custom_paragraph="\npampa has two modules: \n\n - assign, for species identifications \n - build, for construction of custom marker peptides.\n\nType <pampa assign -h> or <pampa build -h> respectively to print the help.\n\n"
group2.add_argument("-s",dest="spectra",help="Path to the spectra files (one spectrum per file). Authorized formats: cvs, mgd, mzML.",type=str,required=True)
group2.add_argument("-e",dest="error",help="Maximal error margin for the observation (in Dalton or ppm). Recommended values: 0.02 for maldi FT and 0.1 for maldi TOF.",type=float,required=True)
group2.add_argument("-o",dest="output",help="Output path (should include the output file name)",type=str,required=True)
group3=assign_parser.add_argument_group('\noptions for organism selection')
group3.add_argument("-d",dest="directory",help="Directory where to find Fasta files.",type=str)
group3.add_argument("-l",dest="limit",help="Limit the set of peptides or fasta sequences to organisms, molecules or sequence ID specified in this file (TSV files)",type=str,required=False)
group4=assign_parser.add_argument_group('\noptions for suboptimal solutions')
group4.add_argument("-n",dest="neighbour",help="Provide near-optimal solutions within a specified percentage margin, ranging between 0 and 100. Default is 100. With this value, only optimal solutions are provided.",type=int,required=False,default=100)
group4.add_argument("-a","--all",dest="all",action='store_true',help="Provide all solutions, and not only suboptimal solutions, within the percentage margin specified with option -n. Default is False.",required=False)
## build module
build_parser=subparsers.add_parser('build',
usage='\n\n pampa [-h] build (-p PEPTIDE TABLE) (-o OUTPUT FILE) (-f FASTA file | -d FASTA dir) [-l LIMIT]',
description='This module is for the construction of custom peptide tables.',
help='This module is for the construction of custom peptide tables.')
build_parser.add_argument("-p",dest="peptide_table",help="TSV file that contains model peptide markers, with sequences.",type=str)
build_parser.add_argument("-o",dest="output",help="Output path (should include the output file name)",type=str)
build_parser.add_argument("-f",dest="fasta",help="FASTA file that contains new sequences with header with species.",type=str)
build_parser.add_argument("-d",dest="directory",help="Directory that contains FASTA files",type=str)