Curated tools for the biodiversity community

communities/biodiversity/resources/curated_tools.tsv

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+Galaxy wrapper id	Galaxy wrapper id	Galaxy tool ids	To keep	Deprecated
+TrimNs	TrimNs	trimns	FALSE	FALSE
+abacas	abacas	abacas	FALSE	FALSE
+abyss	abyss	abyss-pe	FALSE	FALSE
+assembly-stats	assembly-stats	assembly_stats	FALSE	FALSE
+assemblystats	assemblystats	assemblystats	FALSE	FALSE
+bam2mappingstats	bam2mappingstats	bam2mappingstats	FALSE	FALSE
+bionano	bionano	bionano_scaffold	FALSE	FALSE
+biscot	biscot	biscot	FALSE	FALSE
+cap3	cap3	cap3	FALSE	FALSE
+combine_assembly_stats	combine_assembly_stats	combine_stats	FALSE	FALSE
+fastk	fastk	fastk_fastk	FALSE	FALSE
+filter_spades_repeats	filter_spades_repeats	filter_spades_repeat	FALSE	FALSE
+flye	flye	flye	FALSE	FALSE
+getorganelle	getorganelle	get_annotated_regions_from_gb, get_organelle_from_reads	FALSE	FALSE
+graphmap	graphmap	graphmap_align, graphmap_overlap	FALSE	FALSE
+hapcut2	hapcut2	hapcut2	FALSE	FALSE
+hapog	hapog	hapog	FALSE	FALSE
+hifiasm	hifiasm	hifiasm	FALSE	FALSE
+hisat	hisat	hisat	FALSE	FALSE
+hisat2	hisat2	hisat2	TRUE	FALSE
+hypo	hypo	hypo	FALSE	FALSE
+idba_ud	idba_ud	idba_hybrid, idba_tran, idba_ud	FALSE	FALSE
+instagraal	instagraal	instagraal	FALSE	FALSE
+jellyfish	jellyfish	jellyfish	FALSE	FALSE
+links	links	links	FALSE	FALSE
+merqury	merqury	merqury, merquryplot	FALSE	FALSE
+meryl	meryl	meryl_arithmetic_kmers, meryl_count_kmers, meryl_filter_kmers, meryl_groups_kmers, meryl_histogram_kmers, meryl_print, meryl_trio_mode	FALSE	FALSE
+minia	minia	minia	FALSE	FALSE
+miniasm	miniasm	miniasm	FALSE	FALSE
+mitobim	mitobim	mitobim	FALSE	FALSE
+mitohifi	mitohifi	mitohifi	TRUE	FALSE
+necat	necat	necat	FALSE	FALSE
+nextdenovo	nextdenovo	nextdenovo	FALSE	FALSE
+novoplasty	novoplasty	novoplasty	FALSE	FALSE
+plasmidspades	plasmidspades	plasmidspades	FALSE	FALSE
+promer	promer	promer4_substitutions	FALSE	FALSE
+purge_dups	purge_dups	purge_dups	FALSE	FALSE
+quast	quast	quast	FALSE	FALSE
+quickmerge	quickmerge	quickmerge	FALSE	FALSE
+ragtag	ragtag	ragtag	FALSE	FALSE
+raven	raven	raven	FALSE	FALSE
+salsa2	salsa2	salsa	FALSE	FALSE
+shovill	shovill	shovill	FALSE	FALSE
+smudgeplot	smudgeplot	smudgeplot	FALSE	FALSE
+taxonomy_krona_chart	taxonomy_krona_chart	taxonomy_krona_chart	TRUE	FALSE
+tgsgapcloser	tgsgapcloser	tgsgapcloser	FALSE	FALSE
+trycycler	trycycler	trycycler_cluster, trycycler_consensus, trycycler_partition, trycycler_reconcile_msa, trycycler_subsample	FALSE	FALSE
+unicycler	unicycler	unicycler	FALSE	FALSE
+velvet	velvet	velvetg, velveth	FALSE	FALSE
+velvet_optimiser	velvet_optimiser	velvetoptimiser	FALSE	FALSE
+verkko	verkko	verkko	FALSE	FALSE
+wtdbg	wtdbg	wtdbg	FALSE	FALSE
+yahs	yahs	yahs	FALSE	FALSE
+seq_filter_by_mapping	seq_filter_by_mapping	seq_filter_by_mapping	FALSE	FALSE
+sample_seqs	sample_seqs	sample_seqs	FALSE	FALSE
+seq_primer_clip	seq_primer_clip	seq_primer_clip	FALSE	FALSE
+flash	flash	flash	FALSE	FALSE
+shasta	shasta	shasta	FALSE	FALSE
+khmer	khmer	khmer_abundance_distribution_single, khmer_abundance_distribution, khmer_count_median, khmer_partition, khmer_extract_partitions, khmer_filter_abundance, khmer_filter_below_abundance_cutoff, khmer_normalize_by_median	FALSE	FALSE
+clc_assembly_cell	clc_assembly_cell	clc_assembler, clc_mapper	FALSE	FALSE
+samtools_idxstats	samtools_idxstats	samtools_idxstats	FALSE	FALSE
+blastparser_and_hits	blastparser_and_hits	BlastParser_and_hits	FALSE	FALSE
+oases	oases	oasesoptimiserv	FALSE	FALSE
+rnaquast	rnaquast	rna_quast	FALSE	FALSE
+spades	spades	spades_biosyntheticspades, spades_coronaspades, spades_metaplasmidspades, metaspades, spades_metaviralspades, spades_plasmidspades, rnaspades, spades_rnaviralspades, spades	FALSE	FALSE
+count_roi_variants	count_roi_variants	count_roi_variants	FALSE	FALSE
+coverage_stats	coverage_stats	coverage_stats	FALSE	FALSE
+samtools_depad	samtools_depad	samtools_depad	TRUE	FALSE
+samtools_depth	samtools_depth	samtools_depth	TRUE	FALSE
+fermikit	fermikit	fermi2, fermikit_variants	FALSE	FALSE
+EMLassemblyline	EMLassemblyline	eal_table_template, eal_templates, eml2eal, entities_template, geo_cov_template, makeeml, raster_template, taxo_cov_template, vector_template	FALSE	FALSE
+Ecoregionalization_workflow	Ecoregionalization_workflow	ecoregion_brt_analysis, ecoregion_GeoNearestNeighbor, ecoregion_cluster_estimate, ecoregion_clara_cluster, ecoregion_eco_map, ecoregion_taxa_seeker	TRUE	FALSE
+Geom_mean_workflow	Geom_mean_workflow	Map_shp, Mean_geom, bar_plot	FALSE	FALSE
+PAMPA	PAMPA	pampa_communitymetrics, pampa_presabs, pampa_glmcomm, pampa_glmsp, pampa_plotglm	TRUE	FALSE
+aquainfra_importer	aquainfra_importer	aquainfra_importer	FALSE	FALSE
+champ_blocs	champ_blocs	cb_dissim, cb_ivr, cb_div	TRUE	FALSE
+data_exploration	data_exploration	tool_anonymization, ecology_homogeneity_normality, ecology_beta_diversity, ecology_link_between_var, ecology_presence_abs_abund, ecology_stat_presence_abs	TRUE	FALSE
+dose_responses	dose_responses	dr_curve	FALSE	FALSE
+gdal	gdal	gdal_gdal_merge, gdal_gdal_translate, gdal_gdaladdo, gdal_gdalbuildvrt, gdal_gdalinfo, gdal_gdalwarp, gdal_ogr2ogr, gdal_ogrinfo	TRUE	FALSE
+hirondelle_crim_ogc_api_processes	hirondelle_crim_ogc_api_processes	hirondelle_crim	TRUE	FALSE
+interpolation	interpolation	interpolation_run_idw_interpolation	TRUE	FALSE
+obisindicators	obisindicators	obisindicators, obis_data	TRUE	FALSE
+ocean	ocean	argo_getdata	FALSE	FALSE
+ogcProcess_otb_bandmath	ogcProcess_otb_bandmath	otb_band_math	FALSE	FALSE
+ogcProcess_otb_meanShiftSmoothing	ogcProcess_otb_meanShiftSmoothing	otb_mean_shift_smoothing	FALSE	FALSE
+regionalgam	regionalgam	regionalgam_ab_index, regionalgam_autocor_acf, regionalgam_flight_curve, regionalgam_glmmpql, regionalgam_gls_adjusted, regionalgam_gls, regionalgam_plot_trend	TRUE	FALSE
+retrieve_bold	retrieve_bold	retrieve_bold	TRUE	FALSE
+sdmpredictors	sdmpredictors	sdmpredictors_list_layers	TRUE	FALSE
+spocc	spocc	spocc_occ	TRUE	FALSE
+srs_tools	srs_tools	srs_diversity_maps, srs_global_indices, srs_process_data, srs_spectral_indices, srs_pca, srs_preprocess_s2, srs_metadata	TRUE	FALSE
+stoc	stoc	stoceps_filteringsp, stoceps_glm, stoceps_glm_group, stoceps_maketablecarrer, stoceps_trend_indic	TRUE	FALSE
+vigiechiro	vigiechiro	vigiechiro_bilanenrichipf, vigiechiro_bilanenrichirp, vigiechiro_idcorrect_2ndlayer, vigiechiro_idvalid	TRUE	FALSE
+xarray	xarray	timeseries_extraction, xarray_coords_info, xarray_mapplot, xarray_metadata_info, xarray_netcdf2netcdf, xarray_select	FALSE	FALSE
+zoo_project_ogc_api_processes	zoo_project_ogc_api_processes	zoo_project_ogc_api_processes	TRUE	FALSE
+medenv	medenv	iabiodiv_smartbiodiv_med_environ	TRUE	FALSE
+baseline_calculator	baseline_calculator	tt_baseline	FALSE	FALSE
+annotatemyids	annotatemyids	annotatemyids	FALSE	FALSE
+biotradis	biotradis	bacteria_tradis, tradis_essentiality, tradis_gene_insert_sites	FALSE	FALSE
+braker	braker	braker	FALSE	FALSE
+braker3	braker3	braker3	FALSE	FALSE
+deepsig	deepsig	deepsig	FALSE	FALSE
+funannotate	funannotate	funannotate_annotate, funannotate_clean, funannotate_compare, funannotate_predict, funannotate_sort	TRUE	FALSE
+goenrichment	goenrichment	goenrichment, goslimmer	FALSE	FALSE
+helixer	helixer	helixer	FALSE	FALSE
+icescreen	icescreen	icescreen	FALSE	FALSE
+pharokka	pharokka	pharokka	FALSE	FALSE
+prodigal	prodigal	prodigal	FALSE	FALSE
+repeatexplorer2	repeatexplorer2	repeatexplorer_clustering	FALSE	FALSE
+repeatmodeler	repeatmodeler	repeatmodeler	FALSE	FALSE
+telescope	telescope	telescope_assign	FALSE	FALSE
+transit	transit	gff_to_prot, transit_gumbel, transit_hmm, transit_resampling, transit_tn5gaps	FALSE	FALSE
+tsebra	tsebra	tsebra	FALSE	FALSE
+chipseeker	chipseeker	chipseeker	FALSE	FALSE
+disco	disco	disco	FALSE	FALSE
+circexplorer2	circexplorer2	circexplorer2	FALSE	FALSE
+blast_to_scaffold	blast_to_scaffold	blast2scaffold	FALSE	FALSE
+blastx_to_scaffold	blastx_to_scaffold	blastx2scaffold	FALSE	FALSE
+blobtoolkit	blobtoolkit	blobtoolkit	FALSE	FALSE
+ear	ear	make_ear	FALSE	FALSE
+megahit	megahit	megahit	FALSE	FALSE
+megahit_contig2fastg	megahit_contig2fastg	megahit_contig2fastg	FALSE	FALSE
+metaeuk	metaeuk	metaeuk_easy_predict	FALSE	FALSE
+spaln	spaln	list_spaln_tables, spaln	FALSE	FALSE
+taxonomy_filter_refseq	taxonomy_filter_refseq	taxonomy_filter_refseq	TRUE	FALSE
+extract_ipm_date_interval	extract_ipm_date_interval		FALSE	FALSE
+insect_phenology_model	insect_phenology_model		FALSE	FALSE
+test	test		FALSE	FALSE
+validate_temperature_data	validate_temperature_data		FALSE	FALSE
+gdal	gdal		TRUE	FALSE
+mean_per_zone	mean_per_zone		FALSE	FALSE
+netcdf_handler	netcdf_handler		TRUE	FALSE
+run_idw_interpolation	run_idw_interpolation		FALSE	FALSE