Add the CLI doc back.

README.md

@@ -20,7 +20,7 @@ IonQuant is a fast and comprehensive tool for MS1 precursor intensity-based quan
 ## System requirements
 1. Java 1.9+.
 2. `ext` folder from [the latest MSFragger](https://msfragger.arsci.com/upgrader/).
-3. The latest FragPipe from [here](https://github.com/Nesvilab/FragPipe/releases/latest)
+3. The latest FragPipe from [here](https://github.com/Nesvilab/FragPipe/releases/latest) (optional).
 
 **Note:** Bruker's native library needs [Visual C++ Redistributable for Visual Studio 2017](https://aka.ms/vs/16/release/VC_redist.x64.exe) in Windows. If you see an error saying cannot find Bruker native library, please try to install the Visual C++ redistibutable.
 
@@ -32,7 +32,54 @@ Changelog can be found from [here](https://github.com/Nesvilab/IonQuant/blob/mas
 
 ## Usage
 1. Download [FragPipe](http://fragpipe.nesvilab.org/) from [here](https://github.com/Nesvilab/FragPipe/releases/latest).
-2. Follow the [tutorial](https://fragpipe.nesvilab.org/docs/tutorial_lfq.html).
+2. Follow the [tutorial](https://fragpipe.nesvilab.org/docs/tutorial_lfq.html) (recommended).
+
+### Users can also run IonQuant standalone in command line interface
+1. Download the standalone zip file from [here](https://msfragger.arsci.com/ionquant/).
+2. Run `java -jar IonQuant.jar` to print the help document.
+
+```shell
+Usage:
+        java -jar IonQuant.jar <options> --specdir <one directory to the spectral files> --psm <path to psm.tsv file> --psm <path to psm.tsv file>...
+        OR
+        java -jar IonQuant.jar <options> --filelist <path to filelist file>
+Options:
+        --specdir <string>     # Directory containing the spectral files (d/mzml/mzxml/raw/quantindex). One --specdir indicates one spectral directory and can have multiple --specdir.
+        --threads <integer>    # Number of threads. 0 = all logical cores. Default: 0
+        --mztol <float>        # MS1 tolerance in PPM. Default: 10.0
+        --imtol <float>        # 1/K0 tolerance. Default: 0.05
+        --rttol <float>        # Retention time tolerance. Unit: min. Default: 0.4
+        --psm <string>         # Path to Philosopher's psm.tsv. One --psm indicates one psm.tsv and can have multiple --psm.
+        --multidir <string>    # Output directory for the multi-experimental result. Optional. Default: <blank>
+        --normalization 0/1    # Normalize the intensities across all runs. Default: 1
+        --minisotopes 1/2/3    # Minimum isotopes required in feature extraction. Default: 2
+        --minscans <integer>   # Minimum MS1 scans required in feature extraction. Default: 3
+        --minions <integer>    # Minimum ions required in quantifying proteins. Only for MaxLFQ intensity. Default: 2
+        --excludemods <string> # Excluded modifications in quantifying peptide sequences and proteins. Format: <amino acid><mass>;... Default: <blank>
+        --maxlfq 0/1           # Calculate MaxLFQ intensity. 0 = no, 1 = yes. Default: 1
+        --ibaq 0/1             # [experimental] Calculate iBAQ intensity. The iBAQ intensity is normalized by the protein length, not the number of theoretical peptides. 0 = no, 1 = yes. Default: 0
+        --minexps <int>        # Minimum experiments in picking an ion for quantifying proteins. Only for intensity, not for MaxLFQ intensity. Default: 1
+        --minfreq <float>      # Minimum required frequency of an ion being selected for protein quantification. Only for intensity, not for MaxLFQ intensity. Default: 0
+        --tp <int>             # Number of ions used in quantifying each protein. If 0, using all ions. For intensity, not for MaxLFQ intensity. Default: 0
+        --mbr 0/1              # Perform match-between-runs. Default: 0
+        --mbrrttol <float>     # Retention time tolerance used in match-between-runs. Unit: min. Default: 1.0
+        --mbrimtol <float>     # 1/K0 tolerance used in match-between-runs. Default: 0.05
+        --mbrtoprun <integer>  # Maximum number of donor runs for each acceptor run. Default: 10
+        --mbrmincorr <float>   # Minimum correlation coefficient between a donor run and its acceptor run. Default: 0
+        --ionmobility 0/1      # The data has ion mobility information or not (for conventional LC-MS data). Default: 0
+        --ionfdr <float>       # Transferred ion false discovery rate threshold. Default: 0.01
+        --peptidefdr <float>   # Transferred peptide false discovery rate threshold. Default: 1
+        --proteinfdr <float>   # Transferred protein false discovery rate threshold. Default: 1
+        --light <string>       # Light labelling mass. Format: <amino acids><mass>;<amino acids><mass>;... Optional. Default: <blank>
+        --medium <string>      # Medium labelling mass. Format: <amino acids><mass>;<amino acids><mass>;... Optional. Default: <blank>
+        --heavy <string>       # Heavy labelling mass. Format: <amino acids><mass>;<amino acids><mass>;... Optional. Default: <blank>
+        --requantify 0/1       # Re-quantify unidentified feature based on identified feature. Only activate when --light, --medium, or --heavy is not empty. Default: 1
+        --writeindex 0/1       # Write indexed file on disk for further usage. 0 = no, 1 = yes. Default: 0
+        --locprob <float>      # Localization probability threshold. Default: 0
+        --filelist <string>    # A file containing --specdir, and --psm. Default: <blank>
+        --uniqueness 0/1/2     # Peptide-protein uniqueness. 0 = unique+razor, 1 = unique only, 2 = all. Default: 0
+        --modlist <string>     # A file lists modification masses. Those masses are used to remove the mass discrepancy due to rounding errors. Default: <blank>
+```
 
 ## Tutorials:
 - [Using FragPipe coupled with MSFragger and IonQuant to analyze samples](https://fragpipe.nesvilab.org/docs/tutorial_fragpipe.html)