static void *gt_tyr_arguments_new(void)
{
GtToolbox *tyr_toolbox = gt_toolbox_new();
gt_toolbox_add_tool(tyr_toolbox, "mkindex", gt_tyr_mkindex());
gt_toolbox_add_tool(tyr_toolbox, "occratio", gt_tyr_occratio());
gt_toolbox_add_tool(tyr_toolbox, "search", gt_tyr_search());
return tyr_toolbox;
}
static void* gt_condenseq_toolbox_new(void)
{
GtToolbox *condenseq_toolbox = gt_toolbox_new();
gt_toolbox_add_tool(condenseq_toolbox, "compress", gt_condenseq_compress());
gt_toolbox_add_tool(condenseq_toolbox, "search", gt_condenseq_search());
gt_toolbox_add_tool(condenseq_toolbox, "extract", gt_condenseq_extract());
gt_toolbox_add_tool(condenseq_toolbox, "info", gt_condenseq_info());
return condenseq_toolbox;
}
static void *gt_cge_arguments_new(void)
{
GtToolbox *cge_toolbox = gt_toolbox_new();
gt_toolbox_add_tool(cge_toolbox, "spacedseed", gt_cge_spacedseed());
return cge_toolbox;
}
GtToolbox* gtt_tools(void)
{
GtToolbox *tools = gt_toolbox_new();
/* add tools */
gt_toolbox_add(tools, "mgth", gt_mgth);
gt_toolbox_add(tools, "mkfmindex", gt_mkfmindex);
gt_toolbox_add(tools, "suffixerator", gt_suffixerator);
gt_toolbox_add_hidden_tool(tools, "dev", gt_dev());
gt_toolbox_add_hidden_tool(tools, "filter", gt_select());
/* hidden "link from the mutate to the seqmutate tool for backward
compatibility */
gt_toolbox_add_hidden_tool(tools, "mutate", gt_seqmutate());
gt_toolbox_add_hidden_tool(tools, "template", gt_template());
gt_toolbox_add_tool(tools, "bed_to_gff3", gt_bed_to_gff3());
gt_toolbox_add_tool(tools, "cds", gt_cds());
gt_toolbox_add_tool(tools, "chain2dim", gt_chain2dim());
gt_toolbox_add_tool(tools, "chseqids", gt_chseqids());
gt_toolbox_add_tool(tools, "clean", gt_clean());
gt_toolbox_add_tool(tools, "compreads", gt_compreads());
gt_toolbox_add_tool(tools, "condenseq", gt_condenseq());
gt_toolbox_add_tool(tools, "congruence", gt_congruence());
gt_toolbox_add_tool(tools, "convertseq", gt_convertseq());
gt_toolbox_add_tool(tools, "csa", gt_csa());
gt_toolbox_add_tool(tools, "dot", gt_dot());
gt_toolbox_add_tool(tools, "dupfeat", gt_dupfeat());
gt_toolbox_add_tool(tools, "encseq", gt_encseq());
gt_toolbox_add_tool(tools, "encseq2spm", gt_encseq2spm());
gt_toolbox_add_tool(tools, "eval", gt_eval());
gt_toolbox_add_tool(tools, "extractfeat", gt_extractfeat());
gt_toolbox_add_tool(tools, "extractseq", gt_extractseq());
gt_toolbox_add_tool(tools, "fastq_sample", gt_fastq_sample());
gt_toolbox_add_tool(tools, "fingerprint", gt_fingerprint());
gt_toolbox_add_tool(tools, "genomediff", gt_genomediff());
gt_toolbox_add_tool(tools, "gff3", gt_gff3());
gt_toolbox_add_tool(tools, "gff3_to_gtf", gt_gff3_to_gtf());
gt_toolbox_add_tool(tools, "gff3validator", gt_gff3validator());
gt_toolbox_add_tool(tools, "gtf_to_gff3", gt_gtf_to_gff3());
gt_toolbox_add_tool(tools, "hop", gt_hop());
gt_toolbox_add_tool(tools, "id_to_md5", gt_id_to_md5());
gt_toolbox_add_tool(tools, "inlineseq_split", gt_inlineseq_split());
gt_toolbox_add_tool(tools, "inlineseq_add", gt_inlineseq_add());
gt_toolbox_add_tool(tools, "interfeat", gt_interfeat());
gt_toolbox_add_tool(tools, "loccheck", gt_loccheck());
gt_toolbox_add_tool(tools, "ltrclustering", gt_ltrclustering());
gt_toolbox_add_tool(tools, "ltrdigest", gt_ltrdigest());
gt_toolbox_add_tool(tools, "ltrharvest", gt_ltrharvest());
gt_toolbox_add_tool(tools, "matchtool", gt_matchtool());
gt_toolbox_add_tool(tools, "matstat", gt_matstat());
gt_toolbox_add_tool(tools, "md5_to_id", gt_md5_to_id());
gt_toolbox_add_tool(tools, "merge", gt_merge());
gt_toolbox_add_tool(tools, "mergefeat", gt_mergefeat());
gt_toolbox_add_tool(tools, "mmapandread", gt_mmapandread());
gt_toolbox_add_tool(tools, "orffinder", gt_orffinder());
gt_toolbox_add_tool(tools, "packedindex", gt_packedindex());
gt_toolbox_add_tool(tools, "prebwt", gt_prebwt());
gt_toolbox_add_tool(tools, "readjoiner", gt_readjoiner());
gt_toolbox_add_tool(tools, "repfind", gt_repfind());
gt_toolbox_add_tool(tools, "scriptfilter", gt_script_filter());
gt_toolbox_add_tool(tools, "seed_extend", gt_seed_extend());
gt_toolbox_add_tool(tools, "select", gt_select());
gt_toolbox_add_tool(tools, "seq", gt_seq());
gt_toolbox_add_tool(tools, "seqfilter", gt_seqfilter());
gt_toolbox_add_tool(tools, "seqids", gt_seqids());
gt_toolbox_add_tool(tools, "seqmutate", gt_seqmutate());
gt_toolbox_add_tool(tools, "seqorder", gt_seqorder());
gt_toolbox_add_tool(tools, "seqstat", gt_seqstat());
gt_toolbox_add_tool(tools, "seqtransform", gt_seqtransform());
gt_toolbox_add_tool(tools, "seqtranslate", gt_seqtranslate());
gt_toolbox_add_tool(tools, "sequniq", gt_sequniq());
gt_toolbox_add_tool(tools, "shredder", gt_shredder());
gt_toolbox_add_tool(tools, "shulengthdist", gt_shulengthdist());
gt_toolbox_add_tool(tools, "simreads", gt_simreads());
gt_toolbox_add_tool(tools, "snpper", gt_snpper());
gt_toolbox_add_tool(tools, "speck", gt_speck());
gt_toolbox_add_tool(tools, "splicesiteinfo", gt_splicesiteinfo());
gt_toolbox_add_tool(tools, "splitfasta", gt_splitfasta());
gt_toolbox_add_tool(tools, "stat", gt_stat());
gt_toolbox_add_tool(tools, "tagerator", gt_tagerator());
gt_toolbox_add_tool(tools, "tallymer", gt_tallymer());
gt_toolbox_add_tool(tools, "tirvish", gt_tir());
gt_toolbox_add_tool(tools, "uniq", gt_uniq());
gt_toolbox_add_tool(tools, "uniquesub", gt_uniquesub());
gt_toolbox_add_tool(tools, "wtree", gt_wtree());
#ifndef WITHOUT_CAIRO
gt_toolbox_add_tool(tools, "sketch", gt_sketch());
gt_toolbox_add_tool(tools, "sketch_page", gt_sketch_page());
#endif
#if defined (HAVE_MYSQL) || defined (HAVE_SQLITE)
gt_toolbox_add_tool(tools, "featureindex", gt_featureindex());
gt_toolbox_add_tool(tools, "mkfeatureindex", gt_mkfeatureindex());
#endif
return tools;
}
static void* gt_dev_arguments_new(void)
{
GtToolbox *dev_toolbox = gt_toolbox_new();
/* add development tools here with a function call like this:
gt_toolbox_add(dev_toolbox, "devtool", gt_devtool); */
gt_toolbox_add(dev_toolbox, "gthbssmbuild", gt_gthbssmbuild);
gt_toolbox_add(dev_toolbox, "gthbssmfileinfo", gt_gthbssmfileinfo);
gt_toolbox_add(dev_toolbox, "gthbssmprint", gt_gthbssmprint);
gt_toolbox_add(dev_toolbox, "gthmkbssmfiles", gt_gthmkbssmfiles);
gt_toolbox_add(dev_toolbox, "guessprot", gt_guessprot);
gt_toolbox_add(dev_toolbox, "mergeesa", gt_mergeesa);
gt_toolbox_add(dev_toolbox, "paircmp", gt_paircmp);
gt_toolbox_add(dev_toolbox, "patternmatch", gt_patternmatch);
gt_toolbox_add(dev_toolbox, "regioncov", gt_regioncov);
gt_toolbox_add(dev_toolbox, "trieins", gt_trieins);
gt_toolbox_add_tool(dev_toolbox, "compbits", gt_compressedbits());
gt_toolbox_add_tool(dev_toolbox, "condenser", gt_condenser());
gt_toolbox_add_tool(dev_toolbox, "consensus_sa", gt_consensus_sa_tool());
gt_toolbox_add_tool(dev_toolbox, "extracttarget", gt_extracttarget());
gt_toolbox_add_tool(dev_toolbox, "gdiffcalc", gt_gdiffcalc());
gt_toolbox_add_tool(dev_toolbox, "gthbssmrmsd", gt_gthbssmrmsd());
gt_toolbox_add_tool(dev_toolbox, "gthbssmtrain", gt_gthbssmtrain());
gt_toolbox_add_tool(dev_toolbox, "idxlocali", gt_idxlocali());
gt_toolbox_add_tool(dev_toolbox, "kmer_database", gt_kmer_database());
gt_toolbox_add_tool(dev_toolbox, "linspace_align", gt_linspace_align());
gt_toolbox_add_tool(dev_toolbox, "magicmatch", gt_magicmatch());
gt_toolbox_add_tool(dev_toolbox, "parsexrf", gt_parsexrf());
gt_toolbox_add_tool(dev_toolbox, "readreads", gt_readreads());
gt_toolbox_add_tool(dev_toolbox, "sain", gt_sain());
gt_toolbox_add_tool(dev_toolbox, "sambam", gt_sam_interface());
gt_toolbox_add_tool(dev_toolbox, "seqcorrect", gt_seqcorrect());
gt_toolbox_add_tool(dev_toolbox, "seqlensort", gt_seqlensort());
gt_toolbox_add_tool(dev_toolbox, "sfxmap", gt_sfxmap());
gt_toolbox_add_tool(dev_toolbox, "skproto", gt_skproto());
gt_toolbox_add_tool(dev_toolbox, "sortbench", gt_sortbench());
return dev_toolbox;
}
