JSON analysis file

Example JSON analysis file

The example JSON analysis file will be reported by calling PIA with the --example argument, it looks like this:

{
"considerModifications": false,
"createPSMsets": true,
"errorOnNoDecoys": true,
"psmLevelFileID": 0,
"calculateAllFDR": true,
"calculateCombinedFDRScore": true,
"decoyPattern": "DECOY_.*",
"topIdentifications": 0,
"preferredFDRScores": [],
"psmFilters": [
    "psm_score_filter_psm_combined_fdr_score <= 0.01"
],
"psmExportFile": "/tmp/piaExport-PSMs.mzTab",
"inferePeptides": true,
"peptideLevelFileID": 0,
"peptideFilters": [
    "psm_score_filter_psm_combined_fdr_score <= 0.01"
],
"peptideExportWithPSMs": true,
"peptideExportFile": "/tmp/piaExport-peptides.csv",
"infereProteins": true,
"inferenceMethod": "inference_occams_razor",
"inferenceFilters": [
    "psm_score_filter_psm_combined_fdr_score <= 0.01"
],
"scoringMethod": "scoring_multiplicative",
"scoringBaseScore": "psm_combined_fdr_score",
"scoringPSMs": "best",
"proteinFilters": [
    "protein_q_value_filter <= 0.01"
],
"proteinExportFile": "/tmp/piaExport-proteins.mzid",
"proteinExportWithPSMs": false,
"proteinExportWithPeptides": false,
"proteinExportWithProteinSequences": false
}