param = px.get_input_output_parameters(in_out, param)
param = px.get_fastqc_choice(fastqc,param)
param = px.get_adapter_parameters(adapter, param)
param = px.get_quality_parameters(quality, param)
param = px.get_useful_parameters(useful, param)
else :
# get parameters from argparse
# copy arguments [dict]
param = arguments
# CHECK LAYOUT ---------------------------------------------------------
layout = ce.check_layout(param['layout'])
param['layout'] = layout
# CHECK INPUT(s) ACCORDING TO LAYOUT -----------------------------------
# For Single Ends, one input file is expected
if(layout=='SE'):
if not len(param['input']) == 1 :
sys.exit("/!\ Only one file containing reads must be given for \
SE data.")
ce.check_input(param['input'][0], 'for single end data')
# For Paired Ends, two input files are expected
def get_input_output_parameters(Puts, param):
"""
Function that gets inputs and outputs parameters
Takes two arguments : - Puts [ElementTree] : subtree which contains inputs
and outputs information's
- param [dict] : dictionnary containing all
parameters
Returns param[dict] where have been added inputs and outputs parameters
"""
# check if the section 'input-output' contains 4 parameters
if not check_child_number(Puts,4):
sys.exit("/!\ Warning : The XML file must contain exactly 4 parameters \
in the section 'input-output'!")
# LAYOUT -------------------------------------------------------------------
# get the layout text
layout = Puts.find('layout').text
# check that the layout is not empty and is 'SE' or 'PE'
layout = ce.check_layout(layout)
# add the layout to the dictionnary
param['layout'] = layout
# INPUTS -------------------------------------------------------------------
# get input(s)
if(checked_layout == 'SE') :
# get the subtree which contain SE input and get the input file
SE = Puts.find('single-ends')
filename=SE.find('input').text
# check if the file exists
filename = ce.check_input(filename, 'for single-end data')
# add the checked input file
param['input'] = filename
else:
# get the subtree which contain PE input
PE = Puts.find('paired-ends')
# get input files
for filename in PE.findall('input') :
if(filename.get('name') == 'read 1') :
# check the input file for read 1
Read1 = ce.check_input(filename.text, 'reads 1 for paired-end data')
elif(filename.get('name') == 'read 2') :
# check the input file for read 2
Read2 = ce.check_input(filename.text, 'reads 2 for paired-end data')
else :
sys.exit("/!\ The value of 'name' in paired-end section have been \
modified")
# add the checked input files
param['input']= Read1, Read2
# OUTPUTS ------------------------------------------------------------------
# get the working-directory where the new files must be generated
directory = Puts.find('output-directory').text
# check that output-directory is given and if it exists
directory = ce.check_output_dir(directory)
# add into the dictionnary
param['output']= directory
return param