## DE results input files must be in the working directory and have suffix .DE_results
    #import re
    #for $input in $DE_results
        #if re.search('.DE_results$',input.element_identifier)
            ## General case, where DE results files have been previously generated by run_de_analysis.pl
            ln -s '${input}' "${re.sub('[^\w\-_.]', '_', input.element_identifier)}"
        #else
            ## Particular case, where DE results files have non-standard names
            ln -s '${input}' "${re.sub('[^\w\-_.]', '_', input.element_identifier)}.DE_results"
        #end if
        &&
    #end for
    #if str( $additional_params.GO_enrichment.examine_GO_enrichment ) == "yes":
        ## DE matrix input files must be in the working directory and have the same name as DE results input files, but replacing suffix .DE_results by suffix .count_matrix
        #for $DE_matrix in $additional_params.GO_enrichment.DE_matrices
            ## Handle general case, where DE results files and DE matrix files have been previously generated by run_de_analysis.pl
            ln -s '${DE_matrix}' "${re.sub('[^\w\-_.]', '_', DE_matrix.element_identifier)}"
            &&
        #end for
    #end if

    analyze_diff_expr.pl
        --matrix '${matrix}'
        --samples '${samples}'
        -P ${P}
        -C ${C}

        #if str( $additional_params.max_DE_genes_per_comparison ):
            --max_DE_genes_per_comparison ${additional_params.max_DE_genes_per_comparison}
        #end if

        $additional_params.order_columns_by_samples_file

        #if $additional_params.max_genes_clust:
            --max_genes_clust ${additional_params.max_genes_clust}
        #end if

        #if str( $additional_params.GO_enrichment.examine_GO_enrichment ) == "yes":
            --examine_GO_enrichment
            --GO_annots '${$additional_params.GO_enrichment.GO_annots}'
            --gene_lengths '${$additional_params.GO_enrichment.gene_lengths}'
        #end if

        --output results