#for $i, $clib in enumerate($controlLibs):
            #if $clib:
                ln -s -f '$clib' ${i}.c.bam &&
                ln -s -f '$clib.metadata.bam_index' ${i}.c.bam.bai &&
            #end if
        #end for
        #for $j, $elib in enumerate($experimentLibs):
            ln -s -f '$elib' ${j}.e.bam &&
            ln -s -f '$elib.metadata.bam_index' ${j}.e.bam.bai &&
        #end for

        pwd &&
        mkdir ./tmp_output && 
        peakachu 
        ${mode.mode_selector}
        --exp_libs 
        #for $i, $elib in enumerate($experimentLibs):
            '${i}.e.bam'
        #end for
        #for $i, $clib in enumerate($controlLibs):
            #if $clib and $i == 0:
                --ctr_libs 
            #end if
            #if $clib:
                '${i}.c.bam'
            #end if
        #end for
        $pairwise_replicates
        $paired_end
        --max_insert_size $max_insert_size
        --features '$features'
        --sub_features '$sub_features'
        --max_proc "\${GALAXY_SLOTS:-1}"
        --output_folder ./tmp_output
        #if str($mode.mode_selector) == 'adaptive':
            --min_cluster_expr_frac $mode.min_cluster_expr_frac
            --min_block_overlap $mode.min_block_overlap
            --min_max_block_expr $mode.min_max_block_expr
        #elif str($mode.mode_selector) == 'window':
            --window_size $mode.window_size
            --step_size $mode.step_size
            --stat_test $mode.stat_test
            --het_p_val_threshold $mode.het_p_val_threshold
            --rep_pair_p_val_threshold $mode.rep_pair_p_val_threshold
        #end if
       --norm_method $mode.norm_method.norm_method_selector
        #if str($mode.norm_method.norm_method_selector) == 'manual':
            --size_factors '${mode.norm_method.size_factors}'
        #end if
        --mad_multiplier $mad_multiplier
        --fc_cutoff $fc_cutoff
        --padj_threshold $padj_threshold

        &&
        if ls ./tmp_output/peak_tables/*.csv > /dev/null;
        then 
            sed -n 1p ./tmp_output/peak_tables/*.csv > peaks.tsv &&
            tail -n +2 -q ./tmp_output/peak_tables/*.csv >> peaks.tsv &&
            mv peaks.tsv '$peak_tables' &&
            awk '/peak/ {print $0}' ./tmp_output/peak_annotations/*.gff > peak_annotations.gff &&
            mv peak_annotations.gff '$peak_annotations' &&
            mv ./tmp_output/plots/Initial*.png '$MA_plot';
        else 
            echo "No Peaks Found" >&2;
        fi