Commit ace4589e authored by Mathieu Giraud's avatar Mathieu Giraud

vidjil.cpp: CL11, set_type_name()

Closes #2738.
parent 0a0f1ce5
......@@ -292,11 +292,11 @@ int main (int argc, char **argv)
// cerr << "Usage: " << progname << " [options] <reads.fa/.fq/.gz>" << endl << endl;
group = "Files";
app.add_option("reads", f_reads, "reads.fa/.fq/.gz") -> group(group);
app.add_option("reads", f_reads, "reads.fa/.fq/.gz") -> group(group) -> set_type_name("FILE");
group = "Command selection";
app.add_option("-c", command, "command", true) -> group(group);
app.add_option("-c", command, "command") -> group(group) -> set_type_name("COMMAND");
/*
<< " -c <command>"
<< "\t" << COMMAND_CLONES << " \t locus detection, window extraction, clone clustering (default command, most efficient, all outputs)" << endl
......@@ -324,7 +324,7 @@ int main (int argc, char **argv)
group = "Input" ;
app.add_option("--separator", read_header_separator, "separator for headers in the reads file", true) ->group(group); // -> advanced() ;
app.add_option("--separator", read_header_separator, "separator for headers in the reads file", true) -> group(group) -> set_type_name("CHAR"); // -> advanced() ;
group = "Germline presets (at least one -g or -V/(-D)/-J option must be given for all commands except -c " COMMAND_GERMLINES ")";
......@@ -361,9 +361,9 @@ int main (int argc, char **argv)
"multiple locus/germlines, shortcut for '-g <path>/" + DEFAULT_MULTI_GERMLINE_FILE + "'",
<< " processes human TRA, TRB, TRG, TRD, IGH, IGK and IGL locus, possibly with some incomplete/unusal recombinations" << endl
*/
app.add_option("-V", v_reps_V, "custom V germline multi-fasta file") -> group(group);
app.add_option("-D", v_reps_D, "custom D germline multi-fasta file (and resets -m and -w options), will segment into V(D)J components") -> group(group);
app.add_option("-J", v_reps_J, "custom V germline multi-fasta file") -> group(group);
app.add_option("-V", v_reps_V, "custom V germline multi-fasta file") -> group(group) -> set_type_name("FILE");
app.add_option("-D", v_reps_D, "custom D germline multi-fasta file (and resets -m and -w options), will segment into V(D)J components") -> group(group) -> set_type_name("FILE");
app.add_option("-J", v_reps_J, "custom V germline multi-fasta file") -> group(group) -> set_type_name("FILE");
group = "Locus/recombinations";
app.add_flag("-d", several_D, "try to detect several D (experimental)") -> group(group);
......@@ -424,7 +424,7 @@ int main (int argc, char **argv)
// TODO: windows_labels[string(optarg)] = string("-W");
, "label the given sequence") -> group(group);
*/
app.add_option("-l", windows_labels_file, "label a set of sequences given in <file>") -> group(group);
app.add_option("-l", windows_labels_file, "label a set of sequences given in <file>") -> group(group) -> set_type_name("FILE");
app.add_flag("-F", only_labeled_windows, "filter -- keep only the windows related to the labeled sequences") -> group(group);
......@@ -493,8 +493,8 @@ int main (int argc, char **argv)
group = "Output";
app.add_option("-o", out_dir, "output directory", true) -> group(group);
app.add_option("-b", f_basename, "output basename (by default basename of the input file)") -> group(group);
app.add_option("-o", out_dir, "output directory", true) -> group(group) -> set_type_name("PATH");
app.add_option("-b", f_basename, "output basename (by default basename of the input file)") -> group(group) -> set_type_name("FILE");
app.add_flag("-a", output_sequences_by_cluster, "output all sequences by cluster (" CLONE_FILENAME "*), to be used only on small datasets") -> group(group);
// << " -v verbose mode" // verbose += 1 ;
......
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