#set $file_stderr = 'genrich_stderr'

Genrich

###########
## Input ##
###########

## Treatment File(s)
#if str($treatment.t_multi_select) == "Yes":
    -t ${ ','.join( [ "'%s'" %  $x for $x in $treatment.input_treatment_file] ) }
#else
    -t '$treatment.input_treatment_file'
#end if

## Control File(s)
#if str($control.c_select) == "Yes":
    #if str($control.c_multiple.c_multi_select) == "Yes":
        -c ${ ','.join( [ "'%s'" %  $x for $x in $control.c_multiple.input_control_file] ) }
    #else
        -c '$control.c_multiple.input_control_file'
    #end if
#end if

####################
## Filter Options ##
####################

#if $filter_options.duplicates:
    -r -R '${out_dups}'
#end if

#if $filter_options.exclude_chr:
    -e '$filter_options.exclude_chr'
#end if

#if str($cond_exclude.exclude_select) == "Yes":
    -E $cond_exclude.erf
#end if

-m $filter_options.min_mapq
-s $filter_options.alignment_score
$filter_options.unpaired

#if $filter_options.alignment_lengths:
    -w $filter_options.alignment_lengths
#end if

$filter_options.alignment_lengths2

##################
## ATAC Options ##
##################

$atac_options.atac
-d $atac_options.expand_sites

#########################
## Peakcalling Options ##
#########################

-q $peakcalling_options.max_q

#if $peakcalling_options.max_p:
    -p $peakcalling_options.max_p
#end if

-a $peakcalling_options.min_auc
-l $peakcalling_options.min_peak_length
-g $peakcalling_options.max_dist

###################
## Other Options ##
###################

$other_options.skip_peak_calling
-v

####################
## Output Options ##
####################

#if $output_options.bedgraph1:
    -f '${out_bedgraph1}'
#end if

#if $output_options.bedgraph2:
    -k '${out_bedgraph2}'
#end if

#if $output_options.bed:
    -b '${out_bed}'
#end if

-o '${outfile}'

2>&1 > $file_stderr &&
exit_code_for_galaxy=\$? &&
cat $file_stderr 2>&1 &&
exit \$exit_code_for_galaxy