describe programs with 'call' and 'prediction' defintions

Author: elileka

src/metaeuk.cpp

@@ -15,40 +15,40 @@ LocalParameters& localPar = LocalParameters::getLocalInstance();
 std::vector<struct Command> commands = {
         // Main tools (workflows for non-experts)
         {"predictexons",             predictexons,            &localPar.predictexonsworkflow,    COMMAND_MAIN,
-                "Predict eukaryotic exons based on protein similarity",
-                "An analog of 6-frame translation to produce putative protein fragments. Search against protein DB. Compatible exon set identified with respect to each target. Two dynamic programming outputs: predictexonsBaseName_dp_protein_contig_strand_map and predictexonsBaseName_dp_optimal_exon_sets",
+                "Call optimal exon sets based on protein similarity",
+                "An analog of 6-frame translation to produce putative protein fragments. Search against protein DB. Compatible exon set identified with respect to each target.",
                 "Eli Levy Karin <[email protected]>",
-                "<i:contigsDB> <i:targetsDB> <o:predictedExonsDB> <tmpDir>",
+                "<i:contigsDB> <i:targetsDB> <o:calledExonsDB> <tmpDir>",
                 NO_CITATION, {{"contigsDB", DbType::ACCESS_MODE_INPUT, DbType::NEED_DATA, &DbValidator::nuclDb},
                                 {"targetsDB", DbType::ACCESS_MODE_INPUT, DbType::NEED_DATA, &DbValidator::sequenceDb},
-                                {"predictedExonsDB", DbType::ACCESS_MODE_OUTPUT, DbType::NEED_DATA, NULL},
+                                {"calledExonsDB", DbType::ACCESS_MODE_OUTPUT, DbType::NEED_DATA, NULL},
                                 {"tmpDir", DbType::ACCESS_MODE_OUTPUT, DbType::NEED_DATA, &DbValidator::directory}}},
         {"reduceredundancy",             reduceredundancy,            &localPar.reduceredundancy,    COMMAND_MAIN,
-                "Assignment of predictions to cluster",
-                "A greedy examination of predictions accoridng to their contig order, subordered by the number of exons. Predictions in a cluster share an exon with the representative.",
+                "Cluster metaeuk calls that share an exon and select representative prediction",
+                "A greedy examination of calls according to their contig order, subordered by the number of exons. Calls in a cluster share an exon with the representative.",
                 "Eli Levy Karin <[email protected]>",
-                "<i:predictedExonsDB> <o:groupedPredictedExonsDB> <o:repToPred>",
-                NO_CITATION, {{"predictedExonsDB", DbType::ACCESS_MODE_INPUT, DbType::NEED_DATA, &DbValidator::genericDb},
-                                {"groupedPredictedExonsDB", DbType::ACCESS_MODE_OUTPUT, DbType::NEED_DATA, &DbValidator::genericDb},
-                                {"repToPred", DbType::ACCESS_MODE_OUTPUT, DbType::NEED_DATA, &DbValidator::genericDb}}},
+                "<i:calledExonsDB> <o:predictionsExonsDB> <o:predToCall>",
+                NO_CITATION, {{"calledExonsDB", DbType::ACCESS_MODE_INPUT, DbType::NEED_DATA, &DbValidator::genericDb},
+                                {"predictionsExonsDB", DbType::ACCESS_MODE_OUTPUT, DbType::NEED_DATA, &DbValidator::genericDb},
+                                {"predToCall", DbType::ACCESS_MODE_OUTPUT, DbType::NEED_DATA, &DbValidator::genericDb}}},
         {"unitesetstofasta",             unitesetstofasta,            &localPar.unitesetstofasta,    COMMAND_MAIN,
                 "Create a fasta output from optimal exon sets",
                 "Each optimal set is joined to a single sequence of codons or amino-acids",
                 "Eli Levy Karin <[email protected]>",
-                "<i:contigsDB> <i:targetsDB> <i:predictedExonsDB> <o:unitedExonsFasta>",
+                "<i:contigsDB> <i:targetsDB> <i:exonsDB> <o:unitedExonsFasta>",
                 NO_CITATION, {{"contigsDB", DbType::ACCESS_MODE_INPUT, DbType::NEED_DATA, &DbValidator::nuclDb},
                                 {"targetsDB", DbType::ACCESS_MODE_INPUT, DbType::NEED_DATA, &DbValidator::sequenceDb},
-                                {"predictedExonsDB", DbType::ACCESS_MODE_INPUT, DbType::NEED_DATA, &DbValidator::genericDb},
+                                {"exonsDB", DbType::ACCESS_MODE_INPUT, DbType::NEED_DATA, &DbValidator::genericDb},
                                 {"unitedExonsFasta", DbType::ACCESS_MODE_OUTPUT, DbType::NEED_DATA, NULL}}},
         {"groupstoacc",             groupstoacc,            &localPar.onlythreads,    COMMAND_MAIN,
-                "Create a TSV output from representative to member",
+                "Create a TSV output from representative prediction to member",
                 "Replace the internal contig, target and strand identifiers with accessions from the headers",
                 "Eli Levy Karin <[email protected]>",
-                "<i:contigsDB> <i:targetsDB> <i:repToPred> <o:groupsInfoTSV>",
+                "<i:contigsDB> <i:targetsDB> <i:predToCall> <o:predToCallInfoTSV>",
                 NO_CITATION, {{"contigsDB", DbType::ACCESS_MODE_INPUT, DbType::NEED_DATA, &DbValidator::nuclDb},
                                 {"targetsDB", DbType::ACCESS_MODE_INPUT, DbType::NEED_DATA, &DbValidator::sequenceDb},
-                                {"repToPred", DbType::ACCESS_MODE_INPUT, DbType::NEED_DATA, &DbValidator::genericDb},
-                                {"groupsInfoTSV", DbType::ACCESS_MODE_OUTPUT, DbType::NEED_DATA, NULL}}},
+                                {"predToCall", DbType::ACCESS_MODE_INPUT, DbType::NEED_DATA, &DbValidator::genericDb},
+                                {"predToCallInfoTSV", DbType::ACCESS_MODE_OUTPUT, DbType::NEED_DATA, NULL}}},
         // internal modules (COMMAND_EXPERT)
         {"resultspercontig",             resultspercontig,            &localPar.collectoptimalset,    COMMAND_EXPERT,
                 "Swap fragments against targets search and join with contigs",
@@ -63,8 +63,8 @@ std::vector<struct Command> commands = {
                 "Collect the optimal set of exons for a target protein/profile",
                 "A dynamic programming procedure on all candidates of each contig and strand combination",
                 "Eli Levy Karin <[email protected]>",
-                "<i:contigToSearchRes> <i:targetsDB> <o:predictedExonsDB>",
+                "<i:contigToSearchRes> <i:targetsDB> <o:calledExonsDB>",
                 NO_CITATION,{{"contigToSearchRes", DbType::ACCESS_MODE_INPUT, DbType::NEED_DATA, &DbValidator::resultDb},
                                 {"targetsDB", DbType::ACCESS_MODE_INPUT, DbType::NEED_DATA, &DbValidator::sequenceDb},
-                                {"predictedExonsDB", DbType::ACCESS_MODE_OUTPUT, DbType::NEED_DATA, NULL}}}
+                                {"calledExonsDB", DbType::ACCESS_MODE_OUTPUT, DbType::NEED_DATA, NULL}}}
 };