workflow.properties 1.93 KB
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#
# Copyright (C) 2012 INRA
# 
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
# 
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.
# 
# You should have received a copy of the GNU General Public License
# along with this program.  If not, see <http://www.gnu.org/licenses/>.
#

[global]
name = alignment
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description = align reads against a reference genome
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#
# Parameter section
# param.name: the parameter display name
#      .flag: the command line flag to use the argument
#      .help: a brief description of what the parameter does
#      .default [None]: the value produced if the parameter is not provided
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#      .type [str]: the parameter type that should be tested (str|int|date|file|bool)
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#      .choices [None]: a container of the allowable values for the parameter
#      .required [False]: whether or not the command-line option may be omitted
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#      .action [store]: the basic type of action to be taken (store|append)
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#	   .group [None]: gathers arguments into groups when displaying help messages / forms
#	   .exclude [None]: will make sure that there is only one arguments provided
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#
[parameters]
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read_1.name = Read 1
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read_1.flag = --read-1
read_1.help = Which read1 files should be used
read_1.required = True
read_1.action = append
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read_2.name = Read 2
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read_2.flag = --read-2
read_2.help = Which read2 files should be used (if single end, leave empty)
read_2.action = append
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reference_genome.name = Reference genome
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reference_genome.flag = --reference-genome
reference_genome.help = Which genome should the read being align on
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reference_genome.required = True