comparison queue_genotype_workflow.py @ 10:41477ff2ce8e draft

Uploaded

9:0ed7dc418a6d

#!/usr/bin/env python
import argparse
import os
import shutil
import string
import sys
import threading
import time

from bioblend import galaxy
from datetime import datetime
from six.moves import configparser

parser = argparse.ArgumentParser()
parser.add_argument('--affy_metadata', dest='affy_metadata', help='Input Affymetrix 96 well plate metadata file')
parser.add_argument('--annot', dest='annot', help='Probeset annotation file')

    d = {}
    config_parser = configparser.ConfigParser()
    config_parser.read(config_file)
    for key, value in config_parser.items(section):
        if section == 'defaults':
            d[string.upper(key)] = value
        else:
            d[key] = value
    return d

                outputfh.write("Updated step id %s with the following entry:\n%s\n" % (step_id, str(reference_genome_source_cond_dict)))
        if tool_id.find('coral_multilocus_genotype') > 0 and output_nj_phylogeny_tree == 'yes':
            # Reset the default value 'no' of output_nj_phylogeny_tree to 'yes'.
            if parameter_updates is None:
                parameter_updates = {}
            output_nj_phylogeny_tree_dict = {'output_nj_phylogeny_tree' : 'yes'}
            parameter_updates[step_id] = output_nj_phylogeny_tree_dict
            outputfh.write("Updated step id %s with the following entry:\n%s\n" % (step_id, str(output_nj_phylogeny_tree_dict)))
    return parameter_updates

10:41477ff2ce8e

#!/usr/bin/env python
import argparse
import os
import shutil
import sys
import threading
import time
from datetime import datetime

from bioblend import galaxy

from six.moves import configparser

parser = argparse.ArgumentParser()
parser.add_argument('--affy_metadata', dest='affy_metadata', help='Input Affymetrix 96 well plate metadata file')
parser.add_argument('--annot', dest='annot', help='Probeset annotation file')

    d = {}
    config_parser = configparser.ConfigParser()
    config_parser.read(config_file)
    for key, value in config_parser.items(section):
        if section == 'defaults':
            d[key.upper()] = value
        else:
            d[key] = value
    return d

                outputfh.write("Updated step id %s with the following entry:\n%s\n" % (step_id, str(reference_genome_source_cond_dict)))
        if tool_id.find('coral_multilocus_genotype') > 0 and output_nj_phylogeny_tree == 'yes':
            # Reset the default value 'no' of output_nj_phylogeny_tree to 'yes'.
            if parameter_updates is None:
                parameter_updates = {}
            output_nj_phylogeny_tree_dict = {'output_nj_phylogeny_tree': 'yes'}
            parameter_updates[step_id] = output_nj_phylogeny_tree_dict
            outputfh.write("Updated step id %s with the following entry:\n%s\n" % (step_id, str(output_nj_phylogeny_tree_dict)))
    return parameter_updates