detect_cnv.yaml

!mobyle/program
name: detect_cnv
title: detect_cnv
description: Copy Number Variation (CNV) detection from signal intensity data (Illumina
    file)
inputs: !mobyle/inputparagraph
    children:
    - !mobyle/inputprogramparagraph
        prompt: Preprocessing of Illumina intensity file for Copy Number Variation
            (CNV) detection
        name: preprocess
        children:
        - !mobyle/inputprogramparameter {comment: "The input signal intensity file\
                \ is a text file that contains information for one marker per\n  \
                \                       line, and all fields in each line are tab-delimitedThe\
                \ first line of the file specifies the meaning for each tab-delimited\
                \ column. \n        For example, there are six fields in each line\
                \ in the file, corresponding to SNP name, chromosome, \n        position,\
                \ genotype, Log R Ratio (LRR) and B Allele Frequency (BAF), respectively.The\
                \ CNV calling only requires the SNP Name, LRR and BAF values. Note\
                \ that the relative position\n        of LRR and BAF is different\
                \ from the previous file; again the header line tells the program\
                \ that the \n        second column represents BAF values, yet the\
                \ third column is LRR values.", prompt: Input  signal intensity file,
            format: '" " + str(value)', simple: true, argpos: 1, mandatory: true,
            name: infile, command: false}
        - !mobyle/inputprogramparameter
            prompt: Number of tab-delimited column (field) per individual genotyping
                in intensity file
            format: '" split " + str(value) + " -heading 3 --name_by_header -tab --out
                "+ str(infile)'
            simple: true
            argpos: 2
            mandatory: true
            name: split
            command: false
            type: !mobyle/integertype {}
    - !mobyle/inputprogramparagraph
        prompt: Penncnv analyses
        name: analyse
        argpos: 10
        children:
        - !mobyle/inputprogramparameter
            comment: "--test: test a signal intensity file to generate CNV calls.--joint:\
                \ New in July 2008: generate CNV calls for a father-mother-off-\n\
                \               spring trio via a one-step procedure. It is considerably\
                \ slower\n               than the --trio argument, but generates more\
                \ accurate CNV calls\n               with reduced false negative rates\
                \ in simulation studies.--summary:   generate summary statistics on\
                \ signal quality for each input\n               file. Usually the\
                \ summary is provided when calling CNVs and can\n               be\
                \ written to a log file via the --log argument; however, some-\n \
                \              times users forget to use --log, such that the signal\
                \ quality\n               information is lost. The --summary argument\
                \ can calculate the\n               signal quality again quickly without\
                \ calling CNVs."
            prompt: Analyse type without cnv calls file
            format: ( "" , " && detect_cnv.pl " + str(value) )[ value is not None
                and value !=vdef]
            simple: true
            name: type
            command: false
            type: !mobyle/stringtype
                default: 'null'
                options:
                - {label: Choice, value: 'null'}
                - {label: Individual-based CNV calling (test), value: --test}
                - {label: Joint CNV calls for trio (joint), value: --joint}
                - {label: Validate copy number at a pre-specified region (validate),
                    value: --validate}
                - {label: Summary statistics on signal quality (summary), value: --summary}
        - !mobyle/inputprogramparameter
            comment: "--trio:  generate CNV calls for a father-mother-offspring trio,\
                \ given a\n               CNV file containing calls generated on each\
                \ individual separately, a HMM model file, a PFB file, and the three\
                \ signal\n               intensity files.--quartet:    jointly generate\
                \ CNV calls for a father-mother-offspring1-offp-\n               spring2\
                \ quartet, given a CNV file containing calls generated on\n      \
                \         each individual separately, a HMM model file, a PFB file,\
                \ and\n               the four signal intensity files.--cctest: perform\
                \ a case-control test on the frequency of having CNVs for\n      \
                \         each marker within CNVs. A separate phenotype file must\
                \ be\n               specified via the --phenofile argument for this\
                \ to work. The\n               actual test is a two-sided Fisher exact\
                \ test. The --onesided\n               argument can be specified for\
                \ performing one-sided test, and\n               the --type_filter\
                \ argument can be specified so that only \"dup\"\n               or\
                \ \"del\" is compared between cases and controls.--exclude_heterosomic:\
                \ exclude CNV calls from chromosomes showing evidence of heterosomic\
                \ abberations from a given file containing CNV calls. An\n       \
                \        purely empirical method is applied in this procedure, although\n\
                \               I recommended always manually examine the patterns\
                \ of BAF to\n               determine whether heterosomic abberation\
                \ is present in a particular sample, if the sample size is relatively\
                \ small (<100)."
            prompt: Analyse type with cnv calls file
            format: ( "" , " && detect_cnv.pl " + str(value) )[ value is not None
                and value !=vdef]
            simple: true
            argpos: 10
            name: rawcnv
            command: false
            type: !mobyle/stringtype
                default: 'null'
                options:
                - {label: Choice, value: 'null'}
                - {label: Trio-based CNV calling (trio), value: --trio}
                - {label: Posterior CNV calls for quartet (quartet), value: --quartet}
                - {label: Case-control comparison of per-marker CNV frequency (cctest),
                    value: --cctest}
                - {label: Empirically exclude CNVs in heterosomic chromosomes (exclude_heterosomic),
                    value: --exclude_heterosomic}
        - !mobyle/inputprogramparameter
            comment: Specify an output file prefix.
            prompt: Input file name
            format: '" " + infile + ".*"'
            argpos: 18
            name: infile_name
            precond:
                '#or':
                - {type: --test}
                - {type: --joint}
                - {type: --validate}
                - {type: --summary}
                - {rawcnv: --trio}
                - {rawcnv: --quartet}
                - {rawcnv: --cctest}
                - {rawcnv: --exclude_heterosomic}
            command: false
            hidden: true
            type: !mobyle/stringtype {}
        - !mobyle/inputprogramparameter
            comment: "A file containing CNV calls, that could be generated by the\n\
                \               -test operation of this program: trio, quartet, exclude_heterosomic,\
                \ cctest"
            prompt: CNV calls file (cnv)
            format: ( "" , " --cnv " + str(value) )[ value is not None]
            simple: true
            argpos: 12
            name: cnvfile
            precond:
                rawcnv: {'#ne': None}
            command: false
        - !mobyle/inputprogramparameter
            comment: "Specify an output file prefix. By default the output filename\n\
                \               starts with \"gengen\"."
            prompt: Output CNV file name
            format: '" --out " + infile + "_rawcnv "'
            argpos: 12
            name: out_cnv_filename
            precond:
                '#and':
                - {type: --test}
                - infile
            command: false
            hidden: true
            type: !mobyle/stringtype {}
        - !mobyle/inputprogramparameter
            comment: "Specify a HMM model file containing elements necessary for\n\
                \               specifying the hidden Markov model for CNV calling:\
                \ test, validate, joint, trio, quartet"
            prompt: HMM model (hmm)
            format: ( "" , " --hmm /path/to/penncnv/executables/dir/" + str(value)
                )[ value is not None]
            simple: true
            argpos: 11
            mandatory: true
            name: hmmmodel
            precond:
                '#and':
                -   '#or':
                    -   type: {'#ne': None}
                    -   rawcnv: {'#ne': None}
                -   '#and':
                    -   type: {'#ne': --summary}
                    -   '#and':
                        -   rawcnv: {'#ne': --cctest}
                        -   rawcnv: {'#ne': --exclude_heterosomic}
            command: false
            type: !mobyle/stringtype
                default: 'null'
                options:
                - {label: Choose an HMM model, value: 'null'}
                - {label: hhall.hmm, value: hhall.hmm}
                - {label: hh550.hmm, value: hh550.hmm}
        - !mobyle/inputprogramparameter
            comment: "A population frequency of B allele file containing chromosome\n\
                \               coordinates of each SNP, as well as the frequency\
                \ of B allele\n               in a large reference population for\
                \ this SNP: test, validate, joint, summary, trio, quartet, cctest"
            prompt: Population frequency for B allelel file (pfb)
            format: ( "" , " --pfb /path/to/penncnv/shared/data/dir/" + str(value)
                )[ value is not None]
            simple: true
            argpos: 11
            mandatory: true
            name: pfb
            precond:
                '#and':
                -   '#or':
                    -   type: {'#ne': None}
                    -   rawcnv: {'#ne': None}
                -   rawcnv: {'#ne': --exclude_heterosomic}
            command: false
            type: !mobyle/stringtype
                default: 'null'
                options:
                - {label: Choose an population frequency, value: 'null'}
                - {label: hhall.hg18.pfb, value: hhall.hg18.pfb}
                - {label: hh550.hg18.pfb, value: hh550.hg18.pfb}
                - {label: hc12v1.hg18.pfb, value: hc12v1.hg18.pfb}
                - {label: ho1v1.hg18.pfb, value: ho1v1.hg18.pfb}
        - !mobyle/inputprogramparameter
            comment: "A file that contains the GC percentage in the 1Mb region around\n\
                \               each marker for the GC-model based signal adjustment:\
                \ test, joint, validate, trio, quartet"
            prompt: A file containing GC model for wave adjustment (gcmodel)
            format: ( "" , " --gcmodel /path/to/penncnv/shared/data/dir/" + str(value)
                )[ value is not None]
            simple: true
            argpos: 12
            name: gcmodel
            precond:
                '#or':
                -   '#or':
                    - {type: --test}
                    - {type: --joint}
                    - {type: --validate}
                -   '#or':
                    - {rawcnv: --trio}
                    - {rawcnv: --quartet}
            command: false
            type: !mobyle/stringtype
                default: 'null'
                options:
                - {label: Choose an GC model, value: 'null'}
                - {label: hhall.hg18.gcmodel, value: hhall.hg18.gcmodel}
                - {label: hh550.hg18.gcmodel, value: hh550.hg18.gcmodel}
                - {label: hc12v1.hg18.gcmodel, value: hc12v1.hg18.gcmodel}
                - {label: ho1v1.hg18.gcmodel, value: ho1v1.hg18.gcmodel}
    - !mobyle/inputprogramparagraph
        prompt: CNV output format
        name: cnvoutput
        argpos: 20
        children:
        - !mobyle/inputprogramparameter
            prompt: Output format
            format: ( "" , " && visualize_cnv.pl --format %s " % str(value) )[ value
                is not None and value !=vdef]
            name: outputformat
            precond:
                '#or':
                -   type: {'#ne': None}
                -   rawcnv: {'#ne': None}
            command: false
            type: !mobyle/stringtype
                default: output
                options:
                - {label: Program output format, value: output}
                - {label: BED format, value: bed}
                - {label: TAB format, value: tab}
        - !mobyle/inputprogramparameter
            prompt: Output file name for visualize_cnv (.rawcnv)
            format: '" --out " + infile + "_" + outputformat + "cnv " + infile + "_rawcnv
                "'
            argpos: 21
            name: bed_cnv_infile
            precond:
                '#and':
                - {type: --test}
                - infile
                -   outputformat: {'#ne': output}
            command: false
            hidden: true
            type: !mobyle/stringtype {}
        - !mobyle/inputprogramparameter
            prompt: Output file name for visualize_cnv (.out)
            format: '" --out " +  infile + "_" + outputformat + " detect_cnv.out "'
            argpos: 21
            name: bed_infile
            precond:
                '#and':
                -   '#or':
                    -   type: {'#ne': None}
                    -   rawcnv: {'#ne': None}
                -   type: {'#ne': --test}
                -   outputformat: {'#ne': output}
            command: false
            hidden: true
            type: !mobyle/stringtype {}
    - !mobyle/inputprogramparagraph
        prompt: CNV output control
        name: cnvcontrol
        argpos: 12
        children:
        - !mobyle/inputprogramparameter
            comment: "The minimum number of SNPs that a CNV call must contain to be\n\
                \               in output: test, joint, validate, trio, quartet"
            prompt: Minimum number of SNPs within CNV (minsnp)
            format: ( "" , " --minsnp " + str(value) )[ value is not None and value
                != vdef]
            name: minsnp
            precond:
                '#or':
                - {type: --test}
                - {rawcnv: --trio}
                - {rawcnv: --quartet}
                - {type: --joint}
                - {type: --validate}
            command: false
            type: !mobyle/integertype {default: 3}
        - !mobyle/inputprogramparameter
            comment: "The minimum length of base pairs that a CNV call must contain\n\
                \               to be in output: test, joint, validate, trio, quartet"
            prompt: Minimum length of bp within CNV (minlength)
            format: ( "" , " --minlength " + str(value) )[ value is not None ]
            name: minlength
            precond:
                '#or':
                - {type: --test}
                - {rawcnv: --trio}
                - {rawcnv: --quartet}
                - {type: --joint}
                - {type: --validate}
            command: false
            type: !mobyle/integertype {}
        - !mobyle/inputprogramparameter
            comment: "Minimum confidence score for a CNV call to\n               be\
                \ in output. This is an experimental feature, and the\n          \
                \     actual definition of \"confidence score\" may change in\n  \
                \             the future: test, validate"
            prompt: Minimum confidence score of CNV (minconf)
            format: ( "" , " --minconf " + str(value) )[ value is not None ]
            name: minconf
            precond:
                '#or':
                - {type: --test}
                - {type: --validate}
            command: false
            type: !mobyle/integertype {}
        - !mobyle/inputprogramparameter
            comment: "Calculate a confidence score for each CNV call. This is an\n\
                \               experimental feature, and the actual definition of\
                \ \"confidence\n               score\" may change in the future: test,\
                \ validate"
            prompt: Calculate confidence for each CNV (confidence)
            format: ( "" , " --confidence " )[ value ]
            name: confidence
            precond:
                '#or':
                - {type: --test}
                - {type: --validate}
            command: false
            type: !mobyle/booleantype {default: false}
        - !mobyle/inputprogramparameter
            comment: "Process chromosome X specifically. By default only autosomes\n\
                \               will be processed by this program: test, joint, validate,\
                \ trio, quartet."
            prompt: Use chromosomeX-specific treatment (chrx)
            format: ( "" , " --chrx " )[ value ]
            name: chrx
            precond:
                '#or':
                - {type: --test}
                - {rawcnv: --trio}
                - {rawcnv: --quartet}
                - {type: --joint}
                - {type: --validate}
            command: false
            type: !mobyle/booleantype {default: false}
        - !mobyle/inputprogramparameter
            comment: "A 2-column file containing filename and sex (male/female) for\n\
                \               sex chromosome calling with chromosomeX-specific (chrx)\
                \ argument. The first tab-\n               delimited column should\
                \ be the input signal file name, while\n               the second\
                \ tab-delimited column should be male or female.\n               Alternatively,\
                \ abbreviations including m (male), f (female), 1\n              \
                \ (male) or 2 (female) are also fine."
            prompt: Filename and sex (male/female) for chromosomeX (sex)
            format: ( "" , " --sex " + str(value) )[ value is not None]
            argpos: 12
            name: sexfile
            precond:
                '#and':
                - chrx
                - {'#not': bafxhet}
            command: false
        - !mobyle/inputprogramparameter
            comment: "This argument specifies the BAF heterozygosity rate in chrX\
                \ to\n               predict the sex for a sample. Note that this\
                \ rate is based on\n               BAF values so it is not genotype\
                \ heterozygosity rate and indeed\n               quite different/smaller\
                \ than that genotype heterozygosity rate.\n               By default\
                \ if >10% chrX markers have BAF values around 0.5, the\n         \
                \      sample is predicted as female. This threshold however does\
                \ not\n               work for Affymetrix genome-wide arrays (instead\
                \ a 5% threshold\n               is better used). For chrX CNV calling,\
                \ rather than relying on\n               PennCNV prediction of gender,\
                \ it is always best to explicitely\n               specify the sample\
                \ sex using the -sexfile argument."
            prompt: Minimum BAF heterozygosity rate to predict female gender when
                file is not supplied (bafxhet)
            format: ( "" , " --bafxhet " + str(value) )[ value is not None and value
                != vdef]
            name: bafxhet
            precond:
                '#and':
                - chrx
                - {'#not': sexfile}
            command: false
            type: !mobyle/floattype {default: 0.1}
    - !mobyle/inputprogramparagraph
        prompt: Specific Validation-calling arguments (validate)
        name: validateCalling
        precond: {type: --validate}
        argpos: 12
        children:
        - !mobyle/inputprogramparameter
            comment: Specify the start SNP of a pre-specified region used in --validate
                operation
            prompt: Start SNP of a pre-specified region (startsnp)
            format: ( "" , " --startsnp " + str(value) )[ value is not None ]
            simple: true
            mandatory: true
            name: startsnp
            precond: {'#not': candlist}
            command: false
            type: !mobyle/stringtype {}
        - !mobyle/inputprogramparameter
            comment: Specify the end SNP of a pre-specified region used in --validate
                operation
            prompt: End SNP of a pre-specified region (endsnp)
            format: ( "" , " --endsnp " + str(value) )[ value is not None ]
            simple: true
            mandatory: true
            name: endsnp
            precond: {'#not': candlist}
            command: false
            type: !mobyle/stringtype {}
        - !mobyle/inputprogramparameter
            comment: "Specify the prior deletion allele frequency of a pre-specified\n\
                \               region used in --validate operation (this frequency\
                \ can be\n               estimated from CNV calls by --test operation)"
            prompt: Prior deletion frequency of a pre-specified region (delfreq)
            format: ( "" , " --delfreq " + str(value) )[ value is not None ]
            simple: true
            mandatory: true
            name: delfreq
            precond: {'#not': candlist}
            command: false
            type: !mobyle/floattype {}
        - !mobyle/inputprogramparameter
            comment: "Specify the prior duplication allele frequency of a pre-specified\
                \ region used \n            in --validate operation (this frequency\
                \ can be estimated from CNV calls by --test operation)"
            prompt: Prior duplication frequency of a pre-specified region (dupfreq)
            format: ( "" , " --dupfreq " + str(value) )[ value is not None ]
            simple: true
            mandatory: true
            name: dupfreq
            precond: {'#not': candlist}
            command: false
            type: !mobyle/floattype {}
        - !mobyle/inputprogramparameter
            comment: "Background CNV probability for any loci, with default value\
                \ as\n               0.0001. This argument is useful in validation\
                \ calling. When\n               -delfreq/-dupfreq is not specified,\
                \ the background frequency is\n               used to calculate the\
                \ prior probability of different copy number states."
            prompt: Background CNV probability for any loci (backfreq)
            format: ( "" , " --backfreq " + str(value) )[ value is not None ]
            name: backfreq
            precond:
                '#and':
                - {'#not': delfreq}
                - {'#not': dupfreq}
            command: false
            type: !mobyle/floattype {default: 0.0001}
        - !mobyle/inputprogramparameter
            prompt: A file containing all candidate CNV regions to be validated (candlist)
            format: ( "" , " --candlist " + str(value) )[ value is not None]
            name: candlist
            precond:
                '#and':
                - {'#not': startsnp}
                - {'#not': endsnp}
                - {'#not': delfreq}
                - {'#not': dupfreq}
            command: false
    - !mobyle/inputprogramparagraph
        prompt: Specific Case-control comparison arguments (cctest)
        name: cctestCalling
        precond: {rawcnv: --cctest}
        argpos: 12
        children:
        - !mobyle/inputprogramparameter
            comment: "A file containing phenotype informatoin for each individual,\
                \ so\n               that --cctest can be used to compare the frequency\
                \ between\n               cases and controls. Each line has two tab-delimited\
                \ fields:\n               file name and the phenotype. By default,\
                \ \"control\" means\n               control subjects, and other words\
                \ means cases; however, the\n               user can use --control_label\
                \ argument to change the phenotype\n               label for controls."
            prompt: A file containing phenotype information for each input file (phenofile)
            format: ( "" , " --phenofile " + str(value) )[ value is not None]
            simple: true
            argpos: 12
            mandatory: true
            name: phenofile
            precond: {rawcnv: --cctest}
            command: false
        - !mobyle/inputprogramparameter
            comment: "Specify the text label for control subjects in the phenotype\n\
                \               file specified by the --phenofile argument. Normally\
                \ the \"control\" is used to specify \n               controls, and\
                \ all other individuals\n               are treated as cases. However,\
                \ some times users may use 1 to\n               denote controls and\
                \ 2 to denote cases; in such situations the\n               \"--control_label\
                \ 1\" should be used for the --cctest operation."
            prompt: The phenotype label for control subjects in the phenotype file
                (control_label)
            format: ( "" , " --control_label " + str(value) )[ value is not None ]
            name: control_label
            command: false
            type: !mobyle/stringtype {}
        - !mobyle/inputprogramparameter
            prompt: Performed one-sided test (onesided)
            format: ( "" , " --onesided " )[ value ]
            name: onesided
            command: false
            type: !mobyle/booleantype {default: false}
        - !mobyle/inputprogramparameter
            comment: "Specify the particular types of CNVs to be used in the --cctest\n\
                \               operation. By default both duplications and deletions\
                \ are\n               treated as a single group of CNVs and be used\
                \ to compare cases\n               and controls."
            prompt: Used together to specify types of CNVs to be tested (type_filter)
            format: ( "" , " --type_filter " + str(value) )[ value is not None and
                value !=vdef ]
            name: type_filter
            command: false
            type: !mobyle/stringtype
                default: 'null'
                options:
                - {label: Both duplications and deletions, value: 'null'}
                - {label: Duplications, value: dup}
                - {label: Deletions, value: del}
    - !mobyle/inputprogramparagraph
        prompt: Misc options
        name: miscOpt
        argpos: 12
        children:
        - !mobyle/inputprogramparameter
            comment: "The prior probability of 6 hidden states a given CNV call in\n\
                \               father or mother.  This is used for joint calling\
                \ of trios or\n               quartets. It is specified as six numbers\
                \ separated by a comma that sum up to 1.\n               The empirically\
                \ derived default values actually work well: trio, quartet."
            prompt: Prior belief on CN state for regions with CNV calls. Six numbers
                separated by a comma (fmprior)
            format: ( "" , " --fmprior " + str(value) )[ value is not None ]
            name: fmprior
            precond:
                '#or':
                - {rawcnv: --trio}
                - {rawcnv: --quartet}
            command: false
            type: !mobyle/stringtype {}
        - !mobyle/inputprogramparameter
            comment: "Specify the probability that a given CNV is a de novo event\
                \ for\n               family-based CNV calling. The default is 0.0001.\
                \ trio, quartet"
            prompt: Prior belief on genome-wide de novo event rate (denovo_rate)
            format: ( "" , " --denovo_rate " + str(value) )[ value is not None and
                value != vdef]
            name: denovo_rate
            precond:
                '#or':
                - {rawcnv: --trio}
                - {rawcnv: --quartet}
            command: false
            type: !mobyle/floattype {default: 0.0001}
        - !mobyle/inputprogramparameter
            comment: "This option is turned on by default. It adjust the log R Ratio\n\
                \               values of the entire genome by a constant so that\
                \ the median is\n               zero: test, trio, quartet, joint,\
                \ validate."
            prompt: Adjust genome-wide LRR such that median equal 0 (nomedianadjust)
            format: ( "" , " --nomedianadjust " )[ not value ]
            name: medianadjust
            precond:
                '#or':
                - {type: --test}
                - {rawcnv: --trio}
                - {rawcnv: --quartet}
                - {type: --joint}
                - {type: --validate}
            command: false
            type: !mobyle/booleantype {default: false}
        - !mobyle/inputprogramparameter
            comment: "This option is turned ON by default (new July 2008): it adjust\n\
                \               the BAF values genome-wide such that the median value\
                \ is 0.5."
            prompt: Adjust genome-wide BAF such that median equal 0.5 (nobafadjust)
            format: ( "" , " --nobafadjust " )[ not value ]
            name: bafadjust
            precond:
                '#or':
                - {type: --test}
                - {rawcnv: --trio}
                - {rawcnv: --quartet}
                - {type: --joint}
                - {type: --validate}
            command: false
            type: !mobyle/booleantype {default: false}
        - !mobyle/inputprogramparameter
            comment: "This option is turned ON by default: it adjust the SD values\
                \ in\n               HMM model such that the model fits the signal\
                \ quality of the\n               testing sample to reduce false positive\
                \ calls"
            prompt: Adjust SD of hidden Markov model based on input signal (nosdadjust)
            format: ( "" , " --nosdadjust " )[ not value ]
            name: sdadjust
            precond:
                '#or':
                - {type: --test}
                - {rawcnv: --trio}
                - {rawcnv: --quartet}
                - {type: --joint}
                - {type: --validate}
            command: false
            type: !mobyle/booleantype {default: false}
        - !mobyle/inputprogramparameter
            comment: "This argument is turned ON by default. It requires the\n   \
                \            input/output buffer to flush immediately (that is, no\n\
                \               input/output is buffered). When PennCNV is running\
                \ remotely\n               (for example, through a SSH connection)\
                \ or when the output is\n               redirected, this argument\
                \ cause the program to report progress\n               in real-time.\
                \  When running PennCNV in parallel with many processes \n       \
                \        accessing disks simultaneously, this option should be\n \
                \              turned off to decrease system overhead."
            prompt: Flush input/output buffer (noflush)
            format: ( "" , " --noflush " )[ not value ]
            name: flush
            command: false
            type: !mobyle/booleantype {default: false}
    - !mobyle/inputprogramparameter
        prompt: Outfile for detect_cnv and Input file for visualize_cnv
        format: '" --out detect_cnv.out "'
        argpos: 17
        name: outfile_name
        precond:
            '#and':
            -   '#or':
                -   type: {'#ne': None}
                -   rawcnv: {'#ne': None}
            -   type: {'#ne': --test}
        command: false
        hidden: true
        type: !mobyle/stringtype {}
outputs: !mobyle/outputparagraph
    children:
    - !mobyle/outputprogramparameter
        prompt: Split files
        filenames: infile + ".*"
        name: output_split_file
        precond:
            infile: {'#ne': None}
        hidden: true
    - !mobyle/outputprogramparagraph
        prompt: Penncnv analyses
        name: analyse
        argpos: 10
        children:
        - !mobyle/outputprogramparameter
            prompt: CNV file
            filenames: infile + "_rawcnv"
            name: output_cnv_file
            precond:
                '#and':
                - {type: --test}
                - infile
    - !mobyle/outputprogramparagraph
        prompt: CNV output format
        name: cnvoutput
        argpos: 20
        children:
        - !mobyle/outputprogramparameter
            prompt: CNV calls file
            filenames: infile + "_" + outputformat + "cnv"
            name: bed_cnv_file
            precond:
                '#and':
                - {type: --test}
                - infile
                -   outputformat: {'#ne': output}
        - !mobyle/outputprogramparameter
            prompt: Output file
            filenames: infile + "_" + outputformat
            name: bed_file
            precond:
                '#and':
                -   '#or':
                    -   type: {'#ne': None}
                    -   rawcnv: {'#ne': None}
                -   type: {'#ne': --test}
                -   outputformat: {'#ne': output}
    - !mobyle/outputprogramparameter
        prompt: Output file
        filenames: '"detect_cnv.out"'
        name: output_file
        precond:
            type: {'#ne': --test}
        output_type: stdout
    - !mobyle/outputprogramparameter
        prompt: Standard error
        filenames: '"detect_cnv.err"'
        name: stderr
        type: !mobyle/formattedtype
            data_terms: ['EDAM_data:2048']
command: kcolumn.pl
env: {}