#import re

        mkdir stacks_inputs stacks_outputs

        &&

        #set $samples = ""
        #for $input_file in $input_col
            #set $filename = str($input_file.element_identifier)
            #if not filename.endswith('.tsv')
                #set $filename = $filename + ".tsv"
            #end if
            #if not re.search('catalog\.[a-z]+(\.tsv)?$', $filename)
                ln -s '${input_file}' 'stacks_inputs/$filename' &&

                #if $filename.endswith('.tags.tsv')
                    #set samples += " -s 'stacks_inputs/" + $filename[:-9] + "'"
                #end if
            #end if
        #end for

        cstacks

            ## Batch description
            -b 1

            -p \${GALAXY_SLOTS:-1}

            #if $popmap
                -P stacks_inputs -M '$popmap'
            #else
                $samples
                -o stacks_outputs
            #end if

            $g

            -n $n

            $include_multiple

            #if $gapped.use_gapped == "yes"
                --gapped
                --max_gaps $gapped.max_gaps
                --min_aln_len $gapped.min_aln_len
            #end if

            2>&1 | tee cstacks.log

            #if $popmap
                ## When using a popmap, stacks write to the input dir
                && mv stacks_inputs/batch_1.catalog.*.tsv stacks_outputs/
            #end if

            &&

            stacks_summary.py --stacks-prog cstacks --res-dir stacks_outputs --logfile cstacks.log --summary stacks_outputs/summary.html