<commit_before>#
# This module is automatically generated by the gen-valid-commands.pl script
#


package Bio::KBase::InvocationService::ValidCommands;

use strict;

require Exporter;

our @ISA = qw(Exporter);
our @EXPORT_OK = qw(valid_commands command_groups);

our @command_groups = (
   { name => 'modeling_scripts', title => 'Modeling scripts', items => [
	{ cmd => 'exchangeFormat_to_gapfillingFormulation', link => '' },
	{ cmd => 'exchangeformat_to_fbamodel', link => '' },
	{ cmd => 'fbamodel_to_exchangeformat', link => '' },
	{ cmd => 'fbamodel_to_html', link => '' },
	{ cmd => 'fbamodel_to_sbml', link => '' },
	{ cmd => 'gapfill_fbamodel', link => '' },
	{ cmd => 'gapfillingFormulation_to_exchangeFormat', link => '' },
	{ cmd => 'genome_to_fbamodel', link => '' },
	{ cmd => 'get_gapfilling_formulation', link => '' },
	{ cmd => 'runfba', link => '' },
   ]},
   { name => 'scripts', title => 'CDMI Scripts', items => [
	{ cmd => 'all_roles_used_in_models', link => '' },
	{ cmd => 'all_roles_used_in_models_and_subsystems', link => '' },
	{ cmd => 'alleles_to_bp_locs', link => '' },
	{ cmd => 'alleles_to_traits', link => '' },
	{ cmd => 'atomic_regulons_to_fids', link => '' },
	{ cmd => 'close_genomes', link => '' },
	{ cmd => 'co_occurrence_evidence', link => '' },
	{ cmd => 'complexes_to_complex_data', link => '' },
	{ cmd => 'complexes_to_roles', link => '' },
	{ cmd => 'contigs_to_lengths', link => '' },
	{ cmd => 'contigs_to_md5s', link => '' },
	{ cmd => 'contigs_to_sequences', link => '' },
	{ cmd => 'corresponds', link => '' },
	{ cmd => 'dump_relationship', link => '' },
	{ cmd => 'equiv_sequence_assertions', link => '' },
	{ cmd => 'ermodel_to_text', link => '' },
	{ cmd => 'fids_to_annotations', link => '' },
	{ cmd => 'fids_to_atomic_regulons', link => '' },
	{ cmd => 'fids_to_co_occurring_fids', link => '' },
	{ cmd => 'fids_to_coexpressed_fids', link => '' },
	{ cmd => 'fids_to_dna_sequences', link => '' },
	{ cmd => 'fids_to_feature_data', link => '' },
	{ cmd => 'fids_to_functions', link => '' },
	{ cmd => 'fids_to_genomes', link => '' },
	{ cmd => 'fids_to_literature', link => '' },
	{ cmd => 'fids_to_locations', link => '' },
	{ cmd => 'fids_to_protein_families', link => '' },
	{ cmd => 'fids_to_protein_sequences', link => '' },
	{ cmd => 'fids_to_proteins', link => '' },
	{ cmd => 'fids_to_regulon_data', link => '' },
	{ cmd => 'fids_to_roles', link => '' },
	{ cmd => 'fids_to_subsystem_data', link => '' },
	{ cmd => 'fids_to_subsystems', link => '' },
	{ cmd => 'genomes_to_contigs', link => '' },
	{ cmd => 'genomes_to_fids', link => '' },
	{ cmd => 'genomes_to_genome_data', link => '' },
	{ cmd => 'genomes_to_md5s', link => '' },
	{ cmd => 'genomes_to_subsystems', link => '' },
	{ cmd => 'genomes_to_taxonomies', link => '' },
	{ cmd => 'get_abundance_profile', link => '' },
	{ cmd => 'locations_to_dna_sequences', link => '' },
	{ cmd => 'locations_to_fids', link => '' },
	{ cmd => 'md5s_to_genomes', link => '' },
	{ cmd => 'otu_members', link => '' },
	{ cmd => 'ous_with_trait', link => '' },
	{ cmd => 'protein_families_to_co_occurring_families', link => '' },
	{ cmd => 'protein_families_to_fids', link => '' },
	{ cmd => 'protein_families_to_functions', link => '' },
	{ cmd => 'protein_families_to_proteins', link => '' },
	{ cmd => 'proteins_to_fids', link => '' },
	{ cmd => 'proteins_to_functions', link => '' },
	{ cmd => 'proteins_to_literature', link => '' },
	{ cmd => 'proteins_to_protein_families', link => '' },
	{ cmd => 'proteins_to_roles', link => '' },
	{ cmd => 'proteins_to_sequences', link => '' },
	{ cmd => 'reaction_strings', link => '' },
	{ cmd => 'reactions_to_complexes', link => '' },
	{ cmd => 'region_to_alleles', link => '' },
	{ cmd => 'region_to_fids', link => '' },
	{ cmd => 'regulons_to_fids', link => '' },
	{ cmd => 'representative', link => '' },
	{ cmd => 'representative_sequences', link => '' },
	{ cmd => 'roles_to_complexes', link => '' },
	{ cmd => 'roles_to_fids', link => '' },
	{ cmd => 'roles_to_protein_families', link => '' },
	{ cmd => 'roles_to_proteins', link => '' },
	{ cmd => 'roles_to_subsystems', link => '' },
	{ cmd => 'subsystems_to_fids', link => '' },
	{ cmd => 'subsystems_to_genomes', link => '' },
	{ cmd => 'subsystems_to_roles', link => '' },
	{ cmd => 'subsystems_to_spreadsheets', link => '' },
	{ cmd => 'text_search', link => '' },
	{ cmd => 'traits_to_alleles', link => '' },
   ]},
   { name => 'anno_scripts', title => 'Annotation service scripts', items => [
	{ cmd => 'a_and_b', link => '' },
	{ cmd => 'a_not_b', link => '' },
	{ cmd => 'annotate_genome', link => '' },
	{ cmd => 'assign_functions_to_CDSs', link => '' },
	{ cmd => 'call_CDSs', link => '' },
	{ cmd => 'call_CDSs_by_glimmer', link => '' },
	{ cmd => 'call_CDSs_by_projection', link => '' },
	{ cmd => 'call_RNAs', link => '' },
	{ cmd => 'call_pyrrolysoproteins', link => '' },
	{ cmd => 'call_selenoproteins', link => '' },
	{ cmd => 'cluster_objects', link => '' },
	{ cmd => 'cs_to_genome', link => '' },
	{ cmd => 'fasta_to_genome', link => '' },
	{ cmd => 'file_to_spreadsheet', link => '' },
	{ cmd => 'genomeTO_strep_pneumo_repeats', link => '' },
	{ cmd => 'genomeTO_strep_suis_repeats', link => '' },
	{ cmd => 'genomeTO_to_coding_regions', link => '' },
	{ cmd => 'genomeTO_to_feature_data', link => '' },
	{ cmd => 'genomeTO_to_html', link => '' },
	{ cmd => 'genomeTO_to_reconstructionTO', link => '' },
	{ cmd => 'merge_features', link => '' },
	{ cmd => 'reconstructionTO_to_roles', link => '' },
	{ cmd => 'reconstructionTO_to_subsystems', link => '' },
	{ cmd => 'regions_around', link => '' },
	{ cmd => 'rel2tabs', link => '' },
	{ cmd => 'sort_by_id', link => '' },
	{ cmd => 'sort_by_loc', link => '' },
	{ cmd => 'tabs2rel', link => '' },
   ]},
   { name => 'er_scripts', title => 'Entity Relationship Scripts', items => [
	{ cmd => 'all_entities_AlignmentTree', link => '' },
	{ cmd => 'all_entities_AlleleFrequency', link => '' },
	{ cmd => 'all_entities_Annotation', link => '' },
	{ cmd => 'all_entities_Assay', link => '' },
	{ cmd => 'all_entities_AtomicRegulon', link => '' },
	{ cmd => 'all_entities_Attribute', link => '' },
	{ cmd => 'all_entities_Biomass', link => '' },
	{ cmd => 'all_entities_BiomassCompound', link => '' },
	{ cmd => 'all_entities_Compartment', link => '' },
	{ cmd => 'all_entities_Complex', link => '' },
	{ cmd => 'all_entities_Compound', link => '' },
	{ cmd => 'all_entities_Contig', link => '' },
	{ cmd => 'all_entities_ContigChunk', link => '' },
	{ cmd => 'all_entities_ContigSequence', link => '' },
	{ cmd => 'all_entities_CoregulatedSet', link => '' },
	{ cmd => 'all_entities_Diagram', link => '' },
	{ cmd => 'all_entities_EcNumber', link => '' },
	{ cmd => 'all_entities_Experiment', link => '' },
	{ cmd => 'all_entities_Family', link => '' },
	{ cmd => 'all_entities_Feature', link => '' },
	{ cmd => 'all_entities_Genome', link => '' },
	{ cmd => 'all_entities_Identifier', link => '' },
	{ cmd => 'all_entities_Locality', link => '' },
	{ cmd => 'all_entities_Media', link => '' },
	{ cmd => 'all_entities_Model', link => '' },
	{ cmd => 'all_entities_ModelCompartment', link => '' },
	{ cmd => 'all_entities_OTU', link => '' },
	{ cmd => 'all_entities_ObservationalUnit', link => '' },<commit_msg>add strep repeats commands<commit_after>#
# This module is automatically generated by the gen-valid-commands.pl script
#


package Bio::KBase::InvocationService::ValidCommands;

use strict;

require Exporter;

our @ISA = qw(Exporter);
our @EXPORT_OK = qw(valid_commands command_groups);

our @command_groups = (
   { name => 'modeling_scripts', title => 'Modeling scripts', items => [
	{ cmd => 'exchangeFormat_to_gapfillingFormulation', link => '' },
	{ cmd => 'exchangeformat_to_fbamodel', link => '' },
	{ cmd => 'fbamodel_to_exchangeformat', link => '' },
	{ cmd => 'fbamodel_to_html', link => '' },
	{ cmd => 'fbamodel_to_sbml', link => '' },
	{ cmd => 'gapfill_fbamodel', link => '' },
	{ cmd => 'gapfillingFormulation_to_exchangeFormat', link => '' },
	{ cmd => 'genome_to_fbamodel', link => '' },
	{ cmd => 'get_gapfilling_formulation', link => '' },
	{ cmd => 'runfba', link => '' },
   ]},
   { name => 'scripts', title => 'CDMI Scripts', items => [
	{ cmd => 'all_roles_used_in_models', link => '' },
	{ cmd => 'all_roles_used_in_models_and_subsystems', link => '' },
	{ cmd => 'alleles_to_bp_locs', link => '' },
	{ cmd => 'alleles_to_traits', link => '' },
	{ cmd => 'atomic_regulons_to_fids', link => '' },
	{ cmd => 'close_genomes', link => '' },
	{ cmd => 'co_occurrence_evidence', link => '' },
	{ cmd => 'complexes_to_complex_data', link => '' },
	{ cmd => 'complexes_to_roles', link => '' },
	{ cmd => 'contigs_to_lengths', link => '' },
	{ cmd => 'contigs_to_md5s', link => '' },
	{ cmd => 'contigs_to_sequences', link => '' },
	{ cmd => 'corresponds', link => '' },
	{ cmd => 'dump_relationship', link => '' },
	{ cmd => 'equiv_sequence_assertions', link => '' },
	{ cmd => 'ermodel_to_text', link => '' },
	{ cmd => 'fids_to_annotations', link => '' },
	{ cmd => 'fids_to_atomic_regulons', link => '' },
	{ cmd => 'fids_to_co_occurring_fids', link => '' },
	{ cmd => 'fids_to_coexpressed_fids', link => '' },
	{ cmd => 'fids_to_dna_sequences', link => '' },
	{ cmd => 'fids_to_feature_data', link => '' },
	{ cmd => 'fids_to_functions', link => '' },
	{ cmd => 'fids_to_genomes', link => '' },
	{ cmd => 'fids_to_literature', link => '' },
	{ cmd => 'fids_to_locations', link => '' },
	{ cmd => 'fids_to_protein_families', link => '' },
	{ cmd => 'fids_to_protein_sequences', link => '' },
	{ cmd => 'fids_to_proteins', link => '' },
	{ cmd => 'fids_to_regulon_data', link => '' },
	{ cmd => 'fids_to_roles', link => '' },
	{ cmd => 'fids_to_subsystem_data', link => '' },
	{ cmd => 'fids_to_subsystems', link => '' },
	{ cmd => 'genomes_to_contigs', link => '' },
	{ cmd => 'genomes_to_fids', link => '' },
	{ cmd => 'genomes_to_genome_data', link => '' },
	{ cmd => 'genomes_to_md5s', link => '' },
	{ cmd => 'genomes_to_subsystems', link => '' },
	{ cmd => 'genomes_to_taxonomies', link => '' },
	{ cmd => 'get_abundance_profile', link => '' },
	{ cmd => 'locations_to_dna_sequences', link => '' },
	{ cmd => 'locations_to_fids', link => '' },
	{ cmd => 'md5s_to_genomes', link => '' },
	{ cmd => 'otu_members', link => '' },
	{ cmd => 'ous_with_trait', link => '' },
	{ cmd => 'protein_families_to_co_occurring_families', link => '' },
	{ cmd => 'protein_families_to_fids', link => '' },
	{ cmd => 'protein_families_to_functions', link => '' },
	{ cmd => 'protein_families_to_proteins', link => '' },
	{ cmd => 'proteins_to_fids', link => '' },
	{ cmd => 'proteins_to_functions', link => '' },
	{ cmd => 'proteins_to_literature', link => '' },
	{ cmd => 'proteins_to_protein_families', link => '' },
	{ cmd => 'proteins_to_roles', link => '' },
	{ cmd => 'proteins_to_sequences', link => '' },
	{ cmd => 'reaction_strings', link => '' },
	{ cmd => 'reactions_to_complexes', link => '' },
	{ cmd => 'region_to_alleles', link => '' },
	{ cmd => 'region_to_fids', link => '' },
	{ cmd => 'regulons_to_fids', link => '' },
	{ cmd => 'representative', link => '' },
	{ cmd => 'representative_sequences', link => '' },
	{ cmd => 'roles_to_complexes', link => '' },
	{ cmd => 'roles_to_fids', link => '' },
	{ cmd => 'roles_to_protein_families', link => '' },
	{ cmd => 'roles_to_proteins', link => '' },
	{ cmd => 'roles_to_subsystems', link => '' },
	{ cmd => 'subsystems_to_fids', link => '' },
	{ cmd => 'subsystems_to_genomes', link => '' },
	{ cmd => 'subsystems_to_roles', link => '' },
	{ cmd => 'subsystems_to_spreadsheets', link => '' },
	{ cmd => 'text_search', link => '' },
	{ cmd => 'traits_to_alleles', link => '' },
   ]},
   { name => 'anno_scripts', title => 'Annotation service scripts', items => [
	{ cmd => 'a_and_b', link => '' },
	{ cmd => 'a_not_b', link => '' },
	{ cmd => 'annotate_genome', link => '' },
	{ cmd => 'assign_functions_to_CDSs', link => '' },
	{ cmd => 'call_CDSs', link => '' },
	{ cmd => 'call_CDSs_by_glimmer', link => '' },
	{ cmd => 'call_CDSs_by_projection', link => '' },
	{ cmd => 'call_RNAs', link => '' },
	{ cmd => 'call_pyrrolysoproteins', link => '' },
	{ cmd => 'call_selenoproteins', link => '' },
	{ cmd => 'cluster_objects', link => '' },
	{ cmd => 'cs_to_genome', link => '' },
	{ cmd => 'fasta_to_genome', link => '' },
	{ cmd => 'file_to_spreadsheet', link => '' },
	{ cmd => 'genomeTO_strep_pneumo_repeats', link => '' },
	{ cmd => 'genomeTO_strep_suis_repeats', link => '' },
	{ cmd => 'genomeTO_to_coding_regions', link => '' },
	{ cmd => 'genomeTO_to_feature_data', link => '' },
	{ cmd => 'genomeTO_to_html', link => '' },
	{ cmd => 'genomeTO_to_reconstructionTO', link => '' },
	{ cmd => 'merge_features', link => '' },
	{ cmd => 'reconstructionTO_to_roles', link => '' },
	{ cmd => 'reconstructionTO_to_subsystems', link => '' },
	{ cmd => 'regions_around', link => '' },
	{ cmd => 'rel2tabs', link => '' },
	{ cmd => 'sort_by_id', link => '' },
	{ cmd => 'sort_by_loc', link => '' },
	{ cmd => 'tabs2rel', link => '' },
	{ cmd => 'pneumococcal_repeat_annotation.pl', link => '' },
	{ cmd => 'suis_repeat_annotation.pl', link => '' },
   ]},
   { name => 'er_scripts', title => 'Entity Relationship Scripts', items => [
	{ cmd => 'all_entities_AlignmentTree', link => '' },
	{ cmd => 'all_entities_AlleleFrequency', link => '' },
	{ cmd => 'all_entities_Annotation', link => '' },
	{ cmd => 'all_entities_Assay', link => '' },
	{ cmd => 'all_entities_AtomicRegulon', link => '' },
	{ cmd => 'all_entities_Attribute', link => '' },
	{ cmd => 'all_entities_Biomass', link => '' },
	{ cmd => 'all_entities_BiomassCompound', link => '' },
	{ cmd => 'all_entities_Compartment', link => '' },
	{ cmd => 'all_entities_Complex', link => '' },
	{ cmd => 'all_entities_Compound', link => '' },
	{ cmd => 'all_entities_Contig', link => '' },
	{ cmd => 'all_entities_ContigChunk', link => '' },
	{ cmd => 'all_entities_ContigSequence', link => '' },
	{ cmd => 'all_entities_CoregulatedSet', link => '' },
	{ cmd => 'all_entities_Diagram', link => '' },
	{ cmd => 'all_entities_EcNumber', link => '' },
	{ cmd => 'all_entities_Experiment', link => '' },
	{ cmd => 'all_entities_Family', link => '' },
	{ cmd => 'all_entities_Feature', link => '' },
	{ cmd => 'all_entities_Genome', link => '' },
	{ cmd => 'all_entities_Identifier', link => '' },
	{ cmd => 'all_entities_Locality', link => '' },
	{ cmd => 'all_entities_Media', link => '' },
	{ cmd => 'all_entities_Model', link => '' },
	{ cmd => 'all_entities_ModelCompartment', link => '' },
	{ cmd => 'all_entities_OTU', link => '' },
	{ cmd => 'all_entities_ObservationalUnit', link => '' },
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