Mercurial > repos > galaxyp > pmd_fdr
comparison PMD_FDR_package_for_Galaxy.R @ 3:9c517334da45 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 17:29:16 -0400 |
| parents | ece050673770 |
| children |
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| 2:ece050673770 | 3:9c517334da45 |
|---|---|
| 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", |