The only required parameters of cycloquest are address of mgf/mzxml file, and fasta file. the parameters are described below :

cycloquest_html : database search for linear/cyclic peptides
Required arguments:
-------------------
<path to input mzxml/mgf file>
<path to input fasta file>

Optional cycloquest_html arguments: 
----------------------------- 
-out <path to output html file>                                      (default : out.html)
-linear                                                   search only for linear peptides
-cyclic                                                   search only for cyclic peptides
-num_top X                               number of top search hits returned (default: 20)
-num_peaks X 		                             number of top peaks kept in spectra 
-parent_mass X                          Parent Mass in Da (Default : from mzxml/mgf file)
-charge                                                   (Default : from mzxml/mgf file)
-add_decoy                                                          	  search decoy DB
-precursor_ion_tolerance               		                         Default : 0.5 Da
-product_ion_tolerance     	                                	 Default : 0.5 Da
-scan_num X                                                   Default : analyze all scans
-filter_parent_mass X Y         only analyze the species with parent mass between X and Y
-num_cys X                                   only acept peptides with X cysteines
-reduced     	                        		                          	 
-IAM_reduced 	                                                 			 
-MAL_reduced    	                      	                             		 
-PFA_reduced  	                                                      			 
-NaBH4_reduced                          			                         
-CMet_reduced    	                      			                         
-NIPIA_reduced   

