settings.yaml

---
# Global Settings for the DO-MS app and report

#Switch between dia-nn and max_quant mode
do_ms_mode: "dia-nn"
#do_ms_mode: "max_quant"

dia-nn:
  mode_name: 'DIA-NN'
  mode_skin: 'purple'
      
  ChemicalLabels:
      - "(mTRAQ0)"
      - "(mTRAQ4)"
      - "(mTRAQ8)"
          
  channels:
    mtraq0:
      modification: "(mTRAQ0)"
      name: "d0"
      
    mtraq4:
      modification: "(mTRAQ4)"
      name: "d4"
      
    mtraq8:
      modification: "(mTRAQ8)"
      name: "d8"
      
      
  modifications:
    phospho:
      unimod: "(UniMod:21)"
      name: "Phosphorylation"
      
    methyl:
      unimod: "(UniMod:34)"
      name: "Methylation"
      
    acetyl:
      unimod: "(UniMod:1)"
      name: "Acetylation"
      
  misc_input_files:
    allPeptides:
      name: 'allPeptides'
      file: 'allPeptides.txt'
      help: 'MaxQuant allPeptides.txt file'
      default_enabled: false

    XIC_Reference:
      name: 'xic_ref'
      file: 'report.XIC.tsv'
      help: 'Reference XIC file'
      default_enabled: false

    XIC_Standard:
      name: 'xic_standard'
      file: 'report.XIC.tsv'
      help: 'Technical Standard XIC file'
      default_enabled: false
  
  # Input files to load from each search output folder
  input_files:
    report:
      name: 'report'
      file: 'report.parquet'
      help: 'DIA-NN report.parquet'
      default_enabled: true
      
    ms1_extracted:
      name: 'ms1_extracted'
      file: 'report.pr_matrix_channels_ms1_extracted.tsv'
      help: 'DIA-NN ms1_extracted.tsv'
      default_enabled: true
      
    features:
      name: 'features'
      file: 'features.tsv'
      help: 'feature-detection features.tsv'
      default_enabled: true
      
    fill_times:
      name: 'fill_times'
      file: 'fill_times.tsv'
      help: 'feature-detection fill_times.tsv'
      default_enabled: true
      
    tic:
      name: 'tic'
      file: 'tic.tsv'
      help: 'extracted total ion current tic.tsv'
      default_enabled: true
      
    sn:
      name: 'sn'
      file: 'sn.tsv'
      help: 'extracted signal to noise sn.tsv'
      default_enabled: true
      
  # Retention time filter applied to all statistics displaying retention time information
  RT.Start: 0
  RT.End: 90
    
max_quant:
  mode_name: 'Max Quant'
  mode_skin: 'blue'
  
  # Input files to load from each search output folder
  input_files:
    evidence:
      name: 'evidence'
      file: 'evidence.txt'
      help: 'MaxQuant evidence.txt file'
      default_enabled: true
    msms:
      name: 'msms'
      file: 'msms.txt'
      help: 'MaxQuant msms.txt file'
      default_enabled: true
    msmsScans:
      name: 'msmsScans'
      file: 'msmsScans.txt'
      help: 'MaxQuant msmsScans.txt file'
      default_enabled: true
    allPeptides:
      name: 'allPeptides'
      file: 'allPeptides.txt'
      help: 'MaxQuant allPeptides.txt file'
      default_enabled: true
    summary:
      name: 'summary'
      file: 'summary.txt'
      help: 'MaxQuant summary.txt file'
      default_enabled: true
    parameters:
      name: 'parameters'
      file: 'parameters.txt'
      help: 'MaxQuant parameters.txt file'
      default_enabled: true
    msScans:
      name: 'msScans'
      file: 'msScans.txt'
      help: 'MaxQuant msScans.txt file'
      default_enabled: true

  # Misc. input files to provide upload forms for
  misc_input_files:
    inclusion_list:
      name: 'inclusion_list'
      help: 'Inclusion List .txt file'
    Labeling_Efficiency_list:
      name: 'Labeling_Efficiency'
      help: 'Labeling Efficiency .txt file'
    dartid_list:
      name: 'DART-ID'
      help: 'DART-ID evidence_updated.txt file'
        
# Allow addition of folders without MaxQuant txt output files?
allow_all_folders: true
    

## Filtering options

pep_thresh: 1
pif_thresh: 0
remove_decoy: REV_
remove_contam: CON_

exp_name_format: '%e'
exp_name_pattern: ''

## Figure rendering options

ppi: 150

## download figure settings
download_figure_units: 'in'
download_figure_width: 6
download_figure_height: 5

# label font size
figure_title_font_size: 12
# axis tick label font size
figure_axis_font_size: 10
# facet label font size
figure_facet_font_size: 10
# 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

## Structural Display Options

# if there are more tabs than tab colors, will repeat this array
# taken from: c(RColorBrewer::brewer.pal(5, 'Set1'), RColorBrewer::brewer.pal(8, 'Dark2')[c(1, 4, 3, 5, 2)])
tab_colors: ['#E41A1C', '#377EB8', '#4DAF4A', '#984EA3', '#FF7F00', '#1B9E77', '#E7298A', '#7570B3', '#66A61E', '#D95F02']

## Column Aliases
# rename columns to get backwards-compatibility with older versions of MaxQuant
# can also be used to get compatiblity with other search engines or workflows (i.e., ProteomeDiscoverer)

aliases:
  'Raw.file':
    - Run
    - Raw.File
    - RawFile
  'Retention.time':
    - RT
    - Retention.Time
    - RetentionTime