General options that affect the whole pipeline

Output directory for results

type: string
default: ./results

Email address for completion summary

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.

Parameters used to tune library creation (only set if you want to do library idnetification)

set whether you want to do quantification with OpenMS (openms) or XCMS (xcms) in negative ionization (for library)

hidden
type: string

Controls how to perform IPO

hidden
type: string

Possible values:

  • none: don't perform IPO
  • global: performs IPO on all or selected number of samples
  • local: performs IPO on individual samples one at the time

Quantification methods for IPO

hidden
type: string
default: centWave

Only centWave is supported at this stage.

lowest level of noise

hidden
type: number
default: 1000

highest level of noise

hidden
type: number

lowest level of signal to noise threshold

hidden
type: number
default: 10

highest level of signal to noise threshold

hidden
type: number
default: 10

Function for centering the mz

hidden
type: string
default: wMean

Integration method

hidden
type: number
default: 1

logical, if TRUE a Gaussian is fitted

hidden
type: boolean

lower minimum width of peaks

hidden
type: number
default: 12

higher minimum width of peaks

hidden
type: number
default: 28

lower maximum width of peaks

hidden
type: number
default: 35

higher maximum width of peaks

hidden
type: number
default: 65

lower ppm mass deviation

hidden
type: number
default: 17

higher ppm mass deviation

hidden
type: number
default: 32

lower minimum difference in m/z for peaks with overlapping retention times, can be negative to allow overlap

hidden
type: number
default: -0.001

higher minimum difference in m/z for peaks with overlapping retention times, can be negative to allow overlap

hidden
type: number
default: 0.01

maximum charge of molecules (only used in individual setting)

hidden
type: number
default: 1

ppm mass deviation for adducts (only used in individual setting)

hidden
type: number
default: 10

lower value of K in 'prefilter_library_neg=c(k,I)'. Prefilter step for the first phase. Mass traces are only retained if they contain at least 'k' peaks with intensity >_library_neg= 'I'.

hidden
type: number
default: 3

higher value of K in 'prefilter_library_neg=c(k,I)'. Prefilter step for the first phase. Mass traces are only retained if they contain at least 'k' peaks with intensity >_library_neg= 'I'.

hidden
type: number
default: 3

lower I in prefilter

hidden
type: number
default: 100

higher I in prefilter

hidden
type: number
default: 100

number of cores used in IPO

hidden
type: number
default: 5

lower Penalty for Gap opening

hidden
type: number

higher Penalty for Gap opening

hidden
type: number
default: 0.4

lower Penalty for Gap enlargement

hidden
type: number
default: 2.1

higher Penalty for Gap enlargement

hidden
type: number
default: 2.7

lower step size (in m/z) to use for profile generation from the raw data files

hidden
type: number
default: 0.7

higher step size (in m/z) to use for profile generation from the raw data files

hidden
type: number
default: 1

lower Responsiveness of warping. 0 will give a linear warp based on start and end points. 100 will use all bijective anchors

hidden
type: number
default: 1

higher Responsiveness of warping. 0 will give a linear warp based on start and end points. 100 will use all bijective anchors

hidden
type: number
default: 1

lower Local weighting applied to diagonal moves in alignment.

hidden
type: number
default: 2

higher Local weighting applied to diagonal moves in alignment.

hidden
type: number
default: 2

lower Local weighting applied to gap moves in alignment.

hidden
type: number
default: 1

higher Local weighting applied to gap moves in alignment.

hidden
type: number
default: 1

Local rather than global alignment

hidden
type: number

lower bandwidth (consider something like retention time differences)

hidden
type: number
default: 22

higher bandwidth (consider something like retention time differences)

hidden
type: number
default: 38

lower minimum fraction of samples necessary in at least one of the sample groups for it to be a valid group

hidden
type: number
default: 0.3

higher minimum fraction of samples necessary in at least one of the sample groups for it to be a valid group

hidden
type: number
default: 0.7

lower mz width (mz differences)

hidden
type: number
default: 0.015

higher mz width (mz differences)

hidden
type: number
default: 0.035

lower minimum number of samples necessary in at least one of the sample groups for it to be a valid group

hidden
type: number
default: 1

higher minimum number of samples necessary in at least one of the sample groups for it to be a valid group

hidden
type: number
default: 1

lower maximum number of groups to identify in a single m/z slice

hidden
type: number
default: 50

higher maximum number of groups to identify in a single m/z slice

hidden
type: number
default: 50

DistFunc function: cor (Pearson's R) or cor_opt (default, calculate only 10% diagonal band of distance matrix, better runtime), cov (covariance), prd (product), euc (Euclidean distance)

hidden
type: string
default: cor_opt

Only obiwarp is supported

hidden
type: string
default: obiwarp

mass trace deviation in ppm

hidden
type: number
default: 10

lower width of peaks

hidden
type: number
default: 5

highest width of peaks

hidden
type: number
default: 30

level of noise

hidden
type: number
default: 1000

minimum difference in m/z for peaks with overlapping retention times, can be negative to allow overlap

hidden
type: number
default: -0.001

signal to noise ratio cutoff, definition see below.

hidden
type: number
default: 10

K in 'prefilter=c(k,I)'. Prefilter step for the first phase. Mass traces are only retained if they contain at least 'k' peaks with intensity >= 'I'.

hidden
type: number
default: 3

I in prefilter

hidden
type: number
default: 100

Function to calculate the m/z center of the feature: 'wMean' intensity weighted mean of the feature m/z values, 'mean' mean of the feature m/z values, 'apex' use m/z value at peak apex, 'wMeanApex3' intensity weighted mean of the m/z value at peak apex and the m/z value left and right of it, 'meanApex3' mean of the m/z value at peak apex and the m/z value left and right of it.

hidden
type: string
default: wMean

Integration method. If '=1' peak limits are found through descent on the mexican hat filtered data, if '=2' the descent is done on the real data. Method 2 is very accurate but prone to noise, while method 1 is more robust to noise but less exact.

hidden
type: number
default: 1

logical, if TRUE a Gaussian is fitted

hidden
type: boolean

A name for the class of sample

hidden
type: string
default: Sample

sigma value for grouping the peaks across chromatogram

hidden
type: number
default: 8

full width at half maximum for finding overlaping peaks

hidden
type: number
default: 0.6

which intensity value to use

hidden
type: string
default: maxo

ppm deviation between theoritical adduct mass and the experimental one

hidden
type: number
default: 10

this has to be negative (for testing only)!

hidden
type: string
default: negative

number of changes to consider (most often 1 is enough)

hidden
type: number
default: 1

ppm deviation when mapping MS2 parent ion to a mass trace

hidden
type: number
default: 10

rt difference (in second) for mapping MS2 parent ion to a mass trace (the mass trace is a range, star and end of the trace)

hidden
type: number
default: 5

Parameters used to characterize the internal library

name of the column showing which raw files contain which metabolite in the library_description_neg csv file

hidden
type: string
default: rawFile

name of the column showing id of the metabolites in the library_description_neg csv file

hidden
type: string
default: HMDB.YMDB.ID

name of the compount column in the library_description_neg csv file

hidden
type: string
default: PRIMARY_NAME

name of the mz column in the library_description_neg csv file

hidden
type: string
default: mz

"f" or "c", showing whether the Feature range or centroid of the feature should be used for mapping

hidden
type: string

Number of cores for mapping the features

hidden
type: number
default: 1

ppm error for mapping the library characterization masses to the experimental one

hidden
type: number
default: 10

Parameters that control how the results are outputted

relative difference of mass of the ID hit compare to a mass trace (ppm)

type: number
default: 10

retention time difference of ID to mass trace (second)

type: number
default: 5

should we impute adduct and different chance states with the same ID

type: boolean
default: true

Class of the samples (used for statistics and coverage calculations)

type: string
default: Class

what class of samples do you want to keep (anything not matching this in the Class column will be removed)

type: string
default: Sample

you want to rename the files

type: boolean
default: true

which column of the phenotype file to use for renaming

type: string
default: rename

do only want to see the identified mass traces or everything?

type: boolean

do you have technical replicates you want to average ?

type: boolean

which column of the phenotype file show the technical replicates

type: string
default: rep

should we log2 the output

type: boolean
default: true

any mass trace having more pecentage of the missing value will be removed

type: number
default: 50

do you want to normalize the data set to 'NA' if you don't want normalization

type: string
default: 1

Parameters specific to CFM-ID

path to a csv file containing your database

type: string

number of cores that cfm can use

type: number
default: 2

name of the column in the database for id of the molecules

type: string
default: Identifier

name of the column in the database for smile of the molecules

type: string
default: SMILES

name of the column in the database for mass of the molecules

type: string
default: MonoisotopicMass

name of the column in the database for name of the molecules

type: string
default: Name

name of the column in the database for inchi of the molecules

type: string
default: InChI

Parameters only for MetFrag

path to a csv file containing your database

type: string

number of cores that metfrag can use

type: number
default: 2

Parameters only for CSI:FINGERID

IMPORTANT: we don't support database file for csi:fingerid. You will need to provide what database to use here, the rest of the parameters will be taken from there parameter file

type: string
default: hmdb

number of cores that csi can use

type: number
default: 2

number of seconds that each csi ion can rum (time limit)

type: number
default: 600

Parameters that will be used in all the search engines

ppm deviation when mapping MS2 parent ion to a mass trace

type: number
default: 10

rt difference (in second) for mapping MS2 parent ion to a mass trace (the mass trace is a range, star and end of the trace)

type: number
default: 5

relative mass tolerance of the precursor (ppm)

type: number
default: 10

relative mass tolerance of the fragment ions (ppm)

type: number
default: 20

absolute mass tolerance of the fragment ions

type: number
default: 0.05

type of database to use (see metaboIGNITER guide)

type: string
default: LocalCSV

ionization method. This has to be neg (only for testing at this stage)

hidden
type: string
default: neg

adduct rules (primary or extended)

hidden
type: string

ions with less that this number will be removed

type: number
default: 2

Settings for CAMERA to detect adducts and isotopes

sigma value for grouping the peaks across chromatogram

type: number
default: 8

full width at half maximum for finding overlaping peaks

type: number
default: 0.6

which intensity value to use

type: string
default: maxo

ppm deviation between theoritical adduct mass and the experimental one

type: number
default: 10

this has to be negative (for testing only)!

hidden
type: string
default: negative

number of changes to consider (most often 1 is enough)

hidden
type: number
default: 1

Parameters to use for performing QC, blank and dilution filtering

set to true if you want to remove signal from blank

hidden
type: boolean

method of sumarization of signal in blank samples

hidden
type: string
default: max

Name of the class of the blank samples

hidden
type: string
default: Blank

Name of the class of the biological samples

hidden
type: string
default: Sample

set to T to compare blanks only to rest of the samples

hidden
type: string

Whether blank filtereing should be done or not?

hidden
type: boolean

This series will used for calculation of correlation. For example if this parameter is set like 1,2,3 and the class of dilution trends is set as D1,D2,D3 the following the pairs will be used for calculating the correlation: (D1,1),(D2,2),(D3,3)

hidden
type: string
default: 0.5,1,2,4

The class of the samples represneting dilution. This has to be separated by comma!

hidden
type: string
default: D1,D2,D3,D4

p-value of the correlation. Anything higher than this will be removed!

hidden
type: number
default: 0.05

minimum expected correlation. Aniything lower than this will be removed!

hidden
type: number
default: -1

If the tool should consider absolute correlation rather than the typical one from [-1 to 1] (F or T)

hidden
type: string

select to whether perfrom cv filtering or not

hidden
type: boolean

class of your QC samples

hidden
type: string
default: QC

Maximum coefficient of variation you expect. Anything higher than this will be removed!

hidden
type: number
default: 0.3

Parameters for quantification

set whether you want to do quantification with OpenMS (openms) or XCMS (xcms) in negative ionization

hidden
type: string

controls how to perform IPO possible values: "none": don't perform IPO, "global": performs IPO on all or selected number of samples. "global_quant": perform IPO only for quantification (not retention time correction and grouping), "local": performs IPO on individual samples one at the time. "local_quant": performs IPO on individual samples only for quantification, "local_RT": performs IPO on only for retention time correction and grouping.

hidden
type: string

Performs IPO on all the samples irrespective of the class they have

hidden
type: boolean

If ipo_allSamples_neg is false, one must pass the phenotype file to select sample. This parameter select the column of the phenotype file.

hidden
type: string
default: Class

Selects the files only with this value in the columnToSelect column

hidden
type: string
default: QC

Quantification methods for IPO. Only centWave is supported at this stage.

hidden
type: string
default: centWave

lowest level of noise

hidden
type: number

highest level of noise

hidden
type: number

lowest level of signal to noise threshold

hidden
type: number
default: 10

highest level of signal to noise threshold

hidden
type: number
default: 10

Function for centering the mz

hidden
type: string
default: wMean

Integration method. If '=1' peak limits are found through descent on the mexican hat filtered data, if '=2' the descent is done on the real data. Method 2 is very accurate but prone to noise, while method 1 is more robust to noise but less exact.

hidden
type: number
default: 1

logical, if TRUE a Gaussian is fitte

hidden
type: boolean

lower minimum width of peaks

hidden
type: number
default: 12

higher minimum width of peaks

hidden
type: number
default: 28

lower maximum width of peaks

hidden
type: number
default: 35

higher maximum width of peaks

hidden
type: number
default: 65

lower ppm mass deviation

hidden
type: number
default: 17

higher ppm mass deviation

hidden
type: number
default: 32

lower minimum difference in m/z for peaks with overlapping retention times, can be negative to allow overlap

hidden
type: number
default: -0.001

higher minimum difference in m/z for peaks with overlapping retention times, can be negative to allow overlap

hidden
type: number
default: 0.01

maximum charge of molecules (only used in individual setting)

hidden
type: number
default: 1

ppm mass deviation for adducts (only used in individual setting)

hidden
type: number
default: 10

lower value of K in 'prefilter_neg=c(k,I)'. Prefilter step for the first phase. Mass traces are only retained if they contain at least 'k' peaks with intensity >_neg= 'I'.

hidden
type: number
default: 3

higher value of K in 'prefilter_neg=c(k,I)'. Prefilter step for the first phase. Mass traces are only retained if they contain at least 'k' peaks with intensity >_neg= 'I'.

hidden
type: number
default: 3

lower I in prefilter

hidden
type: number
default: 100

higher I in prefilter

hidden
type: number
default: 100

number of cores used in IPO

hidden
type: number
default: 5

lower Penalty for Gap opening

hidden
type: number

higher Penalty for Gap opening

hidden
type: number
default: 0.4

lower Penalty for Gap enlargement

hidden
type: number
default: 2.1

higher Penalty for Gap enlargement

hidden
type: number
default: 2.7

lower step size (in m/z) to use for profile generation from the raw data files

hidden
type: number
default: 0.7

higher step size (in m/z) to use for profile generation from the raw data files

hidden
type: number
default: 1

lower Responsiveness of warping. 0 will give a linear warp based on start and end points. 100 will use all bijective anchors

hidden
type: number
default: 1

higher Responsiveness of warping. 0 will give a linear warp based on start and end points. 100 will use all bijective anchors

hidden
type: number
default: 1

lower Local weighting applied to diagonal moves in alignment

hidden
type: number
default: 2

higher Local weighting applied to diagonal moves in alignment

hidden
type: number
default: 2

lower Local weighting applied to gap moves in alignment

hidden
type: number
default: 1

higher Local weighting applied to gap moves in alignment

hidden
type: number
default: 1

Local rather than global alignment

hidden
type: number

lower bandwidth (consider something like retention time differences)

hidden
type: number
default: 22

higher bandwidth (consider something like retention time differences)

hidden
type: number
default: 38

lower minimum fraction of samples necessary in at least one of the sample groups for it to be a valid group

hidden
type: number
default: 0.3

higher minimum fraction of samples necessary in at least one of the sample groups for it to be a valid group

hidden
type: number
default: 0.7

lower mz width (mz differences)

hidden
type: number
default: 0.015

higher mz width (mz differences)

hidden
type: number
default: 0.035

lower minimum number of samples necessary in at least one of the sample groups for it to be a valid group

hidden
type: number
default: 1

higher minimum number of samples necessary in at least one of the sample groups for it to be a valid group

hidden
type: number
default: 1

lower maximum number of groups to identify in a single m/z slice

hidden
type: number
default: 50

higher maximum number of groups to identify in a single m/z slice

hidden
type: number
default: 50

DistFunc function: cor (Pearson's R) or cor_opt (default, calculate only 10% diagonal band of distance matrix, better runtime), cov (covariance), prd (product), euc (Euclidean distance)

hidden
type: string
default: cor_opt

Only obiwarp is supported

hidden
type: string
default: obiwarp

masstrance deviation in ppm

type: number
default: 10

lower width of peaks

type: number
default: 5

highest width of peaks

type: number
default: 30

level of noise

type: number
default: 1000

minimum difference in m/z for peaks with overlapping retention times, can be negative to allow overlap

type: number
default: -0.001

signal to noise ratio cutoff, definition see below.

type: number
default: 10

K in 'prefilter=c(k,I)'. Prefilter step for the first phase. Mass traces are only retained if they contain at least 'k' peaks with intensity >= 'I'.

type: number
default: 3

I in prefilter

type: number
default: 100

Function to calculate the m/z center of the feature: 'wMean' intensity weighted mean of the feature m/z values, 'mean' mean of the feature m/z values, 'apex' use m/z value at peak apex, 'wMeanApex3' intensity weighted mean of the m/z value at peak apex and the m/z value left and right of it, 'meanApex3' mean of the m/z value at peak apex and the m/z value left and right of it.

type: string
default: wMean

Integration method. If '=1' peak limits are found through descent on the mexican hat filtered data, if '=2' the descent is done on the real data. Method 2 is very accurate but prone to noise, while method 1 is more robust to noise but less exact.

type: number
default: 1

logical, if TRUE a Gaussian is fitted

type: boolean

name of the column in the phenotype_design_neg showing class information of the samples

type: string
default: Class

A name for the class of sample

type: string
default: Sample

step size (in m/z) to use for profile generation from the raw data files

type: number
default: 1

the index of the sample all others will be aligned to. If center==NULL, the sample with the most peaks is chosen as default.

type: string
default: NULL

Responsiveness of warping. 0 will give a linear warp based on start and end points. 100 will use all bijective anchors

type: number
default: 1

DistFunc function: cor (Pearson's R) or cor_opt (default, calculate only 10% diagonal band of distance matrix, better runtime), cov (covariance), prd (product), euc (Euclidean distance)

type: string

Penalty for Gap opening

type: string
default: NULL

Penalty for Gap enlargement

type: string
default: NULL

Local weighting applied to diagonal moves in alignment

type: number
default: 2

Local weighting applied to gap moves in alignment

type: number
default: 1

Local rather than global alignment

type: number

bandwidth (consider something like retention time differences)

type: number
default: 15

mz width (mz differences)

type: number
default: 0.005

minimum fraction of samples necessary in at least one of the sample groups for it to be a valid group

type: number
default: 0.5

minimum number of samples necessary in at least one of the sample groups for it to be a valid group

type: number
default: 1

maximum number of groups to identify in a single m/z slice

type: number
default: 50

Parameters used to tune library creation (only set if you want to do library idnetification)

set whether you want to do quantification with OpenMS (openms) or XCMS (xcms) in positive ionization (for library)

hidden
type: string

controls how to perform IPO possible values: "none": don't perform IPO, "global": performs IPO on all or selected number of samples. "local": performs IPO on individual samples one at the time.

hidden
type: string

Quantification methods for IPO. Only centWave is supported at this stage.

hidden
type: string
default: centWave

lowest level of noise

hidden
type: number

highest level of noise

hidden
type: number

lowest level of signal to noise threshold

hidden
type: number
default: 10

highest level of signal to noise threshold

hidden
type: number
default: 10

Function for centering the mz

hidden
type: string
default: wMean

Integration method. If '=1' peak limits are found through descent on the mexican hat filtered data, if '=2' the descent is done on the real data. Method 2 is very accurate but prone to noise, while method 1 is more robust to noise but less exact.

hidden
type: number
default: 1

logical, if TRUE a Gaussian is fitte

hidden
type: boolean

lower minimum width of peaks

hidden
type: number
default: 12

higher minimum width of peaks

hidden
type: number
default: 28

lower maximum width of peaks

hidden
type: number
default: 35

higher maximum width of peaks

hidden
type: number
default: 65

lower ppm mass deviation

hidden
type: number
default: 17

higher ppm mass deviation

hidden
type: number
default: 32

lower minimum difference in m/z for peaks with overlapping retention times, can be negative to allow overlap

hidden
type: number
default: -0.001

higher minimum difference in m/z for peaks with overlapping retention times, can be negative to allow overlap

hidden
type: number
default: 0.01

maximum charge of molecules (only used in individual setting)

hidden
type: number
default: 1

ppm mass deviation for adducts (only used in individual setting)

hidden
type: number
default: 10

lower value of K in 'prefilter_library_pos=c(k,I)'. Prefilter step for the first phase. Mass traces are only retained if they contain at least 'k' peaks with intensity >_library_pos= 'I'.

hidden
type: number
default: 3

higher value of K in 'prefilter_library_pos=c(k,I)'. Prefilter step for the first phase. Mass traces are only retained if they contain at least 'k' peaks with intensity >_library_pos= 'I'.

hidden
type: number
default: 3

lower I in prefilter

hidden
type: number
default: 100

higher I in prefilter

hidden
type: number
default: 100

number of cores used in IPO

hidden
type: number
default: 5

lower Penalty for Gap opening

hidden
type: number

higher Penalty for Gap opening

hidden
type: number
default: 0.4

lower Penalty for Gap enlargement

hidden
type: number
default: 2.1

higher Penalty for Gap enlargement

hidden
type: number
default: 2.7

lower step size (in m/z) to use for profile generation from the raw data files

hidden
type: number
default: 0.7

higher step size (in m/z) to use for profile generation from the raw data files

hidden
type: number
default: 1

lower Responsiveness of warping. 0 will give a linear warp based on start and end points. 100 will use all bijective anchors

hidden
type: number
default: 1

higher Responsiveness of warping. 0 will give a linear warp based on start and end points. 100 will use all bijective anchors

hidden
type: number
default: 1

lower Local weighting applied to diagonal moves in alignment.

hidden
type: number
default: 2

higher Local weighting applied to diagonal moves in alignment.

hidden
type: number
default: 2

lower Local weighting applied to gap moves in alignment.

hidden
type: number
default: 1

higher Local weighting applied to gap moves in alignment.

hidden
type: number
default: 1

Local rather than global alignment

hidden
type: number

lower bandwidth (consider something like retention time differences)

hidden
type: number
default: 22

higher bandwidth (consider something like retention time differences)

hidden
type: number
default: 38

lower minimum fraction of samples necessary in at least one of the sample groups for it to be a valid group

hidden
type: number
default: 0.3

higher minimum fraction of samples necessary in at least one of the sample groups for it to be a valid group

hidden
type: number
default: 0.7

lower mz width (mz differences)

hidden
type: number
default: 0.015

higher mz width (mz differences)

hidden
type: number
default: 0.035

lower minimum number of samples necessary in at least one of the sample groups for it to be a valid group

hidden
type: number
default: 1

higher minimum number of samples necessary in at least one of the sample groups for it to be a valid group

hidden
type: number
default: 1

lower maximum number of groups to identify in a single m/z slice

hidden
type: number
default: 50

higher maximum number of groups to identify in a single m/z slice

hidden
type: number
default: 50

DistFunc function: cor (Pearson's R) or cor_opt (default, calculate only 10% diagonal band of distance matrix, better runtime), cov (covariance), prd (product), euc (Euclidean distance)

hidden
type: string

Only obiwarp is supported

hidden
type: string
default: obiwarp

mass trace deviation in ppm

hidden
type: number
default: 10

lower width of peaks

hidden
type: number
default: 5

highest width of peaks

hidden
type: number
default: 30

level of noise

hidden
type: number
default: 1000

minimum difference in m/z for peaks with overlapping retention times, can be negative to allow overlap

hidden
type: number
default: -0.001

signal to noise ratio cutoff, definition see below.

hidden
type: number
default: 10

K in 'prefilter=c(k,I)'. Prefilter step for the first phase. Mass traces are only retained if they contain at least 'k' peaks with intensity >= 'I'.

hidden
type: number
default: 3

I in prefilter

hidden
type: number
default: 100

Function to calculate the m/z center of the feature: 'wMean' intensity weighted mean of the feature m/z values, 'mean' mean of the feature m/z values, 'apex' use m/z value at peak apex, 'wMeanApex3' intensity weighted mean of the m/z value at peak apex and the m/z value left and right of it, 'meanApex3' mean of the m/z value at peak apex and the m/z value left and right of it.

hidden
type: string
default: wMean

Integration method. If '=1' peak limits are found through descent on the mexican hat filtered data, if '=2' the descent is done on the real data. Method 2 is very accurate but prone to noise, while method 1 is more robust to noise but less exact.

hidden
type: number
default: 1

logical, if TRUE a Gaussian is fitted

hidden
type: boolean

A name for the class of sample

hidden
type: string
default: Sample

sigma value for grouping the peaks across chromatogram

hidden
type: number
default: 8

full width at half maximum for finding overlaping peaks

hidden
type: number
default: 0.6

which intensity value to use

hidden
type: string
default: maxo

ppm deviation between theoritical adduct mass and the experimental one

hidden
type: number
default: 10

this has to be positive (for testing only)!

hidden
type: string
default: positive

number of changes to consider (most often 1 is enough)

hidden
type: number
default: 1

ppm deviation when mapping MS2 parent ion to a mass trace

hidden
type: number
default: 10

rt difference (in second) for mapping MS2 parent ion to a mass trace (the mass trace is a range, star and end of the trace)

hidden
type: number
default: 5

Parameters used to characterize the internal library

name of the column showing which raw files contain which metabolite in the library_description_pos csv file

hidden
type: string
default: rawFile

name of the column showing id of the metabolites in the library_description_pos csv file

hidden
type: string
default: HMDB.YMDB.ID

name of the compount column in the library_description_pos csv file

hidden
type: string
default: PRIMARY_NAME

name of the mz column in the library_description_pos csv file

hidden
type: string
default: mz

"f" or "c", showing whether the Feature range or centroid of the feature should be used for mapping

hidden
type: string

Number of cores for mapping the features

hidden
type: number
default: 1

ppm error for mapping the library characterization masses to the experimental one

hidden
type: number
default: 10

Parameters that control how the results are outputted

relative difference of mass of the ID hit compare to a mass trace (ppm)

type: number
default: 10

retention time difference of ID to mass trace (second)

type: number
default: 5

should we impute adduct and different chance states with the same ID

type: boolean
default: true

Class of the samples (used for statistics and coverage calculations)

type: string
default: Class

what class of samples do you want to keep (anything not matching this in the Class column will be removed)

type: string
default: Sample

you want to rename the files

type: boolean
default: true

which column of the phenotype file to use for renaming

type: string
default: rename

do only want to see the identified mass traces or everything?

type: boolean

do you have technical replicates you want to average ?

type: boolean

which column of the phenotype file show the technical replicates

type: string
default: rep

should we log2 the output

type: boolean
default: true

any mass trace having more pecentage of the missing value will be removed

type: number
default: 50

do you want to normalize the data set to 'NA' if you don't want normalization

type: string
default: 1

Parameters specific to CFM-ID

path to a csv file containing your database

type: string

number of cores that cfm can use

type: number
default: 2

name of the column in the database for id of the molecules

type: string
default: Identifier

name of the column in the database for smile of the molecules

type: string
default: SMILES

name of the column in the database for mass of the molecules

type: string
default: MonoisotopicMass

name of the column in the database for name of the molecules

type: string
default: Name

name of the column in the database for inchi of the molecules

type: string
default: InChI

Parameters only for MetFrag

path to a csv file containing your database

type: string

number of cores that metfrag can use

type: number
default: 2

Parameters only for CSI:FINGERID

IMPORTANT: we don't support database file for csi:fingerid. You will need to provide what database to use here, the rest of the parameters will be taken from there parameter file

type: string
default: hmdb

number of cores that csi can use

type: number
default: 2

number of seconds that each csi ion can rum (time limit)

type: number
default: 600

Parameters that will be used in all the search engines

ppm deviation when mapping MS2 parent ion to a mass trace

type: number
default: 10

rt difference (in second) for mapping MS2 parent ion to a mass trace (the mass trace is a range, star and end of the trace)

type: number
default: 5

relative mass tolerance of the precursor (ppm)

type: number
default: 10

relative mass tolerance of the fragment ions (ppm)

type: number
default: 20

absolute mass tolerance of the fragment ions

type: number
default: 0.05

type of database to use (see metaboIGNITER guide)

type: string
default: LocalCSV

ionization method. This has to be pos (only for testing at this stage)

hidden
type: string
default: pos

adduct rules (primary or extended)

type: string

ions with less that this number will be removed

type: number
default: 2

Settings for CAMERA to detect adducts and isotopes

sigma value for grouping the peaks across chromatogram

type: number
default: 8

full width at half maximum for finding overlaping peaks

type: number
default: 0.6

which intensity value to use

type: string
default: maxo

ppm deviation between theoritical adduct mass and the experimental one

type: number
default: 10

this has to be positive (for testing only)!

hidden
type: string
default: positive

number of changes to consider (most often 1 is enough)

hidden
type: number
default: 1

Parameters to use for performing QC, blank and dilution filtering

set to true if you want to remove signal from blank

hidden
type: boolean

method of sumarization of signal in blank samples. Must be one of 'max', 'mean' or 'median'. For example, if 'max' is selected, a signal will be removed if it maximum abundance in the blank samples is higher than maximum abundance in biological samples.

hidden
type: string
default: max

Name of the class of the blank samples. This must show the class of blank samples exactly as you refer to them in your phenotype file

hidden
type: string
default: Blank

Name of the class of the biological samples

hidden
type: string
default: Sample

set to T to compare the blanks only to rest of the samples. If F, the blank signals will be compared with the samples with class sample_blankfilter_pos_xcms

hidden
type: string
default: T

Select whether you want to do dilution filtering

hidden
type: boolean

This series will used for calculation of correlation. For example if this parameter is set like 1,2,3 and the class of dilution trends is set as D1,D2,D3 the following the pairs will be used for calculating the correlation: (D1,1),(D2,2),(D3,3)

hidden
type: string
default: 0.5,1,2,4

The class of the samples represneting dilution. This has to be separated by comma! The samples are correlated to the exact order of the sequence provided here

hidden
type: string
default: D1,D2,D3,D4

p-value of the correlation. Anything higher than this will be removed!

hidden
type: number
default: 0.05

minimum expected correlation. Aniything lower than this will be removed!

hidden
type: number
default: -1

If the tool should consider absolute correlation rather than the typical one from [-1 to 1] (F or T)

hidden
type: string

select to whether perfrom cv filtering or not

hidden
type: boolean

class of your QC samples

hidden
type: string
default: QC

Maximum coefficient of variation you expect. Anything higher than this will be removed!

hidden
type: number
default: 0.3

Parameters for quantification

set whether you want to do quantification with OpenMS (openms) or XCMS (xcms) in positive ionization

hidden
type: string

controls how to perform IPO possible values: "none": don't perform IPO, "global": performs IPO on all or selected number of samples. "global_quant": perform IPO only for quantification (not retention time correction and grouping), "local": performs IPO on individual samples one at the time. "local_quant": performs IPO on individual samples only for quantification, "local_RT": performs IPO on only for retention time correction and grouping.

hidden
type: string

Performs IPO on all the samples irrespective of the class they have

hidden
type: boolean

If ipo_allSamples_pos is false, one must pass the phenotype file to select sample. This parameter select the column of the phenotype file.

hidden
type: string
default: Class

Selects the files only with this value in the columnToSelect column

hidden
type: string
default: QC

Quantification methods for IPO. Only centWave is supported at this stage.

hidden
type: string
default: centWave

lowest level of noise

hidden
type: number

highest level of noise

hidden
type: number

lowest level of signal to noise threshold

hidden
type: number
default: 10

highest level of signal to noise threshold

hidden
type: number
default: 10

Function for centering the mz

hidden
type: string
default: wMean

Integration method. If '=1' peak limits are found through descent on the mexican hat filtered data, if '=2' the descent is done on the real data. Method 2 is very accurate but prone to noise, while method 1 is more robust to noise but less exact.

hidden
type: number
default: 1

logical, if TRUE a Gaussian is fitte

hidden
type: boolean

lower minimum width of peaks

hidden
type: number
default: 12

higher minimum width of peaks

hidden
type: number
default: 28

lower maximum width of peaks

hidden
type: number
default: 35

higher maximum width of peaks

hidden
type: number
default: 65

lower ppm mass deviation

hidden
type: number
default: 17

higher ppm mass deviation

hidden
type: number
default: 32

lower minimum difference in m/z for peaks with overlapping retention times, can be negative to allow overlap

hidden
type: number
default: -0.001

higher minimum difference in m/z for peaks with overlapping retention times, can be negative to allow overlap

hidden
type: number
default: 0.01

maximum charge of molecules (only used in individual setting)

hidden
type: number
default: 1

ppm mass deviation for adducts (only used in individual setting)

hidden
type: number
default: 10

lower value of K in 'prefilter_pos=c(k,I)'. Prefilter step for the first phase. Mass traces are only retained if they contain at least 'k' peaks with intensity >_pos= 'I'.

hidden
type: number
default: 3

higher value of K in 'prefilter_pos=c(k,I)'. Prefilter step for the first phase. Mass traces are only retained if they contain at least 'k' peaks with intensity >_pos= 'I'.

hidden
type: number
default: 3

lower I in prefilter

hidden
type: number
default: 100

higher I in prefilter

hidden
type: number
default: 100

number of cores used in IPO

hidden
type: number
default: 5

lower Penalty for Gap opening

hidden
type: number

higher Penalty for Gap opening

hidden
type: number
default: 0.4

lower Penalty for Gap enlargement

hidden
type: number
default: 2.1

higher Penalty for Gap enlargement

hidden
type: number
default: 2.7

lower step size (in m/z) to use for profile generation from the raw data files

hidden
type: number
default: 0.7

higher step size (in m/z) to use for profile generation from the raw data files

hidden
type: number
default: 1

lower Responsiveness of warping. 0 will give a linear warp based on start and end points. 100 will use all bijective anchors

hidden
type: number
default: 1

higher Responsiveness of warping. 0 will give a linear warp based on start and end points. 100 will use all bijective anchors

hidden
type: number
default: 1

lower Local weighting applied to diagonal moves in alignment

hidden
type: number
default: 2

higher Local weighting applied to diagonal moves in alignment

hidden
type: number
default: 2

lower Local weighting applied to gap moves in alignment

hidden
type: number
default: 1

higher Local weighting applied to gap moves in alignment

hidden
type: number
default: 1

Local rather than global alignment

hidden
type: number

lower bandwidth (consider something like retention time differences)

hidden
type: number
default: 22

higher bandwidth (consider something like retention time differences)

hidden
type: number
default: 38

lower minimum fraction of samples necessary in at least one of the sample groups for it to be a valid group

hidden
type: number
default: 0.3

higher minimum fraction of samples necessary in at least one of the sample groups for it to be a valid group

hidden
type: number
default: 0.7

lower mz width (mz differences)

hidden
type: number
default: 0.015

higher mz width (mz differences)

hidden
type: number
default: 0.035

lower minimum number of samples necessary in at least one of the sample groups for it to be a valid group

hidden
type: number
default: 1

higher minimum number of samples necessary in at least one of the sample groups for it to be a valid group

hidden
type: number
default: 1

lower maximum number of groups to identify in a single m/z slice

hidden
type: number
default: 50

higher maximum number of groups to identify in a single m/z slice

hidden
type: number
default: 50

DistFunc function: cor (Pearson's R) or cor_opt (default, calculate only 10% diagonal band of distance matrix, better runtime), cov (covariance), prd (product), euc (Euclidean distance)

hidden
type: string
default: cor_opt

Only obiwarp is supported

hidden
type: string
default: obiwarp

masstrance deviation in ppm

type: number
default: 10

lower width of peaks

type: number
default: 5

highest width of peaks

type: number
default: 30

level of noise

type: number
default: 1000

minimum difference in m/z for peaks with overlapping retention times, can be negative to allow overlap

type: number
default: -0.001

signal to noise ratio cutoff, definition see below.

type: number
default: 10

K in 'prefilter=c(k,I)'. Prefilter step for the first phase. Mass traces are only retained if they contain at least 'k' peaks with intensity >= 'I'.

type: number
default: 3

I in prefilter

type: number
default: 100

Function to calculate the m/z center of the feature: 'wMean' intensity weighted mean of the feature m/z values, 'mean' mean of the feature m/z values, 'apex' use m/z value at peak apex, 'wMeanApex3' intensity weighted mean of the m/z value at peak apex and the m/z value left and right of it, 'meanApex3' mean of the m/z value at peak apex and the m/z value left and right of it.

type: string
default: wMean

Integration method. If '=1' peak limits are found through descent on the mexican hat filtered data, if '=2' the descent is done on the real data. Method 2 is very accurate but prone to noise, while method 1 is more robust to noise but less exact.

type: number
default: 1

logical, if TRUE a Gaussian is fitted

type: boolean

name of the column in the phenotype_design_pos showing class information of the samples

type: string
default: Class

A name for the class of sample

type: string
default: Sample

step size (in m/z) to use for profile generation from the raw data files

type: number
default: 1

the index of the sample all others will be aligned to. If center==NULL, the sample with the most peaks is chosen as default.

type: string
default: NULL

Responsiveness of warping. 0 will give a linear warp based on start and end points. 100 will use all bijective anchors

type: number
default: 1

DistFunc function: cor (Pearson's R) or cor_opt (default, calculate only 10% diagonal band of distance matrix, better runtime), cov (covariance), prd (product), euc (Euclidean distance)

type: string

Penalty for Gap opening

type: string
default: NULL

Penalty for Gap enlargement

type: string
default: NULL

Local weighting applied to diagonal moves in alignment

type: number
default: 2

Local weighting applied to gap moves in alignment

type: number
default: 1

Local rather than global alignment

type: number

bandwidth (consider something like retention time differences)

type: number
default: 15

mz width (mz differences)

type: number
default: 0.005

minimum fraction of samples necessary in at least one of the sample groups for it to be a valid group

type: number
default: 0.5

minimum number of samples necessary in at least one of the sample groups for it to be a valid group

type: number
default: 1

maximum number of groups to identify in a single m/z slice

type: number
default: 50

Input files includes mzML files and settings for performing identification using internal library

if you have already charaztrized your negative library set this to true and specify the path for library_charactrization_file_neg

hidden
type: boolean

path to the file from charaztrized library (negative)

hidden
type: string

Path to a folder containing library mzML files used for doing adduct calcculation (MS1 data in megative ionization method)

hidden
type: string

Path to a folder containing mzML files used for doing identification (MS2 data in negative ionization method)

hidden
type: string

Path to a csv file containing description of the library for negative (see the help)

hidden
type: string

Input files includes mzML files and settings for performing identification using internal library

if you have already charaztrized your positive library set this to true and specify the path for library_charactrization_file_pos

hidden
type: boolean

path to the file from charaztrized library (positive)

hidden
type: string

Path to a folder containing library mzML files used for doing adduct calcculation (MS1 data in positive ionization method)

hidden
type: string

Path to a folder containing mzML files used for doing identification (MS2 data in positive ionization method)

hidden
type: string

Path to a csv file containing description of the library for positive (see the help)

hidden
type: string

Input files includes mzML files for performing identification

ath to a folder containing mzML files used for doing identification (MS2 data in positive ionization method)

type: string

Path to a folder containing mzML files used for doing identification (MS2 data in negative ionization method)

type: string

Used to control functionality of the workflow e.g identification, quantification etc

set to true to publish all the middle stages

type: boolean

Set to false if you don't want to do identification. You will not require to set MS2 related parameters if you set this to false

type: boolean

Should Metfrag be used for doing identification?

type: boolean

Should CSI:FingerID be used for doing identification?

type: boolean

Should CFM-ID be used for doing identification?

type: boolean

Should an internal library be used for doing identification?

hidden
type: boolean

You can either set to 'pos' (only positive), 'neg' (only negative), 'both' (both positive and negative).

type: string

Set to true if your data is in profile mode (only for quantification!)

type: boolean

Used for peak picking and feature detection

Path to the ini file for PeakPickerHiRes

hidden
type: string
default: $baseDir/assets/openms/openms_peak_picker_ini_pos.ini

Path to the ini file for PeakPickerHiRes

hidden
type: string
default: $baseDir/assets/openms/openms_peak_picker_ini_neg.ini

Path to the ini file for OpenMS FeatureFinderMetabo in positive mode

hidden
type: string
default: $baseDir/assets/openms/openms_feature_finder_metabo_ini_pos.ini

Path to the ini file for OpenMS FeatureFinderMetabo in negative mode

hidden
type: string
default: $baseDir/assets/openms/openms_feature_finder_metabo_ini_neg.ini

Path to the ini file for PeakPickerHiRes (for library)

hidden
type: string
default: $baseDir/assets/openms/openms_peak_picker_lib_ini_pos.ini

Path to the ini file for PeakPickerHiRes (for library)

hidden
type: string
default: $baseDir/assets/openms/openms_peak_picker_lib_ini_neg.ini

Path to the ini file for OpenMS FeatureFinderMetabo in positive mode (for library)

hidden
type: string
default: $baseDir/assets/openms/openms_feature_finder_metabo_lib_ini_pos.ini

Path to the ini file for OpenMS FeatureFinderMetabo in negative mode (for library)

hidden
type: string
default: $baseDir/assets/openms/openms_feature_finder_metabo_lib_ini_neg.ini

Input files includes mzML files for performing quantification

Path to a folder containing mzML files used for doing quantification (MS1 data in positive ionization method)

required
type: string

Path to a folder containing mzML files used for doing quantification (MS1 data in negative ionization method)

type: string

Path to a csv file containing the experimental design (MS1 data in positive ionization method)

type: string

Path to a csv file containing the experimental design (MS1 data in negative ionization method)

type: string

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

Display help text.

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.

Boolean whether to validate parameters against the schema at runtime

hidden
type: boolean
default: true

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})$

This works exactly as with --email, except emails are only sent if the workflow is not successful.

Send plain-text email instead of HTML.

hidden
type: boolean

Set to receive plain-text e-mails instead of HTML formatted.

Do not use coloured log outputs.

hidden
type: boolean

Set to disable colourful command line output and live life in monochrome.

Directory to keep pipeline Nextflow logs and reports.

hidden
type: string
default: ${params.outdir}/pipeline_info

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.

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: number
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|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'

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

Git commit id for Institutional configs.

hidden
type: string
default: master

Provide git commit id for custom Institutional configs hosted at nf-core/configs. This was implemented for reproducibility purposes. Default: master.

 Download and use config file with following git commit id  
--custom_config_version d52db660777c4bf36546ddb188ec530c3ada1b96  

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 the custom_config_base option. For example:

 Download and unzip the config files  
cd /path/to/my/configs  
wget https://github.com/nf-core/configs/archive/master.zip  
unzip master.zip  
  
 Run the pipeline  
cd /path/to/my/data  
nextflow run /path/to/pipeline/ --custom_config_base /path/to/my/configs/configs-master/  

Note that the nf-core/tools helper package has a download command to download all required pipeline files + singularity containers + institutional configs in one go for you, to make this process easier.

Institutional configs hostname.

hidden
type: string

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