Skip to content
Permalink
Branch: master
Find file Copy path
Find file Copy path
Fetching contributors…
Cannot retrieve contributors at this time
88 lines (65 sloc) 1.67 KB
## DO-MS command line configuration
## for use with do-ms_cmd.R
## Input/Output
# paths to folders with MaxQuant txt output
input_folders:
- ~/Downloads/example_data_SQC68
# files to load from each folder
load_input_files:
- evidence
- msms
- msmsScans
- allPeptides
- summary
- parameters
# match up with misc_input_files list in global.R
#misc_input_files:
# inclusion_list: /path/to/inclusion_list.txt
output: ~/Downloads/SQC68_DO-MS_report.html
## Filters
# regular expressions to match raw file names against
include_files: 'SQC68D[1-3]'
exclude_files: ~
# experiment name format string
# %i -- index of raw file
# %f -- folder name
# %e -- raw file name
exp_name_format: '%e'
# optional regular expression pattern to extract
# from the experiment names after applying the format string
exp_name_pattern: 'SQC68[A-Z]{1}[0-9]{1}'
# custom names for files
exp_names:
- '250ms IT'
- '500ms IT'
- '1000ms IT'
# custom order for files
exp_order: [1,2,3]
pep_thresh: 1
pif_thresh: 0
remove_decoy: REV_
remove_contam: CON_
## Figure rendering options
ppi: 150
# label font size
figure_title_font_size: 16
# axis tick label font size
figure_axis_font_size: 12
# facet label font size
figure_facet_font_size: 12
# line width
figure_line_width: 1
# show background grid
figure_show_grid: true
## Report options
# choices: pdf, html
report_format: html
# choices: default, cerulean, flatly, darkly, readable,
# spacelab, united, cosmo, lumen, paper, sandstone, simplex, yeti
# previews: https://bootswatch.com/3/
report_theme: readable
# figure size (in inches)
report_figure_width: 5
report_figure_height: 5
# figure format. choices: pdf, png
report_figure_format: png
You can’t perform that action at this time.