Fix FoldMason description in main foldmason entrypoint #33

Author: milot-mirdita

src/foldmason.cpp

@@ -6,8 +6,8 @@
 
 const char* binary_name = "foldmason";
 const char* tool_name = "foldmason";
-const char* tool_introduction = "<< TODO >> .\n\nPlease cite:\n << TODO >>";
-const char* main_author = "Cameron L.M. Gilchrist, Milot Mirdita, Johannes Söding, Martin Steinegger";
+const char* tool_introduction = "FoldMason is a progressive aligner for fast and accurate multiple alignment of hundreds of thousands of protein structures.\n\nPlease cite:\n Gilchrist CLM, Mirdita M, Steinegger S. Multiple Protein Structure Alignment at Scale with FoldMason. bioRxiv, 2024.06.20.44908 (2024).\n";
+const char* main_author = "Cameron L.M. Gilchrist, Milot Mirdita, Martin Steinegger";
 const char* show_extended_help = "1";
 const char* show_bash_info = NULL;
 const char* index_version_compatible = "fs1";
@@ -28,21 +28,21 @@ std::vector<struct Command> foldmasonCommands = {
         {"easy-msa",          easymsa,           &foldmasonPar.easymsaworkflow,   COMMAND_EASY,
                 "Sensitive homology search and build MSAs",
                 "# Align a set of PDB files and create a MSA\n"
-                "foldseek easy-msa example/d1asha_ result.m8 tmp\n",
+                "foldmason easy-msa example/d1asha_ result.m8 tmp\n",
                 "Cameron Gilchrist <gamcil@snu.ac.kr> & Martin Steinegger <martin.steinegger@snu.ac.kr>",
                 "<i:PDB|mmCIF[.gz]> ... <i:PDB|mmCIF[.gz]>|<i:stdin> <o:alignmentFile> <tmpDir>",
                 CITATION_FOLDMASON, {{"PDB|mmCIF[.gz]|stdin", DbType::ACCESS_MODE_INPUT, DbType::NEED_DATA | DbType::VARIADIC, &DbValidator::flatfileStdinAndGeneric },
                                            {"alignmentFile", DbType::ACCESS_MODE_OUTPUT, DbType::NEED_DATA, &DbValidator::flatfile },
                                            {"tmpDir", DbType::ACCESS_MODE_OUTPUT, DbType::NEED_DATA, &DbValidator::directory }}},
         {"structuremsa",      structuremsa,      &foldmasonPar.structuremsa,      COMMAND_ALIGNMENT,
-                "Compute guide tree based on Foldseek scores",
+                "Multiple structure alignment from a set of protein structures in DB format",
                 NULL,
                 "Cameron Gilchrist <gamcil@snu.ac.kr> & Martin Steinegger <martin.steinegger@snu.ac.kr>",
                 "<i:queryDB> <o:alignmentFile>",
                 CITATION_FOLDMASON, {{"queryDB", DbType::ACCESS_MODE_INPUT, DbType::NEED_DATA, &DbValidator::sequenceDb },
                                            {"alignmentFile", DbType::ACCESS_MODE_OUTPUT, DbType::NEED_DATA, &DbValidator::flatfile }}},
         {"structuremsacluster",      structuremsacluster,      &foldmasonPar.structuremsa,      COMMAND_ALIGNMENT,
-                "Compute guide tree based on Foldseek scores",
+                "MSTA based on an existing (pre-)clustering DB",
                 NULL,
                 "Cameron Gilchrist <gamcil@snu.ac.kr> & Martin Steinegger <martin.steinegger@snu.ac.kr>",
                 "<i:queryDB> <i:clusterDB> <o:alignmentFile>",
@@ -80,29 +80,6 @@ std::vector<struct Command> foldmasonCommands = {
                 CITATION_FOLDMASON, {{"queryDB", DbType::ACCESS_MODE_INPUT, DbType::NEED_DATA, &DbValidator::sequenceDb },
                                     {"msaFileIn", DbType::ACCESS_MODE_INPUT, DbType::NEED_DATA, &DbValidator::flatfileAndStdin },
                                     {"msaFileOut", DbType::ACCESS_MODE_OUTPUT, DbType::NEED_DATA, &DbValidator::flatfile },}},
-        {"convertalis",          structureconvertalis,    &foldmasonPar.convertalignments,    COMMAND_FORMAT_CONVERSION,
-                "Convert alignment DB to BLAST-tab, SAM or custom format",
-                "# Create output in BLAST M8 format (12 columns):\n"
-                "#  (1,2) identifiers for query and target sequences/profiles,\n"
-                "#  (3) sequence identity, (4) alignment length, (5) number of mismatches,\n"
-                "#  (6) number of gap openings, (7-8, 9-10) alignment start and end-position in query and in target,\n"
-                "#  (11) E-value, and (12) bit score\n"
-                "foldseek convertalis queryDB targetDB result.m8\n\n"
-                "# Create a TSV containing pairwise alignments\n"
-                "foldseek convertalis queryDB targetDB result.tsv --format-output query,target,qaln,taln\n\n"
-                "# Annotate a alignment result with taxonomy information from targetDB\n"
-                "foldseek convertalis queryDB targetDB result.tsv --format-output query,target,taxid,taxname,taxlineage\n\n"
-                " Create SAM output\n"
-                "foldseek convertalis queryDB targetDB result.sam --format-mode 1\n\n"
-                "# Create a TSV containing which query file a result comes from\n"
-                "foldseek createdb euk_queries.fasta bac_queries.fasta queryDB\n"
-                "foldseek convertalis queryDB targetDB result.tsv --format-output qset,query,target\n",
-                "Martin Steinegger <martin.steinegger@snu.ac.kr>",
-                "<i:queryDb> <i:targetDb> <i:alignmentDB> <o:alignmentFile>",
-                CITATION_MMSEQS2, {{"queryDB", DbType::ACCESS_MODE_INPUT, DbType::NEED_DATA|DbType::NEED_HEADER, &DbValidator::sequenceDb },
-                                           {"targetDB", DbType::ACCESS_MODE_INPUT, DbType::NEED_DATA|DbType::NEED_HEADER, &DbValidator::sequenceDb },
-                                           {"alignmentDB", DbType::ACCESS_MODE_INPUT, DbType::NEED_DATA, &DbValidator::alignmentDb },
-                                           {"alignmentFile", DbType::ACCESS_MODE_OUTPUT, DbType::NEED_DATA, &DbValidator::flatfile}}},
         {"version",              versionstring,        &foldmasonPar.empty,                COMMAND_HIDDEN,
                 "",
                 NULL,