Added one input tabular file input for PS report

moff_all.py

@@ -3,6 +3,7 @@
 import argparse
 import ast
 import configparser
+import gc
 import json
 import logging.config
 import multiprocessing
@@ -178,6 +179,38 @@
  os.makedirs(args.loc_out)
  log.critical("created output folder %r", args.loc_out)
 
+ config = configparser.RawConfigParser()
+ config.read(os.path.join(os.path.dirname(
+ os.path.realpath(sys.argv[0])), 'moff_setting.properties'))
+
+ # just for Galaxy input is possible to use one big input file and a list of raw file.
+ # the big file must have the result of each raw file and the columns 'Spectrum File' should be availabe
+ # This option work only with PS report using only --tsv_list and --raw_list
+ if ( args.tsv_list is not None) and ( args.raw_list is not None) and (len(args.tsv_list)==1) :
+ data_temp= pd.read_csv(args.tsv_list[0],sep="\t")
+ if moff.check_ps_input_data(data_temp.columns.tolist(), ast.literal_eval(config.get('moFF', 'ps_default_export_v1'))) == 1:
+ # split the data input file only if inave more than ONE raw file and tha input file contain identification for more the ONE run
+ if len(data_temp['Spectrum File'].unique())> 1 and len(args.raw_list) > 1:
+
+ output_list_loc=[]
+ for file in data_temp['Spectrum File'].unique():
+ data_temp[data_temp['Spectrum File']== file].to_csv(os.path.join(os.path.split(args.tsv_list[0])[0],file.split('.')[0]+ '.txt')
+ , sep='\t' , index=False )
+ output_list_loc.append(os.path.join(os.path.split(args.tsv_list[0])[0],file.split('.')[0]+ '.txt') )
+
+ if len(args.raw_list) != len(output_list_loc):
+ exit('-- Number of raw file is different to the number of input sources detectd in your one input file --')
+ #sort them to be sure about the association between input - raw file
+ args.raw_list= sorted(args.raw_list)
+ args.tsv_list= sorted(output_list_loc)
+ #clean dataset thta I don use anymore
+ del data_temp
+ gc.collect()
+
+
+
+ ##---
+
  # fixed variable number of split and also number of CPU presence in the macine
  # change this variable with repset to the machine setting of the user
 
@@ -258,9 +291,7 @@
  loc_raw = args.raw_repo if not None else raw_list
  loc_output = args.loc_out
 
- config = configparser.RawConfigParser()
- config.read(os.path.join(os.path.dirname(
- os.path.realpath(sys.argv[0])), 'moff_setting.properties'))
+
  df = pd.read_csv(file_name, sep="\t")
  # add same safety checks len > 1
  # Flag for pride pipeline, or to set from second to minute as input rt time scale