#!/usr/bin/env python

# File created on 28 Mar 2011

from __future__ import division

__author__ = "Jesse Stombaugh"

__copyright__ = "Copyright 2012, The QIIME-webdev project"

__credits__ = ["Jesse Stombaugh"]

__license__ = "GPL"

__version__ = "1.0.0-dev"

__maintainer__ = "Jesse Stombaugh"

__email__ = "[email protected]"

__status__ = "Development"

from os.path import split, splitext, join, dirname, abspath

from qiime.util import get_qiime_scripts_dir

from qiime.workflow import print_to_stdout,\

call_commands_serially,no_status_updates,\

WorkflowError,WorkflowLogger,generate_log_fp,\

get_params_str

def run_make_otu_heatmap_html(otu_table_fp,mapping_fp,output_dir, params,

qiime_config,

command_handler,tree_fp,

status_update_callback=print_to_stdout):

""" This function calls the make_otu_heatmap_html script """

# define upper-level values

python_exe_fp = qiime_config['python_exe_fp']

script_dir = get_qiime_scripts_dir()

commands = []

logger = WorkflowLogger(generate_log_fp(output_dir),

params=params,

qiime_config=qiime_config)

# get the user-defined parameters

try:

params_str = get_params_str(params['make_otu_heatmap_html'])

except KeyError:

params_str = ''

# Build the make_otu_heatmap_html command

heatmap_cmd = '%s %s/make_otu_heatmap_html.py -i %s -m %s -t %s -o %s %s' %\

(python_exe_fp, script_dir, otu_table_fp, mapping_fp,tree_fp, output_dir,

params_str)

commands.append([('OTU Heatmap' , heatmap_cmd)])

# Call the command handler on the list of commands

command_handler(commands, status_update_callback, logger)

return True