defaults for the e-value thresholds are now printed in the usage/help

metaclade2

@@ -50,12 +50,13 @@ function print_usage() {
                         \t(e.g., \"PF00875,PF03441\")\n
     -D, --domain-file <path>\tFile that contains the Pfam accession numbers\n
                             \tof the domains to be considered (one per line)\n
-    -e, --evalue-cutoff <float>\tE-value cutoff\n
-    -E, --evalue-cutconf <float>\tConfidence threshold used by DAMA to add new domains into the architecture.\n
+    -e, --evalue-cutoff <float>\tE-value cutoff (default:${MCLADE_EVALUECUTOFF})\n
+    -E, --evalue-cutconf <float>\tConfidence threshold used by DAMA to add new domains 
+                                \tin the architecture. (default:${MCLADE_EVALUECUTCONF})\n
     -W, --work-dir <path>\tWorking directory, where jobs and results are saved\n
     " | column -t -s $'\t'
-	echo -en "\n"
-	echo -en "  OTHER OPTIONS:\n
+    echo -en "\n"
+    echo -en "  OTHER OPTIONS:\n
     -j, --jobs <num>\tNumber of jobs to be created (default:${NJOBS})\n
     -t, --threads <num>\tNumber of threads for each job (default:${NTHREADS})\n
     -h, --help\tPrint this help message\n