General
create_settings
WarpTools - a collection of tools for EM data pre-processing
Version 2.0.0
Showing all available options for command create_settings:
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-o, --output REQUIRED Path to the new settings file
--folder_processing Processing folder location
--folder_data REQUIRED Raw data folder location
--recursive Recursively search for files in sub-folders (only when pr
ocessing and raw data locations are different)
--extension Import file search term: Use e.g. *.mrc to process all MR
C files, or something more specific like FoilHole1_*.mrc
--angpix REQUIRED Unbinned pixel size in Angstrom. Alternatively s
pecify the path to an image or MDOC file to read the valu
e from. If a wildcard pattern is specified, the first fil
e will be used
--bin 2^x pre-binning factor, applied in Fourier space when loa
ding raw data. 0 = no binning, 1 = 2x2 binning, 2 = 4x4 b
inning, supports non-integer values
--bin_angpix Choose the binning exponent automatically to match this t
arget pixel size in Angstrom
--gain_path Path to gain file, relative to import folder
--defects_path Path to defects file, relative to import folder
--gain_flip_x Flip X axis of the gain image
--gain_flip_y Flip Y axis of the gain image
--gain_transpose Transpose gain image (i.e. swap X and Y axes)
--exposure Default: 1. Overall exposure per Angstrom^2; use negative
value to specify exposure/frame instead
--eer_ngroups Default: 40. Number of groups to combine raw EER frames i
nto, i.e. number of 'virtual' frames in resulting stack;
use negative value to specify the number of frames per vi
rtual frame instead
--eer_groupexposure As an alternative to --eer_ngroups, fractionate the frame
s so that a group will have this exposure in e-/A^2; this
overrides --eer_ngroups
--tomo_dimensions X, Y, and Z dimensions of the full tomogram in unbinned p
ixels, separated by 'x', e.g. 4096x4096x1000
move_data
WarpTools - a collection of tools for EM data pre-processing
Version 2.0.0
Showing all available options for command move_data:
------------------------------Data import settings------------------------------
--settings REQUIRED Path to Warp's .settings file, typically loca
ted in the processing folder. Default file name is 'pr
evious.settings'.
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--to REQUIRED New directory containing raw data; if raw dat
a are located in sub-folders and require recursive sea
rch, specify the top directory here
--new_settings REQUIRED Where to save an updated .settings file conta
ining the new raw data location
----------------------Advanced data import & flow options-----------------------
--input_data Overrides the list of input files specified in the .se
ttings file. Accepts a space-separated list of files,
wildcard patterns, or .txt files with one file name pe
r line.
--input_data_recursive Enables recursive search for files matching the wildca
rd pattern specified in --input_data. Only applicable
when processing and directories are separate. All file
names must be unique.
--input_processing Specifies an alternative directory containing pre-proc
essed results. Overrides the processing directory in t
he .settings file.
--output_processing Specifies an alternative directory to save processing
results. Overrides the processing directory in the .se
ttings file.
filter_quality
WarpTools - a collection of tools for EM data pre-processing
Version 2.0.0
Showing all available options for command filter_quality:
------------------------------Data import settings------------------------------
--settings REQUIRED Path to Warp's .settings file, typically loca
ted in the processing folder. Default file name is 'pr
evious.settings'.
------------------------Output mode (mutually exclusive)------------------------
--histograms Print a histogram for each quality metric and exit
-o, --output Path to a .txt file that will contain a list of series
that pass the filter criteria
----------------------------------CTF metrics-----------------------------------
--defocus Defocus in ยตm: 1 value = min; 2 values = min & max
--astigmatism Astigmatism deviation from the dataset's mean, express
ed in standard deviations: 1 value = min; 2 values = m
in & max
--phase Phase shift as a fraction of ฯ: 1 value = min; 2 value
s = min & max
--resolution Resolution estimate based on CTF fit: 1 value = min; 2
values = min & max
---------------------------------Motion metrics---------------------------------
--motion Average motion in first 1/3 of a frame series in ร
: 1
value = min; 2 values = min & max
-----------------------------Image content metrics------------------------------
--crap Percentage of masked area in an image (frame series on
ly): 1 value = min; 2 values = min & max
--particles Number of particles: 1 value = min; 2 values = min & m
ax; requires --particles_star to be set
--particles_star Path to STAR file(s) with particle information; may co
ntain a wildcard that matches multiple files
------------------------------Tilt series metrics-------------------------------
--ntilts Number of tilts in a tilt series: 1 value = min; 2 val
ues = min & max
----------------------Advanced data import & flow options-----------------------
--input_data Overrides the list of input files specified in the .se
ttings file. Accepts a space-separated list of files,
wildcard patterns, or .txt files with one file name pe
r line.
--input_data_recursive Enables recursive search for files matching the wildca
rd pattern specified in --input_data. Only applicable
when processing and directories are separate. All file
names must be unique.
--input_processing Specifies an alternative directory containing pre-proc
essed results. Overrides the processing directory in t
he .settings file.
--output_processing Specifies an alternative directory to save processing
results. Overrides the processing directory in the .se
ttings file.
change_selection
WarpTools - a collection of tools for EM data pre-processing
Version 2.0.0
Showing all available options for command change_selection:
------------------------------Data import settings------------------------------
--settings REQUIRED Path to Warp's .settings file, typically loca
ted in the processing folder. Default file name is 'pr
evious.settings'.
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--select Change status to selected
--deselect Change status to deselected
--null Change status to null, which is the default status
--invert Invert status if it isn't null
----------------------Advanced data import & flow options-----------------------
--input_data Overrides the list of input files specified in the .se
ttings file. Accepts a space-separated list of files,
wildcard patterns, or .txt files with one file name pe
r line.
--input_data_recursive Enables recursive search for files matching the wildca
rd pattern specified in --input_data. Only applicable
when processing and directories are separate. All file
names must be unique.
--input_processing Specifies an alternative directory containing pre-proc
essed results. Overrides the processing directory in t
he .settings file.
--output_processing Specifies an alternative directory to save processing
results. Overrides the processing directory in the .se
ttings file.
threshold_picks
WarpTools - a collection of tools for EM data pre-processing
Version 2.0.0
Showing all available options for command threshold_picks:
------------------------------Data import settings------------------------------
--settings REQUIRED Path to Warp's .settings file, typically loca
ted in the processing folder. Default file name is 'pr
evious.settings'.
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--in_suffix REQUIRED Suffix for the names of the input STAR files
(file names will be assumed to match {item name}_{--in
_suffix}.star pattern)
--out_suffix REQUIRED Suffix for the names of the output STAR files
(file names will be {item name}_{--in_suffix}_{--outs
uffix}.star)
--out_combined Path to a single STAR file into which all results will
be combined; internal paths will be made relative to
this location
--minimum Remove all particles below this threshold
--maximum Remove all particles above this threshold
--top_series Keep this many top-scoring series
--top_picks Keep this many top-scoring particles for each series
----------------------Advanced data import & flow options-----------------------
--input_data Overrides the list of input files specified in the .se
ttings file. Accepts a space-separated list of files,
wildcard patterns, or .txt files with one file name pe
r line.
--input_data_recursive Enables recursive search for files matching the wildca
rd pattern specified in --input_data. Only applicable
when processing and directories are separate. All file
names must be unique.
--input_processing Specifies an alternative directory containing pre-proc
essed results. Overrides the processing directory in t
he .settings file.
--output_processing Specifies an alternative directory to save processing
results. Overrides the processing directory in the .se
ttings file.
helpgpt
WarpTools - a collection of tools for EM data pre-processing
Version 2.0.0
Showing all available options for command helpgpt:
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--key OpenAI key to be saved to ~/openai.key