#import re

#if $reference_source.reference_source_selector == 'history':
    ln -f -s '$reference_source.ref_file' reference.fa &&
#else:
    ln -f -s '$reference_source.ref_file.fields.path' reference.fa &&
#end if

mkdir ./filter &&
#for $bam in $reads:
    #set $ext = ""
    #set $bam_name = re.sub('[^\w\-\.]', '_', str($bam.element_identifier))
    #if not $bam_name.endswith('.bam')
        #set $ext = ".bam"
    #end if
    ln -s '$bam' './filter/${bam_name}${ext}' &&
    ln -s '$bam.metadata.bam_index' './filter/${bam_name}${ext}.bai' &&
#end for

mkdir ./count &&
#for $tsv in $count_tsvs:
    #set $ext = ""
    #set $tsv_name = re.sub('[^\w\-\.]', '_', str($tsv.element_identifier))
    #if not $tsv_name.endswith('_tcount.tsv')
        #set $ext = "_tcount.tsv"
    #end if
    ln -s '$tsv' './count/${tsv_name}${ext}' &&
#end for

mkdir ./snp &&
#for $vcf in $variants:
    #set $ext = ""
    #set $vcf_name = re.sub('[^\w\-\.]', '_', str($vcf.element_identifier))
    #if not $vcf_name.endswith('_snp.vcf')
        #set $ext = "_snp.vcf"
    #end if
    ln -s '$vcf' './snp/${vcf_name}${ext}' &&
#end for

alleyoop summary -o ./summary.txt -t ./count ./filter/*bam &&

alleyoop rates -o ./stats -r reference.fa -mq $mq ./filter/*bam &&

alleyoop utrrates -o ./stats -r reference.fa -b $reference -t \${GALAXY_SLOTS:-1} -l $l -mq $mq ./filter/*bam &&

alleyoop tcperreadpos -o ./stats -r reference.fa -s ./snp -t \${GALAXY_SLOTS:-1} -l $l -mq $mq ./filter/*bam &&

alleyoop tcperutrpos -o ./stats -r reference.fa -s ./snp -t \${GALAXY_SLOTS:-1} -l $l -b $reference -mq $mq ./filter/*bam

#if $bams:
    && alleyoop read-separator -o ./splitbams -s ./snp -r reference.fa ./filter/*bam
#end if