If true, the centroiding will be skipped

hidden
type: boolean
default: true

If true, the alignment will be skipped

hidden
type: boolean

If true, the adduct detection will be skipped

hidden
type: boolean

If set to true, requantification will be performed

type: boolean

If set to true, identification will be performed. Remember to set identification specific parameters

type: boolean

Polarity of the data

type: string

If set, the linking will be performed in parallel, see nr_partitions in linking

type: boolean

Set wether the MS2 collections have been done on all the MS1 data. If there is a separate MS2 file, set to separate

type: string

If set, the workflow expects the models to be in models_dir_ms2query

hidden
type: boolean

If running offline, this directory has to contain all the files necessary for running MS2Query

hidden
type: string
default: models

If set, the model training will be performed using library_path_ms2query

hidden
type: boolean

path to ms2query library

hidden
type: string

If higher than one, parameter files will be split into the selected number. The result of the identification will be perform on each part separately

hidden
type: integer
default: 1

mz tolerance (ppm) for finding C13

type: number
default: 20

rt tolerance for finding C13

type: number
default: 5

Store the map index of the sub-feature in the peptide ID.

hidden
type: boolean
default: true

Match using RT and m/z of sub-features instead of consensus RT and m/z. A consensus feature matches if any of its sub-features matches.

hidden
type: boolean
default: true

When mapping MS2 precursors to consensus elements, ignore the charge. Specially beneficial in negative mode, if the charges of the consensus features are and spectra are different

hidden
type: boolean

If set, detected adduct will be used in identification

type: boolean

whether feature quality or intensity should be used for feature selection

hidden
type: string

If ture, normalized intesity will be used for selecting the best feature

hidden
type: boolean
default: true

Number of iterations that should be performed to extract the C13 isotope pattern. If no peak is found (C13 distance) the function will abort. Be careful with noisy data - since this can lead to wrong isotope patterns

hidden
type: integer
default: 3

PPM for detecting MS C13

hidden
type: number
default: 10

Just consider compounds with a precursor mz lower or equal this maximum mz. All other compounds in the input file are ignored.=

hidden
type: number
default: -1

Set logging level of the Jobs SIRIUS will execute. Valid values: SEVERE, WARNING, INFO, FINER, ALL

hidden
type: string

Ignore given molecular formula in internal .ms format, while processing.

hidden
type: boolean

Maximum allowed mass deviation in ppm for decomposing masses (ppm)

type: number
default: 10

Maximum allowed mass deviation in ppm for decomposing masses in MS2 (ppm).If not specified, the same value as for the MS1 is used.

type: number
default: 10

Time out in seconds per fragmentation tree computations. 0 for an infinite amount of time

hidden
type: number
default: 100

Time out in seconds per fragmentation tree computations. 0 for an infinite amount of time

hidden
type: number
default: 100

Disable recalibration of input spectra

type: boolean

Name of the configuration profile

type: string

Specify the neutral molecular formula of the measured compound to compute its tree or a list of candidate formulas the method should discriminate. Omit this option if you want to consider all possible molecular formulas

hidden
type: string

The iontype/adduct of the MS/MS data. Example: [M+H]+, [M-H]-, [M+Cl]-, [M+Na]+, [M]+. You can also provide a comma separated list of adducts.

hidden
type: string

The number of formula candidates in the SIRIUS output

type: integer
default: 10

Minimum number of candidates in the output for each ionization. Set to force output of results for each possible ionization, even if not part of highest ranked results.

type: integer
default: 1

Set the allowed elements for rare element detection. Write SBrClBSe to allow the elements S,Br,Cl,B and Se.

hidden
type: string
default: SBrClBSe

Enforce elements for molecular formula determination. Write CHNOPSCl to allow the elements C, H, N, O, P, S and Cl. Add numbers in brackets to restrict the minimal and maximal allowed occurrence of these elements: CHNOP[5]S[8]Cl[1-2]. When one number is given then it is interpreted as upper bound.

hidden
type: string
default: CHNOP

Disable isotope pattern score.

hidden
type: boolean

Disable molecular formula filter. When filtering is enabled, molecular formulas are excluded if their theoretical isotope pattern does not match the theoretical one, even if their MS/MS pattern has high score.

hidden
type: boolean

the iontype/adduct of the MS/MS data. Example: [M+H]+, [M-H]-, [M+Cl]-, [M+Na]+, [M]+. You can also provide a comma separated list of adducts.

type: string
default: [M+H]+,[M+K]+,[M+Na]+,[M+H-H2O]+,[M+H-H4O2]+,[M+NH4]+,[M-H]-,[M+Cl]-,[M-H2O-H]-,[M+Br]-

Search formulas in the Union of the given databases db-name1,db-name2,db-name3. If no database is given all possible molecular formulas will be respected (no database is used). Example: possible DBs: ALL,BIO,PUBCHEM,MESH,HMDB,KNAPSACK,CHEBI,PUBMED,KEGG,HSDB,MACONDA,METACYC,GNPS,ZINCBIO,UNDP,YMDB,PLANTCYC,NORMAN,ADDITIONAL,PUBCHEMANNOTATIONBIO,PUBCHEMANNOTATIONDRUG,PUBCHEMANNOTATIONSAFETYANDTOXIC,PUBCHEMANNOTATIONFOOD,KEGGMINE,ECOCYCMINE,YMDBMINE

type: string

If set, passatutto will be run

type: boolean

Search structures in the Union of the given databases db-name1,db-name2,db-name3. If no database is given all possible molecular formulas will be respected (no database is used). Example: possible DBs: ALL,BIO,PUBCHEM,MESH,HMDB,KNAPSACK,CHEBI,PUBMED,KEGG,HSDB,MACONDA,METACYC,GNPS,ZINCBIO,UNDP,YMDB,PLANTCYC,NORMAN,ADDITIONAL,PUBCHEMANNOTATIONBIO,PUBCHEMANNOTATIONDRUG,PUBCHEMANNOTATIONSAFETYANDTOXIC,PUBCHEMANNOTATIONFOOD,KEGGMINE,ECOCYCMINE,YMDBMINE

type: string

For GUROBI and CPLEX environment variables need to be configured.

hidden
type: string
default: CLP

E-mail for your SIRIUS account.

type: string

Password for your SIRIUS account.

type: string

If set, SIRIUS will be run in parallel. See mgf_splitmgf_pyopenms parameter for segmentation

type: boolean

For running MS2 mapping in parallel set this higher than 1

type: integer
default: 20

If set, MS2Query will be run

type: boolean

If set, FingerID will be run. This has to be run together with run_sirius

type: boolean

If set SIRIUS will run

type: boolean

If set identification will be performed on unmapped MS2 spectra

hidden
type: boolean

Maximal range of charges for a single analyte, i.e. observing q1=[5,6,7] implies span=3. Setting this to 1 will only find adduct variants of the same charge

type: integer
default: 1

Try different values of charge for each feature according to the above settings ('heuristic' [does not test all charges, just the likely ones] or 'all' ), or leave feature charge untouched ('feature').

type: string

Maximum allowed RT difference between any two features if their relation shall be determined

type: number
default: 1

Maximum allowed RT difference between between two co-features, after adduct shifts have been accounted for (if you do not have any adduct shifts, this value should be equal to 'retention_max_diff', otherwise it should be smaller!)

type: number
default: 1

Maximum allowed mass tolerance per feature. Defines a symmetric tolerance window around the feature. When looking at possible feature pairs, the allowed feature-wise errors are combined for consideration of possible adduct shifts. For ppm tolerances, each window is based on the respective observed feature mz (instead of putative experimental mzs causing the observed one)!

type: number
default: 5

Unit of the 'max_difference' parameter

type: string

Maximal number of neutral adducts(q=0) allowed. Add them in the 'potential_adducts' section!

type: integer
default: 1

Prune the considered adduct transitions by transition probabilities.

type: boolean
default: true

Limits allowed adduct compositions and changes between compositions in the underlying graph optimization problem by introducing a probability-based threshold: the minority bound sets the maximum count of the least probable adduct (according to 'potential_adducts' param) within a charge variant with maximum charge only containing the most likely adduct otherwise. E.g., for 'charge_max' 4 and 'max_minority_bound' 2 with most probable adduct being H+ and least probable adduct being Na+, this will allow adduct compositions of '2(H+),2(Na+)' but not of '1(H+),3(Na+)'. Further, adduct compositions/changes less likely than '2(H+),2(Na+)' will be discarded as well.

type: integer
default: 1

Minimum overlap of the convex hull' RT intersection measured against the union from two features (if CHs are given)

type: number
default: 0.66

Enable the intensity filter, which will only allow edges between two equally charged features if the intensity of the feature with less likely adducts is smaller than that of the other feature. It is not used for features of different charge.

type: boolean

Label of map in output consensus file where all features are put by default

hidden
type: string
default: decharged features

possible positive adducts for adduct detection in the format of adduct:charge:probablity

type: string
default: H:+:0.6 Na:+:0.1 NH4:+:0.1 H-1O-1:+:0.1 H-3O-2:+:0.1

possible negative adducts for adduct detection in the format of adduct:charge:probablity

type: string
default: H-1:-:0.8 H-3O-1:-:0.2

The maximal number of peaks/features to be considered per map. To use all, set to '-1'.

type: integer
default: 1000

Maximum of m/z deviation of corresponding elements in different maps. This condition applies to the pairs considered in hashing.

type: number
default: 0.5

Within each of the two maps, the pairs considered for pose clustering must be separated by at least this fraction of the total elution time interval (i.e., max - min).

hidden
type: number
default: 0.1

Maximum number of elements considered in each map (selected by intensity). Use this to reduce the running time and to disregard weak signals during alignment. For using all points, set this to -1.

type: integer
default: 2000

The scaling of the retention time interval is being hashed into buckets of this size during pose clustering. A good choice for this would be a bit smaller than the error you would expect from repeated runs.

hidden
type: number
default: 0.005

The shift at the lower (respectively, higher) end of the retention time interval is being hashed into buckets of this size during pose clustering. A good choice for this would be about the time between consecutive MS scans.

hidden
type: number

Maximal shift which is considered during histogramming (in seconds). This applies for both directions.

hidden
type: number

Maximal scaling which is considered during histogramming. The minimal scaling is the reciprocal of this.

hidden
type: number

[DEBUG] If non-empty, base filename where hash table buckets will be dumped to. A serial number for each invocation will be appended automatically.

hidden
type: string

[DEBUG] If non-empty, base filename where the individual hashed pairs will be dumped to (large!). A serial number for each invocation will be appended automatically.

hidden
type: string

Only link features whose distance to the second nearest neighbors (for both sides) is larger by 'second_nearest_gap' than the distance between the matched pair itself.

hidden
type: number

Never link features that are annotated with different peptides (features without ID's always match; only the best hit per peptide identification is considered).

hidden
type: boolean

false [default]: pairing requires equal charge state (or at least one unknown charge '0'); true: Pairing irrespective of charge state

type: boolean

true [default]: pairing requires equal adducts (or at least one without adduct annotation); true: Pairing irrespective of adducts

hidden
type: boolean
default: true

Never pair features with a larger RT distance (in seconds).

type: number
default: 100

Normalized RT differences ([0-1], relative to 'max_difference') are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)

hidden
type: number

Final RT distances are weighted by this factor

hidden
type: number

Never pair features with larger m/z distance (unit defined by 'unit')

type: number
default: 0.3

Unit of the 'max_difference' parameter

type: string

Normalized ([0-1], relative to 'max_difference') m/z differences are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)

hidden
type: number

Final m/z distances are weighted by this factor

hidden
type: number

Differences in relative intensity ([0-1]) are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)

hidden
type: number

Final intensity distances are weighted by this factor

hidden
type: number

Log-transform intensities? If disabled, d = |int_f2 - int_f1| / int_max. If enabled, d = |log(int_f2 + 1) - log(int_f1 + 1)| / log(int_max + 1))

hidden
type: string

Unit of m/z tolerance

type: string

Number of partitions in m/z space

type: integer
default: 100

Whether or not to internally warp feature RTs using LOWESS transformation before linking (reported RTs in results will always be the original RTs)

type: boolean
default: true

Width of RT tolerance window (sec)

type: number
default: 100

m/z tolerance (in ppm or Da)

type: number
default: 5

Maximum absolute log10 fold change between two compatible signals during compatibility graph construction. Two signals from different maps will not be connected by an edge in the compatibility graph if absolute log fold change exceeds this limit (they might still end up in the same connected component, however). Note: this does not limit fold changes in the linking stage, only during RT alignment, where we try to find high-quality alignment anchor points. Setting this to a value < 0 disables the FC check.

hidden
type: number
default: 0.5

Only connected components containing compatible features from at least max(2, (warp_min_occur * number_of_input_maps)) input maps are considered for computing the warping function

hidden
type: number
default: 0.5

Allow up to this many conflicts (features from the same map) per connected component to be used for alignment (-1 means allow any number of conflicts)

hidden
type: integer

Width of RT tolerance window (sec)

type: number
default: 30

m/z tolerance (in ppm or Da)

type: number
default: 10

whether to disallow charge mismatches (Identical), allow to link charge zero (i.e., unknown charge state) with every charge state, or disregard charges (Any).

type: string

whether to only allow the same adduct for linking (Identical), also allow linking features with adduct-free ones, or disregard adducts (Any).

type: string

Normalized RT differences ([0-1], relative to 'max_difference') are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)

hidden
type: number
default: 1

Final RT distances are weighted by this factor

hidden
type: number
default: 1

Normalized ([0-1], relative to 'max_difference') m/z differences are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)

hidden
type: number
default: 2

Final m/z distances are weighted by this factor

hidden
type: number
default: 1

Differences in relative intensity ([0-1]) are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)

hidden
type: number
default: 1

Final intensity distances are weighted by this factor

hidden
type: number
default: 1

Log-transform intensities? If disabled, d = |int_f2 - int_f1| / int_max. If enabled, d = |log(int_f2 + 1) - log(int_f1 + 1)| / log(int_max + 1))

hidden
type: string

Fraction of datapoints (f) to use for each local regression (determines the amount of smoothing). Choosing this parameter in the range .2 to .8 usually results in a good fit.

hidden
type: number
default: 0.666666666666667

Number of robustifying iterations for lowess fitting.

hidden
type: integer
default: 3

Nonnegative parameter which may be used to save computations (recommended value is 0.01 of the range of the input, e.g. for data ranging from 1000 seconds to 2000 seconds, it could be set to 10). Setting a negative value will automatically do this.

hidden
type: number
default: -1

Method to use for interpolation between datapoints computed by lowess. 'linear': Linear interpolation. 'cspline': Use the cubic spline for interpolation. 'akima': Use an akima spline for interpolation

hidden
type: string

Method to use for extrapolation outside the data range. 'two-point-linear': Uses a line through the first and last point to extrapolate. 'four-point-linear': Uses a line through the first and second point to extrapolate in front and and a line through the last and second-to-last point in the end. 'global-linear': Uses a linear regression to fit a line through all data points and use it for interpolation.

hidden
type: string

For consensusXML input only: If set, the sub-features of the inputs are transferred to the output.

hidden
type: boolean

Invert transformation (approximatively) before applying it

hidden
type: boolean

Store the original retention times (before transformation) as meta data in the output file

hidden
type: boolean

Type of model

hidden
type: string

Perform linear regression on 'y - x' vs. 'y + x', instead of on 'y' vs. 'x'.

hidden
type: boolean

Weight x values

hidden
type: string

Weight y values

hidden
type: string

Minimum x value

hidden
type: number
default: 1e-15

Maximum x value

hidden
type: number
default: 1000000000000000

Minimum y value

hidden
type: number
default: 1e-15

Maximum y value

hidden
type: number
default: 1000000000000000

Determines the amount of smoothing by setting the number of nodes for the B-spline. The number is chosen so that the spline approximates a low-pass filter with this cutoff wavelength. The wavelength is given in the same units as the data; a higher value means more smoothing. '0' sets the number of nodes to twice the number of input points.

hidden
type: number

Number of nodes for B-spline fitting. Overrides 'wavelength' if set (to two or greater). A lower value means more smoothing.

hidden
type: integer

Method to use for extrapolation beyond the original data range. 'linear': Linear extrapolation using the slope of the B-spline at the corresponding endpoint. 'b_spline': Use the B-spline (as for interpolation). 'constant': Use the constant value of the B-spline at the corresponding endpoint. 'global_linear': Use a linear fit through the data (which will most probably introduce discontinuities at the ends of the data range).

hidden
type: string

Boundary condition at B-spline endpoints: 0 (value zero), 1 (first derivative zero) or 2 (second derivative zero)

hidden
type: integer

Fraction of datapoints (f) to use for each local regression (determines the amount of smoothing). Choosing this parameter in the range .2 to .8 usually results in a good fit.

hidden
type: number

Number of robustifying iterations for lowess fitting.

hidden
type: integer

Nonnegative parameter which may be used to save computations (recommended value is 0.01 of the range of the input, e.g. for data ranging from 1000 seconds to 2000 seconds, it could be set to 10). Setting a negative value will automatically do this.

hidden
type: number
default: -1

Method to use for interpolation between datapoints computed by lowess. 'linear': Linear interpolation. 'cspline': Use the cubic spline for interpolation. 'akima': Use an akima spline for interpolation

hidden
type: string

Method to use for extrapolation outside the data range. 'two-point-linear': Uses a line through the first and last point to extrapolate. 'four-point-linear': Uses a line through the first and second point to extrapolate in front and and a line through the last and second-to-last point in the end. 'global-linear': Uses a linear regression to fit a line through all data points and use it for interpolation.

hidden
type: string

Type of interpolation to apply.

hidden
type: string

Type of extrapolation to apply: two-point-linear: use the first and last data point to build a single linear model, four-point-linear: build two linear models on both ends using the first two / last two points, global-linear: use all points to build a single linear model. Note that global-linear may not be continuous at the border.

hidden
type: string

m/z window size for chromatogram extraction (unit: ppm if 1 or greater, else Da/Th)

type: number

RT window size (in sec.) for chromatogram extraction. If set, this parameter takes precedence over 'extract:rt_quantile'.

hidden
type: number

Number of isotopes to include in each peptide assay.

type: integer

Minimum probability for an isotope to be included in the assay for a peptide. If set, this parameter takes precedence over 'extract:n_isotopes'.

hidden
type: number

Expected elution peak width in seconds, for smoothing (Gauss filter). Also determines the RT extration window, unless set explicitly via 'extract:rt_window'.

type: number

Minimum elution peak width. Absolute value in seconds if 1 or greater, else relative to 'peak_width'.

hidden
type: number

Signal-to-noise threshold for OpenSWATH feature detection

hidden
type: number

Type of elution model to fit to features

type: string

Add zero-intensity points outside the feature range to constrain the model fit. This parameter sets the weight given to these points during model fitting; '0' to disable.

hidden
type: number

Suppress weighting of mass traces according to theoretical intensities when fitting elution models

hidden
type: boolean

If fitting the elution model fails for a feature, set its intensity to zero instead of imputing a value from the initial intensity estimate

hidden
type: boolean

Fit elution model to each individual mass trace

hidden
type: boolean

Lower bound for the area under the curve of a valid elution model

hidden
type: number

Time points corresponding to this fraction of the elution model height have to be within the data region used for model fitting

hidden
type: number

Upper limit for acceptable widths of elution models (Gaussian or EGH), expressed in terms of modified (median-based) z-scores. '0' to disable. Not applied to individual mass traces (parameter 'each_trace').

hidden
type: number

Upper limit for acceptable asymmetry of elution models (EGH only), expressed in terms of modified (median-based) z-scores. '0' to disable. Not applied to individual mass traces (parameter 'each_trace').

hidden
type: number

Maximum number of iterations for EMG fitting.

type: integer

Alternative initial parameters for fitting through method of moments.

type: boolean

Minimal signal-to-noise ratio for a peak to be picked (0.0 disables SNT estimation!)

type: number

The extension of a peak is stopped if the spacing between two subsequent data points exceeds 'spacing_difference_gap * min_spacing'. 'min_spacing' is the smaller of the two spacings from the peak apex to its two neighboring points. '0' to disable the constraint. Not applicable to chromatograms.

hidden
type: number

Maximum allowed difference between points during peak extension, in multiples of the minimal difference between the peak apex and its two neighboring points. If this difference is exceeded a missing point is assumed (see parameter 'missing'). A higher value implies a less stringent peak definition, since individual signals within the peak are allowed to be further apart. '0' to disable the constraint. Not applicable to chromatograms.

hidden
type: number

Maximum number of missing points allowed when extending a peak to the left or to the right. A missing data point occurs if the spacing between two subsequent data points exceeds 'spacing_difference * min_spacing'. 'min_spacing' is the smaller of the two spacings from the peak apex to its two neighboring points. Not applicable to chromatograms.

hidden
type: integer

Add metadata for FWHM (as floatDataArray named 'FWHM' or 'FWHM_ppm', depending on param 'report_FWHM_unit') for each picked peak.

hidden
type: boolean

Unit of FWHM. Either absolute in the unit of input, e.g. 'm/z' for spectra, or relative as ppm (only sensible for spectra, not chromatograms).

hidden
type: string

maximal intensity considered for histogram construction. By default, it will be calculated automatically (see auto_mode). Only provide this parameter if you know what you are doing (and change 'auto_mode' to '-1')! All intensities EQUAL/ABOVE 'max_intensity' will be added to the LAST histogram bin. If you choose 'max_intensity' too small, the noise estimate might be too small as well. If chosen too big, the bins become quite large (which you could counter by increasing 'bin_count', which increases runtime). In general, the Median-S/N estimator is more robust to a manual max_intensity than the MeanIterative-S/N.

hidden
type: integer

parameter for 'max_intensity' estimation (if 'auto_mode' == 0): mean + 'auto_max_stdev_factor' * stdev

hidden
type: number

parameter for 'max_intensity' estimation (if 'auto_mode' == 1): auto_max_percentile th percentile

hidden
type: integer

method to use to determine maximal intensity: -1 --> use 'max_intensity'; 0 --> 'auto_max_stdev_factor' method (default); 1 --> 'auto_max_percentile' method

hidden
type: integer

window length in Thomson

hidden
type: number

number of bins for intensity values

hidden
type: integer

minimum number of elements required in a window (otherwise it is considered sparse)

hidden
type: integer

noise value used for sparse windows

hidden
type: number
default: 100000000000000000000

Intensity threshold below which peaks are regarded as noise.

type: number
default: 10

Minimum signal-to-noise a mass trace should have.

type: number
default: 3

Expected chromatographic peak width (in seconds).

type: number
default: 5

Allowed mass deviation (in ppm).

type: number
default: 20

Enables dynamic re-estimation of m/z variance during mass trace collection stage.

type: boolean
default: true

Method of quantification for mass traces. For LC data 'area' is recommended, 'median' for direct injection data. 'max_height' simply uses the most intense peak in the trace.

type: string

Termination criterion for the extension of mass traces. In 'outlier' mode, trace extension cancels if a predefined number of consecutive outliers are found (see trace_termination_outliers parameter). In 'sample_rate' mode, trace extension in both directions stops if ratio of found peaks versus visited spectra falls below the 'min_sample_rate' threshold.

hidden
type: string

Mass trace extension in one direction cancels if this number of consecutive spectra with no detectable peaks is reached.

hidden
type: integer
default: 5

Minimum fraction of scans along the mass trace that must contain a peak.

hidden
type: number
default: 0.5

Minimum expected length of a mass trace (in seconds).

hidden
type: number
default: 5

Maximum expected length of a mass trace (in seconds). Set to a negative value to disable maximal length check during mass trace detection.

hidden
type: number
default: -1

Enable splitting of isobaric mass traces by chromatographic peak detection. Disable for direct injection.

type: boolean
default: true

Enable filtering of unlikely peak widths. The fixed setting filters out mass traces outside the [min_fwhm, max_fwhm] interval (set parameters accordingly!). The auto setting filters with the 5 and 95% quantiles of the peak width distribution.

type: string

Minimum full-width-at-half-maximum of chromatographic peaks (in seconds). Ignored if parameter width_filtering is off or auto.

hidden
type: number
default: 1

Maximum full-width-at-half-maximum of chromatographic peaks (in seconds). Ignored if parameter width_filtering is off or auto.

hidden
type: number
default: 60

Apply post-filtering by signal-to-noise ratio after smoothing.

hidden
type: boolean

RT range where to look for coeluting mass traces

hidden
type: number
default: 10

MZ range where to look for isotopic mass traces

hidden
type: number
default: 6.5

Lowest charge state to consider

hidden
type: integer
default: 1

Highest charge state to consider

hidden
type: integer
default: 1

Set to true for a feature intensity summed up over all traces rather than using monoisotopic trace intensity alone.

hidden
type: boolean

Require sufficient overlap in RT while assembling mass traces. Disable for direct injection data..

type: boolean
default: true

Remove/score candidate assemblies based on isotope intensities. SVM isotope models for metabolites were trained with either 2% or 5% RMS error. For peptides, an averagine cosine scoring is used. Select the appropriate noise model according to the quality of measurement or MS device.

type: string

Use the 13C isotope peak position (~1.003355 Da) as the expected shift in m/z for isotope mass traces (highly recommended for lipidomics!). Disable for general metabolites (as described in Kenar et al. 2014, MCP.).

type: boolean

Use LOWESS intensities instead of raw intensities.

hidden
type: boolean
default: true

Augment each reported feature with the convex hull of the underlying mass traces (increases featureXML file size considerably).

hidden
type: boolean

Remove unassembled traces (single traces).

hidden
type: boolean

Use the m/z range of the assumed elements to detect isotope peaks. A expected m/z range is computed from the isotopes of the assumed elements. If enabled, this ignores 'mz_scoring_13C'

hidden
type: boolean

Elements assumes to be present in the sample (this influences isotope detection).

hidden
type: string
default: CHNOPS

Define where the pipeline should find input data and save output data.

Path to comma-separated file containing information about the samples in the experiment.

required
type: string
pattern: ^\S+\.csv$

You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row. See usage docs.

The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.

required
type: string

Email address for completion summary.

type: string
pattern: ^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$

Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (~/.nextflow/config) then you don't need to specify this on the command line for every run.

MultiQC report title. Printed as page header, used for filename if not otherwise specified.

type: string

Save intermediate files

hidden
type: boolean

Parameters used to describe centralised config profiles. These should not be edited.

Git commit id for Institutional configs.

hidden
type: string
default: master

Base directory for Institutional configs.

hidden
type: string
default: https://raw.githubusercontent.com/nf-core/configs/master

If you're running offline, Nextflow will not be able to fetch the institutional config files from the internet. If you don't need them, then this is not a problem. If you do need them, you should download the files from the repo and tell Nextflow where to find them with this parameter.

Institutional config name.

hidden
type: string

Institutional config description.

hidden
type: string

Institutional config contact information.

hidden
type: string

Institutional config URL link.

hidden
type: string

Set the top limit for requested resources for any single job.

Maximum number of CPUs that can be requested for any single job.

hidden
type: integer
default: 16

Use to set an upper-limit for the CPU requirement for each process. Should be an integer e.g. --max_cpus 1

Maximum amount of memory that can be requested for any single job.

hidden
type: string
default: 128.GB
pattern: ^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$

Use to set an upper-limit for the memory requirement for each process. Should be a string in the format integer-unit e.g. --max_memory '8.GB'

Maximum amount of time that can be requested for any single job.

hidden
type: string
default: 240.h
pattern: ^(\d+\.?\s*(s|m|h|d|day)\s*)+$

Use to set an upper-limit for the time requirement for each process. Should be a string in the format integer-unit e.g. --max_time '2.h'

Less common options for the pipeline, typically set in a config file.

Display help text.

hidden
type: boolean

Display version and exit.

hidden
type: boolean

Method used to save pipeline results to output directory.

hidden
type: string

The Nextflow publishDir option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See Nextflow docs for details.

Email address for completion summary, only when pipeline fails.

hidden
type: string
pattern: ^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$

An email address to send a summary email to when the pipeline is completed - ONLY sent if the pipeline does not exit successfully.

Send plain-text email instead of HTML.

hidden
type: boolean

Do not use coloured log outputs.

hidden
type: boolean

Incoming hook URL for messaging service

hidden
type: string

Incoming hook URL for messaging service. Currently, MS Teams and Slack are supported.

Boolean whether to validate parameters against the schema at runtime

hidden
type: boolean
default: true

Show all params when using --help

hidden
type: boolean

By default, parameters set as hidden in the schema are not shown on the command line when a user runs with --help. Specifying this option will tell the pipeline to show all parameters.

Validation of parameters fails when an unrecognised parameter is found.

hidden
type: boolean

By default, when an unrecognised parameter is found, it returns a warinig.

Validation of parameters in lenient more.

hidden
type: boolean

Allows string values that are parseable as numbers or booleans. For further information see JSONSchema docs.

File size limit when attaching MultiQC reports to summary emails.

hidden
type: string
default: 25.MB
pattern: ^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$

Custom config file to supply to MultiQC.

hidden
type: string

Custom logo file to supply to MultiQC. File name must also be set in the MultiQC config file

hidden
type: string

Custom MultiQC yaml file containing HTML including a methods description.

type: string