Display --tax-fdr parameter in commandline options

src/commons/LocalParameters.h

@@ -66,7 +66,7 @@ class LocalParameters : public Parameters {
         PARAM_REVERSE_SETDB(PARAM_REVERSE_SETDB_ID,"--reverse-setdb", "Create reversed setdb", "Create additional setDB with reversed fragments to compute under null [0,1]", typeid(int), (void *) &reverseSetDb, "^[0-1]{1}$"),
         PARAM_EXTRACTORF_SPACER(PARAM_EXTRACTORF_SPACER_ID,"--extractorf-spacer", "Extract orfs from spacers", "change parameter settings for extractorfs when createsetdb for spacer db [0,1]", typeid(int), (void *) &extractorfsSpacer, "^[0-1]{1}$"),
         PARAM_FDR_CUTOFF(PARAM_FDR_CUTOFF_ID,"--fdr", "FDR cutoff", "FDR cutoff for filtering matches [0.0, 1.0]", typeid(float), (void *) &fdrCutoff, "^0(\\.[0-9]+)?|1(\\.0+)?$"),
-        PARAM_TAX_FDR_CUTOFF(PARAM_FDR_CUTOFF_ID,"--tax-fdr", "Taxonomy FDR cutoff", "FDR cutoff for taxonomy report [0.0, 1.0]", typeid(float), (void *) &taxFdrCutoff, "^0(\\.[0-9]+)?|1(\\.0+)?$"),
+        PARAM_TAX_FDR_CUTOFF(PARAM_TAX_FDR_CUTOFF_ID,"--tax-fdr", "Taxonomy FDR cutoff", "FDR cutoff for taxonomy report [0.0, 1.0]", typeid(float), (void *) &taxFdrCutoff, "^0(\\.[0-9]+)?|1(\\.0+)?$"),
         PARAM_FORMAT_TYPE(PARAM_FORMAT_TYPE_ID,"--fmt", "Output format", "0: short (only matches)\n1: long (matches and hits)\n2: long with nucleotide alignment", typeid(int), (void *) &formatType, "^[0-2]{1}$"),
         PARAM_REPORT_PAM(PARAM_REPORT_PAM_ID,"--report-pam", "Report PAM", "Report protospacer adjacent motifs up and downstream of hits [0,1]", typeid(int), (void *) &reportPam, "^[0-1]{1}$"),
         PARAM_FLANKING_SEQ_LEN(PARAM_FLANKING_SEQ_LEN_ID,"--flanking-seq-len", "Flanking sequence length", "Length of protospacer flanking sequence to extract for possible PAMs scanning", typeid(int), (void *) &flankingSeqLen, "^[0-9]{1}[0-9]*$"),
@@ -131,14 +131,15 @@ class LocalParameters : public Parameters {
         predictmatchworkflow = combineList(searchworkflow, filtermatchbyfdr);
         predictmatchworkflow = combineList(predictmatchworkflow, summarizeresults);
         predictmatchworkflow = combineList(predictmatchworkflow, findpam);
+        predictmatchworkflow.push_back(&PARAM_TAX_FDR_CUTOFF);
         predictmatchworkflow.push_back(&PARAM_RESTRICT_RANKS_MODE);
         predictmatchworkflow = combineList(predictmatchworkflow, restrictranks);
         //predictmatchworkflow.push_back(&PARAM_FDR_CUTOFF);
         //predictmatchworkflow.push_back(&PARAM_FORMAT_TYPE);
         predictmatchworkflow.push_back(&PARAM_DB_OUTPUT);
         predictmatchworkflow.push_back(&PARAM_REPORT_PAM);
         predictmatchworkflow.push_back(&PARAM_PERFORM_NUCLALN);
-        predictmatchworkflow.push_back(&PARAM_TAX_FDR_CUTOFF);
+
 
         easypredictmatchworkflow.push_back(&PARAM_TAX_MAPPING_FILE);
         easypredictmatchworkflow.push_back(&PARAM_NCBI_TAX_DUMP);