Example of Using pbcommand with ipdSummary.py

ipdSummary.py

from pbcommand.models import get_default_contract_parser, TaskTypes, ResourceTypes, FileTypes
from pbcommand.validators import validate_file

def get_pbparser():
    driver_exe = "my-exe"
    p = get_default_contract_parser("pbexample.tasks.my_tool", "My Tool Desc", "0.1.0", driver_exe, TaskTypes.LOCAL, 1, ())
    return p

def add_common(p):
    p.add_input_file_type(FileTypes.DS_BAM, "algn_ds", "Alignment DataSet", "Alignment Set Desc")
    # add common opts here as well
    return p

def add_tc(p):
    p.tool_contract_parser.add_input_file_type(FileTypes.DS_REF, "ref_ds", "Reference Set", "Reference Set desc")
    p.tool_contract_parser.add_output_file_type(FileTypes.GFF, "gff", "Gff", "GFF Desc", "output.gff")
    p.tool_contract_parser.add_output_file_type(FileTypes.CSV, "csv", "CSV", "CSV Desc", "output.csv")
    return p

def add_argparse(p):
    p.arg_parser.parser.add_argument('--gff', type=validate_file, help="Path to Output GFF")
    p.arg_parser.parser.add_argument('--csv', type=validate_file, help="Output CSV") # this should be validate_or_none
    p.arg_parser.parser.add_argument('--reference-fasta', required=True, type=validate_file, help="Path to Fasta or ReferenceSet")
    return p

def to_p():
    p = get_pbparser()
    p = add_common(p)
    p = add_tc(p)
    p = add_argparse(p)
    return p