#import re
mkdir 'bins' &&
#if $bins.select == 'collection'
    #for $b in $bins.bins_coll
        #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($b.element_identifier))
ln -s '$b.file_name' 'bins/${identifier}.fasta' &&
    #end for
#else
    #for $b in $bins.bins_ind
        #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($b.element_identifier))
ln -s '$b.file_name' 'bins/${identifier}.fasta' &&
    #end for
#end if


#if $plot.command == 'gc_plot'
checkm gc_plot
    'bins'
    'output'
    $plot.dist_value
    --extension 'fasta'
    --image_type '$image_type'
    --dpi $dpi
    --font_size $font_size
    --width $width
    --height $height

#else if $plot.command == 'coding_plot'

#for $i in $plot.gff
    #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($i.element_identifier))
mkdir -p 'inputs/bins/${identifier}' &&
ln -s '$i' 'inputs/bins/${identifier}/genes.gff' &&
#end for

checkm coding_plot
    'inputs'
    'bins'
    'output'
    $plot.dist_value
    --extension 'fasta'
    --image_type '$image_type'
    --dpi $dpi
    --font_size $font_size
    --width $width
    --height $height
    --cd_window_size $plot.cd_window_size
    --cd_bin_width $plot.cd_bin_width

#else if $plot.command == 'tetra_plot'

#for $i in $plot.gff
    #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($i.element_identifier))
mkdir -p 'inputs/bins/${identifier}' &&
ln -s '$i' 'inputs/bins/${identifier}/genes.gff' &&
#end for

checkm tetra_plot
    'inputs'
    'bins'
    'output'
    '$tetra_profile'
    $plot.dist_value
    --extension 'fasta'
    --image_type '$image_type'
    --dpi $dpi
    --font_size $font_size
    --width $width
    --height $height
    --td_window_size $plot.td_window_size
    --td_bin_width $plot.td_bin_width

#else if $plot.command == 'dist_plot'

#for $i in $plot.gff
    #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($i.element_identifier))
mkdir -p 'inputs/bins/${identifier}' &&
ln -s '$i' 'inputs/bins/${identifier}/genes.gff' &&
#end for

checkm dist_plot
    'inputs'
    'bins'
    'output'
    '$tetra_profile'
    $plot.dist_value
    --extension 'fasta'
    --image_type '$image_type'
    --dpi $dpi
    --font_size $font_size
    --width $width
    --height $height
    --gc_window_size $plot.gc_window_size
    --gc_bin_width $plot.gc_bin_width
    --cd_window_size $plot.cd_window_size
    --cd_bin_width $plot.cd_bin_width
    --td_window_size $plot.td_window_size
    --td_bin_width $plot.td_bin_width

#else if $plot.command == 'nx_plot'
checkm nx_plot
    'bins'
    'output'
    --extension 'fasta'
    --image_type '$image_type'
    --dpi $dpi
    --font_size $font_size
    --width $width
    --height $height
    --step_size $plot.step_size

#else if $plot.command == 'len_hist'
checkm len_hist
    'bins'
    'output'
    --extension 'fasta'
    --image_type '$image_type'
    --dpi $dpi
    --font_size $font_size
    --width $width
    --height $height

#else if $plot.command == 'marker_plot'
mkdir -p 'inputs/storage/' &&
cp '$marker_gene_stats' 'inputs/storage/marker_gene_stats.tsv' &&
cp '$bin_stats_ext' 'inputs/storage/bin_stats_ext.tsv' &&
#for $b in $plot.genes_fna
    #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($b.element_identifier))
mkdir -p 'inputs/bins/${identifier}' &&
cp '$b.file_name' 'inputs/bins/${identifier}/genes.faa' &&
#end for
checkm marker_plot
    'inputs'
    'bins'
    'output'
    --extension 'fasta'
    --image_type '$image_type'
    --dpi $dpi
    --font_size $font_size
    --width $width
    --height $height
    --fig_padding $plot.fig_padding

#else if $plot.command == 'gc_bias_plot'
mkdir 'mapping' &&
ln -s '$bam_file' 'mapping.bam' &&
samtools index 'mapping.bam' 'mapping.bam.bai' &&

checkm gc_bias_plot
    'bins'
    'output'
    'mapping.bam'
    --extension 'fasta'
    --image_type '$image_type'
    --dpi $dpi
    --font_size $font_size
    --width $width
    --height $height
    --window_size $plot.window_size
    $plot.all_reads       
    --min_align $plot.min_align
    --max_edit_dist $plot.max_edit_dist
    --threads \${GALAXY_SLOTS:-1}
#end if