diff --git a/results/all_tools.tsv b/results/all_tools.tsv
index 13716eae..c1ee0766 100644
--- a/results/all_tools.tsv
+++ b/results/all_tools.tsv
@@ -148,12 +148,12 @@ segmetrics	3.0	2.0	ip_segmetrics	Image segmentation and object detection perform
 slice_image	102.0		ip_slice_image	Slice image	galaxy_image_analysis	Galaxy Image Analysis	Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	slice_image	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/slice_image/	0.3-2	scikit-image		(0/1)	(0/1)	(1/1)
 split_labelmap	42.0		ip_split_labelmap	Split Labelmaps	galaxy_image_analysis	Galaxy Image Analysis	Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	split_labelmap	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_labelmaps/	0.2-2	scikit-image		(0/1)	(0/1)	(1/1)
 spot_detection_2d	16.0	3.0	ip_spot_detection_2d	Spot detection in 2D image sequence	galaxy_image_analysis	Galaxy Image Analysis	Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/BMCV/galaxy-image-analysis	Imaging	spot_detection_2d	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/	0.0.3-2	imageio		(0/1)	(0/1)	(1/1)
-superdsm	16.0	2.0	ip_superdsm	Globally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy images	superdsm	SuperDSM	SuperDSM is a globally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy images and beyond.	Image analysis		To update	https://github.com/bmcv	Imaging	superdsm	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/	0.1.3	superdsm	0.2.0	(0/1)	(0/1)	(1/1)
+superdsm	16.0	2.0	ip_superdsm	Globally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy images	superdsm	SuperDSM	SuperDSM is a globally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy images and beyond.	Image analysis		Up-to-date	https://github.com/bmcv	Imaging	superdsm	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/	0.2.0	superdsm	0.2.0	(0/1)	(0/1)	(1/1)
 unzip	5370.0	508.0	unzip	Unzip file						To update	https://github.com/bmcv	Convert Formats	unzip	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/unzip/	6.0	unzip		(0/1)	(1/1)	(1/1)
 visceral-evaluatesegmentation			ip_visceral_evaluatesegmentation	Visceral Project - Evaluate Segmentation Tool						To update	https://github.com/bmcv	Imaging	visceral_evaluatesegmentation	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/visceral-evaluatesegmentation	0.5-2	visceral-evaluatesegmentation	2015.07.03	(0/1)	(0/1)	(1/1)
 wsi_extract_top_view	38.0		ip_wsi_extract_top_view	WSI Extract Top View						To update	https://github.com/bmcv	Imaging	wsi_extract_top_view	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/wsi_extract_top_view/	0.2-2	scikit-image		(0/1)	(0/1)	(1/1)
 add_value	33763.0	356.0	addValue	Add a value as a new column.						To update		Text Manipulation	add_value	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/add_value	1.0.1	perl		(1/1)	(1/1)	(1/1)
-annotation_profiler	2.0		Annotation_Profiler_0	Profile Annotations for a set of genomic intervals						To update		Genomic Interval Operations	annotation_profiler	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/annotation_profiler	1.0.0	bx-python	0.10.0	(1/1)	(0/1)	(1/1)
+annotation_profiler	2.0		Annotation_Profiler_0	Profile Annotations for a set of genomic intervals						To update		Genomic Interval Operations	annotation_profiler	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/annotation_profiler	1.0.0	bx-python	0.11.0	(1/1)	(0/1)	(1/1)
 best_regression_subsets	3.0		BestSubsetsRegression1	Perform Best-subsets Regression						To update		Sequence Analysis, Variant Analysis	best_regression_subsets	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/best_regression_subsets	1.0.0	numpy		(1/1)	(0/1)	(1/1)
 blat_coverage_report			generate_coverage_report	Polymorphism of the Reads						To update		Next Gen Mappers, Sequence Analysis	blat_coverage_report	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/blat_coverage_report	1.0.0			(0/1)	(0/1)	(0/1)
 blat_mapping			blat2wig	Coverage of the Reads in wiggle format						To update		Next Gen Mappers, Sequence Analysis	blat_mapping	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/blat_mapping	1.0.0			(0/1)	(0/1)	(0/1)
@@ -186,15 +186,15 @@ dwt_var_perclass			compute_p-values_max_variances_feature_occurrences_in_one_dat
 dwt_var_perfeature	36.0		dwt_var1	Wavelet variance using Discrete Wavelet Transfoms						To update		Statistics	dwt_var_perfeature	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perfeature	1.0.2	r-bitops		(1/1)	(1/1)	(1/1)
 express	325.0	12.0	express	Quantify the abundances of a set of target sequences from sampled subsequences						To update		RNA	express	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/express	1.1.1	eXpress	1.5.1	(0/1)	(1/1)	(1/1)
 fasta_compute_length	7758.0	380.0	fasta_compute_length	Compute sequence length						To update		Fasta Manipulation	fasta_compute_length	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_compute_length	1.0.3	python		(1/1)	(1/1)	(1/1)
-fasta_concatenate_by_species	35793.0	88.0	fasta_concatenate0	Concatenate FASTA alignment by species						To update		Fasta Manipulation	fasta_concatenate_by_species	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_concatenate_by_species	0.0.1	bx-python	0.10.0	(1/1)	(1/1)	(1/1)
+fasta_concatenate_by_species	35793.0	88.0	fasta_concatenate0	Concatenate FASTA alignment by species						To update		Fasta Manipulation	fasta_concatenate_by_species	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_concatenate_by_species	0.0.1	bx-python	0.11.0	(1/1)	(1/1)	(1/1)
 fasta_filter_by_length	48649.0	350.0	fasta_filter_by_length	Filter sequences by length						To update		Fasta Manipulation	fasta_filter_by_length	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length	1.2	python		(1/1)	(1/1)	(1/1)
 fasta_to_tabular	105841.0	622.0	fasta2tab	FASTA-to-Tabular converter						To update		Fasta Manipulation	fasta_to_tabular	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_to_tabular	1.1.1	python		(1/1)	(1/1)	(1/1)
 fastq_trimmer_by_quality	5485.0	459.0	fastq_quality_trimmer	FASTQ Quality Trimmer by sliding window						Up-to-date		Fastq Manipulation	fastq_trimmer_by_quality	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastq_trimmer_by_quality	1.1.5	galaxy_sequence_utils	1.1.5	(1/1)	(1/1)	(1/1)
 fastqsolexa_to_fasta_qual			fastqsolexa_to_fasta_qual	FASTQSOLEXA-to-FASTA-QUAL extracts sequences and quality scores from FASTQSOLEXA data						To update		Convert Formats, Fastq Manipulation	fastqsolexa_to_fasta_qual	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/fastqsolexa_to_fasta_qual	1.0.0			(0/1)	(0/1)	(0/1)
-featurecounter	22384.0	6.0	featureCoverage1	Feature coverage						To update		Sequence Analysis, Variant Analysis	featurecounter	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/featurecounter	2.0.0	bx-python	0.10.0	(1/1)	(0/1)	(1/1)
+featurecounter	22384.0	6.0	featureCoverage1	Feature coverage						To update		Sequence Analysis, Variant Analysis	featurecounter	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/featurecounter	2.0.0	bx-python	0.11.0	(1/1)	(0/1)	(1/1)
 filter_transcripts_via_tracking	20.0	1.0	filter_combined_via_tracking	Filter Combined Transcripts						To update		RNA	filter_transcripts_via_tracking	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/filter_transcripts_via_tracking	0.1			(1/1)	(1/1)	(1/1)
 generate_pc_lda_matrix	119.0	12.0	generate_matrix_for_pca_and_lda1	Generate a Matrix for using PC and LDA						To update		Sequence Analysis	generate_pc_lda_matrix	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/generate_pc_lda_matrix	1.0.0			(1/1)	(1/1)	(1/1)
-getindelrates_3way			indelRates_3way	Estimate Indel Rates for 3-way alignments						To update		Sequence Analysis, Variant Analysis	getindelrates_3way	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/getindelrates_3way	1.0.0	bx-python	0.10.0	(1/1)	(0/1)	(0/1)
+getindelrates_3way			indelRates_3way	Estimate Indel Rates for 3-way alignments						To update		Sequence Analysis, Variant Analysis	getindelrates_3way	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/getindelrates_3way	1.0.0	bx-python	0.11.0	(1/1)	(0/1)	(0/1)
 getindels_2way			getIndels_2way	Fetch Indels from pairwise alignments						To update		Sequence Analysis, Variant Analysis	getindels_2way	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/getindels_2way	1.0.0	numpy		(1/1)	(0/1)	(0/1)
 gmaj	11.0	4.0	gmaj_1	GMAJ Multiple Alignment Viewer						To update		Visualization	gmaj	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/gmaj	2.0.1			(1/1)	(1/1)	(1/1)
 hisat	228.0		hisat	HISAT is a fast and sensitive spliced alignment program.						To update	http://ccb.jhu.edu/software/hisat/index.shtml	Assembly	hisat	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat	1.0.3	hisat		(0/1)	(0/1)	(0/1)
@@ -206,24 +206,24 @@ lastz_paired_reads	9.0	1.0	lastz_paired_reads_wrapper	Galaxy wrapper for the Las
 lda_analysis	148.0	18.0	lda_analy1	Perform Linear Discriminant Analysis						To update		Graphics, Statistics	lda_analysis	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/lda_analysis	1.0.1	R		(1/1)	(0/1)	(1/1)
 linear_regression			LinearRegression1	Perform Linear Regression						To update		Statistics	linear_regression	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/linear_regression	1.0.1	R		(1/1)	(0/1)	(0/1)
 logistic_regression_vif			LogisticRegression	Perform Logistic Regression with vif						To update		Sequence Analysis, Variant Analysis, Statistics	logistic_regression_vif	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/logistic_regression_vif	1.0.1	numpy		(0/1)	(0/1)	(0/1)
-maf_cpg_filter			cpgFilter	Mask CpG/non-CpG sites from MAF file						To update		Sequence Analysis, Variant Analysis	maf_cpg_filter	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/maf_cpg_filter	1.0.0	bx-python	0.10.0	(1/1)	(0/1)	(0/1)
+maf_cpg_filter			cpgFilter	Mask CpG/non-CpG sites from MAF file						To update		Sequence Analysis, Variant Analysis	maf_cpg_filter	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/maf_cpg_filter	1.0.0	bx-python	0.11.0	(1/1)	(0/1)	(0/1)
 mapping_to_ucsc			mapToUCSC	Format mapping data as UCSC custom track						To update		Visualization, Convert Formats, Next Gen Mappers	mapping_to_ucsc	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/mapping_to_ucsc	1.0.0			(0/1)	(0/1)	(0/1)
 megablast_xml_parser	338.0	36.0	megablast_xml_parser	Parse blast XML output						To update		Next Gen Mappers, Convert Formats	megablast_xml_parser	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/megablast_xml_parser	1.0.1	python		(1/1)	(0/1)	(1/1)
 merge_cols	21906.0	536.0	mergeCols1	Merge columns together.						To update		Text Manipulation	merge_cols	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols	1.0.3	python		(1/1)	(1/1)	(1/1)
 microsatellite_birthdeath			microsatellite_birthdeath	Identify microsatellite births and deaths						To update		Sequence Analysis	microsatellite_birthdeath	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsatellite_birthdeath	1.0.0			(0/1)	(0/1)	(0/1)
 microsats_alignment_level			microsats_align1	Extract Orthologous Microsatellites from pair-wise alignments						To update		Sequence Analysis, Variant Analysis	microsats_alignment_level	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsats_alignment_level	1.0.0	sputnik		(1/1)	(0/1)	(0/1)
-microsats_mutability			microsats_mutability1	Estimate microsatellite mutability by specified attributes						To update		Sequence Analysis, Variant Analysis	microsats_mutability	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsats_mutability	1.1.0	bx-python	0.10.0	(1/1)	(0/1)	(0/1)
+microsats_mutability			microsats_mutability1	Estimate microsatellite mutability by specified attributes						To update		Sequence Analysis, Variant Analysis	microsats_mutability	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsats_mutability	1.1.0	bx-python	0.11.0	(1/1)	(0/1)	(0/1)
 mine	11.0	2.0	maximal_information_based_nonparametric_exploration	Maximal Information-based Nonparametric Exploration						To update		Variant Analysis	mine	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/mine	0.0.1	MINE		(1/1)	(0/1)	(1/1)
 multispecies_orthologous_microsats			multispecies_orthologous_microsats	Extract orthologous microsatellites						To update		Sequence Analysis, Variant Analysis	multispecies_orthologous_microsats	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/multispecies_orthologous_microsats	1.0.0	bx-sputnik		(0/1)	(0/1)	(0/1)
 mutate_snp_codon	47.0		mutate_snp_codon_1	Mutate Codons with SNPs						To update		Variant Analysis	mutate_snp_codon	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/mutate_snp_codon	1.0.0			(1/1)	(0/1)	(1/1)
 partialr_square			partialRsq	Compute partial R square						To update		Statistics	partialr_square	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/partialr_square	1.0.0	R		(1/1)	(0/1)	(0/1)
 pearson_correlation			Pearson_and_apos_Correlation1	Pearson and apos Correlation between any two numeric columns						To update		Statistics	pearson_correlation	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/pearson_correlation	1.0.0			(0/1)	(0/1)	(0/1)
 pgsnp2gd_snp			pgSnp2gd_snp	Convert from pgSnp to gd_snp						To update		Variant Analysis	pgsnp2gd_snp	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/pgsnp2gd_snp	1.0.0			(0/1)	(0/1)	(0/1)
-pileup_interval	632.0	15.0	pileup_interval	Pileup-to-Interval condenses pileup format into ranges of bases						To update		SAM	pileup_interval	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/pileup_interval	1.0.3	bx-python	0.10.0	(1/1)	(1/1)	(1/1)
+pileup_interval	632.0	15.0	pileup_interval	Pileup-to-Interval condenses pileup format into ranges of bases						To update		SAM	pileup_interval	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/pileup_interval	1.0.3	bx-python	0.11.0	(1/1)	(1/1)	(1/1)
 pileup_parser	3158.0	169.0	pileup_parser	Filter pileup on coverage and SNPs						To update	https://github.com/galaxyproject/tools-devteam/	SAM	pileup_parser	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/pileup_parser	1.0.2	perl		(1/1)	(1/1)	(1/1)
 plot_from_lda	73.0	9.0	plot_for_lda_output1	"Draw ROC plot on ""Perform LDA"" output"						To update		Graphics, Statistics	plot_from_lda	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/plot_from_lda	1.0.1	R		(1/1)	(0/1)	(1/1)
 principal_component_analysis	9986.0	88.0	pca1	Principal Component Analysis						To update		Statistics	principal_component_analysis	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/principal_component_analysis	1.0.2	rpy		(1/1)	(0/1)	(1/1)
-quality_filter			qualityFilter	Filter nucleotides based on quality scores						To update		Sequence Analysis, Variant Analysis	quality_filter	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/quality_filter	1.0.1	bx-python	0.10.0	(0/1)	(0/1)	(0/1)
+quality_filter			qualityFilter	Filter nucleotides based on quality scores						To update		Sequence Analysis, Variant Analysis	quality_filter	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/quality_filter	1.0.1	bx-python	0.11.0	(0/1)	(0/1)	(0/1)
 rcve			rcve1	Compute RCVE						To update		Sequence Analysis, Variant Analysis	rcve	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/rcve	1.0.0	R		(1/1)	(0/1)	(0/1)
 remove_beginning			Remove beginning1	Remove lines from the beginning of a file.						To update		Text Manipulation	remove_beginning	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/remove_beginning	1.0.0			(1/1)	(1/1)	(1/1)
 rmap			rmap_wrapper	RMAP for Solexa Short Reads Alignment						To update		Next Gen Mappers	rmap	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/rmap	1.0.0	rmap	2.1	(0/1)	(0/1)	(0/1)
@@ -239,7 +239,7 @@ show_tail			Show tail1	Select lines from the end of a file.						To update		Text
 sicer	374.0	5.0	peakcalling_sicer	Statistical approach for the Identification of ChIP-Enriched Regions						Up-to-date	https://home.gwu.edu/~wpeng/Software.htm	ChIP-seq	sicer	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer	1.1	SICER	1.1	(1/1)	(1/1)	(1/1)
 split_paired_reads			split_paired_reads	Split paired end reads						To update		Fastq Manipulation	split_paired_reads	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/split_paired_reads	1.0.0			(0/1)	(0/1)	(0/1)
 substitution_rates			subRate1	Estimate substitution rates for non-coding regions						To update		Sequence Analysis, Variant Analysis	substitution_rates	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/substitution_rates	1.0.0			(0/1)	(0/1)	(0/1)
-substitutions			substitutions1	Fetch substitutions from pairwise alignments						To update		Sequence Analysis, Variant Analysis	substitutions	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/substitutions	1.0.1	bx-python	0.10.0	(1/1)	(0/1)	(0/1)
+substitutions			substitutions1	Fetch substitutions from pairwise alignments						To update		Sequence Analysis, Variant Analysis	substitutions	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/substitutions	1.0.1	bx-python	0.11.0	(1/1)	(0/1)	(0/1)
 t_test_two_samples	210.0	6.0	t_test_two_samples	T Test for Two Samples						To update		Statistics	t_test_two_samples	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/t_test_two_samples	1.0.1	R		(1/1)	(1/1)	(1/1)
 table_annovar			table_annovar	Annotate a VCF file using ANNOVAR annotations to produce a tabular file that can be filtered						To update		Variant Analysis	table_annovar	devteam	Nonehttps://github.com/galaxyproject/tools-devteam/tree/master/tools/table_annovar	0.2	annovar		(0/1)	(0/1)	(0/1)
 tabular_to_fasta	319234.0	601.0	tab2fasta	Tabular-to-FASTA						To update		Convert Formats	tabular_to_fasta	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/tabular_to_fasta	1.1.1	python		(1/1)	(1/1)	(1/1)
@@ -255,20 +255,20 @@ vcf_extract			vcf_extract	Extract reads from a specified region						To update
 vcf_filter	388.0	63.0	vcf_filter	Filter a VCF file						To update		Variant Analysis	vcf_filter	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_filter	1.0.0			(0/1)	(0/1)	(1/1)
 vcf_intersect	19.0		vcf_intersect	Generate the intersection of two VCF files						To update		Variant Analysis	vcf_intersect	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_intersect	1.0.0			(0/1)	(0/1)	(0/1)
 weightedaverage			wtavg	Assign weighted-average of the values of features overlapping an interval						To update		Sequence Analysis, Variant Analysis	weightedaverage	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/weightedaverage	1.0.1	galaxy-ops	1.1.0	(1/1)	(0/1)	(0/1)
-windowsplitter			winSplitter	Make windows						To update		Sequence Analysis, Variant Analysis	windowsplitter	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter	1.0.1	bx-python	0.10.0	(1/1)	(0/1)	(0/1)
+windowsplitter			winSplitter	Make windows						To update		Sequence Analysis, Variant Analysis	windowsplitter	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter	1.0.1	bx-python	0.11.0	(1/1)	(0/1)	(0/1)
 xy_plot	5890.0	344.0	XY_Plot_1	Plotting tool for multiple series and graph types						To update		Graphics, Statistics	xy_plot	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/xy_plot	1.0.2	r-base		(1/1)	(1/1)	(1/1)
-basecoverage	307.0	2.0	gops_basecoverage_1	Base Coverage of all intervals						To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	basecoverage	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/basecoverage	1.0.0	bx-python	0.10.0	(1/1)	(1/1)	(1/1)
-cluster	791.0	1.0	gops_cluster_1	Cluster the intervals of a dataset						To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	cluster	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/cluster	1.0.0	bx-python	0.10.0	(1/1)	(1/1)	(1/1)
-complement	233.0	1.0	gops_complement_1	Complement intervals of a dataset						To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	complement	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/complement	1.0.0	bx-python	0.10.0	(1/1)	(1/1)	(1/1)
-concat	564897.0	309.0	gops_concat_1	Concatenate two bed files						To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	concat	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/concat	1.0.1	bx-python	0.10.0	(1/1)	(1/1)	(1/1)
-coverage	1489.0	17.0	gops_coverage_1	Coverage of a set of intervals on second set of intervals						To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	coverage	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/coverage	1.0.0	bx-python	0.10.0	(1/1)	(1/1)	(1/1)
-flanking_features	671.0	20.0	flanking_features_1	Fetch closest non-overlapping feature for every interval						To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	flanking_features	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features	4.0.1	bx-python	0.10.0	(1/1)	(1/1)	(1/1)
-get_flanks	324380.0	555.0	get_flanks1	Get flanks returns flanking region/s for every gene						To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	get_flanks	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/get_flanks	1.0.0	bx-python	0.10.0	(1/1)	(1/1)	(1/1)
-intersect	347919.0	1003.0	gops_intersect_1	Intersect the intervals of two datasets						To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	intersect	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect	1.0.0	bx-python	0.10.0	(1/1)	(1/1)	(1/1)
-join	329478.0	284.0	gops_join_1	Join the intervals of two datasets side-by-side						To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	join	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/join	1.0.0	bx-python	0.10.0	(1/1)	(1/1)	(1/1)
-merge	563676.0	193.0	gops_merge_1	Merge the overlapping intervals of a dataset						To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	merge	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/merge	1.0.0	bx-python	0.10.0	(1/1)	(1/1)	(1/1)
-subtract	564149.0	182.0	gops_subtract_1	Subtract the intervals of two datasets						To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	subtract	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract	1.0.0	bx-python	0.10.0	(1/1)	(1/1)	(1/1)
-subtract_query	1014.0	55.0	subtract_query1	Subtract Whole Dataset from another dataset						To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	subtract_query	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract_query	0.1	bx-python	0.10.0	(1/1)	(1/1)	(1/1)
+basecoverage	307.0	2.0	gops_basecoverage_1	Base Coverage of all intervals						To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	basecoverage	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/basecoverage	1.0.0	bx-python	0.11.0	(1/1)	(1/1)	(1/1)
+cluster	791.0	1.0	gops_cluster_1	Cluster the intervals of a dataset						To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	cluster	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/cluster	1.0.0	bx-python	0.11.0	(1/1)	(1/1)	(1/1)
+complement	233.0	1.0	gops_complement_1	Complement intervals of a dataset						To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	complement	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/complement	1.0.0	bx-python	0.11.0	(1/1)	(1/1)	(1/1)
+concat	564897.0	309.0	gops_concat_1	Concatenate two bed files						To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	concat	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/concat	1.0.1	bx-python	0.11.0	(1/1)	(1/1)	(1/1)
+coverage	1489.0	17.0	gops_coverage_1	Coverage of a set of intervals on second set of intervals						To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	coverage	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/coverage	1.0.0	bx-python	0.11.0	(1/1)	(1/1)	(1/1)
+flanking_features	671.0	20.0	flanking_features_1	Fetch closest non-overlapping feature for every interval						To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	flanking_features	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/flanking_features	4.0.1	bx-python	0.11.0	(1/1)	(1/1)	(1/1)
+get_flanks	324380.0	555.0	get_flanks1	Get flanks returns flanking region/s for every gene						To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	get_flanks	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/get_flanks	1.0.0	bx-python	0.11.0	(1/1)	(1/1)	(1/1)
+intersect	347919.0	1003.0	gops_intersect_1	Intersect the intervals of two datasets						To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	intersect	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect	1.0.0	bx-python	0.11.0	(1/1)	(1/1)	(1/1)
+join	329478.0	284.0	gops_join_1	Join the intervals of two datasets side-by-side						To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	join	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/join	1.0.0	bx-python	0.11.0	(1/1)	(1/1)	(1/1)
+merge	563676.0	193.0	gops_merge_1	Merge the overlapping intervals of a dataset						To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	merge	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/merge	1.0.0	bx-python	0.11.0	(1/1)	(1/1)	(1/1)
+subtract	564149.0	182.0	gops_subtract_1	Subtract the intervals of two datasets						To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	subtract	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract	1.0.0	bx-python	0.11.0	(1/1)	(1/1)	(1/1)
+subtract_query	1014.0	55.0	subtract_query1	Subtract Whole Dataset from another dataset						To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	subtract_query	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract_query	0.1	bx-python	0.11.0	(1/1)	(1/1)	(1/1)
 tables_arithmetic_operations	2207.0	14.0	tables_arithmetic_operations	Arithmetic Operations on tables						To update	https://github.com/galaxyproject/gops	Genomic Interval Operations	tables_arithmetic_operations	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/tables_arithmetic_operations	1.0.0	perl		(0/1)	(0/1)	(1/1)
 hgv_fundo			hgv_funDo	FunDO human genes associated with disease terms						To update		Sequence Analysis	hgv_fundo	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/hgv_fundo	1.0.0			(1/1)	(0/1)	(1/1)
 hgv_hilbertvis			hgv_hilbertvis	HVIS visualization of genomic data with the Hilbert curve						To update	https://www.ebi.ac.uk/huber-srv/hilbert/	Graphics, Visualization	hgv_hilbertvis	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/hgv_hilbertvis	1.0.0	R		(1/1)	(0/1)	(1/1)
@@ -301,7 +301,7 @@ PrepareForMlocarna			preMloc	This tool prepares files for locarna step.						To
 Preprocessing			preproc	Preprocessing input for GraphClust						To update		RNA	graphclust_preprocessing	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust	0.5	graphclust-wrappers	0.6.0	(0/1)	(0/1)	(1/1)
 Structure_GSPAN			structure_to_gspan	Convert RNA structure to GSPAN graphs						To update		RNA	structure_to_gspan	rnateam	https://github.com/mmiladi/galaxytools/blob/graphclust-gspan/tools/GraphClust/Structure_GSPAN	0.4	graphclust-wrappers	0.6.0	(0/1)	(0/1)	(1/1)
 agat	481.0	42.0	agat	GTF/GFF analysis toolkit	agat	AGAT	Another Gff Analysis Toolkit (AGAT)Suite of tools to handle gene annotations in any GTF/GFF format.	Data handling, Genome annotation	Genomics	Up-to-date	https://github.com/NBISweden/AGAT	Convert Formats, Statistics, Fasta Manipulation	agat	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/agat	1.2.0	agat	1.2.0	(0/1)	(0/1)	(1/1)
-antismash	14596.0	279.0	antismash	Antismash allows the genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters	antismash	antiSMASH	Rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genomes. It integrates and cross-links with a large number of in silico secondary metabolite analysis tools that have been published earlier.	Sequence clustering, Gene prediction, Differential gene expression analysis	Molecular interactions, pathways and networks, Gene and protein families	Up-to-date	https://antismash.secondarymetabolites.org	Sequence Analysis	antismash	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash	6.1.1	antismash	6.1.1	(1/1)	(1/1)	(1/1)
+antismash	14596.0	279.0	antismash	Antismash allows the genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters	antismash	antiSMASH	Rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genomes. It integrates and cross-links with a large number of in silico secondary metabolite analysis tools that have been published earlier.	Sequence clustering, Gene prediction, Differential gene expression analysis	Molecular interactions, pathways and networks, Gene and protein families	To update	https://antismash.secondarymetabolites.org	Sequence Analysis	antismash	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash	6.1.1	antismash	7.1.0	(1/1)	(1/1)	(1/1)
 atactk_trim_adapters	257.0	26.0	atactk_trim_adapters	Trim adapters from paired-end HTS reads.						To update	https://github.com/ParkerLab/atactk/	Fastq Manipulation	atactk_trim_adapters	rnateam	https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters	0.1.6	atactk	0.1.9	(0/1)	(0/1)	(1/1)
 augustus	8864.0	516.0	augustus	AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences.						To update	http://bioinf.uni-greifswald.de/augustus/	Sequence Analysis	augustus	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/augustus	3.1.0	augustus	3.5.0	(1/1)	(1/1)	(1/1)
 bamhash	169.0	15.0	bamhash	Hash BAM and FASTQ files to verify data integrity						Up-to-date	https://github.com/DecodeGenetics/BamHash	Sequence Analysis	bamhash	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/bamhash	1.1	bamhash	1.1	(0/1)	(0/1)	(1/1)
@@ -405,7 +405,7 @@ dotknot	83.0	1.0	dotknot	DotKnot is a heuristic method for pseudoknot prediction
 exparna			exparna	ExpaRNA is a fast, motif-based comparison and alignment tool for RNA molecules.						Up-to-date	http://rna.informatik.uni-freiburg.de/ExpaRNA/Input.jsp	RNA	exparna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/exparna	1.0.1	exparna	1.0.1	(0/1)	(0/1)	(0/1)
 graphprot			graphprot_predict_profile	GraphProt models binding preferences of RNA-binding proteins.						To update	https://github.com/dmaticzka/GraphProt	Sequence Analysis, RNA, CLIP-seq	graphprot	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot	1.1.7+galaxy1	graphprot	1.1.7	(0/1)	(0/1)	(1/1)
 htseq-clip			htseq_clip	htseq-clip is a toolset for the analysis of eCLIP/iCLIP datasets						To update	https://github.com/EMBL-Hentze-group/htseq-clip	Sequence Analysis, RNA, CLIP-seq	htseq_clip	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip	0.1.0+galaxy0	htseq-clip	2.19.0b0	(0/1)	(0/1)	(1/1)
-infernal	100230.0	67.0	infernal_cmalign, infernal_cmbuild, infernal_cmpress, infernal_cmscan, infernal_cmsearch, infernal_cmstat	"Infernal (""INFERence of RNA ALignment"") is for searching DNA sequence databases for RNA structure and sequence similarities."	infernal	Infernal	"Infernal (""INFERence of RNA ALignment"") is for searching DNA sequence databases for RNA structure and sequence similarities. It is an implementation of a special case of profile stochastic context-free grammars called covariance models (CMs). A CM is like a sequence profile, but it scores a combination of sequence consensus and RNA secondary structure consensus, so in many cases, it is more capable of identifying RNA homologs that conserve their secondary structure more than their primary sequence."	Nucleic acid feature detection	Sequence sites, features and motifs	Up-to-date	http://infernal.janelia.org/	RNA	infernal	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/infernal	1.1.4	infernal	1.1.4	(0/6)	(6/6)	(6/6)
+infernal	100230.0	67.0	infernal_cmalign, infernal_cmbuild, infernal_cmpress, infernal_cmscan, infernal_cmsearch, infernal_cmstat	"Infernal (""INFERence of RNA ALignment"") is for searching DNA sequence databases for RNA structure and sequence similarities."	infernal	Infernal	"Infernal (""INFERence of RNA ALignment"") is for searching DNA sequence databases for RNA structure and sequence similarities. It is an implementation of a special case of profile stochastic context-free grammars called covariance models (CMs). A CM is like a sequence profile, but it scores a combination of sequence consensus and RNA secondary structure consensus, so in many cases, it is more capable of identifying RNA homologs that conserve their secondary structure more than their primary sequence."	Nucleic acid feature detection	Sequence sites, features and motifs	To update	http://infernal.janelia.org/	RNA	infernal	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/infernal	1.1.4	infernal	1.1.5	(0/6)	(6/6)	(6/6)
 inforna				INFO-RNA is a service for the design of RNA sequences that fold into a given pseudo-knot free RNA secondary structure.						To update	http://rna.informatik.uni-freiburg.de/INFORNA/Input.jsp	RNA	inforna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/inforna				(0/1)	(0/1)	(0/1)
 intarna	7569.0	23.0	intarna	Efficient RNA-RNA interaction prediction incorporating accessibility and seeding of interaction sites.						Up-to-date	https://github.com/BackofenLab/IntaRNA	RNA	intarna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna	3.4.0	intarna	3.4.0	(0/1)	(0/1)	(1/1)
 kinwalker	70.0	3.0		Kinwalker splits the folding process into a series of events where each event can either be a folding event or a transcription event.						To update	http://www.bioinf.uni-leipzig.de/Software/Kinwalker/	RNA	kinwalker	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/kinwalker				(0/1)	(0/1)	(0/1)
@@ -443,6 +443,7 @@ sklearn			sklearn_mlxtend_association_rules, sklearn_clf_metrics, sklearn_discri
 splitfasta	1295.0	96.0	rbc_splitfasta	Split a multi-sequence fasta file into files containing single sequences						To update		Text Manipulation	splitfasta	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/splitfasta	0.4.0	biopython	1.70	(1/1)	(0/1)	(1/1)
 statistics			bg_statistical_hypothesis_testing	Tool for computing statistical tests.						To update	https://github.com/bgruening/galaxytools/tree/master/tools/statistics	Statistics	bg_statistical_hypothesis_testing	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/statistics	0.3	numpy		(0/1)	(0/1)	(1/1)
 stress_ng	47.0		stress_ng	stress test a computer system in various selectable ways						To update		Web Services	stress_ng	bgruening-util	https://github.com/ColinIanKing/stress-ng	0.12.04	stress-ng		(0/1)	(0/1)	(0/1)
+tapscan			tapscan_classify	Search for transcription associated proteins (TAPs)						To update	https://plantcode.cup.uni-freiburg.de/tapscan/	Proteomics	tapscan	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/tapscan	4.74+galaxy0	hmmer	3.4	(0/1)	(0/1)	(1/1)
 add_line_to_file	14480.0	193.0	add_line_to_file	Adds a text line to the beginning or end of a file.						To update		Text Manipulation	add_line_to_file	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/add_line_to_file	0.1.0	coreutils	8.25	(1/1)	(1/1)	(1/1)
 column_arrange_by_header	3781.0	179.0	bg_column_arrange_by_header	Column arrange by header name						To update		Text Manipulation	column_arrange_by_header	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/column_arrange_by_header	0.2			(1/1)	(1/1)	(1/1)
 join_files_on_column_fuzzy	2448.0	117.0	join_files_on_column_fuzzy	Join two files on a common column, allowing a certain difference.						To update		Text Manipulation	join_files_on_column_fuzzy	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy	1.0.1	python		(0/1)	(1/1)	(1/1)
@@ -541,7 +542,7 @@ bwameth	10619.0	201.0	bwameth	Fast and accurate alignment of BS-seq reads						T
 cactus			cactus_cactus, cactus_export	Cactus is a reference-free whole-genome multiple alignment program	cactus	Cactus	Cactus is a reference-free whole-genome multiple alignment program.	Multiple sequence alignment, Genome alignment	Genomics, Sequence analysis, Phylogeny, Sequence assembly, Mapping, Phylogenetics	To update	https://github.com/ComparativeGenomicsToolkit/cactus	Sequence Analysis	cactus	galaxy-australia	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cactus	2.7.1			(0/2)	(2/2)	(2/2)
 calculate_contrast_threshold			calculate_contrast_threshold	Calculates a contrast threshold from the CDT file generated by ``tag_pileup_frequency``. The calculated values are then used to set a uniform contrast for all the heatmaps generated downstream.						To update	https://github.com/CEGRcode/ChIP-QC-tools/tree/master/calculate_contrast_threshold	Visualization, Genomic Interval Operations, SAM	calculate_contrast_threshold	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/calculate_contrast_threshold	1.0.0	numpy		(0/1)	(0/1)	(0/1)
 calculate_numeric_param	1393.0	8.0	calculate_numeric_param	Calculate a numeric parameter value using integer and float values.						To update		Text Manipulation	calculate_numeric_param	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/calculate_numeric_param	0.1.0			(0/1)	(0/1)	(1/1)
-cat			cat_add_names, cat_bins, cat_contigs, cat_prepare, cat_summarise	Contig Annotation Tool (CAT)						To update	https://github.com/dutilh/CAT	Metagenomics	contig_annotation_tool	iuc	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat	5.2.3	cat	5.3	(5/5)	(2/5)	(5/5)
+cat			cat_add_names, cat_bins, cat_contigs, cat_prepare, cat_summarise	Contig Annotation Tool (CAT)	cat_bins	CAT and BAT	Contig Annotation Tool (CAT) and Bin Annotation Tool (BAT) are pipelines for the taxonomic classification of long DNA sequences and metagenome assembled genomes (MAGs/bins) of both known and (highly) unknown microorganisms, as generated by contemporary metagenomics studies. The core algorithm of both programs involves gene calling, mapping of predicted ORFs against the nr protein database, and voting-based classification of the entire contig / MAG based on classification of the individual ORFs.	Taxonomic classification, Sequence assembly, Coding region prediction	Metagenomics, Metagenomic sequencing, Taxonomy, Sequence assembly	To update	https://github.com/dutilh/CAT	Metagenomics	contig_annotation_tool	iuc	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat	5.2.3	cat	5.3	(5/5)	(2/5)	(5/5)
 cdhit	8278.0	6.0	cd_hit	Cluster or compare biological sequence datasets	cd-hit	cd-hit	Cluster a nucleotide dataset into representative sequences.	Sequence clustering	Sequencing	Up-to-date	http://weizhongli-lab.org/cd-hit/	Sequence Analysis, Fasta Manipulation	cd_hit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cdhit	4.8.1	cd-hit	4.8.1	(0/1)	(0/1)	(1/1)
 cemitool	98.0	9.0	cemitool	Gene co-expression network analysis tool	cemitool	CEMiTool	It unifies the discovery and the analysis of coexpression gene modules in a fully automatic manner, while providing a user-friendly html report with high quality graphs. Our tool evaluates if modules contain genes that are over-represented by specific pathways or that are altered in a specific sample group. Additionally, CEMiTool is able to integrate transcriptomic data with interactome information, identifying the potential hubs on each network.	Enrichment analysis, Pathway or network analysis	Gene expression, Transcriptomics, Microarray experiment	To update	https://www.bioconductor.org/packages/release/bioc/html/CEMiTool.html	Transcriptomics, RNA, Statistics	cemitool	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool	1.18.1	bioconductor-cemitool	1.26.0	(1/1)	(0/1)	(1/1)
 charts	3589.0	287.0	charts	Enables advanced visualization options in Galaxy Charts						To update		Visualization	charts	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/	1.0.1	r-getopt		(0/1)	(0/1)	(0/1)
@@ -566,6 +567,7 @@ collection_element_identifiers	5059.0	912.0	collection_element_identifiers	Extra
 column_maker	3882097.0	2379.0	Add_a_column1	Compute an expression on every row						To update		Text Manipulation	column_maker	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker	2.0	python		(1/1)	(1/1)	(1/1)
 column_order_header_sort	3258.0	80.0	column_order_header_sort	Sort Column Order by heading						To update		Text Manipulation	column_order_header_sort	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_order_header_sort	0.0.1	python		(1/1)	(0/1)	(1/1)
 column_remove_by_header	8424.0	199.0	column_remove_by_header	Remove columns by header						To update		Text Manipulation	column_remove_by_header	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_remove_by_header	1.0	python		(1/1)	(1/1)	(1/1)
+compleasm			compleasm	Compleasm: a faster and more accurate reimplementation of BUSCO						Up-to-date	https://github.com/huangnengCSU/compleasm	Sequence Analysis	compleasm	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/compleasm/	0.2.5	compleasm	0.2.5	(0/1)	(0/1)	(1/1)
 compose_text_param	35084.0	375.0	compose_text_param	Compose a text parameter value using text, integer and float values						To update		Text Manipulation	compose_text_param	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/compose_text_param	0.1.1			(1/1)	(1/1)	(1/1)
 compress_file	3674.0	164.0	compress_file	Compress files.						To update		Text Manipulation	compress_file	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/compress_file	0.1.0	gzip		(1/1)	(1/1)	(1/1)
 concoct	250.0	29.0	concoct, concoct_coverage_table, concoct_cut_up_fasta, concoct_extract_fasta_bins, concoct_merge_cut_up_clustering	CONCOCT (Clustering cONtigs with COverage and ComposiTion) does unsupervised binning of metagenomic contigs byusing nucleotide composition - kmer frequencies - and coverage data for multiple samples. CONCOCT can accurately(up to species level) bin metagenomic contigs.	concoct	CONCOCT	A program for unsupervised binning of metagenomic contigs by using nucleotide composition, coverage data in multiple samples and linkage data from paired end reads.	Sequence clustering, Read binning	Metagenomics	Up-to-date	https://github.com/BinPro/CONCOCT	Metagenomics	concoct	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct	1.1.0	concoct	1.1.0	(0/5)	(0/5)	(5/5)
@@ -593,7 +595,7 @@ deseq2	95752.0	4990.0	deseq2	Differential gene expression analysis based on the
 dexseq	16064.0	218.0	dexseq, dexseq_count, plotdexseq	Inference of differential exon usage in RNA-Seq	dexseq	DEXSeq	The package is focused on finding differential exon usage using RNA-seq exon counts between samples with different experimental designs. It provides functions that allows the user to make the necessary statistical tests based on a model that uses the negative binomial distribution to estimate the variance between biological replicates and generalized linear models for testing. The package also provides functions for the visualization and exploration of the results.	Enrichment analysis, Exonic splicing enhancer prediction	RNA-Seq	To update	https://www.bioconductor.org/packages/release/bioc/html/DEXSeq.html	Transcriptomics, RNA, Statistics	dexseq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq	1.44	bioconductor-dexseq	1.48.0	(3/3)	(3/3)	(3/3)
 diamond	49711.0	963.0	bg_diamond, bg_diamond_makedb, bg_diamond_view	DIAMOND is a new alignment tool for aligning short DNA sequencing reads to a protein reference database such as NCBI-NR.	diamond	Diamond	Sequence aligner for protein and translated DNA searches and functions as a drop-in replacement for the NCBI BLAST software tools. It is suitable for protein-protein search as well as DNA-protein search on short reads and longer sequences including contigs and assemblies, providing a speedup of BLAST ranging up to x20,000.	Sequence alignment analysis	Sequence analysis, Proteins	To update	https://github.com/bbuchfink/diamond	Sequence Analysis	diamond	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond	2.0.15	diamond	2.1.9	(3/3)	(3/3)	(3/3)
 diffbind	6264.0	250.0	diffbind	Diffbind provides functions for  processing  ChIP-Seq  data.	diffbind	DiffBind	Compute differentially bound sites from multiple ChIP-seq experiments using affinity (quantitative) data. Also enables occupancy (overlap) analysis and plotting functions.	Differential binding analysis	ChIP-seq	To update	http://bioconductor.org/packages/release/bioc/html/DiffBind.html	ChIP-seq	diffbind	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind	2.10.0	bioconductor-diffbind	3.12.0	(1/1)	(1/1)	(1/1)
-dimet			dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@	DIMet is a bioinformatics pipeline for differential analysis of isotopic targeted labeling data.						To update	https://github.com/cbib/DIMet	Metabolomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet	0.1.4	dimet	0.2.1	(0/1)	(0/1)	(0/1)
+dimet			dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@	DIMet is a bioinformatics pipeline for differential analysis of isotopic targeted labeling data.						Up-to-date	https://github.com/cbib/DIMet	Metabolomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet	0.2.1	dimet	0.2.1	(0/1)	(0/1)	(0/1)
 disco	369.0	42.0	disco	DISCO is a overlap-layout-consensus (OLC) metagenome assembler	disco	DISCO	DISCO is software to perform structure determination of protein homo-oligomers with cyclic symmetry.DISCO computes oligomeric protein structures using geometric constraints derived from RDCs and intermolecular distance restraints such as NOEs or disulfide bonds. When a reliable subunit structure can be calculated from intramolecular restraints, DISCO guarantees that all satisfying oligomer structures will be discovered, yet can run in minutes to hours on only a single desktop-class computer.	Protein sequence analysis	Structure determination	To update	http://disco.omicsbio.org/	Metagenomics, Assembly	disco	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/		disco	1.2	(1/1)	(0/1)	(1/1)
 dnabot			dnabot	DNA assembly using BASIC on OpenTrons						To update	https://github.com/BASIC-DNA-ASSEMBLY/DNA-BOT	Synthetic Biology	dnabot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/dnabot	3.1.0	dnabot		(0/1)	(0/1)	(0/1)
 dnaweaver			dnaweaver	Given a SBOL input, calculate assembly parts for Gibson or Golden Gate.						Up-to-date	https://github.com/Edinburgh-Genome-Foundry/DnaWeaver	Synthetic Biology	dnaweaver	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/dnaweaver	1.0.2	dnaweaver_synbiocad	1.0.2	(0/1)	(0/1)	(0/1)
@@ -611,7 +613,7 @@ episcanpy			episcanpy_build_matrix, episcanpy_cluster_embed, episcanpy_preproces
 exomedepth	410.0	29.0	exomedepth	ExomeDepth: Calls copy number variants (CNVs) from targeted sequence data	exomedepth	ExomeDepth	Copy number variant (CNV) calling algorithm designed to control technical variability between samples. It calls CNVs from targeted sequence data, typically exome sequencing experiments designed to identify the genetic basis of Mendelian disorders.	Sequence analysis, Variant calling, Genotyping, Copy number estimation	Exome sequencing, Gene transcripts, Mapping, Sequencing, Genetic variation, Rare diseases	To update	https://cran.r-project.org/package=ExomeDepth	Sequence Analysis, Variant Analysis	exomedepth	crs4	https://github.com/galaxyproject/tools-iuc/tree/master/tools/exomedepth	1.1.0	r-exomedepth	1.1.16	(1/1)	(0/1)	(1/1)
 exonerate	988.0	59.0	exonerate	Exonerate is a generic tool for pairwise sequence comparison.	exonerate	Exonerate	A tool for pairwise sequence alignment. It enables alignment for DNA-DNA and DNA-protein pairs and also gapped and ungapped alignment.	Pairwise sequence alignment, Protein threading, Genome alignment	Sequence analysis, Sequence sites, features and motifs, Molecular interactions, pathways and networks	Up-to-date	https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate	Sequence Analysis	exonerate	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate	2.4.0	exonerate	2.4.0	(1/1)	(1/1)	(1/1)
 export2graphlan	5265.0	200.0	export2graphlan	export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn	export2graphlan	export2graphlan	export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn. In particular, the annotation file tries to highlight specific sub-trees deriving automatically from input file what nodes are important.	Conversion	Taxonomy, Metabolomics, Biomarkers	To update	https://bitbucket.org/CibioCM/export2graphlan/overview	Metagenomics	export2graphlan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/	0.20	export2graphlan	0.22	(1/1)	(1/1)	(1/1)
-extract_genomic_dna	11348.0	285.0	Extract genomic DNA 1	Contains a tool that extracts genomic DNA using coordinates from ASSEMBLED genomes and UNassembled genomes.						To update		Genomic Interval Operations	extract_genomic_dna	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna	3.0.3+galaxy2	bx-python	0.10.0	(1/1)	(0/1)	(1/1)
+extract_genomic_dna	11348.0	285.0	Extract genomic DNA 1	Contains a tool that extracts genomic DNA using coordinates from ASSEMBLED genomes and UNassembled genomes.						To update		Genomic Interval Operations	extract_genomic_dna	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna	3.0.3+galaxy2	bx-python	0.11.0	(1/1)	(0/1)	(1/1)
 fargene	459.0	52.0	fargene	fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr )	fargene	fARGene	fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr ) is a tool that takes either fragmented metagenomic data or longer sequences as input and predicts and delivers full-length antiobiotic resistance genes as output.	Antimicrobial resistance prediction	Metagenomics, Microbiology, Public health and epidemiology	Up-to-date	https://github.com/fannyhb/fargene	Sequence Analysis	fargene	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene	0.1	fargene	0.1	(1/1)	(0/1)	(1/1)
 fasta_nucleotide_color_plot	322.0	39.0	fasta_nucleotide_color_plot	Contains a tool that produces a graphical representation of FASTA data with each nucleotide represented by a selected color.						To update	https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/fourcolorplot	Visualization	fasta_nucleotide_color_plot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_nucleotide_color_plot	1.0.1	openjdk		(1/1)	(0/1)	(1/1)
 fasta_stats	35332.0	1080.0	fasta-stats	Display summary statistics for a fasta file.						To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/	Sequence Analysis	fasta_stats	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/	2.0	numpy		(1/1)	(1/1)	(1/1)
@@ -639,7 +641,7 @@ fsd			fsd, fsd_beforevsafter, fsd_regions, td	Tool that plots a histogram of siz
 funannotate			funannotate_annotate, funannotate_clean, funannotate_compare, funannotate_predict, funannotate_sort	Funannotate is a genome prediction, annotation, and comparison software package.	"
                 funannotate
             "					To update	https://funannotate.readthedocs.io	Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate	1.8.15			(3/5)	(5/5)	(5/5)
-gatk4			gatk4_mutect2	A Galaxy wrapper for Mutect2 from GATK						To update	https://software.broadinstitute.org/gatk/gatk4	Variant Analysis	gatk4_mutect2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk4	4.1.7.0	gatk4	4.4.0.0	(1/1)	(0/1)	(1/1)
+gatk4			gatk4_mutect2	A Galaxy wrapper for Mutect2 from GATK						To update	https://software.broadinstitute.org/gatk/gatk4	Variant Analysis	gatk4_mutect2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk4	4.1.7.0	gatk4	4.5.0.0	(1/1)	(0/1)	(1/1)
 gdcwebapp			data_source_gdcwebapp	GDCWebApp automatically filter, extract, and convert genomic data from the Genomic Data Commons portal to BED format						To update	http://bioinf.iasi.cnr.it/gdcwebapp/	Data Source, Convert Formats	gdcwebapp	iuc	https://github.com/fabio-cumbo/GDCWebApp4Galaxy	1.0.0	python		(1/1)	(0/1)	(1/1)
 gecko	519.0	112.0	gecko	Ungapped genome comparison						Up-to-date	https://github.com/otorreno/gecko	Sequence Analysis	gecko	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko	1.2	gecko	1.2	(0/1)	(1/1)	(1/1)
 gemini	1209.0		gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_db_info, gemini_@BINARY@, gemini_@BINARY@, gemini_inheritance, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@	GEMINI: a flexible framework for exploring genome variation	gemini	GEMINI	GEMINI (GEnome MINIng) is a flexible framework for exploring genetic variation in the context of the wealth of genome annotations available for the human genome. By placing genetic variants, sample phenotypes and genotypes, as well as genome annotations into an integrated database framework, GEMINI provides a simple, flexible, and powerful system for exploring genetic variation for disease and population genetics.	Sequence analysis, Genetic variation analysis	Sequence analysis	To update	https://github.com/arq5x/gemini	Sequence Analysis, Next Gen Mappers	gemini	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini	0.20.1	gemini	0.30.2	(1/3)	(2/3)	(2/3)
@@ -677,7 +679,7 @@ happy			som.py	A tool to perform comparisons only based on chromosome, position,
 heatmap2			ggplot2_heatmap2	heatmap.2 function from the R gplots package						To update	https://github.com/cran/gplots	Visualization	ggplot2_heatmap2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2	3.1.3	r-gplots	2.17.0	(1/1)	(1/1)	(1/1)
 heinz	1186.0	242.0	heinz_bum, heinz, heinz_scoring, heinz_visualization	An algorithm for identification of the optimal scoring subnetwork.	bionet	BioNet	This package provides functions for the integrated analysis of protein-protein interaction networks and the detection of functional modules. Different datasets can be integrated into the network by assigning p-values of statistical tests to the nodes of the network. By fitting a beta-uniform mixture model and calculating scores from these p-values, overall scores of network regions can be calculated and an integer linear programming algorithm identifies the maximum scoring subnetwork.	Protein interaction analysis	Molecular interactions, pathways and networks, Protein interactions	To update	https://github.com/ls-cwi/heinz	Transcriptomics, Visualization, Statistics	heinz	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz	1.0	bioconductor-bionet	1.62.0	(4/4)	(4/4)	(4/4)
 hicexplorer			hicexplorer_chicaggregatestatistic, hicexplorer_chicdifferentialtest, hicexplorer_chicexportdata, hicexplorer_chicplotviewpoint, hicexplorer_chicqualitycontrol, hicexplorer_chicsignificantinteractions, hicexplorer_chicviewpoint, hicexplorer_chicviewpointbackgroundmodel, hicexplorer_hicadjustmatrix, hicexplorer_hicaggregatecontacts, hicexplorer_hicaverageregions, hicexplorer_hicbuildmatrix, hicexplorer_hiccomparematrices, hicexplorer_hiccompartmentspolarization, hicexplorer_hicconvertformat, hicexplorer_hiccorrectmatrix, hicexplorer_hiccorrelate, hicexplorer_hicdetectloops, hicexplorer_hicdifferentialtad, hicexplorer_hicfindrestrictionsites, hicexplorer_hicfindtads, hicexplorer_hichyperoptDetectLoops, hicexplorer_hicinfo, hicexplorer_hicinterintratad, hicexplorer_hicmergedomains, hicexplorer_hicmergeloops, hicexplorer_hicmergematrixbins, hicexplorer_hicnormalize, hicexplorer_hicpca, hicexplorer_hicplotaverageregions, hicexplorer_hicplotdistvscounts, hicexplorer_hicplotmatrix, hicexplorer_hicplotsvl, hicexplorer_hicplotviewpoint, hicexplorer_hicquickqc, hicexplorer_hicsummatrices, hicexplorer_hictadclassifier, hicexplorer_hictraintadclassifier, hicexplorer_hictransform, hicexplorer_hicvalidatelocations	HiCExplorer: Set of programs to process, analyze and visualize Hi-C data.						To update	https://github.com/deeptools/HiCExplorer	Sequence Analysis, Visualization	hicexplorer	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer	3.7.2	hicexplorer	3.7.3	(0/40)	(5/40)	(40/40)
-hicstuff			hicstuff_pipeline							To update	https://github.com/koszullab/hicstuff	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicstuff	3.1.5	hicstuff	3.2.1	(0/1)	(0/1)	(0/1)
+hicstuff			hicstuff_pipeline							To update	https://github.com/koszullab/hicstuff	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicstuff	3.1.5	hicstuff	3.2.2	(0/1)	(0/1)	(0/1)
 hifiasm_meta	137.0	12.0	hifiasm_meta	A hifiasm fork for metagenome assembly using Hifi reads.	hifiasm-meta	Hifiasm-meta	Hifiasm_meta - de novo metagenome assembler, based on hifiasm, a haplotype-resolved de novo assembler for PacBio Hifi reads.	Sequence assembly	Sequence assembly, Metagenomics	To update	https://github.com/xfengnefx/hifiasm-meta	Metagenomics	hifiasm_meta	galaxy-australia	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hifiasm_meta	0.3.1	hifiasm_meta	hamtv0.3.1	(0/1)	(1/1)	(1/1)
 hisat2	299104.0	4183.0	hisat2	HISAT2 is a fast and sensitive spliced alignment program.	hisat2	HISAT2	Alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome).	Sequence alignment	RNA-seq	Up-to-date	http://ccb.jhu.edu/software/hisat2/	Assembly	hisat2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2	2.2.1	hisat2	2.2.1	(1/1)	(1/1)	(1/1)
 hivclustering			hivclustering	Infers transmission networks from pairwise distances inferred by tn93						To update	https://pypi.org/project/hivclustering/	Next Gen Mappers	hivclustering	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hivclustering/	1.3.1	python-hivclustering	1.6.8	(0/1)	(0/1)	(0/1)
@@ -688,7 +690,7 @@ humann	5856.0	247.0	humann, humann_associate, humann_barplot, humann_join_tables
 hybpiper			hybpiper	Analyse targeted sequence capture data	HybPiper	HybPiper	Paralogs and off-target sequences improve phylogenetic resolution in a densely-sampled study of the breadfruit genus (Artocarpus, Moraceae).Recovering genes from targeted sequence capture data.Current version: 1.3.1 (August 2018).-- Read our article in Applications in Plant Sciences (Open Access).HybPiper was designed for targeted sequence capture, in which DNA sequencing libraries are enriched for gene regions of interest, especially for phylogenetics. HybPiper is a suite of Python scripts that wrap and connect bioinformatics tools in order to extract target sequences from high-throughput DNA sequencing reads.	Sequence trimming, Sequence assembly, Read mapping	Phylogenetics, Plant biology, Gene transcripts, Sequence assembly, Phylogenomics	Up-to-date	https://github.com/mossmatters/HybPiper	Sequence Analysis, Phylogenetics	hybpiper	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper	2.1.6	hybpiper	2.1.6	(0/1)	(1/1)	(0/1)
 hyphy			hyphy_absrel, hyphy_annotate, hyphy_bgm, hyphy_busted, hyphy_cfel, hyphy_conv, hyphy_fade, hyphy_fel, hyphy_fubar, hyphy_gard, hyphy_meme, hyphy_prime, hyphy_relax, hyphy_slac, hyphy_sm19, hyphy_strike_ambigs, hyphy_summary	Hypothesis Testing using Phylogenies	HyPhy	HyPhy	Software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning.	Statistical calculation	Phylogeny, Small molecules, Molecular interactions, pathways and networks	To update	http://www.hyphy.org	Phylogenetics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/	2.5.47	hyphy	2.5.59	(17/17)	(2/17)	(17/17)
 hypo	354.0	39.0	hypo	Super Fast & Accurate Polisher for Long Read Genome Assemblies	HyPo	HyPo	HyPo, a Hybrid Polisher, utilizes short as well as long reads within a single run to polish a long reads assembly of small and large genomes.	Optimisation and refinement, Genome assembly	Sequence assembly, Genomics	Up-to-date	https://github.com/kensung-lab/hypo	Assembly	hypo	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo	1.0.3	hypo	1.0.3	(0/1)	(0/1)	(1/1)
-icescreen			icescreen	ICEscreen identifies Integrative Conjugative Elements (ICEs) and Integrative Mobilizable Elements (IMEs) in Bacillota genomes.	icescreen	ICEscreen	A tool to detect Firmicute ICEs and IMEs, isolated or enclosed in composite structures.	Database search, Protein feature detection	Mobile genetic elements, Sequence sites, features and motifs, Genomics, Molecular interactions, pathways and networks, Structural variation	Up-to-date	https://icescreen.migale.inrae.fr/	Genome annotation	icescreen	iuc	https://forgemia.inra.fr/ices_imes_analysis/icescreen	1.3.1	icescreen	1.3.1	(0/1)	(0/1)	(0/1)
+icescreen			icescreen	ICEscreen identifies Integrative Conjugative Elements (ICEs) and Integrative Mobilizable Elements (IMEs) in Bacillota genomes.	icescreen	ICEscreen	A tool to detect Firmicute ICEs and IMEs, isolated or enclosed in composite structures.	Database search, Protein feature detection	Mobile genetic elements, Sequence sites, features and motifs, Genomics, Molecular interactions, pathways and networks, Structural variation	To update	https://icescreen.migale.inrae.fr/	Genome annotation	icescreen	iuc	https://forgemia.inra.fr/ices_imes_analysis/icescreen	1.3.1	icescreen	1.3.2	(0/1)	(0/1)	(0/1)
 idba_ud	721.0	43.0	idba_hybrid, idba_tran, idba_ud	Wrappers for the idba assembler variants.	idba	IDBA	A short read assembler based on iterative De Bruijn graph. It is developed under 64-bit Linux, but should be suitable for all unix-like system.	Sequence assembly	Sequence assembly	To update	https://i.cs.hku.hk/~alse/hkubrg/projects/index.html	Assembly	idba	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud		idba	1.1.3	(3/3)	(0/3)	(3/3)
 idr	2873.0	30.0	idr	Galaxy wrappers for the IDR package from Nathan Boleu						To update	https://github.com/nboley/idr	Sequence Analysis	idr	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/	2.0.3	idr	2.0.4.2	(1/1)	(0/1)	(1/1)
 idr_download			idr_download_by_ids	Image Data Resource downloading tool						To update	https://idr.openmicroscopy.org	Data Source	idr_download_by_ids	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download	0.44.1	omero-py	5.11.1	(0/1)	(0/1)	(1/1)
@@ -697,7 +699,7 @@ instrain			instrain_compare, instrain_profile	InStrain is a tool for analysis of
 integron_finder	52965.0	58.0	integron_finder	"""IntegronFinder identify integrons with high accuracy and sensitivity.It searches for attC sites using covariance models, for integron-integrases using HMM profiles, and for other features (promoters, attI site) using pattern matching"""	integron_finder	Integron Finder	A tool to detect Integron in DNA sequences.	Nucleic acid feature detection, Sequence motif recognition, Protein feature detection, Genome annotation	Functional genomics, Mobile genetic elements, Molecular biology, Sequence analysis	To update	https://github.com/gem-pasteur/Integron_Finder	Sequence Analysis	integronfinder	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/integron_finder	2.0.2	hmmer	3.4	(0/1)	(1/1)	(1/1)
 intermine_galaxy_exchange	44.0	1.0	galaxy_intermine_exchange	InterMine Exporter						To update		Convert Formats	intermine_galaxy_exchange	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/intermine_galaxy_exchange	0.0.1	coreutils	8.25	(1/1)	(1/1)	(1/1)
 interproscan	5294.0	554.0	interproscan	Interproscan queries the interpro database and provides annotations.	interproscan_ebi	InterProScan (EBI)	Scan sequences against the InterPro protein signature databases.	Sequence motif recognition, Protein feature detection	Gene and protein families, Sequence analysis	To update	http://www.ebi.ac.uk/Tools/pfa/iprscan5/	Sequence Analysis	interproscan	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan	5.59-91.0	interproscan	5.59_91.0	(1/1)	(1/1)	(1/1)
-interval2maf	14.0	3.0	Interval2Maf1	Extract MAF blocks given a set of intervals	bx-python	bx-python	Tools for manipulating biological data, particularly multiple sequence alignments.		Sequence analysis	To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/	Genomic Interval Operations	interval2maf	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/	1.0.1+galaxy1	bx-python	0.10.0	(1/1)	(1/1)	(1/1)
+interval2maf	14.0	3.0	Interval2Maf1	Extract MAF blocks given a set of intervals	bx-python	bx-python	Tools for manipulating biological data, particularly multiple sequence alignments.		Sequence analysis	To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/	Genomic Interval Operations	interval2maf	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/	1.0.1+galaxy1	bx-python	0.11.0	(1/1)	(1/1)	(1/1)
 intervene	1497.0	136.0	intervene_pairwise, intervene_upset	Create pairwise and upset plots	intervene	Intervene	Tool for intersection and visualization of multiple gene or genomic region sets. Intervene contains three modules: venn to generate Venn diagrams of up to six sets, upset to generate UpSet plots of multiple sets, and pairwise to compute and visualize intersections of multiple sets as clustered heat maps.	Sequence comparison, Sequence visualisation	Computational biology	Up-to-date	https://intervene.readthedocs.io	Statistics	intervene	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/intervene	0.6.5	intervene	0.6.5	(2/2)	(0/2)	(2/2)
 iqtree	21598.0	681.0	iqtree	Efficient phylogenomic software by maximum likelihood						To update	http://www.iqtree.org/	Phylogenetics	iqtree	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/	2.1.2	iqtree	2.2.6	(1/1)	(1/1)	(1/1)
 irissv	29.0	4.0	irissv	Refine insertion sequences						To update	https://github.com/mkirsche/Iris	Variant Analysis	irissv	iuc	https://github.com/galaxyproject/tools-iuc/tools/irissv/	1.0.4	samtools	1.19.2	(0/1)	(0/1)	(1/1)
@@ -720,7 +722,7 @@ kleborate	319.0	38.0	kleborate	Screen genome assemblies of Klebsiella pneumoniae
 kma			kma_map	Map with KMA						To update	https://bitbucket.org/genomicepidemiology/kma	Next Gen Mappers	kma	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/kma	1.2.21	kma	1.4.14	(0/1)	(0/1)	(1/1)
 kofamscan	594.0	33.0	kofamscan	Gene function annotation tool based on KEGG Orthology and hidden Markov model						Up-to-date	https://github.com/takaram/kofam_scan	Sequence Analysis	kofamscan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan	1.3.0	kofamscan	1.3.0	(0/1)	(0/1)	(1/1)
 kraken_biom	1444.0	182.0	kraken_biom	Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/)						Up-to-date	https://github.com/smdabdoub/kraken-biom	Metagenomics	kraken_biom	iuc	https://github.com/smdabdoub/kraken-biom	1.2.0	kraken-biom	1.2.0	(0/1)	(1/1)	(1/1)
-kraken_taxonomy_report	2527.0	354.0	kraken_taxonomy_report	Kraken taxonomy report						To update	https://github.com/blankenberg/Kraken-Taxonomy-Report	Metagenomics	kraken_taxonomy_report	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report	0.0.3	biopython	1.70	(1/1)	(0/1)	(1/1)
+kraken_taxonomy_report	2527.0	354.0	kraken_taxonomy_report	Kraken taxonomy report						To update	https://github.com/blankenberg/Kraken-Taxonomy-Report	Metagenomics	kraken_taxonomy_report	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report	0.0.3	biopython	1.70	(1/1)	(1/1)	(1/1)
 krakentools			krakentools_alpha_diversity, krakentools_beta_diversity, krakentools_combine_kreports, krakentools_extract_kraken_reads, krakentools_kreport2krona, krakentools_kreport2mpa	KrakenTools is a suite of scripts to be used alongside the Kraken	krakentools	KrakenTools	KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files	Visualisation, Aggregation	Taxonomy, Metagenomics	Up-to-date	https://github.com/jenniferlu717/KrakenTools	Metagenomics	krakentools	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools	1.2	krakentools	1.2	(1/6)	(4/6)	(6/6)
 krocus			krocus	Predict MLST directly from uncorrected long reads						To update	https://github.com/quadram-institute-bioscience/krocus	Sequence Analysis	krocus	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/krocus	1.0.1	krocus	1.0.3	(0/1)	(0/1)	(0/1)
 last	227.0	41.0	last_al, last_db, last_split, last_train, last_maf_convert	LAST finds similar regions between sequences.	last	LAST	Short read alignment program incorporating quality scores	Sequence alignment	Genomics, Comparative genomics	To update	http://last.cbrc.jp/	Sequence Analysis	last	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/last	1205	last	1541	(0/5)	(0/5)	(5/5)
@@ -755,7 +757,7 @@ meme			meme_dreme, meme_fimo, meme_meme, meme_psp_gen	The MEME Suite allows the
 meme_chip	6584.0	287.0	meme_chip	Performs motif discovery, motif enrichment analysis and clustering on large nucleotide datasets.						To update	http://meme-suite.org/	ChIP-seq	meme_chip	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip	4.11.2	graphicsmagick	1.3.26	(1/1)	(0/1)	(1/1)
 meningotype			meningotype	Assign sequence type to N. meningitidis genome assemblies						Up-to-date	https://github.com/MDU-PHL/meningotype	Sequence Analysis	meningotype	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype	0.8.5	meningotype	0.8.5	(0/1)	(0/1)	(0/1)
 merlin			merlin	Pedigree Analysis package	merlin	Merlin	Can be used for parametric and non-parametric linkage analysis, regression-based linkage analysis or association analysis for quantitative traits, ibd and kinship estimation, haplotyping, error detection and simulation	Haplotype mapping, Genetic mapping	GWAS study, Mapping	Up-to-date	http://csg.sph.umich.edu/abecasis/Merlin/	Variant Analysis	merlin	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/merlin/	1.1.2	merlin	1.1.2	(0/1)	(0/1)	(0/1)
-merqury	2483.0	244.0	merqury	Merqury is a tool for evaluating genomes assemblies based of k-mer operations.	merqury	Merqury	Reference-free quality, completeness, and phasing assessment for genome assemblies.Evaluate genome assemblies with k-mers and more.Often, genome assembly projects have illumina whole genome sequencing reads available for the assembled individual.Merqury provides a set of tools for this purpose.	Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly	Sequence assembly, Whole genome sequencing, Plant biology	Up-to-date	https://github.com/marbl/merqury	Assembly	merqury	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury	1.3	merqury	1.3	(1/1)	(1/1)	(1/1)
+merqury	2483.0	244.0	merqury, merquryplot	Merqury is a tool for evaluating genomes assemblies based of k-mer operations.	merqury	Merqury	Reference-free quality, completeness, and phasing assessment for genome assemblies.Evaluate genome assemblies with k-mers and more.Often, genome assembly projects have illumina whole genome sequencing reads available for the assembled individual.Merqury provides a set of tools for this purpose.	Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly	Sequence assembly, Whole genome sequencing, Plant biology	Up-to-date	https://github.com/marbl/merqury	Assembly	merqury	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury	1.3	merqury	1.3	(1/2)	(1/2)	(1/2)
 meryl	6785.0	350.0	meryl	Meryl a k-mer counter.	meryl	Meryl	Meryl is a tool for counting and working with sets of k-mers that was originally developed for use in the Celera Assembler and has since been migrated and maintained as part of Canu.	k-mer counting	Whole genome sequencing, Genomics, Sequence analysis, Sequencing	Up-to-date	https://github.com/marbl/meryl	Assembly	meryl	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl	1.3	merqury	1.3	(1/1)	(1/1)	(1/1)
 metabat2	4072.0	154.0	metabat2_jgi_summarize_bam_contig_depths, metabat2	MetaBAT2 (Metagenome Binning based on Abundance and Tetranucleotide frequency) is an automated metagenome binningsoftware that integrates empirical probabilistic distances of genome abundance and tetranucleotide frequency.	MetaBAT_2	MetaBAT 2	"an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies | MetaBAT2 clusters metagenomic contigs into different ""bins"", each of which should correspond to a putative genome | MetaBAT2 uses nucleotide composition information and source strain abundance (measured by depth-of-coverage by aligning the reads to the contigs) to perform binning"	Read binning, Sequence assembly, Genome annotation	Metagenomics, Sequence assembly, Metagenomic sequencing	Up-to-date	https://bitbucket.org/berkeleylab/metabat/src/master/	Metagenomics	metabat2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/	2.15	metabat2	2.15	(1/2)	(1/2)	(2/2)
 metaeuk			metaeuk_easy_predict	MetaEuk is a modular toolkit designed for large-scale gene discovery andannotation in eukaryotic metagenomic contigs. Metaeuk combines the fast andsensitive homology search capabilities of MMseqs2 with a dynamic programmingprocedure to recover optimal exons sets. It reduces redundancies in multiplediscoveries of the same gene and resolves conflicting gene predictions onthe same strand. 	MetaEuk	MetaEuk	MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics	Homology-based gene prediction	Metagenomics, Gene and protein families	To update	https://github.com/soedinglab/metaeuk	Sequence Analysis, Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk	5.34c21f2	metaeuk	6.a5d39d9	(0/1)	(0/1)	(1/1)
@@ -776,7 +778,7 @@ mothur			mothur_align_check, mothur_align_seqs, mothur_amova, mothur_anosim, mot
 msaboot	803.0	34.0	msaboot	A multiple sequences alignment bootstrapping tool.						Up-to-date	https://github.com/phac-nml/msaboot	Fasta Manipulation	msaboot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/msaboot	0.1.2	msaboot	0.1.2	(1/1)	(0/1)	(1/1)
 multigps			multigps	Analyzes collections of multi-condition ChIP-seq data.						To update	http://mahonylab.org/software/multigps/	ChIP-seq	multigps	iuc		0.74.0	fonts-conda-ecosystem		(1/1)	(0/1)	(0/1)
 multigsea	53.0	2.0	multigsea	GSEA-based pathway enrichment analysis for multi-omics data	multiGSEA	multiGSEA	A GSEA-based pathway enrichment analysis for multi-omics data.multiGSEA: a GSEA-based pathway enrichment analysis for multi-omics data, BMC Bioinformatics 21, 561 (2020).Combining GSEA-based pathway enrichment with multi omics data integration.	Gene-set enrichment analysis, Aggregation, Pathway analysis	Metabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules	To update	https://bioconductor.org/packages/devel/bioc/html/multiGSEA.html	Transcriptomics, Proteomics, Statistics	multigsea	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigsea	1.8.0	bioconductor-multigsea	1.12.0	(0/1)	(0/1)	(1/1)
-multiqc	162790.0	8320.0	multiqc	MultiQC aggregates results from bioinformatics analyses across many samples into a single report	multiqc	MultiQC	MultiQC aggregates results from multiple bioinformatics analyses across many samples into a single report. It searches a given directory for analysis logs and compiles a HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools.	Validation	Sequencing, Bioinformatics	To update	http://multiqc.info/	Fastq Manipulation, Statistics, Visualization	multiqc	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc	1.11	multiqc	1.19	(1/1)	(1/1)	(1/1)
+multiqc	162790.0	8320.0	multiqc	MultiQC aggregates results from bioinformatics analyses across many samples into a single report	multiqc	MultiQC	MultiQC aggregates results from multiple bioinformatics analyses across many samples into a single report. It searches a given directory for analysis logs and compiles a HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools.	Validation	Sequencing, Bioinformatics	To update	http://multiqc.info/	Fastq Manipulation, Statistics, Visualization	multiqc	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc	1.11	multiqc	1.20	(1/1)	(1/1)	(1/1)
 mummer4			mummer_delta_filter, mummer_dnadiff, mummer_mummer, mummer_mummerplot, mummer_nucmer, mummer_show_coords	Mummer4 Tools	mumer4	MUMmer4	System for rapidly aligning large DNA sequences to one another.	Multiple sequence alignment	Sequence analysis, Human genetics	Up-to-date	https://github.com/mummer4/mummer	Sequence Analysis	mummer4	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4	4.0.0rc1	mummer4	4.0.0rc1	(6/6)	(6/6)	(6/6)
 mykrobe			mykrobe_predict	Antibiotic resistance predictions	Mykrobe	Mykrobe	Antibiotic resistance prediction for Mycobacterium tuberculosis from genome sequence data with Mykrobe.Antibiotic resistance prediction in minutes.Table of Contents generated with DocToc.AMR prediction (Mykrobe predictor).Before attempting to install with bioconda, please ensure you have your channels set up as specified in the documentation. If you don't, you may run into issues with an older version of mykrobe being installed	Antimicrobial resistance prediction, Variant calling, Genotyping, Sequence trimming	Whole genome sequencing, Genotype and phenotype, Probes and primers, Genetic variation, Metagenomics	To update	https://github.com/Mykrobe-tools/mykrobe	Sequence Analysis	mykrobe	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe	0.10.0	mykrobe	0.13.0	(0/1)	(0/1)	(0/1)
 mzmine			mzmine_batch	mass-spectrometry data processing, with the main focus on LC-MS data	mzmine	MZmine	Toolbox for visualization and analysis of LC-MS data in netCDF or mzXML.	Natural product identification, Standardisation and normalisation, Peptide database search, Deisotoping, Clustering, Filtering, Chromatographic alignment, Peak detection, Peptide identification, Chromatogram visualisation, Mass spectrum visualisation, Structure visualisation, Plotting, Heat map generation	Proteomics, Metabolomics, Proteomics experiment, Small molecules	Up-to-date	http://mzmine.github.io/	Metabolomics	mzmine_batch	iuc	https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/	3.9.0	mzmine	3.9.0	(0/1)	(0/1)	(1/1)
@@ -835,7 +837,7 @@ polypolish	239.0	24.0	polypolish	"""Polypolish is a tool for polishing genome as
 porechop	185468.0	1046.0	porechop	Porechop - Finding and removing adapters from Oxford Nanopore reads						To update	https://github.com/rrwick/Porechop	Fasta Manipulation, Fastq Manipulation	porechop	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/porechop		porechop	0.2.4	(1/1)	(1/1)	(1/1)
 poretools			poretools_events, poretools_extract, poretools_hist, poretools_nucdist, poretools_occupancy, poretools_qualdist, poretools_qualpos, poretools_squiggle, poretools_stats, poretools_tabular, poretools_times, poretools_winner, poretools_yield_plot	A flexible toolkit for exploring datasets generated by nanopore sequencing devices from MinION for the purposes of quality control and downstream analysis.	poretools	Poretools	Flexible toolkit for exploring datasets generated by nanopore sequencing devices from MinION for the purposes of quality control and downstream analysis.	Nucleic acid sequence analysis	DNA, Sequencing	Up-to-date	https://poretools.readthedocs.io/en/latest/	Fasta Manipulation, Fastq Manipulation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools	0.6.1a1	poretools	0.6.1a1	(13/13)	(13/13)	(13/13)
 presto			presto_alignsets, presto_assemblepairs, presto_buildconsensus, presto_collapseseq, presto_filterseq, presto_maskprimers, presto_pairseq, presto_parseheaders, presto_parselog, presto_partition, prestor_abseq3	pRESTO toolkit for immune repertoire analysis.	presto	pRESTO	Integrated collection of platform-independent Python modules for processing raw reads from high-throughput (next-generation) sequencing of lymphocyte repertoires.	Nucleic acid sequence analysis	Sequencing, DNA, Immunology	To update	https://presto.readthedocs.io/	Sequence Analysis	presto	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto	0.6.2	presto	0.7.2	(11/11)	(0/11)	(0/11)
-pretext			pretext_map, pretext_snapshot	Process genome contacts maps processing images.						Up-to-date	https://github.com/wtsi-hpag/PretextSnapshot	Sequence Analysis	suite_pretext	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext	0.1.9	pretextmap	0.1.9	(2/2)	(2/2)	(2/2)
+pretext			pretext_graph, pretext_map, pretext_snapshot	Process genome contacts maps processing images.						Up-to-date	https://github.com/wtsi-hpag/PretextSnapshot	Sequence Analysis	suite_pretext	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext	0.0.6	pretextgraph	0.0.6	(2/3)	(2/3)	(2/3)
 prinseq	7881.0	70.0	prinseq	PRINSEQ is a tool for easy and rapid quality control and data processing of metagenomic and metatranscriptomic datasets	prinseq	PRINSEQ	PRINSEQ is a sequence processing tool that can be used to filter, reformat and trim genomic and metagenomic sequence data. It generates summary statistics of the input in graphical and tabular formats that can be used for quality control steps. PRINSEQ is available as both standalone and web-based versions.	Read pre-processing, Sequence trimming, Sequence contamination filtering	Transcriptomics, Metagenomics, Genomics	To update	http://prinseq.sourceforge.net/manual.html	Fastq Manipulation, Metagenomics	prinseq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/	@TOOL_VERSION+galaxy2	prinseq	0.20.4	(1/1)	(0/1)	(1/1)
 progressivemauve	1734.0	286.0	progressivemauve, xmfa2gff3	Mauve/ProgressiveMauve Multiple Sequence Aligner						To update		Sequence Analysis	progressivemauve	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve		progressivemauve	snapshot_2015_02_13	(2/2)	(0/2)	(2/2)
 prokka	371445.0	3233.0	prokka	Rapid annotation of prokaryotic genomes	prokka	Prokka	Software tool to annotate bacterial, archaeal and viral genomes quickly and produce standards-compliant output files.	Gene prediction, Coding region prediction, Genome annotation	Genomics, Model organisms, Virology	Up-to-date	http://github.com/tseemann/prokka	Sequence Analysis	prokka	crs4	https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/	1.14.6	prokka	1.14.6	(1/1)	(1/1)	(1/1)
@@ -878,7 +880,7 @@ rnaquast	1110.0	109.0	rna_quast	rnaQuast (RNA Quality Assessment Tool) evaluates
 roary	12225.0	656.0	roary	Roary the pangenome pipeline	roary	Roary	A high speed stand alone pan genome pipeline, which takes annotated assemblies in GFF3 format (produced by Prokka (Seemann, 2014)) and calculates the pan genome.	Genome assembly	DNA, Genomics, Mapping	Up-to-date	https://sanger-pathogens.github.io/Roary/	Sequence Analysis	roary	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary	3.13.0	roary	3.13.0	(1/1)	(1/1)	(1/1)
 rp2biosensor			rp2biosensor	Build Sensing-Enabling Metabolic Pathways from RetroPath2.0 output						To update	https://github.com/brsynth/rp2biosensor	Synthetic Biology	rp2biosensor	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rp2biosensor	3.2.1	rp2biosensor		(0/1)	(0/1)	(0/1)
 rp2paths			rp2paths	Enumerate and seperate the different pathways generated by RetroPath2.0						To update	https://github.com/brsynth/rp2paths	Synthetic Biology	rp2paths	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rp2paths	1.5.1	rp2paths		(0/1)	(0/1)	(0/1)
-rpbasicdesign			rpbasicdesign	Extracting enzyme IDs from rpSBML files						To update	https://github.com/brsynth/rpbasicdesign	Synthetic Biology	rpbasicdesign	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rpbasicdesign	1.1.1	rpbasicdesign		(0/1)	(0/1)	(0/1)
+rpbasicdesign			rpbasicdesign	Extracting enzyme IDs from rpSBML files						To update	https://github.com/brsynth/rpbasicdesign	Synthetic Biology	rpbasicdesign	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rpbasicdesign	1.2.2	rpbasicdesign		(0/1)	(0/1)	(0/1)
 rpfba			rpfba	Perform FBA for the RetroPath2.0 heterologous pathways						To update	https://github.com/brsynth/rptools/releases	Synthetic Biology	rpfba	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rpfba	5.12.3	rptools		(0/1)	(0/1)	(0/1)
 rptools			rptools_rpextractsink, rptools_rpfba, rptools_rpranker, rptools_rpreport, rptools_rpviz	Suite of tools that work on rpSBML format						To update	https://github.com/brsynth/rptools	Synthetic Biology	rptools	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools	5.13.1	rptools		(0/5)	(0/5)	(0/5)
 rrparser			rrparser	Reaction Rules Parser						To update	https://github.com/brsynth/RRParser	Synthetic Biology	rrparser	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser	2.5.2	rrparser		(0/1)	(0/1)	(0/1)
@@ -903,6 +905,7 @@ semibin	183.0	10.0	semibin_bin, semibin_concatenate_fasta, semibin_generate_cann
 seq2hla	288.0	16.0	seq2hla	Precision HLA typing and expression from RNAseq data	seq2hla	Seq2HLA	seq2HLA is a computational tool to determine Human Leukocyte Antigen (HLA) directly from existing and future short RNA-Seq reads. It takes standard RNA-Seq sequence reads in fastq format as input, uses a bowtie index comprising known HLA alleles and outputs the most likely HLA class I and class II types, a p-value for each call, and the expression of each class.	Read mapping, Genetic variation analysis	Transcriptomics, Mapping	Up-to-date	https://github.com/TRON-Bioinformatics/seq2HLA	Sequence Analysis	seq2hla	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla	2.3	seq2hla	2.3	(0/1)	(0/1)	(1/1)
 seqcomplexity	68.0	16.0	seqcomplexity	Sequence complexity for raw reads						Up-to-date	https://github.com/stevenweaver/seqcomplexity	Sequence Analysis		iuc	https://github.com/stephenshank/tools-iuc/tree/seqcomplexity/tools/seqcomplexity/	0.1.2	seqcomplexity	0.1.2	(1/1)	(0/1)	(1/1)
 seqkit			seqkit_fx2tab, seqkit_locate, seqkit_stats	A cross-platform and ultrafast toolkit for FASTA/Q file manipulation	seqkit	seqkit	FASTA and FASTQ are basic and ubiquitous formats for storing nucleotide and protein sequences. Common manipulations of FASTA/Q file include converting, searching, filtering, deduplication, splitting, shuffling, and sampling. Existing tools only implement some of these manipulations, and not particularly efficiently, and some are only available for certain operating systems. Furthermore, the complicated installation process of required packages and running environments can render these programs less user friendly. SeqKit demonstrates competitive performance in execution time and memory usage compared to similar tools. The efficiency and usability of SeqKit enable researchers to rapidly accomplish common FASTA/Q file manipulations.	DNA transcription, Sequence trimming, DNA translation, Sequence conversion	Database management, Sequence analysis	To update	https://bioinf.shenwei.me/seqkit/	Sequence Analysis	seqkit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit	2.3.1	seqkit	2.7.0	(0/3)	(0/3)	(3/3)
+seqprep			seqprep	Tool for merging paired-end Illumina reads and trimming adapters.	seqprep	SeqPrep	Strips adapters and optionally merges overlapping paired-end (or paired-end contamination in mate-pair libraries) illumina style reads.	Nucleic acid design	Genomics, Sequence assembly, Sequencing, Probes and primers	Up-to-date	https://github.com/jstjohn/SeqPrep	Fastq Manipulation, Sequence Analysis	seqprep	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep	1.3.2	seqprep	1.3.2	(0/1)	(0/1)	(0/1)
 seqsero2	12.0		seqsero2	Salmonella serotype prediction from genome sequencing data						Up-to-date	https://github.com/denglab/SeqSero2	Sequence Analysis	seqsero2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2	1.2.1	seqsero2	1.2.1	(0/1)	(0/1)	(1/1)
 seqtk	59668.0	753.0	seqtk_comp, seqtk_cutN, seqtk_dropse, seqtk_fqchk, seqtk_hety, seqtk_listhet, seqtk_mergefa, seqtk_mergepe, seqtk_mutfa, seqtk_randbase, seqtk_sample, seqtk_seq, seqtk_subseq, seqtk_telo, seqtk_trimfq	Toolkit for processing sequences in FASTA/Q formats	seqtk	seqtk	A tool for processing sequences in the FASTA or FASTQ format. It parses both FASTA and FASTQ files which can also be optionally compressed by gzip.	Data handling, Sequence file editing	Data management	Up-to-date	https://github.com/lh3/seqtk	Sequence Analysis	seqtk	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk	1.4	seqtk	1.4	(15/15)	(15/15)	(15/15)
 seqwish	271.0		seqwish	Alignment to variation graph inducer						To update	https://github.com/ekg/seqwish	Sequence Analysis, Variant Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqwish/	0.7.5	seqwish	0.7.9	(0/1)	(0/1)	(1/1)
@@ -928,7 +931,7 @@ snpeff-covid19			snpeff_sars_cov_2	SnpEff, the COVID-19 version, is a genetic va
 snpfreqplot	3530.0	156.0	snpfreqplot	Generates a heatmap of allele frequencies grouped by variant type for SARS-CoV-2 data						To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/	Variant Analysis	snpfreqplot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/	1.0	r-base		(1/1)	(1/1)	(1/1)
 socru	621.0	13.0	socru	Order and orientation of complete bacterial genomes						To update	https://github.com/quadram-institute-bioscience/socru	Sequence Analysis	socru	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/socru	2.1.7	socru	2.2.4	(1/1)	(0/1)	(1/1)
 sonneityping	1.0	1.0	sonneityping	Scripts for parsing Mykrobe predict results for Shigella sonnei.						Up-to-date	https://github.com/katholt/sonneityping	Sequence Analysis	sonneityping	iuc	https://github.com/katholt/sonneityping	20210201	sonneityping	20210201	(0/1)	(0/1)	(1/1)
-spades	58834.0	2309.0	spades_biosyntheticspades, spades_coronaspades, spades_metaplasmidspades, metaspades, spades_metaviralspades, spades_plasmidspades, rnaspades, spades_rnaviralspades, spades	SPAdes is an assembly toolkit containing various assembly pipelines. It implements the following 4 stages: assembly graph construction, k-bimer adjustment, construction of paired assembly graph and contig construction.						Up-to-date	https://github.com/ablab/spades	Assembly, RNA, Metagenomics	spades	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades	3.15.5	spades	3.15.5	(9/9)	(9/9)	(9/9)
+spades	58834.0	2309.0	spades_biosyntheticspades, spades_coronaspades, spades_metaplasmidspades, metaspades, spades_metaviralspades, spades_plasmidspades, rnaspades, spades_rnaviralspades, spades	SPAdes is an assembly toolkit containing various assembly pipelines. It implements the following 4 stages: assembly graph construction, k-bimer adjustment, construction of paired assembly graph and contig construction.	biosyntheticspades	biosyntheticSPAdes	biosyntheticSPAdes - biosynthetic gene cluster assembly with paired-end reads	Sequence assembly	Sequence assembly, Sequence sites, features and motifs, Genetic engineering	Up-to-date	https://github.com/ablab/spades	Assembly, RNA, Metagenomics	spades	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades	3.15.5	spades	3.15.5	(9/9)	(9/9)	(9/9)
 spaln	446.0	34.0	list_spaln_tables, spaln	Spaln (space-efficient spliced alignment) maps and aligns a set of cDNA or protein sequences onto a whole genomic sequence.						To update	http://www.genome.ist.i.kyoto-u.ac.jp/~aln_user/spaln/	Sequence Analysis, Genome annotation	spaln	iuc	https://github.com/ogotoh/spaln	2.4.9	python		(2/2)	(0/2)	(2/2)
 spotyping	1278.0	12.0	spotyping	SpoTyping allows fast and accurate in silico Mycobacterium spoligotyping from sequence reads	spotyping	SpoTyping	Fast and accurate in silico Mycobacterium spoligotyping from sequence reads.	Variant pattern analysis	Microbiology, Sequencing, Sequence composition, complexity and repeats, Genetic variation	Up-to-date	https://github.com/xiaeryu/SpoTyping-v2.0	Sequence Analysis	spotyping	iuc	https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine	2.1	spotyping	2.1	(0/1)	(0/1)	(1/1)
 spyboat	67.0	1.0	spyboat	Wavelet analysis for 3d-image stacks						To update	http://github.com/tensionhead/spyboat	Imaging, Graphics	spyboat	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat	0.1.2	spyboat		(0/1)	(0/1)	(1/1)
@@ -963,10 +966,10 @@ transdecoder	5468.0	348.0	transdecoder	TransDecoder finds coding regions within
 transit			gff_to_prot, transit_gumbel, transit_hmm, transit_resampling, transit_tn5gaps	TRANSIT	transit	TRANSIT	A tool for the analysis of Tn-Seq data. It provides an easy to use graphical interface and access to three different analysis methods that allow the user to determine essentiality in a single condition as well as between conditions.	Transposon prediction	DNA, Sequencing, Mobile genetic elements	To update	https://github.com/mad-lab/transit/	Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/	3.0.2	transit	3.2.3	(5/5)	(4/5)	(5/5)
 transtermhp	229.0	5.0	transtermhp	Finds rho-independent transcription terminators in bacterial genomes						To update		Sequence Analysis	transtermhp	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp		transtermhp	2.09	(1/1)	(0/1)	(1/1)
 trimmomatic	305866.0	5862.0	trimmomatic	A flexible read trimming tool for Illumina NGS data						Up-to-date	http://www.usadellab.org/cms/?page=trimmomatic	Fastq Manipulation	trimmomatic	pjbriggs	https://github.com/galaxyproject/tools-iuc/tree/main/packages/trimmomatic	0.39	trimmomatic	0.39	(1/1)	(1/1)	(1/1)
-trinity	12733.0	678.0	trinity_abundance_estimates_to_matrix, trinity_align_and_estimate_abundance, trinity_analyze_diff_expr, trinity_contig_exn50_statistic, trinity_define_clusters_by_cutting_tree, describe_samples, trinity_filter_low_expr_transcripts, trinity_gene_to_trans_map, trinity_run_de_analysis, trinity_samples_qccheck, trinity_super_transcripts, trinity, trinity_stats	Trinity represents a method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq datahttps://github.com/trinityrnaseq/trinityrnaseq	trinity	Trinity	Trinity is a transcriptome assembler which relies on three different tools, inchworm an assembler, chrysalis which pools contigs and butterfly which amongst others compacts a graph resulting from butterfly with reads.	Transcriptome assembly	Transcriptomics, Gene expression, Gene transcripts	Up-to-date	https://github.com/trinityrnaseq/trinityrnaseq	Transcriptomics, RNA		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity	2.15.1	trinity	2.15.1	(8/13)	(12/13)	(13/13)
+trinity	12733.0	678.0	trinity_abundance_estimates_to_matrix, trinity_align_and_estimate_abundance, trinity_analyze_diff_expr, trinity_contig_exn50_statistic, trinity_define_clusters_by_cutting_tree, describe_samples, trinity_filter_low_expr_transcripts, trinity_gene_to_trans_map, trinity_run_de_analysis, trinity_samples_qccheck, trinity_super_transcripts, trinity, trinity_stats	Trinity represents a method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq datahttps://github.com/trinityrnaseq/trinityrnaseq	trinity	Trinity	Trinity is a transcriptome assembler which relies on three different tools, inchworm an assembler, chrysalis which pools contigs and butterfly which amongst others compacts a graph resulting from butterfly with reads.	Transcriptome assembly	Transcriptomics, Gene expression, Gene transcripts	Up-to-date	https://github.com/trinityrnaseq/trinityrnaseq	Transcriptomics, RNA		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity	2.15.1	trinity	2.15.1	(9/13)	(12/13)	(13/13)
 trinotate	1796.0	151.0	trinotate	Trinotate is a comprehensive annotation suite designed for automatic functional annotation of de novo transcriptomes.	trinotate	Trinotate	Comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms.	Gene functional annotation	Gene expression, Transcriptomics	To update	https://trinotate.github.io/	Transcriptomics, RNA	trinotate	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate	3.2.2	trinotate	4.0.2	(1/1)	(1/1)	(1/1)
 trycycler			trycycler_cluster, trycycler_consensus, trycycler_partition, trycycler_reconcile_msa, trycycler_subsample	Trycycler toolkit wrappers						Up-to-date	https://github.com/rrwick/Trycycler	Assembly	trycycler	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler	0.5.4	trycycler	0.5.4	(0/5)	(5/5)	(5/5)
-tsebra	5.0		tsebra	This tool has been developed to combine BRAKER predictions.						To update	https://github.com/Gaius-Augustus/TSEBRA	Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra	1.1.2	tsebra	1.1.2.2	(0/1)	(0/1)	(1/1)
+tsebra	5.0		tsebra	This tool has been developed to combine BRAKER predictions.						To update	https://github.com/Gaius-Augustus/TSEBRA	Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra	1.1.2	tsebra	1.1.2.3	(0/1)	(0/1)	(1/1)
 tsne	368.0	10.0	tsne	T-Distributed Stochastic Neighbor Embedding using a Barnes-Hut Implementation						To update	https://cran.r-project.org/web/packages/Rtsne/	Text Manipulation	tsne	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsne	0.0.2	r-rtsne	0.13	(1/1)	(0/1)	(1/1)
 tximport	1408.0	88.0	tximport	Wrapper for the Bioconductor package tximport	tximport	tximport	An R/Bioconductor package that imports transcript-level abundance, estimated counts and transcript lengths, and summarizes into matrices for use with downstream gene-level analysis packages.	Pathway or network analysis, Formatting, RNA-Seq analysis	Transcriptomics, Gene transcripts, Workflows	To update	http://bioconductor.org/packages/tximport/	Transcriptomics	tximport	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport	1.22.0	bioconductor-tximport	1.30.0	(1/1)	(0/1)	(1/1)
 ucsc_blat			ucsc_blat	Standalone blat sequence search command line tool	blat	BLAT	Fast, accurate spliced alignment of DNA sequences.	Sequence alignment	Sequence analysis	To update	http://genome.ucsc.edu/goldenPath/help/blatSpec.html	Sequence Analysis	ucsc_blat	yating-l		377	ucsc-blat	445	(0/1)	(0/1)	(0/1)
@@ -974,7 +977,7 @@ fasplit			fasplit	faSplit is a tool to split a single FASTA file into several fi
 fatovcf			fatovcf	Convert a FASTA alignment file to Variant Call Format (VCF) single-nucleotide diffs	UCSC_Genome_Browser_Utilities	UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	http://hgdownload.cse.ucsc.edu/admin/exe/	Convert Formats	ucsc_fatovcf	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/fatovcf	448	ucsc-fatovcf	448	(1/1)	(0/1)	(1/1)
 twobittofa			ucsc-twobittofa	twoBitToFa is a tool to convert all or part of .2bit file to FASTA	UCSC_Genome_Browser_Utilities	UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	To update	https://genome.ucsc.edu/goldenpath/help/twoBit.html	Convert Formats	ucsc_twobittofa	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/twobittofa	377	ucsc-twobittofa	455	(1/1)	(1/1)	(1/1)
 wigtobigwig			ucsc_wigtobigwig	converts bedGraph (wig) files into binary bigwig	UCSC_Genome_Browser_Utilities	UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	https://genome.ucsc.edu/goldenPath/help/bigWig.html	Convert Formats	ucsc_wigtobigwig	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/wigtobigwig	447	ucsc-wigtobigwig	447	(0/1)	(0/1)	(1/1)
-umi_tools			umi_tools_count, umi_tools_dedup, umi_tools_extract, umi_tools_group, umi_tools_whitelist	UMI-tools extract - Extract UMIs from fastq	umi-tools	UMI-tools	Tools for handling Unique Molecular Identifiers in NGS data sets.	Sequencing quality control	NGS, Sequence sites, features and motifs, Quality affairs	To update	https://github.com/CGATOxford/UMI-tools	Sequence Analysis, Transcriptomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools	1.1.2	umi_tools	1.1.4	(5/5)	(5/5)	(5/5)
+umi_tools			umi_tools_count, umi_tools_dedup, umi_tools_extract, umi_tools_group, umi_tools_whitelist	UMI-tools extract - Extract UMIs from fastq	umi-tools	UMI-tools	Tools for handling Unique Molecular Identifiers in NGS data sets.	Sequencing quality control	NGS, Sequence sites, features and motifs, Quality affairs	To update	https://github.com/CGATOxford/UMI-tools	Sequence Analysis, Transcriptomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools	1.1.2	umi_tools	1.1.5	(5/5)	(5/5)	(5/5)
 unicycler	65732.0	1558.0	unicycler	Unicycler is a hybrid assembly pipeline for bacterial genomes.	unicycler	Unicycler	A tool for assembling bacterial genomes from a combination of short (2nd generation) and long (3rd generation) sequencing reads.	Genome assembly, Aggregation	Microbiology, Genomics, Sequencing, Sequence assembly	Up-to-date	https://github.com/rrwick/Unicycler	Assembly	unicycler	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler	0.5.0	unicycler	0.5.0	(1/1)	(1/1)	(1/1)
 usher	1060.0	5.0	usher_matutils, usher	UShER toolkit wrappers						To update	https://github.com/yatisht/usher	Phylogenetics	usher	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher	0.2.1	usher	0.6.3	(0/2)	(0/2)	(2/2)
 valet	637.0	20.0	valet	A pipeline for detecting mis-assemblies in metagenomic assemblies.						To update	https://github.com/marbl/VALET	Metagenomics	valet	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet		valet	1.0	(1/1)	(0/1)	(1/1)
@@ -1120,13 +1123,13 @@ msstats	2036.0	144.0	msstats	MSstats tool for analyzing mass spectrometry proteo
 msstatstmt	726.0	71.0	msstatstmt	MSstatsTMT protein significance analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling						To update	http://msstats.org/msstatstmt/	Proteomics	msstatstmt	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt	2.0.0	bioconductor-msstatstmt	2.10.0	(0/1)	(1/1)	(1/1)
 mt2mq	270.0	19.0	mt2mq	Tool to prepare metatranscriptomic outputs from ASaiM for Metaquantome						To update		Proteomics	mt2mq	galaxyp		1.1.0	r-tidyverse		(0/1)	(0/1)	(1/1)
 mz_to_sqlite	844.0	33.0	mz_to_sqlite	Creates a SQLite database for proteomics data						To update		Proteomics	mz_to_sqlite	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite	2.1.1+galaxy0	mztosqlite	2.1.1	(1/1)	(1/1)	(1/1)
-openms			AccurateMassSearch, AssayGeneratorMetabo, BaselineFilter, CVInspector, ClusterMassTraces, ClusterMassTracesByPrecursor, CometAdapter, CompNovo, CompNovoCID, ConsensusID, ConsensusMapNormalizer, CruxAdapter, DTAExtractor, DatabaseFilter, DatabaseSuitability, DeMeanderize, Decharger, DecoyDatabase, Digestor, DigestorMotif, EICExtractor, ERPairFinder, Epifany, ExternalCalibration, FFEval, FalseDiscoveryRate, FeatureFinderCentroided, FeatureFinderIdentification, FeatureFinderIsotopeWavelet, FeatureFinderMRM, FeatureFinderMetabo, FeatureFinderMetaboIdent, FeatureFinderMultiplex, FeatureLinkerLabeled, FeatureLinkerUnlabeled, FeatureLinkerUnlabeledKD, FeatureLinkerUnlabeledQT, FidoAdapter, FileConverter, FileFilter, FileInfo, FileMerger, FuzzyDiff, GNPSExport, HighResPrecursorMassCorrector, IDConflictResolver, IDExtractor, IDFileConverter, IDFilter, IDMapper, IDMassAccuracy, IDMerger, IDPosteriorErrorProbability, IDRTCalibration, IDRipper, IDScoreSwitcher, IDSplitter, InternalCalibration, IsobaricAnalyzer, LabeledEval, LuciphorAdapter, MRMMapper, MRMPairFinder, MRMTransitionGroupPicker, MSFraggerAdapter, MSGFPlusAdapter, MSSimulator, MSstatsConverter, MaRaClusterAdapter, MapAlignerIdentification, MapAlignerPoseClustering, MapAlignerSpectrum, MapAlignerTreeGuided, MapNormalizer, MapRTTransformer, MapStatistics, MascotAdapter, MascotAdapterOnline, MassCalculator, MassTraceExtractor, MetaProSIP, MetaboliteAdductDecharger, MetaboliteSpectralMatcher, MultiplexResolver, MyriMatchAdapter, MzMLSplitter, MzTabExporter, NoiseFilterGaussian, NoiseFilterSGolay, NovorAdapter, NucleicAcidSearchEngine, OMSSAAdapter, OpenMSDatabasesInfo, OpenPepXL, OpenPepXLLF, OpenSwathAnalyzer, OpenSwathAssayGenerator, OpenSwathChromatogramExtractor, OpenSwathConfidenceScoring, OpenSwathDIAPreScoring, OpenSwathDecoyGenerator, OpenSwathFeatureXMLToTSV, OpenSwathFileSplitter, OpenSwathMzMLFileCacher, OpenSwathRTNormalizer, OpenSwathRewriteToFeatureXML, OpenSwathWorkflow, PSMFeatureExtractor, PTModel, PeakPickerHiRes, PeakPickerIterative, PeakPickerWavelet, PepNovoAdapter, PeptideIndexer, PercolatorAdapter, PhosphoScoring, PrecursorIonSelector, PrecursorMassCorrector, ProteinInference, ProteinQuantifier, ProteinResolver, QCCalculator, QCEmbedder, QCExporter, QCExtractor, QCImporter, QCMerger, QCShrinker, QualityControl, RNADigestor, RNAMassCalculator, RNPxlSearch, RNPxlXICFilter, RTEvaluation, RTModel, SeedListGenerator, SemanticValidator, SequenceCoverageCalculator, SimpleSearchEngine, SiriusAdapter, SpecLibCreator, SpecLibSearcher, SpectraFilterBernNorm, SpectraFilterMarkerMower, SpectraFilterNLargest, SpectraFilterNormalizer, SpectraFilterParentPeakMower, SpectraFilterScaler, SpectraFilterSqrtMower, SpectraFilterThresholdMower, SpectraFilterWindowMower, SpectraMerger, SpectraSTSearchAdapter, StaticModification, SvmTheoreticalSpectrumGeneratorTrainer, TICCalculator, TOFCalibration, TargetedFileConverter, TextExporter, TransformationEvaluation, TriqlerConverter, XFDR, XMLValidator, XTandemAdapter	OpenMS Suite for LC/MS data management and analyses						To update	https://www.openms.de/	Proteomics	openms	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms	2.8	openms	3.1.0	(1/164)	(36/164)	(160/164)
+openms			AccurateMassSearch, AssayGeneratorMetabo, BaselineFilter, CVInspector, ClusterMassTraces, ClusterMassTracesByPrecursor, CometAdapter, CompNovo, CompNovoCID, ConsensusID, ConsensusMapNormalizer, CruxAdapter, DTAExtractor, DatabaseFilter, DatabaseSuitability, DeMeanderize, Decharger, DecoyDatabase, Digestor, DigestorMotif, EICExtractor, ERPairFinder, Epifany, ExternalCalibration, FFEval, FalseDiscoveryRate, FeatureFinderCentroided, FeatureFinderIdentification, FeatureFinderIsotopeWavelet, FeatureFinderMRM, FeatureFinderMetabo, FeatureFinderMetaboIdent, FeatureFinderMultiplex, FeatureLinkerLabeled, FeatureLinkerUnlabeled, FeatureLinkerUnlabeledKD, FeatureLinkerUnlabeledQT, FidoAdapter, FileConverter, FileFilter, FileInfo, FileMerger, FuzzyDiff, GNPSExport, HighResPrecursorMassCorrector, IDConflictResolver, IDExtractor, IDFileConverter, IDFilter, IDMapper, IDMassAccuracy, IDMerger, IDPosteriorErrorProbability, IDRTCalibration, IDRipper, IDScoreSwitcher, IDSplitter, InternalCalibration, IsobaricAnalyzer, LabeledEval, LuciphorAdapter, MRMMapper, MRMPairFinder, MRMTransitionGroupPicker, MSFraggerAdapter, MSGFPlusAdapter, MSSimulator, MSstatsConverter, MaRaClusterAdapter, MapAlignerIdentification, MapAlignerPoseClustering, MapAlignerSpectrum, MapAlignerTreeGuided, MapNormalizer, MapRTTransformer, MapStatistics, MascotAdapter, MascotAdapterOnline, MassCalculator, MassTraceExtractor, MetaProSIP, MetaboliteAdductDecharger, MetaboliteSpectralMatcher, MultiplexResolver, MyriMatchAdapter, MzMLSplitter, MzTabExporter, NoiseFilterGaussian, NoiseFilterSGolay, NovorAdapter, NucleicAcidSearchEngine, OMSSAAdapter, OpenMSDatabasesInfo, OpenPepXL, OpenPepXLLF, OpenSwathAnalyzer, OpenSwathAssayGenerator, OpenSwathChromatogramExtractor, OpenSwathConfidenceScoring, OpenSwathDIAPreScoring, OpenSwathDecoyGenerator, OpenSwathFeatureXMLToTSV, OpenSwathFileSplitter, OpenSwathMzMLFileCacher, OpenSwathRTNormalizer, OpenSwathRewriteToFeatureXML, OpenSwathWorkflow, PSMFeatureExtractor, PTModel, PeakPickerHiRes, PeakPickerIterative, PeakPickerWavelet, PepNovoAdapter, PeptideIndexer, PercolatorAdapter, PhosphoScoring, PrecursorIonSelector, PrecursorMassCorrector, ProteinInference, ProteinQuantifier, ProteinResolver, QCCalculator, QCEmbedder, QCExporter, QCExtractor, QCImporter, QCMerger, QCShrinker, QualityControl, RNADigestor, RNAMassCalculator, RNPxlSearch, RNPxlXICFilter, RTEvaluation, RTModel, SeedListGenerator, SemanticValidator, SequenceCoverageCalculator, SimpleSearchEngine, SiriusAdapter, SpecLibCreator, SpecLibSearcher, SpectraFilterBernNorm, SpectraFilterMarkerMower, SpectraFilterNLargest, SpectraFilterNormalizer, SpectraFilterParentPeakMower, SpectraFilterScaler, SpectraFilterSqrtMower, SpectraFilterThresholdMower, SpectraFilterWindowMower, SpectraMerger, SpectraSTSearchAdapter, StaticModification, SvmTheoreticalSpectrumGeneratorTrainer, TICCalculator, TOFCalibration, TargetedFileConverter, TextExporter, TransformationEvaluation, TriqlerConverter, XFDR, XMLValidator, XTandemAdapter	OpenMS Suite for LC/MS data management and analyses						To update	https://www.openms.de/	Proteomics	openms	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms	2.8	openms	3.1.0	(1/164)	(35/164)	(160/164)
 pathwaymatcher			reactome_pathwaymatcher	Reactome Pathway Matcher						To update	https://github.com/LuisFranciscoHS/PathwayMatcher	Proteomics	reactome_pathwaymatcher	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher		pathwaymatcher	1.9.1	(0/1)	(0/1)	(1/1)
 pep_pointer	498.0	9.0	pep_pointer	PepPointer categorizes peptides by their genomic coordinates.						To update		Genomic Interval Operations, Proteomics	pep_pointer	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pep_pointer	0.1.3+galaxy1	python		(1/1)	(1/1)	(1/1)
 pepquery	4862.0	23.0	pepquery	A peptide-centric MS search engine for novel peptide identification and validation.						To update	https://pepquery.org	Proteomics	pepquery	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery	1.6.2	pepquery	2.0.2	(0/1)	(0/1)	(1/1)
 pepquery2	707.0	10.0	pepquery2, pepquery2_index, pepquery2_show_sets	PepQuery2 peptide-centric MS search for peptide identification and validation						Up-to-date	https://pepquery.org	Proteomics	pepquery2	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2	2.0.2	pepquery	2.0.2	(0/3)	(0/3)	(3/3)
 peptide_genomic_coordinate	468.0	9.0	peptide_genomic_coordinate	Gets genomic coordinate of peptides based on the information in mzsqlite and genomic mapping sqlite files						To update		Proteomics	peptide_genomic_coordinate	galaxyp		1.0.0	python		(1/1)	(1/1)	(1/1)
-peptideshaker	17477.0	485.0	fasta_cli, ident_params, peptide_shaker, search_gui	PeptideShaker and SearchGUI						To update	http://compomics.github.io	Proteomics	peptideshaker	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker		searchgui	4.3.5	(4/4)	(4/4)	(4/4)
+peptideshaker	17477.0	485.0	fasta_cli, ident_params, peptide_shaker, search_gui	PeptideShaker and SearchGUI						To update	http://compomics.github.io	Proteomics	peptideshaker	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker		searchgui	4.3.6	(4/4)	(4/4)	(4/4)
 pepxml_to_xls				Convert PepXML to Tabular						To update		Proteomics	pepxml_to_xls	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepxml_to_xls				(0/1)	(0/1)	(0/1)
 percolator	368.0	5.0	batched_set_list_creator, percolator, percolator_input_converters, pout2mzid	Percolator						Up-to-date		Proteomics	percolator	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator	3.5	percolator	3.5	(0/4)	(4/4)	(4/4)
 pi_db_tools			calc_delta_pi, pi_db_split, pi_dbspec_align	HiRIEF tools						To update		Proteomics	hirieftools	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools	1.3	python		(0/3)	(0/3)	(0/3)
@@ -1151,7 +1154,7 @@ protxml_to_xls			protxml_to_xls							To update			protxml_to_xls	galaxyp		0.1.0
 psm_eval			psm_eval							To update			psm_eval	galaxyp		0.1.0	binaries_for_psm_eval		(0/1)	(0/1)	(0/1)
 psm_validation	20.0		psmvalidator	Validate PSM from Ion Fragmentation						To update	https://github.com/galaxyproteomics/psm_fragments.git	Proteomics	psm_validation	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation	1.0.3			(0/1)	(0/1)	(1/1)
 pyprophet			pyprophet_export, pyprophet_merge, pyprophet_peptide, pyprophet_protein, pyprophet_score, pyprophet_subsample	Semi-supervised learning and scoring of OpenSWATH results.						To update	https://github.com/PyProphet/pyprophet	Proteomics		galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet	2.1.4	pyprophet	2.2.5	(0/6)	(4/6)	(6/6)
-pyteomics			mztab2tsv	Tools using the pyteomics library	pyteomics	Pyteomics	Framework for proteomics data analysis, supporting mzML, MGF, pepXML and more.	Protein identification	Proteomics, Proteomics experiment	To update	https://pyteomics.readthedocs.io/en/latest/	Proteomics, Metabolomics	pyteomics	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics	4.4.1	pyteomics	4.7	(0/1)	(0/1)	(1/1)
+pyteomics			mztab2tsv	Tools using the pyteomics library	pyteomics	Pyteomics	Framework for proteomics data analysis, supporting mzML, MGF, pepXML and more.	Protein identification	Proteomics, Proteomics experiment	To update	https://pyteomics.readthedocs.io/en/latest/	Proteomics, Metabolomics	pyteomics	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics	4.4.1	pyteomics	4.7.1	(0/1)	(0/1)	(1/1)
 quantp	230.0	6.0	quantp	Correlation between protein and transcript abundance						To update		Proteomics	quantp	galaxyp		1.1.2	r-data.table	1.11.6	(0/1)	(0/1)	(1/1)
 quantwiz_iq	32.0	1.0	quantwiz_iq	Isobaric Quantitation using QuantWiz-IQ						Up-to-date	https://sourceforge.net/projects/quantwiz/	Proteomics	quantwiz_iq	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/quantwiz_iq	2.0	quantwiz-iq	2.0	(0/1)	(0/1)	(1/1)
 qupath_roi_splitter	59.0	5.0	qupath_roi_splitter	Split ROI coordinates of QuPath TMA annotation by cell type						To update	https://github.com/npinter/ROIsplitter	Imaging	qupath_roi_splitter	galaxyp	hhttps://github.com/npinter/ROIsplitter	0.1.0+galaxy1	geojson		(0/1)	(0/1)	(1/1)
@@ -1195,7 +1198,7 @@ embl2fa			embl2fa	Converts EMBL flat format to fasta format						To update	http:
 ez_histograms			ez_histograms	ggplot2 histograms and density plots						To update	https://github.com/tidyverse/ggplot2	Visualization, Statistics	ez_histograms	artbio	https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms	3.4.4	r-ggplot2	2.2.1	(0/1)	(0/1)	(0/1)
 fetch_fasta_from_ncbi			retrieve_fasta_from_NCBI	Fetch fasta sequences from NCBI using eutils wrappers						To update	http://artbio.fr	Fasta Manipulation, Data Source	fetch_fasta_from_ncbi	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/fetch_fasta_from_ncbi	3.1.0	urllib3	1.12	(0/1)	(0/1)	(0/1)
 fisher_test			fishertest	Fisher's exact test on two-column hit lists.						To update	http://artbio.fr	RNA, Statistics	fishertest	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/fisher_test	2.32.0+galaxy0	bioconductor-qvalue	2.34.0	(0/1)	(0/1)	(0/1)
-gatk4			filtermutectcalls, mergemutectstats, mutect2	Find somatic variations						To update	http://artbio.fr	Variant Analysis	gatk4	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/gatk4	4.1.7.0	gatk4	4.4.0.0	(0/3)	(0/3)	(0/3)
+gatk4			filtermutectcalls, mergemutectstats, mutect2	Find somatic variations						To update	http://artbio.fr	Variant Analysis	gatk4	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/gatk4	4.1.7.0	gatk4	4.5.0.0	(0/3)	(0/3)	(0/3)
 get_reference_fasta			get_fasta_reference	Obtain reference genome sequence.						To update	http://artbio.fr	Data Source, Fasta Manipulation	get_reference_fasta	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/get_reference_fasta	0.3.2			(0/1)	(0/1)	(0/1)
 gsc_center_scale			center_scale	Center or scale (standardize) data						To update	http://artbio.fr	Statistics	gsc_center_scale	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_center_scale	4.3.1+galaxy0	r-optparse	1.3.2	(0/1)	(0/1)	(0/1)
 gsc_filter_cells			filter_cells	Filter single cell RNAseq data on libray depth and number of detected genes						To update	http://artbio.fr	Transcriptomics	gsc_filter_cells	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_filter_cells	4.3.1+galaxy0	r-optparse	1.3.2	(0/1)	(0/1)	(0/1)
@@ -1214,9 +1217,9 @@ manta	93.0	8.0	manta	Structural variant and indel caller for mapped sequencing d
 mapping_quality_stats			mapqstatistics	Collects and shows the distribution of MAPQ values in a BAM alignment file						To update	http://artbio.fr	Sequence Analysis, Statistics	mapping_quality_stats	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/mapping_quality_stats	0.22.0	r-optparse	1.3.2	(0/1)	(0/1)	(0/1)
 mircounts			mircounts	Generates miRNA count lists from read alignments to mirBase.						To update	http://artbio.fr	RNA, Transcriptomics	mircounts	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts	1.6	tar		(0/1)	(1/1)	(0/1)
 mutational_patterns			mutational_patterns	Mutational patterns and signatures in base substitution catalogs						Up-to-date	http://artbio.fr	Variant Analysis	mutational_patterns	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/mutational_patterns	3.12.0	bioconductor-mutationalpatterns	3.12.0	(0/1)	(0/1)	(0/1)
-oases			oasesoptimiserv	Short read assembler						To update	http://artbio.fr	Assembly, RNA	oases	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/oases	1.3.0	oases	0.2.09	(0/1)	(0/1)	(0/1)
-pathifier	228.0	10.0	pathifier	pathifier						To update	https://	Transcriptomics, Statistics	pathifier	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier	1.0.2	r-optparse	1.3.2	(0/1)	(0/1)	(1/1)
-pindel			pindel	Pindel detects genome-wide structural variation.						To update	http://artbio.fr	Variant Analysis	pindel	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel	0.2.5b8+galaxy1	pindel	0.2.5b9	(0/1)	(0/1)	(0/1)
+oases			oasesoptimiserv	Short read assembler						To update	http://artbio.fr	Assembly, RNA	oases	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/oases	1.4.0	oases	0.2.09	(0/1)	(0/1)	(0/1)
+pathifier	228.0	10.0	pathifier	pathifier						Up-to-date	https://	Transcriptomics, Statistics	pathifier	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/pathifier	1.40.0	bioconductor-pathifier	1.40.0	(0/1)	(0/1)	(1/1)
+pindel			pindel	Pindel detects genome-wide structural variation.						Up-to-date	http://artbio.fr	Variant Analysis	pindel	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel	0.2.5b9	pindel	0.2.5b9	(0/1)	(0/1)	(0/1)
 probecoverage			probecoverage	computes and plots read coverage of genomic regions by sequencing datasets						To update	http://artbio.fr	Sequence Analysis, Genomic Interval Operations, Graphics, Statistics	probecoverage	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/probecoverage	0.7.0	samtools	1.19.2	(0/1)	(0/1)	(0/1)
 repenrich			edger-repenrich, repenrich	Repeat element profiling						To update	https://github.com/nskvir/RepEnrich	Transcriptomics, Variant Analysis	repenrich	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich	1.5.2	bioconductor-edger	4.0.2	(0/2)	(2/2)	(0/2)
 rsem	2273.0	199.0	extract_transcript_to_gene_map_from_trinity, purgegtffrommultichromgenes, rsembowtie2, rsembowtie	transcript quantification from RNA-Seq data						To update	https://github.com/deweylab/RSEM	Transcriptomics, RNA	rsem	artbio	https://github.com/artbio/tools-artbio/tree/master/tools/rsem		rsem	1.3.3	(0/4)	(0/4)	(1/4)
@@ -1244,6 +1247,7 @@ data_exploration			tool_anonymization, ecology_homogeneity_normality, ecology_be
 xarray			timeseries_extraction, xarray_coords_info, xarray_mapplot, xarray_metadata_info, xarray_netcdf2netcdf, xarray_select	xarray (formerly xray) is an open source project and Python package that makes working withlabelled multi-dimensional arrays simple, efficient, and fun!xarray integrates with Dask to support parallel computations and streaming computation on datasetsthat don’t fit into memory.						To update	http://xarray.pydata.org	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/	2022.3.0	xarray		(5/6)	(2/6)	(6/6)
 gdal			gdal_gdal_merge, gdal_gdal_translate, gdal_gdaladdo, gdal_gdalbuildvrt, gdal_gdalinfo, gdal_gdalwarp, gdal_ogr2ogr, gdal_ogrinfo	Geospatial Data Abstraction Library tools are all dedicated to manipulate raster and vector geospatial data formats.						To update	https://www.gdal.org	Ecology	gdal	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/gdal	3.0.0			(0/8)	(0/8)	(8/8)
 interpolation			interpolation_run_idw_interpolation	Run IDW interpolation based on a .csv and .geojson file						To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation	1.0	r-getopt		(0/1)	(0/1)	(1/1)
+medenv			iabiodiv_smartbiodiv_med_environ	Retrieve environmental data from etopo, cmems and woa						To update	https://github.com/jeremyfix/medenv	Ecology, Data Source		ecology	https://github.com/jeremyfix/medenv	0.0.1	pandas		(0/1)	(0/1)	(0/1)
 obisindicators	45.0	4.0	obisindicators, obis_data	Compute biodiveristy indicators for marine data from obis						To update	https://github.com/Marie59/obisindicators	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators	0.0.2	r-base		(1/2)	(0/2)	(2/2)
 ocean			argo_getdata	Access, process, visualise oceanographic data for the Earth System						To update	https://github.com/Marie59/FE-ft-ESG/tree/main/argo	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean	0.1.15			(0/1)	(0/1)	(1/1)
 regionalgam			regionalgam_ab_index, regionalgam_autocor_acf, regionalgam_flight_curve, regionalgam_glmmpql, regionalgam_gls_adjusted, regionalgam_gls, regionalgam_plot_trend							To update	https://github.com/RetoSchmucki/regionalGAM	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam	1.5	r-mgcv		(0/7)	(0/7)	(7/7)
@@ -1279,14 +1283,14 @@ dropletutils	3934.0	126.0	dropletutils_empty_drops, dropletutils_read_10x	De-com
 garnett			garnett_check_markers, garnett_classify_cells, garnett_get_feature_genes, garnett_get_std_output, garnett_train_classifier, garnett_transform_markers, update_marker_file	De-composed Garnett functionality tools, see https://github.com/ebi-gene-expression-group/garnett-cli and r-garnett 0.2.8						To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_garnett	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	0.2.8	garnett-cli	0.0.5	(0/7)	(0/7)	(7/7)
 monocle3			monocle3_create, monocle3_diffExp, monocle3_learnGraph, monocle3_orderCells, monocle3_partition, monocle3_plotCells, monocle3_preprocess, monocle3_reduceDim, monocle3_topmarkers	De-composed monocle3 functionality tools, based on https://github.com/ebi-gene-expression-group/monocle-scripts and monocle3 0.1.2.						To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_monocle3	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	0.1.4	monocle3-cli	0.0.9	(9/9)	(0/9)	(9/9)
 sc3			sc3_calc_biology, sc3_calc_consens, sc3_calc_dists, sc3_calc_transfs, sc3_estimate_k, sc3_kmeans, sc3_prepare	De-composed SC3 functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-sc3-scripts and SC3 1.8.0.						To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_sc3	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	1.8.0	sc3-scripts	0.0.6	(0/7)	(0/7)	(7/7)
-scanpy			anndata_ops, scanpy_filter_cells, scanpy_filter_genes, scanpy_find_cluster, scanpy_find_markers, scanpy_find_variable_genes, scanpy_integrate_bbknn, scanpy_integrate_combat, scanpy_integrate_harmony, scanpy_integrate_mnn, scanpy_plot_scrublet, scanpy_multiplet_scrublet, scanpy_compute_graph, scanpy_normalise_data, scanpy_parameter_iterator, scanpy_plot_embed, scanpy_plot_trajectory, scanpy_read_10x, scanpy_regress_variable, scanpy_run_diffmap, scanpy_run_dpt, scanpy_run_fdg, scanpy_run_paga, scanpy_run_pca, scanpy_run_tsne, scanpy_run_umap, scanpy_scale_data	scanpy-scripts, command-line wrapper scripts around Scanpy.						To update	https://scanpy.readthedocs.io	Transcriptomics, Sequence Analysis, RNA	scanpy_scripts	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy	1.8.1	scanpy-scripts	1.1.6	(17/27)	(27/27)	(27/27)
+scanpy			anndata_ops, scanpy_filter_cells, scanpy_filter_genes, scanpy_find_cluster, scanpy_find_markers, scanpy_find_variable_genes, scanpy_integrate_bbknn, scanpy_integrate_combat, scanpy_integrate_harmony, scanpy_integrate_mnn, scanpy_plot_scrublet, scanpy_multiplet_scrublet, scanpy_compute_graph, scanpy_normalise_data, scanpy_parameter_iterator, scanpy_plot_embed, scanpy_plot_trajectory, scanpy_read_10x, scanpy_regress_variable, scanpy_run_diffmap, scanpy_run_dpt, scanpy_run_fdg, scanpy_run_paga, scanpy_run_pca, scanpy_run_tsne, scanpy_run_umap, scanpy_scale_data	scanpy-scripts, command-line wrapper scripts around Scanpy.						To update	https://scanpy.readthedocs.io	Transcriptomics, Sequence Analysis, RNA	scanpy_scripts	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy	1.8.1	scanpy-scripts	1.9.0	(17/27)	(27/27)	(27/27)
 scater			scater_calculate_cpm, scater_calculate_qc_metrics, scater_filter, scater_is_outlier, scater_normalize, scater_read_10x_results	De-composed Scater functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-scater-scripts and Scater 1.8.4.						To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_scater	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	1.10.0	scater-scripts	0.0.5	(0/6)	(1/6)	(6/6)
 sccaf			run_sccaf, sccaf_asses, sccaf_asses_merger, sccaf_regress_out	SCCAF: Single Cell Clustering Assessment Framework.						To update	https://github.com/sccaf/sccaf	Transcriptomics	SCCAF	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sccaf	0.0.9	sccaf	0.0.10	(0/4)	(0/4)	(4/4)
 sceasy			sceasy_convert	Convert scRNA data object between popular formats						To update		Transcriptomics	sceasy	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	0.0.5	r-sceasy	0.0.7	(1/1)	(0/1)	(1/1)
 scmap			scmap_get_std_output, scmap_index_cell, scmap_index_cluster, scmap_preprocess_sce, scmap_scmap_cell, scmap_scmap_cluster, scmap_select_features	De-composed scmap functionality tools, based on https://github.com/ebi-gene-expression-group/scmap-cli and scmap 1.6.0.						To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_scmap	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	1.6.3	scmap-cli	0.1.0	(0/7)	(0/7)	(7/7)
 scpred			scpred_get_feature_space, scpred_get_std_output, scpred_predict_labels, scpred_train_model	De-composed scPred functionality tools, see https://github.com/ebi-gene-expression-group/scpred-cli and r-scPred 1.0						To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_scpred	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	1.0.2	scpred-cli	0.1.0	(0/4)	(0/4)	(4/4)
 seurat	1543.0	66.0	seurat_convert, seurat_dim_plot, seurat_export_cellbrowser, seurat_filter_cells, seurat_find_clusters, seurat_find_markers, seurat_find_neighbours, seurat_find_variable_genes, seurat_normalise_data, seurat_read10x, seurat_run_pca, seurat_run_tsne, seurat_scale_data	De-composed Seurat functionality tools, based on https://github.com/ebi-gene-expression-group/r-seurat-scripts and Seurat 2.3.1						To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_seurat	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	0.3.0	seurat-scripts	4.0.0	(0/13)	(0/13)	(12/13)
-ucsc-cell-browser			ucsc_cell_browser	Python pipeline and Javascript scatter plot library for single-cell datasets						To update	https://cells.ucsc.edu/	Transcriptomics	ucsc_cell_browser	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/ucsc-cell-browser/.shed.yml	1.0.0+galaxy1	ucsc-cell-browser	1.2.4	(0/1)	(0/1)	(1/1)
+ucsc-cell-browser			ucsc_cell_browser	Python pipeline and Javascript scatter plot library for single-cell datasets						To update	https://cells.ucsc.edu/	Transcriptomics	ucsc_cell_browser	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/ucsc-cell-browser/.shed.yml	1.0.0+galaxy1	ucsc-cell-browser	1.2.5	(0/1)	(0/1)	(1/1)
 biotransformer			biotransformer	BioTransformer is a tool for prediction of small molecule metabolism in mammals.	biotransformer	BioTransformer	BioTransformer is a freely available web server that supports accurate, rapid and comprehensive in silico metabolism prediction.	Metabolic pathway prediction, PTM site prediction, Natural product identification	Small molecules, Endocrinology and metabolism, Metabolomics, Carbohydrates, NMR	Up-to-date	https://bitbucket.org/djoumbou/biotransformerjar/src/master/	Metabolomics	biotransformer	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer	3.0.20230403	biotransformer	3.0.20230403	(0/1)	(1/1)	(1/1)
 filter_compounds			filter_orgmet_anorg	Tool for filtering organometallics/anorganic compounds from a list of compounds.						To update	https://github.com/RECETOX/galaxytools/	Metabolomics	filter_compounds	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds	3.1.1	openbabel	2.3.90dev7d621d9	(0/1)	(0/1)	(0/1)
 matchms			matchms_add_key, matchms_convert, matchms_filtering, matchms_fingerprint_similarity, matchms_formatter, matchms_metadata_export, matchms_metadata_match, matchms_metadata_merge, matchms_networking, matchms_remove_key, matchms_spectral_similarity, matchms_split, matchms_subsetting	Searching, filtering and converting mass spectral libraries.	matchms	Matchms	Tool to import, process, clean, and compare mass spectrometry data.	Spectral library search, Format validation, Filtering	Metabolomics	To update	https://github.com/matchms/matchms	Metabolomics	matchms	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/matchms	0.24.0	matchms	0.24.2	(2/13)	(9/13)	(13/13)
@@ -1300,7 +1304,7 @@ recetox_msfinder			recetox_msfinder		recetox-msfinder	recetox-msfinder	This is a
 recetox_xmsannotator			recetox_xmsannotator_advanced		recetox-xmsannotator	recetox-xMSannotator	Annotation tool for untargeted LCMS1 data. Uses a database and adduct list for compound annotation and intensity networks, isotopic patterns and pathways for annotation scoring.	Expression profile pathway mapping, Structure comparison, Isotopic distributions calculation, Annotation		Up-to-date	https://github.com/RECETOX/recetox-xMSannotator	Metabolomics		recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator	0.10.0	r-recetox-xmsannotator	0.10.0	(0/1)	(1/1)	(1/1)
 rem_complex			rem_complex	Removes molecular coordination complexes.						To update	https://github.com/RECETOX/galaxytools	Metabolomics	rem_complex	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/rem_complex	1.0.0	pandas		(0/1)	(0/1)	(1/1)
 retip			retip_apply, retip_descriptors, retip_filter_rt, retip_train		retip	Retip	Retention Time Prediction for Compound Annotation in Untargeted Metabolomics.Retip is an R package for predicting Retention Time (RT) for small molecules in a high pressure liquid chromatography (HPLC) Mass Spectrometry analysis.Retip - Retention Time prediction for Metabolomics.Retip: Retention Time Prediction for Compound Annotation in Untargeted Metabolomics Paolo Bonini, Tobias Kind, Hiroshi Tsugawa, Dinesh Kumar Barupal, and Oliver Fiehn Analytical Chemistry 2020 92 (11), 7515-7522 DOI: 10.1021/acs.analchem.9b05765.	Retention time prediction, Spectrum calculation, Deisotoping, Formatting, Deposition	Metabolomics, Proteomics experiment, Machine learning, Cheminformatics, Chemistry	To update	https://github.com/PaoloBnn/Retip	Metabolomics		recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/retip	0.5.4			(0/4)	(0/4)	(0/4)
-riassigner	15.0	3.0	riassigner		riassigner	RIAssigner	RIAssigner is a python tool for retention index (RI) computation for GC-MS data.	Standardisation and normalisation	Metabolomics, Compound libraries and screening, Data submission, annotation and curation	Up-to-date	https://github.com/RECETOX/RIAssigner	Metabolomics		recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/riassigner	0.3.4	riassigner	0.3.4	(1/1)	(0/1)	(1/1)
+riassigner	15.0	3.0	riassigner		riassigner	RIAssigner	RIAssigner is a python tool for retention index (RI) computation for GC-MS data.	Standardisation and normalisation	Metabolomics, Compound libraries and screening, Data submission, annotation and curation	To update	https://github.com/RECETOX/RIAssigner	Metabolomics		recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/riassigner	0.3.4	riassigner	0.4.0	(1/1)	(0/1)	(1/1)
 rmassbank			rmassbank	RMassBank is an R package for processing tandem MS files and building of MassBank records.						To update	https://github.com/MassBank/RMassBank	Metabolomics	rmassbank	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/rmassbank	3.0.0	python		(0/1)	(1/1)	(1/1)
 spec2vec			spec2vec_similarity, spec2vec_training	Mass spectra similarity scoring using a trained Spec2Vec model.	spec2vec	Spec2Vec	Improved mass spectral similarity scoring through learning of structural relationships.Spec2vec is a novel spectral similarity score inspired by a natural language processing algorithm -- Word2Vec. Where Word2Vec learns relationships between words in sentences, spec2vec does so for mass fragments and neutral losses in MS/MS spectra. The spectral similarity score is based on spectral embeddings learnt from the fragmental relationships within a large set of spectral data.Analysis and benchmarking of mass spectra similarity measures using gnps data set.	Spectrum calculation, Spectral library search, Database search, Natural product identification	Proteomics experiment, Metabolomics, Natural language processing, Proteomics	Up-to-date	https://github.com/iomega/spec2vec	Metabolomics	spec2vec	recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/spec2vec	0.8.0	spec2vec	0.8.0	(0/2)	(0/2)	(0/2)
 waveica	6.0		waveica	Removal of batch effects for large-scale untargeted metabolomics data based on wavelet analysis.	waveica	WaveICA	Removal of batch effects for large-scale untargeted metabolomics data based on wavelet transform.	Standardisation and normalisation	Metabolomics	Up-to-date	https://github.com/RECETOX/WaveICA	Metabolomics		recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/waveica	0.2.0	r-recetox-waveica	0.2.0	(1/1)	(0/1)	(1/1)
@@ -1326,7 +1330,7 @@ measure_gastruloids			measureGastruloids	Get the ROI coordinates around the gast
 omero_clean_rois_tables			omero_clean_rois_tables	Remove all ROIs and all tables on OMERO associated to an omero object and recursively up and down						To update		Imaging	omero_clean_rois_tables	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_clean_rois_tables	20230623	fiji	20231211	(0/1)	(0/1)	(0/1)
 omero_get_children_ids			omero_get_children_ids	Get omero id of children of an omero object id						To update		Imaging	omero_get_children_ids	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_children_ids	0.1.0	omero-py	5.11.1	(0/1)	(0/1)	(0/1)
 omero_hyperstack_to_fluo_measurements_on_gastruloid			omero_hyperstack_to_fluo_measurements_on_gastruloid	Analyse Hyperstack on OMERO server to measure fluorescence levels						To update		Imaging	omero_hyperstack_to_fluo_measurements_on_gastruloid	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_fluo_measurements_on_gastruloid	20230809	fiji	20231211	(0/1)	(0/1)	(0/1)
-omero_hyperstack_to_gastruloid_measurements			omero_hyperstack_to_gastruloid_measurements	Analyse Hyperstack on OMERO server to segment gastruloid and compute measurements						To update		Imaging	omero_hyperstack_to_gastruloid_measurements	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_gastruloid_measurements	20231220	fiji	20231211	(0/1)	(0/1)	(0/1)
+omero_hyperstack_to_gastruloid_measurements			omero_hyperstack_to_gastruloid_measurements	Analyse Hyperstack on OMERO server to segment gastruloid and compute measurements						To update		Imaging	omero_hyperstack_to_gastruloid_measurements	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_hyperstack_to_gastruloid_measurements	20240214	fiji	20231211	(0/1)	(0/1)	(0/1)
 revertR2orientationInBam			revertR2orientationInBam	Revert the mapped orientation of R2 mates in a bam.						To update		SAM	revertr2orientationinbam	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/revertR2orientationInBam	0.0.2	samtools	1.19.2	(1/1)	(0/1)	(1/1)
 upload_roi_and_measures_to_omero			uploadROIandMeasuresToOMERO	Upload the ROI coordinates and the measurements to the omero server						To update		Imaging	upload_roi_and_measures_to_omero	lldelisle	https://github.com/lldelisle/tools-lldelisle/tree/master/tools/upload_roi_and_measures_to_omero	0.0.5	omero-py	5.11.1	(0/1)	(0/1)	(0/1)
 blast2go	1232.0	101.0	blast2go	Maps BLAST results to GO annotation terms						To update	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go	Ontology Manipulation, Sequence Analysis	blast2go	peterjc	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go	0.0.11	b2g4pipe		(0/1)	(0/1)	(0/1)
diff --git a/results/all_tools_wordcloud.png b/results/all_tools_wordcloud.png
index 86d269a5..5e516baf 100644
Binary files a/results/all_tools_wordcloud.png and b/results/all_tools_wordcloud.png differ
diff --git a/results/index.html b/results/index.html
index 3348bdbd..c4ed122b 100644
--- a/results/index.html
+++ b/results/index.html
@@ -3060,17 +3060,17 @@
     <tr>
       <td></td>
       <td>superdsm</td>
-      <td>0.1.3</td>
+      <td>0.2.0</td>
       <td>0.2.0</td>
       <td>superdsm</td>
-      <td>To update</td>
+      <td>Up-to-date</td>
       <td>superdsm</td>
       <td>SuperDSM</td>
       <td>Image analysis</td>
       <td></td>
       <td>Globally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy images</td>
       <td>SuperDSM is a globally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy images and beyond.</td>
-      <td>To update</td>
+      <td>Up-to-date</td>
       <td>https://github.com/bmcv</td>
       <td>Imaging</td>
       <td>superdsm</td>
@@ -3161,7 +3161,7 @@
       <td></td>
       <td>annotation_profiler</td>
       <td>1.0.0</td>
-      <td>0.10.0</td>
+      <td>0.11.0</td>
       <td>bx-python</td>
       <td>To update</td>
       <td></td>
@@ -3821,7 +3821,7 @@
       <td></td>
       <td>fasta_concatenate_by_species</td>
       <td>0.0.1</td>
-      <td>0.10.0</td>
+      <td>0.11.0</td>
       <td>bx-python</td>
       <td>To update</td>
       <td></td>
@@ -3921,7 +3921,7 @@
       <td></td>
       <td>featurecounter</td>
       <td>2.0.0</td>
-      <td>0.10.0</td>
+      <td>0.11.0</td>
       <td>bx-python</td>
       <td>To update</td>
       <td></td>
@@ -3981,7 +3981,7 @@
       <td></td>
       <td>getindelrates_3way</td>
       <td>1.0.0</td>
-      <td>0.10.0</td>
+      <td>0.11.0</td>
       <td>bx-python</td>
       <td>To update</td>
       <td></td>
@@ -4221,7 +4221,7 @@
       <td></td>
       <td>maf_cpg_filter</td>
       <td>1.0.0</td>
-      <td>0.10.0</td>
+      <td>0.11.0</td>
       <td>bx-python</td>
       <td>To update</td>
       <td></td>
@@ -4341,7 +4341,7 @@
       <td></td>
       <td>microsats_mutability</td>
       <td>1.1.0</td>
-      <td>0.10.0</td>
+      <td>0.11.0</td>
       <td>bx-python</td>
       <td>To update</td>
       <td></td>
@@ -4481,7 +4481,7 @@
       <td></td>
       <td>pileup_interval</td>
       <td>1.0.3</td>
-      <td>0.10.0</td>
+      <td>0.11.0</td>
       <td>bx-python</td>
       <td>To update</td>
       <td></td>
@@ -4561,7 +4561,7 @@
       <td></td>
       <td>quality_filter</td>
       <td>1.0.1</td>
-      <td>0.10.0</td>
+      <td>0.11.0</td>
       <td>bx-python</td>
       <td>To update</td>
       <td></td>
@@ -4881,7 +4881,7 @@
       <td></td>
       <td>substitutions</td>
       <td>1.0.1</td>
-      <td>0.10.0</td>
+      <td>0.11.0</td>
       <td>bx-python</td>
       <td>To update</td>
       <td></td>
@@ -5201,7 +5201,7 @@
       <td></td>
       <td>windowsplitter</td>
       <td>1.0.1</td>
-      <td>0.10.0</td>
+      <td>0.11.0</td>
       <td>bx-python</td>
       <td>To update</td>
       <td></td>
@@ -5241,7 +5241,7 @@
       <td></td>
       <td>basecoverage</td>
       <td>1.0.0</td>
-      <td>0.10.0</td>
+      <td>0.11.0</td>
       <td>bx-python</td>
       <td>To update</td>
       <td></td>
@@ -5261,7 +5261,7 @@
       <td></td>
       <td>cluster</td>
       <td>1.0.0</td>
-      <td>0.10.0</td>
+      <td>0.11.0</td>
       <td>bx-python</td>
       <td>To update</td>
       <td></td>
@@ -5281,7 +5281,7 @@
       <td></td>
       <td>complement</td>
       <td>1.0.0</td>
-      <td>0.10.0</td>
+      <td>0.11.0</td>
       <td>bx-python</td>
       <td>To update</td>
       <td></td>
@@ -5301,7 +5301,7 @@
       <td></td>
       <td>concat</td>
       <td>1.0.1</td>
-      <td>0.10.0</td>
+      <td>0.11.0</td>
       <td>bx-python</td>
       <td>To update</td>
       <td></td>
@@ -5321,7 +5321,7 @@
       <td></td>
       <td>coverage</td>
       <td>1.0.0</td>
-      <td>0.10.0</td>
+      <td>0.11.0</td>
       <td>bx-python</td>
       <td>To update</td>
       <td></td>
@@ -5341,7 +5341,7 @@
       <td></td>
       <td>flanking_features</td>
       <td>4.0.1</td>
-      <td>0.10.0</td>
+      <td>0.11.0</td>
       <td>bx-python</td>
       <td>To update</td>
       <td></td>
@@ -5361,7 +5361,7 @@
       <td></td>
       <td>get_flanks</td>
       <td>1.0.0</td>
-      <td>0.10.0</td>
+      <td>0.11.0</td>
       <td>bx-python</td>
       <td>To update</td>
       <td></td>
@@ -5381,7 +5381,7 @@
       <td></td>
       <td>intersect</td>
       <td>1.0.0</td>
-      <td>0.10.0</td>
+      <td>0.11.0</td>
       <td>bx-python</td>
       <td>To update</td>
       <td></td>
@@ -5401,7 +5401,7 @@
       <td></td>
       <td>join</td>
       <td>1.0.0</td>
-      <td>0.10.0</td>
+      <td>0.11.0</td>
       <td>bx-python</td>
       <td>To update</td>
       <td></td>
@@ -5421,7 +5421,7 @@
       <td></td>
       <td>merge</td>
       <td>1.0.0</td>
-      <td>0.10.0</td>
+      <td>0.11.0</td>
       <td>bx-python</td>
       <td>To update</td>
       <td></td>
@@ -5441,7 +5441,7 @@
       <td></td>
       <td>subtract</td>
       <td>1.0.0</td>
-      <td>0.10.0</td>
+      <td>0.11.0</td>
       <td>bx-python</td>
       <td>To update</td>
       <td></td>
@@ -5461,7 +5461,7 @@
       <td></td>
       <td>subtract_query</td>
       <td>0.1</td>
-      <td>0.10.0</td>
+      <td>0.11.0</td>
       <td>bx-python</td>
       <td>To update</td>
       <td></td>
@@ -6121,16 +6121,16 @@
       <td></td>
       <td>antismash</td>
       <td>6.1.1</td>
-      <td>6.1.1</td>
+      <td>7.1.0</td>
       <td>antismash</td>
-      <td>Up-to-date</td>
+      <td>To update</td>
       <td>antismash</td>
       <td>antiSMASH</td>
       <td>Sequence clustering, Gene prediction, Differential gene expression analysis</td>
       <td>Molecular interactions, pathways and networks, Gene and protein families</td>
       <td>Antismash allows the genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters</td>
       <td>Rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genomes. It integrates and cross-links with a large number of in silico secondary metabolite analysis tools that have been published earlier.</td>
-      <td>Up-to-date</td>
+      <td>To update</td>
       <td>https://antismash.secondarymetabolites.org</td>
       <td>Sequence Analysis</td>
       <td>antismash</td>
@@ -8201,16 +8201,16 @@
       <td></td>
       <td>infernal</td>
       <td>1.1.4</td>
-      <td>1.1.4</td>
+      <td>1.1.5</td>
       <td>infernal</td>
-      <td>Up-to-date</td>
+      <td>To update</td>
       <td>infernal</td>
       <td>Infernal</td>
       <td>Nucleic acid feature detection</td>
       <td>Sequence sites, features and motifs</td>
       <td>Infernal ("INFERence of RNA ALignment") is for searching DNA sequence databases for RNA structure and sequence similarities.</td>
       <td>Infernal ("INFERence of RNA ALignment") is for searching DNA sequence databases for RNA structure and sequence similarities. It is an implementation of a special case of profile stochastic context-free grammars called covariance models (CMs). A CM is like a sequence profile, but it scores a combination of sequence consensus and RNA secondary structure consensus, so in many cases, it is more capable of identifying RNA homologs that conserve their secondary structure more than their primary sequence.</td>
-      <td>Up-to-date</td>
+      <td>To update</td>
       <td>http://infernal.janelia.org/</td>
       <td>RNA</td>
       <td>infernal</td>
@@ -8957,6 +8957,26 @@
       <td>bgruening-util</td>
       <td>https://github.com/ColinIanKing/stress-ng</td>
     </tr>
+    <tr>
+      <td></td>
+      <td>tapscan</td>
+      <td>4.74+galaxy0</td>
+      <td>3.4</td>
+      <td>hmmer</td>
+      <td>To update</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Search for transcription associated proteins (TAPs)</td>
+      <td></td>
+      <td>To update</td>
+      <td>https://plantcode.cup.uni-freiburg.de/tapscan/</td>
+      <td>Proteomics</td>
+      <td>tapscan</td>
+      <td>bgruening</td>
+      <td>https://github.com/bgruening/galaxytools/tree/master/tools/tapscan</td>
+    </tr>
     <tr>
       <td></td>
       <td>add_line_to_file</td>
@@ -10924,12 +10944,12 @@
       <td>5.3</td>
       <td>cat</td>
       <td>To update</td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
+      <td>cat_bins</td>
+      <td>CAT and BAT</td>
+      <td>Taxonomic classification, Sequence assembly, Coding region prediction</td>
+      <td>Metagenomics, Metagenomic sequencing, Taxonomy, Sequence assembly</td>
       <td>Contig Annotation Tool (CAT)</td>
-      <td></td>
+      <td>Contig Annotation Tool (CAT) and Bin Annotation Tool (BAT) are pipelines for the taxonomic classification of long DNA sequences and metagenome assembled genomes (MAGs/bins) of both known and (highly) unknown microorganisms, as generated by contemporary metagenomics studies. The core algorithm of both programs involves gene calling, mapping of predicted ORFs against the nr protein database, and voting-based classification of the entire contig / MAG based on classification of the individual ORFs.</td>
       <td>To update</td>
       <td>https://github.com/dutilh/CAT</td>
       <td>Metagenomics</td>
@@ -11377,6 +11397,26 @@
       <td>iuc</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_remove_by_header</td>
     </tr>
+    <tr>
+      <td></td>
+      <td>compleasm</td>
+      <td>0.2.5</td>
+      <td>0.2.5</td>
+      <td>compleasm</td>
+      <td>Up-to-date</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Compleasm: a faster and more accurate reimplementation of BUSCO</td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/huangnengCSU/compleasm</td>
+      <td>Sequence Analysis</td>
+      <td>compleasm</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/compleasm/</td>
+    </tr>
     <tr>
       <td></td>
       <td>compose_text_param</td>
@@ -11880,17 +11920,17 @@
     <tr>
       <td></td>
       <td>dimet</td>
-      <td>0.1.4</td>
+      <td>0.2.1</td>
       <td>0.2.1</td>
       <td>dimet</td>
-      <td>To update</td>
+      <td>Up-to-date</td>
       <td></td>
       <td></td>
       <td></td>
       <td></td>
       <td>DIMet is a bioinformatics pipeline for differential analysis of isotopic targeted labeling data.</td>
       <td></td>
-      <td>To update</td>
+      <td>Up-to-date</td>
       <td>https://github.com/cbib/DIMet</td>
       <td>Metabolomics</td>
       <td></td>
@@ -12241,7 +12281,7 @@
       <td></td>
       <td>extract_genomic_dna</td>
       <td>3.0.3+galaxy2</td>
-      <td>0.10.0</td>
+      <td>0.11.0</td>
       <td>bx-python</td>
       <td>To update</td>
       <td></td>
@@ -12681,7 +12721,7 @@
       <td></td>
       <td>gatk4</td>
       <td>4.1.7.0</td>
-      <td>4.4.0.0</td>
+      <td>4.5.0.0</td>
       <td>gatk4</td>
       <td>To update</td>
       <td></td>
@@ -13441,7 +13481,7 @@
       <td></td>
       <td>hicstuff</td>
       <td>3.1.5</td>
-      <td>3.2.1</td>
+      <td>3.2.2</td>
       <td>hicstuff</td>
       <td>To update</td>
       <td></td>
@@ -13661,16 +13701,16 @@
       <td></td>
       <td>icescreen</td>
       <td>1.3.1</td>
-      <td>1.3.1</td>
+      <td>1.3.2</td>
       <td>icescreen</td>
-      <td>Up-to-date</td>
+      <td>To update</td>
       <td>icescreen</td>
       <td>ICEscreen</td>
       <td>Database search, Protein feature detection</td>
       <td>Mobile genetic elements, Sequence sites, features and motifs, Genomics, Molecular interactions, pathways and networks, Structural variation</td>
       <td>ICEscreen identifies Integrative Conjugative Elements (ICEs) and Integrative Mobilizable Elements (IMEs) in Bacillota genomes.</td>
       <td>A tool to detect Firmicute ICEs and IMEs, isolated or enclosed in composite structures.</td>
-      <td>Up-to-date</td>
+      <td>To update</td>
       <td>https://icescreen.migale.inrae.fr/</td>
       <td>Genome annotation</td>
       <td>icescreen</td>
@@ -13841,7 +13881,7 @@
       <td></td>
       <td>interval2maf</td>
       <td>1.0.1+galaxy1</td>
-      <td>0.10.0</td>
+      <td>0.11.0</td>
       <td>bx-python</td>
       <td>To update</td>
       <td>bx-python</td>
@@ -15421,7 +15461,7 @@
       <td></td>
       <td>multiqc</td>
       <td>1.11</td>
-      <td>1.19</td>
+      <td>1.20</td>
       <td>multiqc</td>
       <td>To update</td>
       <td>multiqc</td>
@@ -16520,9 +16560,9 @@
     <tr>
       <td></td>
       <td>pretext</td>
-      <td>0.1.9</td>
-      <td>0.1.9</td>
-      <td>pretextmap</td>
+      <td>0.0.6</td>
+      <td>0.0.6</td>
+      <td>pretextgraph</td>
       <td>Up-to-date</td>
       <td></td>
       <td></td>
@@ -17380,7 +17420,7 @@
     <tr>
       <td></td>
       <td>rpbasicdesign</td>
-      <td>1.1.1</td>
+      <td>1.2.2</td>
       <td></td>
       <td>rpbasicdesign</td>
       <td>To update</td>
@@ -17877,6 +17917,26 @@
       <td>iuc</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit</td>
     </tr>
+    <tr>
+      <td></td>
+      <td>seqprep</td>
+      <td>1.3.2</td>
+      <td>1.3.2</td>
+      <td>seqprep</td>
+      <td>Up-to-date</td>
+      <td>seqprep</td>
+      <td>SeqPrep</td>
+      <td>Nucleic acid design</td>
+      <td>Genomics, Sequence assembly, Sequencing, Probes and primers</td>
+      <td>Tool for merging paired-end Illumina reads and trimming adapters.</td>
+      <td>Strips adapters and optionally merges overlapping paired-end (or paired-end contamination in mate-pair libraries) illumina style reads.</td>
+      <td>Up-to-date</td>
+      <td>https://github.com/jstjohn/SeqPrep</td>
+      <td>Fastq Manipulation, Sequence Analysis</td>
+      <td>seqprep</td>
+      <td>iuc</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep</td>
+    </tr>
     <tr>
       <td></td>
       <td>seqsero2</td>
@@ -18384,12 +18444,12 @@
       <td>3.15.5</td>
       <td>spades</td>
       <td>Up-to-date</td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
+      <td>biosyntheticspades</td>
+      <td>biosyntheticSPAdes</td>
+      <td>Sequence assembly</td>
+      <td>Sequence assembly, Sequence sites, features and motifs, Genetic engineering</td>
       <td>SPAdes is an assembly toolkit containing various assembly pipelines. It implements the following 4 stages: assembly graph construction, k-bimer adjustment, construction of paired assembly graph and contig construction.</td>
-      <td></td>
+      <td>biosyntheticSPAdes - biosynthetic gene cluster assembly with paired-end reads</td>
       <td>Up-to-date</td>
       <td>https://github.com/ablab/spades</td>
       <td>Assembly, RNA, Metagenomics</td>
@@ -19141,7 +19201,7 @@
       <td></td>
       <td>tsebra</td>
       <td>1.1.2</td>
-      <td>1.1.2.2</td>
+      <td>1.1.2.3</td>
       <td>tsebra</td>
       <td>To update</td>
       <td></td>
@@ -19301,7 +19361,7 @@
       <td></td>
       <td>umi_tools</td>
       <td>1.1.2</td>
-      <td>1.1.4</td>
+      <td>1.1.5</td>
       <td>umi_tools</td>
       <td>To update</td>
       <td>umi-tools</td>
@@ -22341,7 +22401,7 @@
       <td></td>
       <td>peptideshaker</td>
       <td></td>
-      <td>4.3.5</td>
+      <td>4.3.6</td>
       <td>searchgui</td>
       <td>To update</td>
       <td></td>
@@ -22841,7 +22901,7 @@
       <td></td>
       <td>pyteomics</td>
       <td>4.4.1</td>
-      <td>4.7</td>
+      <td>4.7.1</td>
       <td>pyteomics</td>
       <td>To update</td>
       <td>pyteomics</td>
@@ -23721,7 +23781,7 @@
       <td></td>
       <td>gatk4</td>
       <td>4.1.7.0</td>
-      <td>4.4.0.0</td>
+      <td>4.5.0.0</td>
       <td>gatk4</td>
       <td>To update</td>
       <td></td>
@@ -24100,7 +24160,7 @@
     <tr>
       <td></td>
       <td>oases</td>
-      <td>1.3.0</td>
+      <td>1.4.0</td>
       <td>0.2.09</td>
       <td>oases</td>
       <td>To update</td>
@@ -24115,42 +24175,42 @@
       <td>Assembly, RNA</td>
       <td>oases</td>
       <td>artbio</td>
-      <td>https://github.com/ARTbio/tools-artbio/tree/master/tools/oases</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/oases</td>
     </tr>
     <tr>
       <td></td>
       <td>pathifier</td>
-      <td>1.0.2</td>
-      <td>1.3.2</td>
-      <td>r-optparse</td>
-      <td>To update</td>
+      <td>1.40.0</td>
+      <td>1.40.0</td>
+      <td>bioconductor-pathifier</td>
+      <td>Up-to-date</td>
       <td></td>
       <td></td>
       <td></td>
       <td></td>
       <td>pathifier</td>
       <td></td>
-      <td>To update</td>
+      <td>Up-to-date</td>
       <td>https://</td>
       <td>Transcriptomics, Statistics</td>
       <td>pathifier</td>
       <td>artbio</td>
-      <td>https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/pathifier</td>
     </tr>
     <tr>
       <td></td>
       <td>pindel</td>
-      <td>0.2.5b8+galaxy1</td>
+      <td>0.2.5b9</td>
       <td>0.2.5b9</td>
       <td>pindel</td>
-      <td>To update</td>
+      <td>Up-to-date</td>
       <td></td>
       <td></td>
       <td></td>
       <td></td>
       <td>Pindel detects genome-wide structural variation.</td>
       <td></td>
-      <td>To update</td>
+      <td>Up-to-date</td>
       <td>http://artbio.fr</td>
       <td>Variant Analysis</td>
       <td>pindel</td>
@@ -24697,6 +24757,26 @@
       <td>ecology</td>
       <td>https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation</td>
     </tr>
+    <tr>
+      <td></td>
+      <td>medenv</td>
+      <td>0.0.1</td>
+      <td></td>
+      <td>pandas</td>
+      <td>To update</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Retrieve environmental data from etopo, cmems and woa</td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/jeremyfix/medenv</td>
+      <td>Ecology, Data Source</td>
+      <td></td>
+      <td>ecology</td>
+      <td>https://github.com/jeremyfix/medenv</td>
+    </tr>
     <tr>
       <td></td>
       <td>obisindicators</td>
@@ -25401,7 +25481,7 @@
       <td></td>
       <td>scanpy</td>
       <td>1.8.1</td>
-      <td>1.1.6</td>
+      <td>1.9.0</td>
       <td>scanpy-scripts</td>
       <td>To update</td>
       <td></td>
@@ -25541,7 +25621,7 @@
       <td></td>
       <td>ucsc-cell-browser</td>
       <td>1.0.0+galaxy1</td>
-      <td>1.2.4</td>
+      <td>1.2.5</td>
       <td>ucsc-cell-browser</td>
       <td>To update</td>
       <td></td>
@@ -25821,16 +25901,16 @@
       <td></td>
       <td>riassigner</td>
       <td>0.3.4</td>
-      <td>0.3.4</td>
+      <td>0.4.0</td>
       <td>riassigner</td>
-      <td>Up-to-date</td>
+      <td>To update</td>
       <td>riassigner</td>
       <td>RIAssigner</td>
       <td>Standardisation and normalisation</td>
       <td>Metabolomics, Compound libraries and screening, Data submission, annotation and curation</td>
       <td></td>
       <td>RIAssigner is a python tool for retention index (RI) computation for GC-MS data.</td>
-      <td>Up-to-date</td>
+      <td>To update</td>
       <td>https://github.com/RECETOX/RIAssigner</td>
       <td>Metabolomics</td>
       <td></td>
@@ -26340,7 +26420,7 @@
     <tr>
       <td></td>
       <td>omero_hyperstack_to_gastruloid_measurements</td>
-      <td>20231220</td>
+      <td>20240214</td>
       <td>20231211</td>
       <td>fiji</td>
       <td>To update</td>