.09}
            ctrls:
            -   message: requires a float value between 0.0 and 1.0
                test:
                    '#and':
                    -   value: {'#gte': '0.0'}
                    -   value: {'#lte': '1.0'}
        - !mobyle/inputprogramparameter
            comment: 'Assembled transfrags supported by fewer than this many aligned
                RNA-Seq fragments are not reported. Default: 10.'
            prompt: Minimum number of fragments needed For new transfrags (--min-frags-per-transfrag)
            format: ("", " --min-frags-per-transfrag " + str(value)) [value is not
                None and value != vdef]
            name: min_frags
            command: false
            type: !mobyle/integertype {default: 10}
        - !mobyle/inputprogramparameter
            comment: The number of bp allowed to enter the intron of a transcript
                when determining if a read or another transcript is mappable to/compatible
                with it. The default is 8 bp based on the default bowtie/TopHat parameters.
            prompt: Number of terminal exon bp to tolerate in introns (--overhang-tolerance)
            format: ("", " --overhang-tolerance " + str(value)) [value is not None
                and value != vdef]
            name: overhang_tolerance
            command: false
            type: !mobyle/integertype {default: 8}
        - !mobyle/inputprogramparameter
            comment: Maximum genomic length allowed for a given bundle. The default
                is 3,500,000 bp.
            prompt: Maximum genomic length allowed for a given bundle (--max-bundle-length)
            format: ("", " --max-bundle-length " + str(value)) [value is not None
                and value != vdef]
            name: max_bundle_length
            command: false
            type: !mobyle/integertype {default: 3500000}
        - !mobyle/inputprogramparameter
            comment: 'Sets the maximum number of fragments a locus may have before
                being skipped. Skipped loci are listed in skipped.gtf. Default: 1,000,000'
            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: Minimum intron size allowed in genome. The default is 50 bp.
            prompt: Minimum intron size allowed in genome (--min-intron-length)
            format: ("", " --min-intron-length " + str(value)) [value is not None
                and value != vdef]
            name: min_intron_length
            command: false
            type: !mobyle/integertype {default: 50}
        - !mobyle/inputprogramparameter
            comment: Minimum average coverage required to attempt 3' trimming. The
                default is 10.
            prompt: Minimum average coverage required to attempt 3' trimming (--trim-3-avgcov-thresh)
            format: ("", " --trim-3-avgcov-thresh " + str(value)) [value is not None
                and value != vdef]
            name: avgcov_thresh
            command: false
            type: !mobyle/integertype {default: 10}
        - !mobyle/inputprogramparameter
            comment: The fraction of average coverage below which to trim the 3' end
                of an assembled transcript. The default is 0.1.
            prompt: Fraction of average coverage below which to trim 3' end (--trim-3-dropoff-frac)
            format: ("", " --trim-3-dropoff-frac " + str(value)) [value is not None
                and value != vdef]
            name: dropoff_frac
            command: false
            type: !mobyle/floattype {default: 0.1}
    - !mobyle/inputprogramparagraph
        prompt: Reference Annotation Based Transcript (RABT) Assembly Options
        name: ReferenceBasedAssemblyOptions
        children:
        - !mobyle/inputprogramparameter
            comment: This option disables tiling of the reference transcripts with
                faux reads. Use this if you only want to use sequencing reads in assembly
                but do not want to output assembled transcripts that lay within reference
                transcripts. All reference transcripts in the input annotation will
                also be included in the output.
            prompt: Disable tiling by faux reads (--no-faux-reads)
            format: ("", " --no-faux-reads")[value]
            name: no_faux_reads
            command: false
            type: !mobyle/booleantype {default: false}
        - !mobyle/inputprogramparameter
            comment: The number of bp allowed to overhang the 3' end of a reference
                transcript when determining if an assembled transcript should be merged
                with it (ie, the assembled transcript is not novel). The default is
                600 bp.
            prompt: Overhang allowed on 3' end when merging with reference (--3-overhang-tolerance)
            format: ("", " --3-overhang-tolerance " + str(value)) [value is not None
                and value != vdef]
            name: three_overhang_tolerance
            command: false
            type: !mobyle/integertype {default: 600}
        - !mobyle/inputprogramparameter
            comment: The number of bp allowed to enter the intron of a reference transcript
                when determining if an assembled transcript should be merged with
                it (ie, the assembled transcript is not novel). The default is 50
                bp.
            prompt: Overhang allowed inside reference intron when merging (--intron-overhang-tolerance)
            format: ("", " --intron-overhang-tolerance " + str(value)) [value is not
                None and value != vdef]
            name: intron_overhang_tolerance
            command: false
            type: !mobyle/integertype {default: 30}
    - !mobyle/inputprogramparagraph
        prompt: Output
        name: output2
        argpos: 12
        children:
        - !mobyle/inputprogramparameter
            comment: Sets the name of the directory in which Cufflinks will write
                all of its output. The default is "./".
            prompt: Write all output files to this directory (-o)
            format: '" -o ./"'
            name: output_dir
            command: false
            hidden: true
            type: !mobyle/stringtype {}
outputs: !mobyle/outputparagraph
    children:
    - !mobyle/outputprogramparagraph
        prompt: Output
        name: output2
        argpos: 12
        children:
        - !mobyle/outputprogramparameter
            prompt: GTF Out
            filenames: '"transcripts.gtf"'
            name: gtf_out
            type: !mobyle/formattedtype
                data_terms: ['EDAM_data:2044']
        - !mobyle/outputprogramparameter
            prompt: Isoforms tracking file
            filenames: '"isoforms.fpkm_tracking"'
            name: iso_track
            type: !mobyle/formattedtype
                data_terms: ['EDAM_data:2048']
        - !mobyle/outputprogramparameter
            prompt: FPKM tracking file
            filenames: '"genes.fpkm_tracking"'
            name: fpkm_track
            type: !mobyle/formattedtype
                data_terms: ['EDAM_data:2048']
    - !mobyle/outputprogramparameter
        prompt: Standard output
        filenames: '"cufflinks.out"'
        name: stdout
        output_type: stdout
        type: !mobyle/formattedtype
            data_terms: ['EDAM_data:2048']
    - !mobyle/outputprogramparameter
        prompt: Standard error
        filenames: '"cufflinks.err"'
        name: stderr
        type: !mobyle/formattedtype
            data_terms: ['EDAM_data:2048']
operations: ['EDAM_operation:2495']
topics: ['EDAM_topic:0203']
command: cufflinks
env: {}