diff --git a/docs/mode_merge.txt b/docs/mode_merge.txt index e4a404a..fe47ade 100644 --- a/docs/mode_merge.txt +++ b/docs/mode_merge.txt @@ -41,6 +41,12 @@ REQUIRED PARAMETERS taxonomic data files) +MERGING RESULTS OUTPUT + + Redirect output to file . + If not specified, output will be written to stdout. + + CLASSIFICATION -lowest Do not classify on ranks below @@ -85,7 +91,7 @@ CLASSIFICATION default: off -GENERAL OUTPUT +GENERAL OUTPUT FORMATTING -silent|-verbose information level during build: silent => none / verbose => most detailed diff --git a/src/options.cpp b/src/options.cpp index ec496c6..9879ac2 100644 --- a/src/options.cpp +++ b/src/options.cpp @@ -1683,10 +1683,18 @@ merge_mode_cli(merge_options& opt, error_messages& err) % "directory with taxonomic hierarchy data (see NCBI's taxonomic data files)" ) , + "MERGING RESULTS OUTPUT" % + ( option("-out") & + value("file", qry.queryMappingsFile) + .if_missing([&]{ err += "Output filename missing after '-out'!"; }) + % "Redirect output to file .\n" + "If not specified, output will be written to stdout." + ) + , "CLASSIFICATION" % classification_params_cli(qry.classify, err) , - "GENERAL OUTPUT" % ( + "GENERAL OUTPUT FORMATTING" % ( info_level_cli(opt.infoLevel, err) , option("-no-summary", "-nosummary").set(qry.output.showSummary,false)