singjust/dialignr repository overview

$docker run -it --rm -v `pwd`:/data singjust/dialignr:2.0.0

Name: 
        Run DIAlignR's alignTargetedRuns via the Command Line

    Usage: 
        Rscript alignTargetedRuns_cli.R --dataPath=/data/ [args] | --help

        Example: Rscript alignTargetedRuns_cli.R --dataPath=/data/osw/ --params=context:experiment-wide,maxFdrQuery:0.01

        Example2: Rscript alignTargetedRuns_cli.R --dataPath=/data/osw/ --oswMerged=FALSE --params=context:experiment-wide,maxFdrQuery:0.01 --runs=run0,run1,run2 --peps=0,1 --applyFun=BiocParallel::bplapply --regBioCP=BiocParallel::register(BiocParallel::MulticoreParam(workers=4,progressbar=TRUE))

    Options: 
        --dataPath: path to xics and osw directory.
        --outFile: name of the output file.
        --oswMerged: TRUE for experiment-wide FDR and FALSE for run-specific FDR by pyprophet.
        --params: Parameters for the alignment functions generated from DIAlignR::paramsDIAlignR(). Separate keys and values using a ':', and separate parameters using ','. Example: --params=context:experiment-wide,maxFdrQuery:0.01,fitEMG:TRUE
        --runs: names of xics file without extension. Separate runs using ','. Example: --runs=run0,run1,run2
        --refRun: reference for alignment. If no run is provided, m-score is used to select reference run.
        --peps: ids of peptides to be aligned. If NULL, align all peptides. Separate peptide ids using ','. Example--peps=1,2,3
        --appyFun: value must be either lapply or BiocParallel::bplapply.
        --regBioCP: If using BiocParallel::bplapply, register cores to use. Example: --regBioCP=BiocParallel::register(BiocParallel::MulticoreParam(workers=4,progressbar=TRUE)) . Make sure there are no spaces in this command
        --help: Display this help message

$docker run -it --rm -v `pwd`:/data singjust/dialignr:2.0.0 --dataPath=/data/ --outFile=/data/dialignr