comparison PMD_FDR_package_for_Galaxy.R @ 1:460edeedeb7d draft default tip

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit d87c44ec8fd5bc03d7bb06f65a1a6ec247daee36"
author galaxyp
date Thu, 10 Oct 2019 17:29:37 -0400
parents 5cc0c32d05a2
children
comparison
equal deleted inserted replaced
0:5cc0c32d05a2 1:460edeedeb7d
2943 local_add_argument("--psm_report_1_percent", default = "" , help="full name and path to the PSM report for 1% FDR") 2943 local_add_argument("--psm_report_1_percent", default = "" , help="full name and path to the PSM report for 1% FDR")
2944 local_add_argument("--output_i_fdr" , default = "" , help="full name and path to the i-FDR output file ") 2944 local_add_argument("--output_i_fdr" , default = "" , help="full name and path to the i-FDR output file ")
2945 local_add_argument("--output_g_fdr" , default = "" , help="full name and path to the g-FDR output file ") 2945 local_add_argument("--output_g_fdr" , default = "" , help="full name and path to the g-FDR output file ")
2946 local_add_argument("--output_densities" , default = "" , help="full name and path to the densities output file ") 2946 local_add_argument("--output_densities" , default = "" , help="full name and path to the densities output file ")
2947 #local_add_argument("--score_field_name" , default = "" , help="name of score field (in R format)") 2947 #local_add_argument("--score_field_name" , default = "" , help="name of score field (in R format)")
2948 local_add_argument("--input_file_type" , default = "PMD_FDR_input_file", help="type of input file (currently supports: PSM_Report)") 2948 local_add_argument("--input_file_type" , default = "PMD_FDR_input_file", help="type of input file (currently supports: PMD_FDR_file_type, PSM_Report, MaxQuant_Evidence)")
2949 } 2949 }
2950 ) 2950 )###############################################################################
2951 ###############################################################################
2952 # Class: Data_Object_Parser 2951 # Class: Data_Object_Parser
2953 ############################################################################### 2952 ###############################################################################
2954 Data_Object_Parser <- setRefClass("Data_Object_Parser", 2953 Data_Object_Parser <- setRefClass("Data_Object_Parser",
2955 contains = c("Data_Object"), 2954 contains = c("Data_Object"),
2956 fields =list(parser = "ModuleArgParser_PMD_FDR", 2955 fields =list(parser = "ModuleArgParser_PMD_FDR",