#import os

#if str($input_type_cond.input_type) in ['single', 'pair']:
    #set read1 = $input_type_cond.read1
    ## Tadpole uses the file extension to determine the input format.
    #set ext = '.fastq'
    #if $read1.ext.endswith('.gz'):
        #set ext = $ext + '.gz'
    #end if
    #set read1_file = 'forward' + $ext
    ln -s '${read1}' '${read1_file}' &&
    #if str($input_type_cond.input_type) == 'pair':
        #set read2 = $input_type_cond.read2
        #set read2_file = 'reverse' + $ext
        ln -s '${read2}' '${read2_file}' &&
    #end if
#else:
    #set read1 = $input_type_cond.reads_collection['forward']
    #set read1_identifier = re.sub('[^\s\w\-]', '_', str($read1.element_identifier))
    ## Tadpole uses the file extension to determine the input format.
    #set ext = $read1_identifier + '.fastq'
    #if $read1.ext.endswith('.gz'):
        #set ext = $ext + '.gz'
    #end if
    #set read1_file = $read1_identifier + $ext
    ln -s '${read1}' '${read1_file}' &&
    #set read2 = $input_type_cond.reads_collection['reverse']
    #set read2_identifier = re.sub('[^\s\w\-]', '_', str($read2.element_identifier))
    #set read2_file = $read2_identifier + $ext
    ln -s '${read2}' '${read2_file}' &&
#end if

tadpole.sh

#### Input parameters
in='${read1_file}'
#if str($input_type_cond.input_type) in ['pair', 'paired']:
    in2='${read2_file}'
#end if

#### Output parameters
fastadump='$output_options.fastadump'
mincounttodump='$output_options.mincounttodump'
#if str($output_options.fastadump):
    dump='${outputdump}'
#end if
out='${output}'
#if str($input_type_cond.input_type) in ['pair', 'paired'] and str($mode_options.mode) != 'contig':
    out2='${output2}'
#end if

#### Processing modes
#if str($mode_options.mode) == 'contig':
    mode=contig
#elif str($mode_options.mode) == 'extend':
    mode=extend
#elif str($mode_options.mode) == 'correct':
    mode=correct
#end if
threads=\${GALAXY_SLOTS:-4}
overwrite=true