#import re

trap ">&2 cat '$output_log'" err exit &&
mkdir stacks_inputs stacks_outputs &&


    #set $samples = []
    #for $input_file in $input_stacks
        #set $filename = str($input_file.element_identifier)
        #if not filename.endswith('.tsv')
            #set $filename = $filename + ".tsv"
        #end if
        #if re.search('^(?!catalog).+\.(tags|alleles|snps)\.tsv$', $filename)
            ln -s '${input_file}' 'stacks_inputs/$filename' &&
            #if $filename.endswith('.tags.tsv')
                $samples.append($filename[:-9])
            #end if
        #end if
    #end for
    
    
cstacks

-p \${GALAXY_SLOTS:-1}

#if $popmap
    -P stacks_inputs
    -M '$popmap'
#else
    #for $sample in $samples
        -s 'stacks_inputs/$sample'
    #end for
    -o stacks_outputs
#end if

-n $n
## -c not implemented in Galaxy (appending can be done in Galaxy)


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

## Advanced Options
#if $k_len:
    --k_len $k_len
#end if
$report_mmatches

        #if $output_log
            2> '$output_log'
        #end if
    

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