diff --git a/results/repositories02.list_tools.json b/results/repositories02.list_tools.json
index 9dd7a491..d46f4a6d 100644
--- a/results/repositories02.list_tools.json
+++ b/results/repositories02.list_tools.json
@@ -67,7 +67,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 591,
+        "Total tool usage (usegalaxy.eu)": 367167
     },
     {
         "Galaxy wrapper id": "annotation_profiler",
@@ -137,7 +139,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+        "Total tool usage (usegalaxy.eu)": 2
     },
     {
         "Galaxy wrapper id": "best_regression_subsets",
@@ -208,7 +212,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+        "Total tool usage (usegalaxy.eu)": 3
     },
     {
         "Galaxy wrapper id": "blat_coverage_report",
@@ -279,7 +285,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 0,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+        "Total tool usage (usegalaxy.eu)": 0
     },
     {
         "Galaxy wrapper id": "blat_mapping",
@@ -350,7 +358,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 0,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+        "Total tool usage (usegalaxy.eu)": 0
     },
     {
         "Galaxy wrapper id": "bowtie_wrappers",
@@ -420,7 +430,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 506,
+        "Total tool usage (usegalaxy.eu)": 22988
     },
     {
         "Galaxy wrapper id": "canonical_correlation_analysis",
@@ -490,7 +502,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 10,
+        "Total tool usage (usegalaxy.eu)": 74
     },
     {
         "Galaxy wrapper id": "categorize_elements_satisfying_criteria",
@@ -560,7 +574,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 1,
+        "Total tool usage (usegalaxy.eu)": 40
     },
     {
         "Galaxy wrapper id": "ccat",
@@ -630,7 +646,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 15,
+        "Total tool usage (usegalaxy.eu)": 173
     },
     {
         "Galaxy wrapper id": "cd_hit_dup",
@@ -701,7 +719,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 0,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+        "Total tool usage (usegalaxy.eu)": 0
     },
     {
         "Galaxy wrapper id": "change_case",
@@ -771,7 +791,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 931,
+        "Total tool usage (usegalaxy.eu)": 10965
     },
     {
         "Galaxy wrapper id": "compute_motif_frequencies_for_all_motifs",
@@ -842,7 +864,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 2,
+        "Total tool usage (usegalaxy.eu)": 94
     },
     {
         "Galaxy wrapper id": "compute_motifs_frequency",
@@ -913,7 +937,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+        "Total tool usage (usegalaxy.eu)": 65
     },
     {
         "Galaxy wrapper id": "compute_q_values",
@@ -983,7 +1009,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 0,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+        "Total tool usage (usegalaxy.eu)": 35
     },
     {
         "Galaxy wrapper id": "condense_characters",
@@ -1053,7 +1081,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 0,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+        "Total tool usage (usegalaxy.eu)": 0
     },
     {
         "Galaxy wrapper id": "convert_characters",
@@ -1123,7 +1153,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 475,
+        "Total tool usage (usegalaxy.eu)": 23829
     },
     {
         "Galaxy wrapper id": "convert_solid_color2nuc",
@@ -1193,7 +1225,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 0,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+        "Total tool usage (usegalaxy.eu)": 0
     },
     {
         "Galaxy wrapper id": "correlation",
@@ -1263,7 +1297,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 47,
+        "Total tool usage (usegalaxy.eu)": 837
     },
     {
         "Galaxy wrapper id": "count_gff_features",
@@ -1333,7 +1369,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 49,
+        "Total tool usage (usegalaxy.eu)": 271
     },
     {
         "Galaxy wrapper id": "ctd_batch",
@@ -1403,7 +1441,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 13,
+        "Total tool usage (usegalaxy.eu)": 203
     },
     {
         "Galaxy wrapper id": "cummerbund",
@@ -1474,7 +1514,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 31,
+        "Total tool usage (usegalaxy.eu)": 1782
     },
     {
         "Galaxy wrapper id": "cummerbund_to_tabular",
@@ -1545,7 +1587,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 13,
+        "Total tool usage (usegalaxy.eu)": 1204
     },
     {
         "Galaxy wrapper id": "cut_columns",
@@ -1615,7 +1659,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 5064,
+        "Total tool usage (usegalaxy.eu)": 1957541
     },
     {
         "Galaxy wrapper id": "delete_overlapping_indels",
@@ -1685,7 +1731,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 2,
+        "Total tool usage (usegalaxy.eu)": 39
     },
     {
         "Galaxy wrapper id": "dgidb_annotator",
@@ -1756,7 +1804,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 7,
+        "Total tool usage (usegalaxy.eu)": 65
     },
     {
         "Galaxy wrapper id": "divide_pg_snp",
@@ -1826,7 +1876,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+        "Total tool usage (usegalaxy.eu)": 32
     },
     {
         "Galaxy wrapper id": "draw_stacked_barplots",
@@ -1897,7 +1949,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 12,
+        "Total tool usage (usegalaxy.eu)": 173
     },
     {
         "Galaxy wrapper id": "dwt_cor_ava_perclass",
@@ -1967,7 +2021,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 0,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+        "Total tool usage (usegalaxy.eu)": 0
     },
     {
         "Galaxy wrapper id": "dwt_cor_avb_all",
@@ -2037,7 +2093,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 0,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+        "Total tool usage (usegalaxy.eu)": 0
     },
     {
         "Galaxy wrapper id": "dwt_ivc_all",
@@ -2107,7 +2165,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 0,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+        "Total tool usage (usegalaxy.eu)": 0
     },
     {
         "Galaxy wrapper id": "dwt_var_perclass",
@@ -2177,7 +2237,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 0,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+        "Total tool usage (usegalaxy.eu)": 0
     },
     {
         "Galaxy wrapper id": "dwt_var_perfeature",
@@ -2247,7 +2309,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+        "Total tool usage (usegalaxy.eu)": 36
     },
     {
         "Galaxy wrapper id": "express",
@@ -2317,7 +2381,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 12,
+        "Total tool usage (usegalaxy.eu)": 325
     },
     {
         "Galaxy wrapper id": "fasta_compute_length",
@@ -2387,7 +2453,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 380,
+        "Total tool usage (usegalaxy.eu)": 7758
     },
     {
         "Galaxy wrapper id": "fasta_concatenate_by_species",
@@ -2457,7 +2525,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 88,
+        "Total tool usage (usegalaxy.eu)": 35793
     },
     {
         "Galaxy wrapper id": "fasta_filter_by_length",
@@ -2527,7 +2597,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 350,
+        "Total tool usage (usegalaxy.eu)": 48649
     },
     {
         "Galaxy wrapper id": "fasta_to_tabular",
@@ -2597,7 +2669,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 622,
+        "Total tool usage (usegalaxy.eu)": 105935
     },
     {
         "Galaxy wrapper id": "fastq_trimmer_by_quality",
@@ -2667,7 +2741,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 459,
+        "Total tool usage (usegalaxy.eu)": 5676
     },
     {
         "Galaxy wrapper id": "fastqsolexa_to_fasta_qual",
@@ -2738,7 +2814,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 0,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+        "Total tool usage (usegalaxy.eu)": 0
     },
     {
         "Galaxy wrapper id": "featurecounter",
@@ -2809,7 +2887,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 6,
+        "Total tool usage (usegalaxy.eu)": 22385
     },
     {
         "Galaxy wrapper id": "filter_transcripts_via_tracking",
@@ -2879,7 +2959,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 1,
+        "Total tool usage (usegalaxy.eu)": 20
     },
     {
         "Galaxy wrapper id": "generate_pc_lda_matrix",
@@ -2949,7 +3031,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 12,
+        "Total tool usage (usegalaxy.eu)": 119
     },
     {
         "Galaxy wrapper id": "getindelrates_3way",
@@ -3020,7 +3104,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 0,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+        "Total tool usage (usegalaxy.eu)": 0
     },
     {
         "Galaxy wrapper id": "getindels_2way",
@@ -3091,7 +3177,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 0,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+        "Total tool usage (usegalaxy.eu)": 0
     },
     {
         "Galaxy wrapper id": "gmaj",
@@ -3161,7 +3249,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 4,
+        "Total tool usage (usegalaxy.eu)": 11
     },
     {
         "Galaxy wrapper id": "hisat",
@@ -3231,7 +3321,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 0,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+        "Total tool usage (usegalaxy.eu)": 228
     },
     {
         "Galaxy wrapper id": "histogram",
@@ -3302,7 +3394,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 242,
+        "Total tool usage (usegalaxy.eu)": 4350
     },
     {
         "Galaxy wrapper id": "indels_3way",
@@ -3372,7 +3466,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+        "Total tool usage (usegalaxy.eu)": 22
     },
     {
         "Galaxy wrapper id": "kernel_canonical_correlation_analysis",
@@ -3442,7 +3538,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 2,
+        "Total tool usage (usegalaxy.eu)": 69
     },
     {
         "Galaxy wrapper id": "kernel_principal_component_analysis",
@@ -3512,7 +3610,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 13,
+        "Total tool usage (usegalaxy.eu)": 156
     },
     {
         "Galaxy wrapper id": "lastz_paired_reads",
@@ -3582,7 +3682,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 1,
+        "Total tool usage (usegalaxy.eu)": 9
     },
     {
         "Galaxy wrapper id": "lda_analysis",
@@ -3653,7 +3755,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 18,
+        "Total tool usage (usegalaxy.eu)": 148
     },
     {
         "Galaxy wrapper id": "linear_regression",
@@ -3723,7 +3827,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 0,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+        "Total tool usage (usegalaxy.eu)": 0
     },
     {
         "Galaxy wrapper id": "logistic_regression_vif",
@@ -3795,7 +3901,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 0,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+        "Total tool usage (usegalaxy.eu)": 0
     },
     {
         "Galaxy wrapper id": "maf_cpg_filter",
@@ -3866,7 +3974,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 0,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+        "Total tool usage (usegalaxy.eu)": 0
     },
     {
         "Galaxy wrapper id": "mapping_to_ucsc",
@@ -3938,7 +4048,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 0,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+        "Total tool usage (usegalaxy.eu)": 0
     },
     {
         "Galaxy wrapper id": "megablast_xml_parser",
@@ -4009,7 +4121,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 36,
+        "Total tool usage (usegalaxy.eu)": 338
     },
     {
         "Galaxy wrapper id": "merge_cols",
@@ -4079,7 +4193,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 542,
+        "Total tool usage (usegalaxy.eu)": 28593
     },
     {
         "Galaxy wrapper id": "microsatellite_birthdeath",
@@ -4149,7 +4265,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 0,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+        "Total tool usage (usegalaxy.eu)": 0
     },
     {
         "Galaxy wrapper id": "microsats_alignment_level",
@@ -4220,7 +4338,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 0,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+        "Total tool usage (usegalaxy.eu)": 0
     },
     {
         "Galaxy wrapper id": "microsats_mutability",
@@ -4291,7 +4411,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 0,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+        "Total tool usage (usegalaxy.eu)": 0
     },
     {
         "Galaxy wrapper id": "mine",
@@ -4361,7 +4483,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 2,
+        "Total tool usage (usegalaxy.eu)": 11
     },
     {
         "Galaxy wrapper id": "multispecies_orthologous_microsats",
@@ -4432,7 +4556,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 0,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+        "Total tool usage (usegalaxy.eu)": 0
     },
     {
         "Galaxy wrapper id": "mutate_snp_codon",
@@ -4502,7 +4628,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+        "Total tool usage (usegalaxy.eu)": 47
     },
     {
         "Galaxy wrapper id": "partialr_square",
@@ -4572,7 +4700,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 0,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+        "Total tool usage (usegalaxy.eu)": 0
     },
     {
         "Galaxy wrapper id": "pearson_correlation",
@@ -4642,7 +4772,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 0,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+        "Total tool usage (usegalaxy.eu)": 0
     },
     {
         "Galaxy wrapper id": "pgsnp2gd_snp",
@@ -4712,7 +4844,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 0,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+        "Total tool usage (usegalaxy.eu)": 0
     },
     {
         "Galaxy wrapper id": "pileup_interval",
@@ -4782,7 +4916,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 15,
+        "Total tool usage (usegalaxy.eu)": 632
     },
     {
         "Galaxy wrapper id": "pileup_parser",
@@ -4852,7 +4988,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 169,
+        "Total tool usage (usegalaxy.eu)": 3158
     },
     {
         "Galaxy wrapper id": "plot_from_lda",
@@ -4923,7 +5061,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 9,
+        "Total tool usage (usegalaxy.eu)": 73
     },
     {
         "Galaxy wrapper id": "principal_component_analysis",
@@ -4993,7 +5133,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 88,
+        "Total tool usage (usegalaxy.eu)": 9989
     },
     {
         "Galaxy wrapper id": "quality_filter",
@@ -5064,7 +5206,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 0,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+        "Total tool usage (usegalaxy.eu)": 0
     },
     {
         "Galaxy wrapper id": "rcve",
@@ -5135,7 +5279,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 0,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+        "Total tool usage (usegalaxy.eu)": 0
     },
     {
         "Galaxy wrapper id": "remove_beginning",
@@ -5205,7 +5351,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 1409,
+        "Total tool usage (usegalaxy.eu)": 137310
     },
     {
         "Galaxy wrapper id": "rmap",
@@ -5275,7 +5423,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 0,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+        "Total tool usage (usegalaxy.eu)": 0
     },
     {
         "Galaxy wrapper id": "rmapq",
@@ -5345,7 +5495,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 0,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+        "Total tool usage (usegalaxy.eu)": 0
     },
     {
         "Galaxy wrapper id": "sam2interval",
@@ -5415,7 +5567,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 20,
+        "Total tool usage (usegalaxy.eu)": 1189
     },
     {
         "Galaxy wrapper id": "sam_bitwise_flag_filter",
@@ -5485,7 +5639,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 1,
+        "Total tool usage (usegalaxy.eu)": 278
     },
     {
         "Galaxy wrapper id": "scatterplot",
@@ -5556,7 +5712,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 61,
+        "Total tool usage (usegalaxy.eu)": 1677
     },
     {
         "Galaxy wrapper id": "short_reads_figure_high_quality_length",
@@ -5627,7 +5785,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 0,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+        "Total tool usage (usegalaxy.eu)": 0
     },
     {
         "Galaxy wrapper id": "short_reads_figure_score",
@@ -5698,7 +5858,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 13,
+        "Total tool usage (usegalaxy.eu)": 163
     },
     {
         "Galaxy wrapper id": "short_reads_trim_seq",
@@ -5768,7 +5930,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 21,
+        "Total tool usage (usegalaxy.eu)": 220
     },
     {
         "Galaxy wrapper id": "show_beginning",
@@ -5838,7 +6002,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 704,
+        "Total tool usage (usegalaxy.eu)": 32112
     },
     {
         "Galaxy wrapper id": "show_tail",
@@ -5908,7 +6074,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 128,
+        "Total tool usage (usegalaxy.eu)": 2513
     },
     {
         "Galaxy wrapper id": "sicer",
@@ -5978,7 +6146,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 5,
+        "Total tool usage (usegalaxy.eu)": 374
     },
     {
         "Galaxy wrapper id": "split_paired_reads",
@@ -6048,7 +6218,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 0,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+        "Total tool usage (usegalaxy.eu)": 0
     },
     {
         "Galaxy wrapper id": "substitution_rates",
@@ -6119,7 +6291,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 0,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+        "Total tool usage (usegalaxy.eu)": 0
     },
     {
         "Galaxy wrapper id": "substitutions",
@@ -6190,7 +6364,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 0,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+        "Total tool usage (usegalaxy.eu)": 0
     },
     {
         "Galaxy wrapper id": "t_test_two_samples",
@@ -6260,7 +6436,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 6,
+        "Total tool usage (usegalaxy.eu)": 210
     },
     {
         "Galaxy wrapper id": "table_annovar",
@@ -6330,7 +6508,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 0,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+        "Total tool usage (usegalaxy.eu)": 0
     },
     {
         "Galaxy wrapper id": "tabular_to_fasta",
@@ -6400,7 +6580,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 601,
+        "Total tool usage (usegalaxy.eu)": 319334
     },
     {
         "Galaxy wrapper id": "tophat",
@@ -6471,7 +6653,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 0,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+        "Total tool usage (usegalaxy.eu)": 1
     },
     {
         "Galaxy wrapper id": "tophat2",
@@ -6542,7 +6726,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 312,
+        "Total tool usage (usegalaxy.eu)": 24167
     },
     {
         "Galaxy wrapper id": "tophat_fusion_post",
@@ -6612,7 +6798,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 15,
+        "Total tool usage (usegalaxy.eu)": 216
     },
     {
         "Galaxy wrapper id": "trimmer",
@@ -6682,7 +6870,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 188,
+        "Total tool usage (usegalaxy.eu)": 6058
     },
     {
         "Galaxy wrapper id": "ucsc_custom_track",
@@ -6752,7 +6942,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 45,
+        "Total tool usage (usegalaxy.eu)": 394
     },
     {
         "Galaxy wrapper id": "varscan_version_2",
@@ -6822,7 +7014,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 246,
+        "Total tool usage (usegalaxy.eu)": 5191
     },
     {
         "Galaxy wrapper id": "vcf2pgsnp",
@@ -6892,7 +7086,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 15,
+        "Total tool usage (usegalaxy.eu)": 206
     },
     {
         "Galaxy wrapper id": "vcf_annotate",
@@ -6962,7 +7158,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 0,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+        "Total tool usage (usegalaxy.eu)": 1
     },
     {
         "Galaxy wrapper id": "vcf_extract",
@@ -7032,7 +7230,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 0,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+        "Total tool usage (usegalaxy.eu)": 0
     },
     {
         "Galaxy wrapper id": "vcf_filter",
@@ -7102,7 +7302,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 63,
+        "Total tool usage (usegalaxy.eu)": 388
     },
     {
         "Galaxy wrapper id": "vcf_intersect",
@@ -7172,7 +7374,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 0,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+        "Total tool usage (usegalaxy.eu)": 19
     },
     {
         "Galaxy wrapper id": "weightedaverage",
@@ -7243,7 +7447,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 0,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+        "Total tool usage (usegalaxy.eu)": 0
     },
     {
         "Galaxy wrapper id": "windowsplitter",
@@ -7314,7 +7520,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 0,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+        "Total tool usage (usegalaxy.eu)": 11
     },
     {
         "Galaxy wrapper id": "xy_plot",
@@ -7385,7 +7593,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 344,
+        "Total tool usage (usegalaxy.eu)": 5892
     },
     {
         "Galaxy wrapper id": "basecoverage",
@@ -7455,7 +7665,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 2,
+        "Total tool usage (usegalaxy.eu)": 308
     },
     {
         "Galaxy wrapper id": "cluster",
@@ -7525,7 +7737,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 1,
+        "Total tool usage (usegalaxy.eu)": 801
     },
     {
         "Galaxy wrapper id": "complement",
@@ -7595,7 +7809,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 1,
+        "Total tool usage (usegalaxy.eu)": 233
     },
     {
         "Galaxy wrapper id": "concat",
@@ -7665,7 +7881,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 309,
+        "Total tool usage (usegalaxy.eu)": 564900
     },
     {
         "Galaxy wrapper id": "coverage",
@@ -7735,7 +7953,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 17,
+        "Total tool usage (usegalaxy.eu)": 1502
     },
     {
         "Galaxy wrapper id": "flanking_features",
@@ -7805,7 +8025,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 20,
+        "Total tool usage (usegalaxy.eu)": 671
     },
     {
         "Galaxy wrapper id": "get_flanks",
@@ -7875,7 +8097,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 555,
+        "Total tool usage (usegalaxy.eu)": 324598
     },
     {
         "Galaxy wrapper id": "intersect",
@@ -7945,7 +8169,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 1003,
+        "Total tool usage (usegalaxy.eu)": 348449
     },
     {
         "Galaxy wrapper id": "join",
@@ -8015,7 +8241,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 284,
+        "Total tool usage (usegalaxy.eu)": 329556
     },
     {
         "Galaxy wrapper id": "merge",
@@ -8085,7 +8313,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 193,
+        "Total tool usage (usegalaxy.eu)": 563676
     },
     {
         "Galaxy wrapper id": "subtract",
@@ -8155,7 +8385,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 182,
+        "Total tool usage (usegalaxy.eu)": 564229
     },
     {
         "Galaxy wrapper id": "subtract_query",
@@ -8225,7 +8457,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 55,
+        "Total tool usage (usegalaxy.eu)": 1019
     },
     {
         "Galaxy wrapper id": "tables_arithmetic_operations",
@@ -8295,7 +8529,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 14,
+        "Total tool usage (usegalaxy.eu)": 2207
     },
     {
         "Galaxy wrapper id": "hgv_fundo",
@@ -8365,7 +8601,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+        "Total tool usage (usegalaxy.eu)": 0
     },
     {
         "Galaxy wrapper id": "hgv_hilbertvis",
@@ -8436,7 +8674,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+        "Total tool usage (usegalaxy.eu)": 0
     },
     {
         "Galaxy wrapper id": "snpfreq",
@@ -8507,7 +8747,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 7,
+        "Total tool usage (usegalaxy.eu)": 37
     },
     {
         "Galaxy wrapper id": "find_diag_hits",
@@ -8577,7 +8819,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 5,
+        "Total tool usage (usegalaxy.eu)": 69
     },
     {
         "Galaxy wrapper id": "gi2taxonomy",
@@ -8659,7 +8903,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 27,
+        "Total tool usage (usegalaxy.eu)": 660
     },
     {
         "Galaxy wrapper id": "kraken2tax",
@@ -8729,7 +8975,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 481,
+        "Total tool usage (usegalaxy.eu)": 14683
     },
     {
         "Galaxy wrapper id": "lca_wrapper",
@@ -8799,7 +9047,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 2,
+        "Total tool usage (usegalaxy.eu)": 137
     },
     {
         "Galaxy wrapper id": "poisson2test",
@@ -8870,7 +9120,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 6,
+        "Total tool usage (usegalaxy.eu)": 116
     },
     {
         "Galaxy wrapper id": "t2ps",
@@ -8950,7 +9202,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 31,
+        "Total tool usage (usegalaxy.eu)": 457
     },
     {
         "Galaxy wrapper id": "t2t_report",
@@ -9020,7 +9274,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 26,
+        "Total tool usage (usegalaxy.eu)": 947
     },
     {
         "Galaxy wrapper id": "vcftools_annotate",
@@ -9090,7 +9346,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 24,
+        "Total tool usage (usegalaxy.eu)": 171
     },
     {
         "Galaxy wrapper id": "vcftools_compare",
@@ -9160,7 +9418,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 34,
+        "Total tool usage (usegalaxy.eu)": 531
     },
     {
         "Galaxy wrapper id": "vcftools_consensus",
@@ -9230,7 +9490,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 0,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+        "Total tool usage (usegalaxy.eu)": 0
     },
     {
         "Galaxy wrapper id": "vcftools_isec",
@@ -9300,7 +9562,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 35,
+        "Total tool usage (usegalaxy.eu)": 498
     },
     {
         "Galaxy wrapper id": "vcftools_merge",
@@ -9370,7 +9634,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 68,
+        "Total tool usage (usegalaxy.eu)": 953
     },
     {
         "Galaxy wrapper id": "vcftools_slice",
@@ -9440,7 +9706,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 24,
+        "Total tool usage (usegalaxy.eu)": 411
     },
     {
         "Galaxy wrapper id": "vcftools_subset",
@@ -9510,7 +9778,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 17,
+        "Total tool usage (usegalaxy.eu)": 137
     },
     {
         "Galaxy wrapper id": "10x_bamtofastq",
@@ -9580,7 +9850,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 46,
+        "Total tool usage (usegalaxy.eu)": 228
     },
     {
         "Galaxy wrapper id": "AggregateAlignments",
@@ -9650,7 +9922,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 6,
+        "Total tool usage (usegalaxy.eu)": 116
     },
     {
         "Galaxy wrapper id": "AlignCluster",
@@ -9720,7 +9994,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 0,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 10,
+        "Total tool usage (usegalaxy.eu)": 3060
     },
     {
         "Galaxy wrapper id": "CMFinder",
@@ -9790,7 +10066,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 14,
+        "Total tool usage (usegalaxy.eu)": 45191
     },
     {
         "Galaxy wrapper id": "CollectResults",
@@ -9860,7 +10138,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 14,
+        "Total tool usage (usegalaxy.eu)": 1961
     },
     {
         "Galaxy wrapper id": "CollectResultsNoAlign",
@@ -9930,7 +10210,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+        "Total tool usage (usegalaxy.eu)": 108
     },
     {
         "Galaxy wrapper id": "GSPAN",
@@ -10000,7 +10282,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 4,
+        "Total tool usage (usegalaxy.eu)": 133
     },
     {
         "Galaxy wrapper id": "LocARNAGraphClust",
@@ -10070,7 +10354,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 13,
+        "Total tool usage (usegalaxy.eu)": 45325
     },
     {
         "Galaxy wrapper id": "NSPDK",
@@ -10141,7 +10427,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 2,
-        "Tools available on UseGalaxy.no": 2
+        "Tools available on UseGalaxy.no": 2,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 28,
+        "Total tool usage (usegalaxy.eu)": 62388
     },
     {
         "Galaxy wrapper id": "Plotting",
@@ -10211,7 +10499,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 3,
+        "Total tool usage (usegalaxy.eu)": 68
     },
     {
         "Galaxy wrapper id": "PrepareForMlocarna",
@@ -10281,7 +10571,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 15,
+        "Total tool usage (usegalaxy.eu)": 1932
     },
     {
         "Galaxy wrapper id": "Preprocessing",
@@ -10351,7 +10643,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 18,
+        "Total tool usage (usegalaxy.eu)": 1758
     },
     {
         "Galaxy wrapper id": "Structure_GSPAN",
@@ -10421,7 +10715,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 16,
+        "Total tool usage (usegalaxy.eu)": 2925
     },
     {
         "Galaxy wrapper id": "agat",
@@ -10505,7 +10801,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 42,
+        "Total tool usage (usegalaxy.eu)": 481
     },
     {
         "Galaxy wrapper id": "antismash",
@@ -10591,7 +10889,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 279,
+        "Total tool usage (usegalaxy.eu)": 14596
     },
     {
         "Galaxy wrapper id": "atactk_trim_adapters",
@@ -10661,7 +10961,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 26,
+        "Total tool usage (usegalaxy.eu)": 257
     },
     {
         "Galaxy wrapper id": "augustus",
@@ -10731,7 +11033,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 516,
+        "Total tool usage (usegalaxy.eu)": 8864
     },
     {
         "Galaxy wrapper id": "bamhash",
@@ -10801,7 +11105,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 15,
+        "Total tool usage (usegalaxy.eu)": 169
     },
     {
         "Galaxy wrapper id": "barcode_collapse",
@@ -10872,7 +11178,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 0,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+        "Total tool usage (usegalaxy.eu)": 0
     },
     {
         "Galaxy wrapper id": "bigwig_to_bedgraph",
@@ -10942,7 +11250,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 200,
+        "Total tool usage (usegalaxy.eu)": 5749
     },
     {
         "Galaxy wrapper id": "biomodelsML",
@@ -11013,7 +11323,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 0,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+        "Total tool usage (usegalaxy.eu)": 13
     },
     {
         "Galaxy wrapper id": "bionano",
@@ -11083,7 +11395,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 112,
+        "Total tool usage (usegalaxy.eu)": 531
     },
     {
         "Galaxy wrapper id": "bismark",
@@ -11157,7 +11471,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 4,
         "Tools available on UseGalaxy.cz": 4,
-        "Tools available on UseGalaxy.no": 4
+        "Tools available on UseGalaxy.no": 4,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 332,
+        "Total tool usage (usegalaxy.eu)": 12876
     },
     {
         "Galaxy wrapper id": "blobtoolkit",
@@ -11228,7 +11544,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 21,
+        "Total tool usage (usegalaxy.eu)": 685
     },
     {
         "Galaxy wrapper id": "blockbuster",
@@ -11299,7 +11617,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 34,
+        "Total tool usage (usegalaxy.eu)": 3009
     },
     {
         "Galaxy wrapper id": "canu",
@@ -11377,7 +11697,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 533,
+        "Total tool usage (usegalaxy.eu)": 13021
     },
     {
         "Galaxy wrapper id": "cellpose",
@@ -11447,7 +11769,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 0,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+        "Total tool usage (usegalaxy.eu)": 0
     },
     {
         "Galaxy wrapper id": "cellprofiler",
@@ -11557,7 +11881,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 19,
         "Tools available on UseGalaxy.cz": 23,
-        "Tools available on UseGalaxy.no": 19
+        "Tools available on UseGalaxy.no": 19,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 178,
+        "Total tool usage (usegalaxy.eu)": 4614
     },
     {
         "Galaxy wrapper id": "cellprofiler_v4",
@@ -11627,7 +11953,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 8,
+        "Total tool usage (usegalaxy.eu)": 43
     },
     {
         "Galaxy wrapper id": "chipseeker",
@@ -11698,7 +12026,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 418,
+        "Total tool usage (usegalaxy.eu)": 15690
     },
     {
         "Galaxy wrapper id": "circexplorer",
@@ -11769,7 +12099,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 8,
+        "Total tool usage (usegalaxy.eu)": 251
     },
     {
         "Galaxy wrapper id": "combine_metaphlan_humann",
@@ -11851,7 +12183,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 9,
+        "Total tool usage (usegalaxy.eu)": 147
     },
     {
         "Galaxy wrapper id": "compare_humann2_output",
@@ -11933,7 +12267,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 10,
+        "Total tool usage (usegalaxy.eu)": 332
     },
     {
         "Galaxy wrapper id": "cpat",
@@ -12003,7 +12339,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 21,
+        "Total tool usage (usegalaxy.eu)": 134
     },
     {
         "Galaxy wrapper id": "crt",
@@ -12073,7 +12411,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 74,
+        "Total tool usage (usegalaxy.eu)": 3389
     },
     {
         "Galaxy wrapper id": "diff",
@@ -12143,7 +12483,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 30,
+        "Total tool usage (usegalaxy.eu)": 235
     },
     {
         "Galaxy wrapper id": "diffbind",
@@ -12211,7 +12553,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 0,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+        "Total tool usage (usegalaxy.eu)": 0
     },
     {
         "Galaxy wrapper id": "ear",
@@ -12282,7 +12626,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 0,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+        "Total tool usage (usegalaxy.eu)": 0
     },
     {
         "Galaxy wrapper id": "edta",
@@ -12374,7 +12720,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 58,
+        "Total tool usage (usegalaxy.eu)": 484
     },
     {
         "Galaxy wrapper id": "epicseg",
@@ -12444,7 +12792,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 5,
+        "Total tool usage (usegalaxy.eu)": 245
     },
     {
         "Galaxy wrapper id": "fastq_info",
@@ -12514,7 +12864,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 679,
+        "Total tool usage (usegalaxy.eu)": 5765
     },
     {
         "Galaxy wrapper id": "file_manipulation",
@@ -12584,7 +12936,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 176,
+        "Total tool usage (usegalaxy.eu)": 8496
     },
     {
         "Galaxy wrapper id": "find_subsequences",
@@ -12652,7 +13006,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 31,
+        "Total tool usage (usegalaxy.eu)": 763
     },
     {
         "Galaxy wrapper id": "flye",
@@ -12743,7 +13099,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 1499,
+        "Total tool usage (usegalaxy.eu)": 20904
     },
     {
         "Galaxy wrapper id": "footprint",
@@ -12813,7 +13171,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+        "Total tool usage (usegalaxy.eu)": 57
     },
     {
         "Galaxy wrapper id": "format_cd_hit_output",
@@ -12883,7 +13243,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 20,
+        "Total tool usage (usegalaxy.eu)": 166
     },
     {
         "Galaxy wrapper id": "format_metaphlan2_output",
@@ -12965,7 +13327,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 166,
+        "Total tool usage (usegalaxy.eu)": 5588
     },
     {
         "Galaxy wrapper id": "gfastats",
@@ -13045,7 +13409,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 418,
+        "Total tool usage (usegalaxy.eu)": 8159
     },
     {
         "Galaxy wrapper id": "glimmer_hmm",
@@ -13113,7 +13479,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 0,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+        "Total tool usage (usegalaxy.eu)": 0
     },
     {
         "Galaxy wrapper id": "gotohscan",
@@ -13183,7 +13551,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 1,
+        "Total tool usage (usegalaxy.eu)": 71
     },
     {
         "Galaxy wrapper id": "graph_converter",
@@ -13253,7 +13623,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 0,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+        "Total tool usage (usegalaxy.eu)": 0
     },
     {
         "Galaxy wrapper id": "graphclust",
@@ -13323,7 +13695,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 0,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+        "Total tool usage (usegalaxy.eu)": 6
     },
     {
         "Galaxy wrapper id": "graphmap",
@@ -13412,7 +13786,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 2,
         "Tools available on UseGalaxy.cz": 2,
-        "Tools available on UseGalaxy.no": 2
+        "Tools available on UseGalaxy.no": 2,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 136,
+        "Total tool usage (usegalaxy.eu)": 6651
     },
     {
         "Galaxy wrapper id": "hclust2",
@@ -13482,7 +13858,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 0,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+        "Total tool usage (usegalaxy.eu)": 0
     },
     {
         "Galaxy wrapper id": "hictk",
@@ -13553,7 +13931,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 0,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+        "Total tool usage (usegalaxy.eu)": 0
     },
     {
         "Galaxy wrapper id": "hicup",
@@ -13629,7 +14009,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 7,
-        "Tools available on UseGalaxy.no": 6
+        "Tools available on UseGalaxy.no": 6,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 76,
+        "Total tool usage (usegalaxy.eu)": 921
     },
     {
         "Galaxy wrapper id": "hifiasm",
@@ -13699,7 +14081,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 297,
+        "Total tool usage (usegalaxy.eu)": 1410
     },
     {
         "Galaxy wrapper id": "homer",
@@ -13767,7 +14151,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 0,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+        "Total tool usage (usegalaxy.eu)": 0
     },
     {
         "Galaxy wrapper id": "illumina_methylation_analyser",
@@ -13837,7 +14223,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 0,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+        "Total tool usage (usegalaxy.eu)": 0
     },
     {
         "Galaxy wrapper id": "bia-ftplinks",
@@ -13907,7 +14295,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 0,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+        "Total tool usage (usegalaxy.eu)": 2
     },
     {
         "Galaxy wrapper id": "graphicsmagick",
@@ -13979,7 +14369,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 2,
         "Tools available on UseGalaxy.cz": 2,
-        "Tools available on UseGalaxy.no": 2
+        "Tools available on UseGalaxy.no": 2,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 43,
+        "Total tool usage (usegalaxy.eu)": 2605
     },
     {
         "Galaxy wrapper id": "imagej2",
@@ -14089,7 +14481,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 27,
-        "Tools available on UseGalaxy.no": 27
+        "Tools available on UseGalaxy.no": 27,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 26,
+        "Total tool usage (usegalaxy.eu)": 1537
     },
     {
         "Galaxy wrapper id": "woundhealing",
@@ -14159,7 +14553,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 0,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+        "Total tool usage (usegalaxy.eu)": 0
     },
     {
         "Galaxy wrapper id": "instagraal",
@@ -14253,7 +14649,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 14,
+        "Total tool usage (usegalaxy.eu)": 139
     },
     {
         "Galaxy wrapper id": "iprscan5",
@@ -14321,7 +14719,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 0,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+        "Total tool usage (usegalaxy.eu)": 0
     },
     {
         "Galaxy wrapper id": "itsx",
@@ -14403,7 +14803,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 38,
+        "Total tool usage (usegalaxy.eu)": 868
     },
     {
         "Galaxy wrapper id": "jbrowse2",
@@ -14475,7 +14877,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 0,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+        "Total tool usage (usegalaxy.eu)": 0
     },
     {
         "Galaxy wrapper id": "jupyter_job",
@@ -14545,7 +14949,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 0,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 2,
+        "Total tool usage (usegalaxy.eu)": 30
     },
     {
         "Galaxy wrapper id": "labels",
@@ -14615,7 +15021,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 0,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+        "Total tool usage (usegalaxy.eu)": 0
     },
     {
         "Galaxy wrapper id": "lighter",
@@ -14707,7 +15115,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 9,
+        "Total tool usage (usegalaxy.eu)": 152
     },
     {
         "Galaxy wrapper id": "mafft",
@@ -14788,7 +15198,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 2,
         "Tools available on UseGalaxy.cz": 2,
-        "Tools available on UseGalaxy.no": 2
+        "Tools available on UseGalaxy.no": 2,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 817,
+        "Total tool usage (usegalaxy.eu)": 143045
     },
     {
         "Galaxy wrapper id": "mavedb",
@@ -14858,7 +15270,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 0,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+        "Total tool usage (usegalaxy.eu)": 0
     },
     {
         "Galaxy wrapper id": "methtools",
@@ -14935,7 +15349,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 0,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+        "Total tool usage (usegalaxy.eu)": 5461
     },
     {
         "Galaxy wrapper id": "methyldackel",
@@ -15005,7 +15421,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 200,
+        "Total tool usage (usegalaxy.eu)": 16573
     },
     {
         "Galaxy wrapper id": "methylkit",
@@ -15075,7 +15493,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 0,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+        "Total tool usage (usegalaxy.eu)": 0
     },
     {
         "Galaxy wrapper id": "metilene",
@@ -15146,7 +15566,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 103,
+        "Total tool usage (usegalaxy.eu)": 3966
     },
     {
         "Galaxy wrapper id": "mgnify_seqprep",
@@ -15233,7 +15655,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 0,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+        "Total tool usage (usegalaxy.eu)": 0
     },
     {
         "Galaxy wrapper id": "miclip",
@@ -15303,7 +15727,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 0,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+        "Total tool usage (usegalaxy.eu)": 0
     },
     {
         "Galaxy wrapper id": "minced",
@@ -15373,7 +15799,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 53,
+        "Total tool usage (usegalaxy.eu)": 895
     },
     {
         "Galaxy wrapper id": "minipolish",
@@ -15457,7 +15885,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 21,
+        "Total tool usage (usegalaxy.eu)": 185
     },
     {
         "Galaxy wrapper id": "mitohifi",
@@ -15527,7 +15957,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 56,
+        "Total tool usage (usegalaxy.eu)": 613
     },
     {
         "Galaxy wrapper id": "molecule2gspan",
@@ -15597,7 +16029,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 0,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+        "Total tool usage (usegalaxy.eu)": 0
     },
     {
         "Galaxy wrapper id": "music_deconvolution",
@@ -15671,7 +16105,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 5,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 240,
+        "Total tool usage (usegalaxy.eu)": 1872
     },
     {
         "Galaxy wrapper id": "nanopolish",
@@ -15742,7 +16178,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 4,
         "Tools available on UseGalaxy.cz": 4,
-        "Tools available on UseGalaxy.no": 4
+        "Tools available on UseGalaxy.no": 4,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 78,
+        "Total tool usage (usegalaxy.eu)": 8366
     },
     {
         "Galaxy wrapper id": "netboxr",
@@ -15812,7 +16250,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 5,
+        "Total tool usage (usegalaxy.eu)": 11
     },
     {
         "Galaxy wrapper id": "nextdenovo",
@@ -15896,7 +16336,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 84,
+        "Total tool usage (usegalaxy.eu)": 268
     },
     {
         "Galaxy wrapper id": "nucleosome_prediction",
@@ -15982,7 +16424,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 2,
+        "Total tool usage (usegalaxy.eu)": 861
     },
     {
         "Galaxy wrapper id": "numeric_clustering",
@@ -16052,7 +16496,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 0,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+        "Total tool usage (usegalaxy.eu)": 486
     },
     {
         "Galaxy wrapper id": "openms",
@@ -16261,7 +16707,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 19,
         "Tools available on UseGalaxy.cz": 135,
-        "Tools available on UseGalaxy.no": 134
+        "Tools available on UseGalaxy.no": 134,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 916,
+        "Total tool usage (usegalaxy.eu)": 105743
     },
     {
         "Galaxy wrapper id": "pandas_rolling_window",
@@ -16331,7 +16779,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 7,
+        "Total tool usage (usegalaxy.eu)": 269
     },
     {
         "Galaxy wrapper id": "peakachu",
@@ -16402,7 +16852,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 78,
+        "Total tool usage (usegalaxy.eu)": 3109
     },
     {
         "Galaxy wrapper id": "perf",
@@ -16470,7 +16922,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 0,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+        "Total tool usage (usegalaxy.eu)": 0
     },
     {
         "Galaxy wrapper id": "pfamscan",
@@ -16550,7 +17004,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 19,
+        "Total tool usage (usegalaxy.eu)": 165
     },
     {
         "Galaxy wrapper id": "pg_tools",
@@ -16623,7 +17079,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 0,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+        "Total tool usage (usegalaxy.eu)": 0
     },
     {
         "Galaxy wrapper id": "pharmcat",
@@ -16693,7 +17151,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 14,
+        "Total tool usage (usegalaxy.eu)": 82
     },
     {
         "Galaxy wrapper id": "piranha",
@@ -16764,7 +17224,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 39,
+        "Total tool usage (usegalaxy.eu)": 1809
     },
     {
         "Galaxy wrapper id": "platypus",
@@ -16834,7 +17296,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 0,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+        "Total tool usage (usegalaxy.eu)": 0
     },
     {
         "Galaxy wrapper id": "plotly_ml_performance_plots",
@@ -16904,7 +17368,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 71,
+        "Total tool usage (usegalaxy.eu)": 1323
     },
     {
         "Galaxy wrapper id": "plotly_parallel_coordinates_plot",
@@ -16974,7 +17440,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 37,
+        "Total tool usage (usegalaxy.eu)": 652
     },
     {
         "Galaxy wrapper id": "plotly_regression_performance_plots",
@@ -17044,7 +17512,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 79,
+        "Total tool usage (usegalaxy.eu)": 843
     },
     {
         "Galaxy wrapper id": "protease_prediction",
@@ -17115,7 +17585,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 7,
+        "Total tool usage (usegalaxy.eu)": 154
     },
     {
         "Galaxy wrapper id": "protein_properties",
@@ -17185,7 +17657,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 30,
+        "Total tool usage (usegalaxy.eu)": 604
     },
     {
         "Galaxy wrapper id": "improviser",
@@ -17255,7 +17729,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 0,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+        "Total tool usage (usegalaxy.eu)": 0
     },
     {
         "Galaxy wrapper id": "racon",
@@ -17339,7 +17815,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 309,
+        "Total tool usage (usegalaxy.eu)": 21353
     },
     {
         "Galaxy wrapper id": "repeat_masker",
@@ -17409,7 +17887,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 248,
+        "Total tool usage (usegalaxy.eu)": 3750
     },
     {
         "Galaxy wrapper id": "replaceColumn",
@@ -17479,7 +17959,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 189,
+        "Total tool usage (usegalaxy.eu)": 576111
     },
     {
         "Galaxy wrapper id": "rest_tool",
@@ -17549,7 +18031,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 0,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+        "Total tool usage (usegalaxy.eu)": 0
     },
     {
         "Galaxy wrapper id": "antarna",
@@ -17619,7 +18103,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 2,
+        "Total tool usage (usegalaxy.eu)": 52
     },
     {
         "Galaxy wrapper id": "aresite2",
@@ -17691,7 +18177,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 4,
+        "Total tool usage (usegalaxy.eu)": 65
     },
     {
         "Galaxy wrapper id": "blockclust",
@@ -17761,7 +18249,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 15,
+        "Total tool usage (usegalaxy.eu)": 1478
     },
     {
         "Galaxy wrapper id": "cmsearch_deoverlap",
@@ -17845,7 +18335,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 1,
+        "Total tool usage (usegalaxy.eu)": 102
     },
     {
         "Galaxy wrapper id": "cmv",
@@ -17918,7 +18410,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 2,
-        "Tools available on UseGalaxy.no": 2
+        "Tools available on UseGalaxy.no": 2,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 1,
+        "Total tool usage (usegalaxy.eu)": 108
     },
     {
         "Galaxy wrapper id": "cofold",
@@ -17988,7 +18482,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 8,
+        "Total tool usage (usegalaxy.eu)": 342
     },
     {
         "Galaxy wrapper id": "compalignp",
@@ -18059,7 +18555,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+        "Total tool usage (usegalaxy.eu)": 220
     },
     {
         "Galaxy wrapper id": "coprarna",
@@ -18130,7 +18628,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 0,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+        "Total tool usage (usegalaxy.eu)": 0
     },
     {
         "Galaxy wrapper id": "dewseq",
@@ -18202,7 +18702,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 11,
+        "Total tool usage (usegalaxy.eu)": 72
     },
     {
         "Galaxy wrapper id": "dorina",
@@ -18273,7 +18775,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 1,
+        "Total tool usage (usegalaxy.eu)": 1576
     },
     {
         "Galaxy wrapper id": "dot2ct",
@@ -18344,7 +18848,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 0,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+        "Total tool usage (usegalaxy.eu)": 0
     },
     {
         "Galaxy wrapper id": "dotknot",
@@ -18415,7 +18921,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 1,
+        "Total tool usage (usegalaxy.eu)": 83
     },
     {
         "Galaxy wrapper id": "exparna",
@@ -18485,7 +18993,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 0,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+        "Total tool usage (usegalaxy.eu)": 0
     },
     {
         "Galaxy wrapper id": "graphprot",
@@ -18557,7 +19067,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 6,
+        "Total tool usage (usegalaxy.eu)": 474
     },
     {
         "Galaxy wrapper id": "htseq-clip",
@@ -18629,7 +19141,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 15,
+        "Total tool usage (usegalaxy.eu)": 77
     },
     {
         "Galaxy wrapper id": "infernal",
@@ -18716,7 +19230,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 6,
-        "Tools available on UseGalaxy.no": 6
+        "Tools available on UseGalaxy.no": 6,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 67,
+        "Total tool usage (usegalaxy.eu)": 100294
     },
     {
         "Galaxy wrapper id": "inforna",
@@ -18784,7 +19300,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 0,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+        "Total tool usage (usegalaxy.eu)": 0
     },
     {
         "Galaxy wrapper id": "intarna",
@@ -18854,7 +19372,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 23,
+        "Total tool usage (usegalaxy.eu)": 7569
     },
     {
         "Galaxy wrapper id": "kinwalker",
@@ -18922,7 +19442,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 0,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+        "Total tool usage (usegalaxy.eu)": 0
     },
     {
         "Galaxy wrapper id": "locarna",
@@ -18996,7 +19518,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 11,
+        "Total tool usage (usegalaxy.eu)": 339
     },
     {
         "Galaxy wrapper id": "mea",
@@ -19066,7 +19590,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 3,
+        "Total tool usage (usegalaxy.eu)": 85
     },
     {
         "Galaxy wrapper id": "mqc",
@@ -19136,7 +19662,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 5,
+        "Total tool usage (usegalaxy.eu)": 76
     },
     {
         "Galaxy wrapper id": "nastiseq",
@@ -19206,7 +19734,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+        "Total tool usage (usegalaxy.eu)": 40
     },
     {
         "Galaxy wrapper id": "paralyzer",
@@ -19276,7 +19806,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 7,
+        "Total tool usage (usegalaxy.eu)": 299
     },
     {
         "Galaxy wrapper id": "pipmir",
@@ -19346,7 +19878,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 21,
+        "Total tool usage (usegalaxy.eu)": 275
     },
     {
         "Galaxy wrapper id": "rRNA",
@@ -19416,7 +19950,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 0,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+        "Total tool usage (usegalaxy.eu)": 0
     },
     {
         "Galaxy wrapper id": "rbpbench",
@@ -19502,7 +20038,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 0,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+        "Total tool usage (usegalaxy.eu)": 36
     },
     {
         "Galaxy wrapper id": "rcas",
@@ -19572,7 +20110,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 38,
+        "Total tool usage (usegalaxy.eu)": 1226
     },
     {
         "Galaxy wrapper id": "reago",
@@ -19659,7 +20199,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 0,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+        "Total tool usage (usegalaxy.eu)": 0
     },
     {
         "Galaxy wrapper id": "remurna",
@@ -19729,7 +20271,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 2,
+        "Total tool usage (usegalaxy.eu)": 42
     },
     {
         "Galaxy wrapper id": "ribotaper",
@@ -19811,7 +20355,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 3,
-        "Tools available on UseGalaxy.no": 3
+        "Tools available on UseGalaxy.no": 3,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 44,
+        "Total tool usage (usegalaxy.eu)": 628
     },
     {
         "Galaxy wrapper id": "rna_shapes",
@@ -19881,7 +20427,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 11,
+        "Total tool usage (usegalaxy.eu)": 129
     },
     {
         "Galaxy wrapper id": "rnabob",
@@ -19951,7 +20499,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 3,
+        "Total tool usage (usegalaxy.eu)": 164
     },
     {
         "Galaxy wrapper id": "rnacode",
@@ -20021,7 +20571,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 5,
+        "Total tool usage (usegalaxy.eu)": 1358
     },
     {
         "Galaxy wrapper id": "rnacommender",
@@ -20091,7 +20643,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 6,
+        "Total tool usage (usegalaxy.eu)": 1074
     },
     {
         "Galaxy wrapper id": "rnalien",
@@ -20162,7 +20716,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 4,
+        "Total tool usage (usegalaxy.eu)": 33
     },
     {
         "Galaxy wrapper id": "rnasnp",
@@ -20232,7 +20788,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 5,
+        "Total tool usage (usegalaxy.eu)": 86
     },
     {
         "Galaxy wrapper id": "rnaz",
@@ -20307,7 +20865,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 6,
-        "Tools available on UseGalaxy.no": 6
+        "Tools available on UseGalaxy.no": 6,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 28,
+        "Total tool usage (usegalaxy.eu)": 43279
     },
     {
         "Galaxy wrapper id": "selectsequencesfrommsa",
@@ -20378,7 +20938,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 27,
+        "Total tool usage (usegalaxy.eu)": 457
     },
     {
         "Galaxy wrapper id": "sortmerna",
@@ -20463,7 +21025,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 376,
+        "Total tool usage (usegalaxy.eu)": 18183
     },
     {
         "Galaxy wrapper id": "sshmm",
@@ -20534,7 +21098,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 5,
+        "Total tool usage (usegalaxy.eu)": 223
     },
     {
         "Galaxy wrapper id": "targetfinder",
@@ -20604,7 +21170,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 37,
+        "Total tool usage (usegalaxy.eu)": 713
     },
     {
         "Galaxy wrapper id": "trna_prediction",
@@ -20675,7 +21243,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 2,
-        "Tools available on UseGalaxy.no": 2
+        "Tools available on UseGalaxy.no": 2,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 236,
+        "Total tool usage (usegalaxy.eu)": 2935
     },
     {
         "Galaxy wrapper id": "vienna_rna",
@@ -20767,7 +21337,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 21,
-        "Tools available on UseGalaxy.no": 21
+        "Tools available on UseGalaxy.no": 21,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 123,
+        "Total tool usage (usegalaxy.eu)": 7864
     },
     {
         "Galaxy wrapper id": "sailfish",
@@ -20838,7 +21410,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 55,
+        "Total tool usage (usegalaxy.eu)": 4024
     },
     {
         "Galaxy wrapper id": "salmon",
@@ -20929,7 +21503,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 3,
         "Tools available on UseGalaxy.cz": 3,
-        "Tools available on UseGalaxy.no": 3
+        "Tools available on UseGalaxy.no": 3,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 969,
+        "Total tool usage (usegalaxy.eu)": 61937
     },
     {
         "Galaxy wrapper id": "sambamba",
@@ -20963,11 +21539,11 @@
         "EDAM topic (no superclasses)": [],
         "Available on UseGalaxy.org (Main)": 0,
         "Available on UseGalaxy.org.au": 0,
-        "Available on UseGalaxy.eu": 0,
+        "Available on UseGalaxy.eu": 4,
         "Available on UseGalaxy.fr": 0,
         "Tools available on UseGalaxy.org (Main)": 0,
         "Tools available on UseGalaxy.org.au": 0,
-        "Tools available on UseGalaxy.eu": 0,
+        "Tools available on UseGalaxy.eu": 4,
         "Tools available on UseGalaxy.fr": 0,
         "Tools available on ANASTASIA": 0,
         "Tools available on APOSTL": 0,
@@ -21002,7 +21578,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 0,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+        "Total tool usage (usegalaxy.eu)": 0
     },
     {
         "Galaxy wrapper id": "sed",
@@ -21072,7 +21650,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 0,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 2,
+        "Total tool usage (usegalaxy.eu)": 2276
     },
     {
         "Galaxy wrapper id": "segemehl",
@@ -21142,7 +21722,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 30,
+        "Total tool usage (usegalaxy.eu)": 1276
     },
     {
         "Galaxy wrapper id": "sklearn",
@@ -21245,7 +21827,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 29,
         "Tools available on UseGalaxy.cz": 31,
-        "Tools available on UseGalaxy.no": 27
+        "Tools available on UseGalaxy.no": 27,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 958,
+        "Total tool usage (usegalaxy.eu)": 113932
     },
     {
         "Galaxy wrapper id": "splitfasta",
@@ -21315,7 +21899,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 96,
+        "Total tool usage (usegalaxy.eu)": 1295
     },
     {
         "Galaxy wrapper id": "statistics",
@@ -21385,7 +21971,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 21,
+        "Total tool usage (usegalaxy.eu)": 304
     },
     {
         "Galaxy wrapper id": "stress_ng",
@@ -21455,7 +22043,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 0,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+        "Total tool usage (usegalaxy.eu)": 47
     },
     {
         "Galaxy wrapper id": "tapscan",
@@ -21525,7 +22115,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 0,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+        "Total tool usage (usegalaxy.eu)": 0
     },
     {
         "Galaxy wrapper id": "add_line_to_file",
@@ -21595,7 +22187,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 193,
+        "Total tool usage (usegalaxy.eu)": 14480
     },
     {
         "Galaxy wrapper id": "column_arrange_by_header",
@@ -21665,7 +22259,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 179,
+        "Total tool usage (usegalaxy.eu)": 3781
     },
     {
         "Galaxy wrapper id": "join_files_on_column_fuzzy",
@@ -21735,7 +22331,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 117,
+        "Total tool usage (usegalaxy.eu)": 2448
     },
     {
         "Galaxy wrapper id": "split_file_on_column",
@@ -21805,7 +22403,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 159,
+        "Total tool usage (usegalaxy.eu)": 5507
     },
     {
         "Galaxy wrapper id": "split_file_to_collection",
@@ -21875,7 +22475,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 412,
+        "Total tool usage (usegalaxy.eu)": 15358
     },
     {
         "Galaxy wrapper id": "text_processing",
@@ -21964,7 +22566,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 19,
         "Tools available on UseGalaxy.cz": 19,
-        "Tools available on UseGalaxy.no": 19
+        "Tools available on UseGalaxy.no": 19,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 15048,
+        "Total tool usage (usegalaxy.eu)": 3864895
     },
     {
         "Galaxy wrapper id": "tgsgapcloser",
@@ -22058,7 +22662,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 36,
+        "Total tool usage (usegalaxy.eu)": 460
     },
     {
         "Galaxy wrapper id": "tiara",
@@ -22152,7 +22758,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 0,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+        "Total tool usage (usegalaxy.eu)": 0
     },
     {
         "Galaxy wrapper id": "tool_recommendation_model",
@@ -22222,7 +22830,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 15,
+        "Total tool usage (usegalaxy.eu)": 445
     },
     {
         "Galaxy wrapper id": "trim_galore",
@@ -22307,7 +22917,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 2334,
+        "Total tool usage (usegalaxy.eu)": 238699
     },
     {
         "Galaxy wrapper id": "uniprot_rest_interface",
@@ -22378,7 +22990,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 132,
+        "Total tool usage (usegalaxy.eu)": 2406
     },
     {
         "Galaxy wrapper id": "vt",
@@ -22450,7 +23064,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 0,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+        "Total tool usage (usegalaxy.eu)": 0
     },
     {
         "Galaxy wrapper id": "whisper",
@@ -22520,7 +23136,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 0,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+        "Total tool usage (usegalaxy.eu)": 0
     },
     {
         "Galaxy wrapper id": "wtdbg",
@@ -22604,7 +23222,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 116,
+        "Total tool usage (usegalaxy.eu)": 1660
     },
     {
         "Galaxy wrapper id": "align_back_trans",
@@ -22675,7 +23295,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 11,
+        "Total tool usage (usegalaxy.eu)": 329
     },
     {
         "Galaxy wrapper id": "chromosome_diagram",
@@ -22747,7 +23369,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 0,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+        "Total tool usage (usegalaxy.eu)": 0
     },
     {
         "Galaxy wrapper id": "clc_assembly_cell",
@@ -22820,7 +23444,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 0,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+        "Total tool usage (usegalaxy.eu)": 0
     },
     {
         "Galaxy wrapper id": "clinod",
@@ -22900,7 +23526,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 0,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+        "Total tool usage (usegalaxy.eu)": 0
     },
     {
         "Galaxy wrapper id": "count_roi_variants",
@@ -22971,7 +23599,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 0,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+        "Total tool usage (usegalaxy.eu)": 0
     },
     {
         "Galaxy wrapper id": "coverage_stats",
@@ -23042,7 +23672,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 0,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+        "Total tool usage (usegalaxy.eu)": 0
     },
     {
         "Galaxy wrapper id": "effectiveT3",
@@ -23122,7 +23754,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 0,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+        "Total tool usage (usegalaxy.eu)": 0
     },
     {
         "Galaxy wrapper id": "fasta_filter_by_id",
@@ -23194,7 +23828,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 0,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+        "Total tool usage (usegalaxy.eu)": 0
     },
     {
         "Galaxy wrapper id": "fastq_filter_by_id",
@@ -23266,7 +23902,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 0,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+        "Total tool usage (usegalaxy.eu)": 0
     },
     {
         "Galaxy wrapper id": "fastq_pair_names",
@@ -23336,7 +23974,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 0,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+        "Total tool usage (usegalaxy.eu)": 0
     },
     {
         "Galaxy wrapper id": "fastq_paired_unpaired",
@@ -23407,7 +24047,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 0,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+        "Total tool usage (usegalaxy.eu)": 0
     },
     {
         "Galaxy wrapper id": "get_orfs_or_cdss",
@@ -23477,7 +24119,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 15,
+        "Total tool usage (usegalaxy.eu)": 186
     },
     {
         "Galaxy wrapper id": "mummer",
@@ -23549,7 +24193,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 83,
+        "Total tool usage (usegalaxy.eu)": 652
     },
     {
         "Galaxy wrapper id": "nlstradamus",
@@ -23620,7 +24266,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 0,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+        "Total tool usage (usegalaxy.eu)": 0
     },
     {
         "Galaxy wrapper id": "predictnls",
@@ -23690,7 +24338,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 0,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+        "Total tool usage (usegalaxy.eu)": 0
     },
     {
         "Galaxy wrapper id": "protein_analysis",
@@ -23765,7 +24415,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 6,
         "Tools available on UseGalaxy.cz": 6,
-        "Tools available on UseGalaxy.no": 6
+        "Tools available on UseGalaxy.no": 6,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 451,
+        "Total tool usage (usegalaxy.eu)": 6428
     },
     {
         "Galaxy wrapper id": "sample_seqs",
@@ -23838,7 +24490,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 149,
+        "Total tool usage (usegalaxy.eu)": 3765
     },
     {
         "Galaxy wrapper id": "samtools_depad",
@@ -23910,7 +24564,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 0,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+        "Total tool usage (usegalaxy.eu)": 0
     },
     {
         "Galaxy wrapper id": "samtools_depth",
@@ -23982,7 +24638,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 296,
+        "Total tool usage (usegalaxy.eu)": 4948
     },
     {
         "Galaxy wrapper id": "samtools_idxstats",
@@ -24054,7 +24712,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 1,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 1450,
+        "Total tool usage (usegalaxy.eu)": 48426
     },
     {
         "Galaxy wrapper id": "seq_composition",
@@ -24124,7 +24784,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 71,
+        "Total tool usage (usegalaxy.eu)": 874
     },
     {
         "Galaxy wrapper id": "seq_filter_by_id",
@@ -24196,7 +24858,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 306,
+        "Total tool usage (usegalaxy.eu)": 25302
     },
     {
         "Galaxy wrapper id": "seq_filter_by_mapping",
@@ -24270,7 +24934,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 82,
+        "Total tool usage (usegalaxy.eu)": 3784
     },
     {
         "Galaxy wrapper id": "seq_length",
@@ -24342,7 +25008,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 0,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+        "Total tool usage (usegalaxy.eu)": 0
     },
     {
         "Galaxy wrapper id": "seq_primer_clip",
@@ -24414,7 +25082,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 0,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+        "Total tool usage (usegalaxy.eu)": 0
     },
     {
         "Galaxy wrapper id": "seq_rename",
@@ -24486,7 +25156,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 0,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+        "Total tool usage (usegalaxy.eu)": 0
     },
     {
         "Galaxy wrapper id": "seq_select_by_id",
@@ -24558,7 +25230,9 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 0,
-        "Tools available on UseGalaxy.no": 0
+        "Tools available on UseGalaxy.no": 0,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 0,
+        "Total tool usage (usegalaxy.eu)": 0
     },
     {
         "Galaxy wrapper id": "venn_list",
@@ -24630,6 +25304,8 @@
         "Tools available on Protologger": 0,
         "Tools available on UseGalaxy.be": 0,
         "Tools available on UseGalaxy.cz": 1,
-        "Tools available on UseGalaxy.no": 1
+        "Tools available on UseGalaxy.no": 1,
+        "No. of tool users (2022-2023) (usegalaxy.eu)": 248,
+        "Total tool usage (usegalaxy.eu)": 5067
     }
 ]
\ No newline at end of file
diff --git a/results/repositories02.list_tools.tsv b/results/repositories02.list_tools.tsv
index df94e57d..380f2b91 100644
--- a/results/repositories02.list_tools.tsv
+++ b/results/repositories02.list_tools.tsv
@@ -1,339 +1,339 @@
-Galaxy wrapper id	Total tool usage (usegalaxy.eu)	No. of tool users (2022-2023) (usegalaxy.eu)	Galaxy tool ids	Description	bio.tool id	bio.tool ids	biii	bio.tool name	bio.tool description	EDAM operation	EDAM topic	Status	Source	ToolShed categories	ToolShed id	Galaxy wrapper owner	Galaxy wrapper source	Galaxy wrapper parsed folder	Galaxy wrapper version	Conda id	Conda version	EDAM operation (no superclasses)	EDAM topic (no superclasses)	Available on UseGalaxy.org (Main)	Available on UseGalaxy.org.au	Available on UseGalaxy.eu	Available on UseGalaxy.fr	Tools available on UseGalaxy.org (Main)	Tools available on UseGalaxy.org.au	Tools available on UseGalaxy.eu	Tools available on UseGalaxy.fr	Tools available on ANASTASIA	Tools available on APOSTL	Tools available on ARGs-OAP	Tools available on BF2I-MAP	Tools available on BioBix	Tools available on CIRM-CFBP	Tools available on Center for Phage Technology (CPT)	Tools available on ChemFlow	Tools available on Coloc-stats	Tools available on CorGAT	Tools available on CropGalaxy	Tools available on Dintor	Tools available on FreeBioinfo	Tools available on GASLINI	Tools available on Galaxy@AuBi	Tools available on Galaxy@Pasteur	Tools available on GalaxyTrakr	Tools available on Genomic Hyperbrowser	Tools available on GigaGalaxy	Tools available on HyPhy HIV NGS Tools	Tools available on IPK Galaxy Blast Suite	Tools available on ImmPort Galaxy	Tools available on InteractoMIX	Tools available on MISSISSIPPI	Tools available on Mandoiu Lab	Tools available on MiModD NacreousMap	Tools available on Oqtans	Tools available on Palfinder	Tools available on PepSimili	Tools available on PhagePromotor	Tools available on Protologger	Tools available on UseGalaxy.be	Tools available on UseGalaxy.cz	Tools available on UseGalaxy.no
-10x_bamtofastq	228.0	46.0	10x_bamtofastq	Converts 10x Genomics BAM to FASTQ								Up-to-date	https://github.com/10XGenomics/bamtofastq	Convert Formats	10x_bamtofastq	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq	https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq	1.4.1	10x_bamtofastq	1.4.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0
-AggregateAlignments			graphclust_aggregate_alignments	Aggregate and filter alignment metrics of individual clusters, like the output of graphclust_align_cluster.								Up-to-date		RNA	graphclust_aggregate_alignments	rnateam	https://github.com/bgruening/galaxytools/tools/GraphClust/AggregateAlignments	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/AggregateAlignments	0.6.0	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1
-AlignCluster			graphclust_align_cluster	Align predicted clusters of glob_report_no_align step with locarna and conservation analysis and visualizations.								To update		RNA	graphclust_align_cluster	rnateam	https://github.com/bgruening/galaxytools/tools/GraphClust/AlignCluster	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/AlignCluster	0.1	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1
-CMFinder			cmFinder	Determines consensus motives for sequences.								To update		RNA	graphclust_cmfinder	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CMFinder	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CMFinder	0.4	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1
-CollectResults			glob_report	Post-processing. Redundant clusters are merged and instances that belong to multiple clusters are assigned unambiguously. For every pair of clusters, the relative overlap (i.e. the fraction of instances that occur in both clusters) is computed and clusters are merged if the overlap exceeds 50%. instances that occur in both clusters) is computed and clusters are merged if the overlap exceeds 50%.								To update		RNA	graphclust_postprocessing	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResults	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResults	0.5	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1
-CollectResultsNoAlign			graphclust_glob_report_no_align	Redundant GraphClust clusters are merged and instances that belong to multiple clusters are assigned unambiguously.								To update		RNA	graphclust_postprocessing_no_align	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign	0.5	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1
-GSPAN			gspan	Second step of GraphClust								To update		RNA	graphclust_fasta_to_gspan	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/GSPAN	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/GSPAN	0.4	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1
-LocARNAGraphClust			locarna_best_subtree	MLocARNA computes a multiple sequence-structure alignment of RNA sequences.								To update		RNA	graphclust_mlocarna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/LocARNAGraphClust	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/LocARNAGraphClust	0.4	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1
-NSPDK			NSPDK_candidateClust, nspdk_sparse	Produces an explicit sparse feature encoding and copmutes global feature index and returns top dense sets.								To update		RNA	graphclust_nspdk	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/NSPDK	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/NSPDK	9.2.3.1	graphclust-wrappers	0.6.0			0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2
-Plotting			motifFinderPlot	Plotting results for GraphClust								To update		RNA	graphclust_motif_finder_plot	rnateam	https://github.com/eteriSokhoyan/galaxytools/tree/master/tools/GraphClust/Plotting	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/Plotting	0.4	seaborn				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1
-PrepareForMlocarna			preMloc	This tool prepares files for locarna step.								To update		RNA	graphclust_prepocessing_for_mlocarna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/PrepareForMlocarna	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/PrepareForMlocarna	0.4	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1
-Preprocessing			preproc	Preprocessing input for GraphClust								To update		RNA	graphclust_preprocessing	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/Preprocessing	0.5	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/Structure_GSPAN	0.4	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/add_line_to_file	0.1.0	coreutils	8.25			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0
-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	https://github.com/galaxyproject/tools-devteam/tree/main/tools/add_value	1.0.1	perl				1	1	1	1	1	1	1	1	0	1	1	1	1	0	1	0	1	1	1	1	0	1	1	1	1	1	1	0	0	0	0	1	0	0	1	0	1	1	0	1	1	1
-agat	481.0	42.0	agat	GTF/GFF analysis toolkit	agat	agat		AGAT	Another Gff Analysis Toolkit (AGAT)Suite of tools to handle gene annotations in any GTF/GFF format.	Data handling, Genome annotation	Genomics	To update	https://github.com/NBISweden/AGAT	Convert Formats, Statistics, Fasta Manipulation	agat	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/agat	https://github.com/bgruening/galaxytools/tree/master/tools/agat	1.2.0	agat	1.4.0	Data handling, Genome annotation	Genomics	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0
-align_back_trans	329.0	11.0	align_back_trans	Thread nucleotides onto a protein alignment (back-translation)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans	Fasta Manipulation, Sequence Analysis	align_back_trans	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans	https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans	0.0.10	biopython	1.70			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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	https://github.com/galaxyproject/tools-devteam/tree/main/tools/annotation_profiler	1.0.0	bx-python	0.11.0			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1
-antarna	52.0	2.0	antarna	antaRNA uses ant colony optimization to solve the inverse folding problem in RNA research .								To update		RNA	antarna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna	1.1	antarna	2.0.1.2			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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		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	https://github.com/bgruening/galaxytools/tree/master/tools/antismash	6.1.1	antismash	7.1.0	Sequence clustering, Gene prediction, Differential gene expression analysis	Molecular interactions, pathways and networks, Gene and protein families	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1
-aresite2	65.0	4.0	AREsite2_REST	AREsite2 REST Interface								To update	http://rna.tbi.univie.ac.at/AREsite	RNA, Data Source, Sequence Analysis	aresite2	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2	0.1.2	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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	https://github.com/bgruening/galaxytools/tree/master/tools/atactk_trim_adapters	0.1.6	atactk	0.1.9			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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	https://github.com/bgruening/galaxytools/tree/master/tools/augustus	3.1.0	augustus	3.5.0			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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	https://github.com/bgruening/galaxytools/tree/master/tools/bamhash	1.1	bamhash	1.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1
-barcode_collapse			barcode_collapse	Paired End randomer aware duplicate removal algorithm								To update	https://github.com/YeoLab/gscripts	RNA, Sequence Analysis	barcode_collapse	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse	https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse	0.1.0	pysam	0.22.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-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	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/basecoverage	1.0.0	bx-python	0.11.0			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	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	https://github.com/galaxyproject/tools-devteam/tree/main/tools/best_regression_subsets	1.0.0	numpy				1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1
-bia-ftplinks			bia_download	Tool to query ftp links for study from bioimage archive								To update		Imaging	bia_download	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools	https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/bia-ftplinks	0.1.0	wget				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-bigwig_to_bedgraph	5749.0	200.0	bigwig_to_bedgraph	Convert from bigWig to bedGraph format								To update		Convert Formats	bigwig_to_bedgraph	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/bigwig_to_bedgraph	https://github.com/bgruening/galaxytools/tree/master/tools/bigwig_to_bedgraph	0.1.0	ucsc_tools				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1
-biomodelsML			biomodels_biomd0000001066, biomodels_biomd0000001076	Wrappers for tools to bring BioModels AI models into Galaxy.								To update	https://www.ebi.ac.uk/biomodels/	Machine Learning	biomodels	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools	https://github.com/bgruening/galaxytools/tree/master/tools/biomodelsML	1.1					0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-bionano			bionano_scaffold	Bionano Solve is a set of tools for analyzing Bionano data								To update	https://bionanogenomics.com/	Assembly	bionano	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/bionano	https://github.com/bgruening/galaxytools/tree/master/tools/bionano	3.7.0					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0
-bismark	13575.0	404.0	bismark_pretty_report, bismark_bowtie2, bismark_deduplicate, bismark_methylation_extractor	A tool to map bisulfite converted sequence reads and determine cytosine methylation states								To update	https://www.bioinformatics.babraham.ac.uk/projects/bismark/	Sequence Analysis, Next Gen Mappers	bismark	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/bismark	https://github.com/bgruening/galaxytools/tree/master/tools/bismark	0.22.1	bismark	0.24.2			0	4	4	4	0	4	4	4	0	0	0	4	0	0	0	0	0	0	0	0	0	0	4	0	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	4	4	4
-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	https://github.com/galaxyproject/tools-devteam/tree/main/tools/blat_coverage_report	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-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	https://github.com/galaxyproject/tools-devteam/tree/main/tools/blat_mapping	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-blobtoolkit	685.0	21.0	blobtoolkit	Identification and isolation non-target data in draft and publicly available genome assemblies.								To update	https://blobtoolkit.genomehubs.org/	Sequence Analysis, Assembly	blobtoolkit	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit	https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit	4.0.7					0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0
-blockbuster	3009.0	34.0	blockbuster	Blockbuster detects blocks of overlapping reads using a gaussian-distribution approach.								To update	http://hoffmann.bioinf.uni-leipzig.de/LIFE/blockbuster.html	RNA, Sequence Analysis	blockbuster	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster	https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster	0.1.2	blockbuster	0.0.1.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	1
-blockclust	1478.0	15.0	blockclust	BlockClust detects transcripts with similar processing patterns.								Up-to-date	https://github.com/bgruening/galaxytools/tree/master/workflows/blockclust	RNA	blockclust	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/blockclust	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/blockclust	1.1.1	blockclust	1.1.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	1
-bowtie_wrappers	22988.0	506.0	bowtie_wrapper	Galaxy wrappers for the Bowtie short read mapping tools.								To update	http://bowtie-bio.sourceforge.net/	Next Gen Mappers	bowtie_wrappers	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers	https://github.com/galaxyproject/tools-devteam/tree/main/tools/bowtie_wrappers	1.2.0	bowtie	1.3.1			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	1
-canonical_correlation_analysis	72.0	10.0	cca1	Canonical Correlation Analysis								To update		Statistics	canonical_correlation_analysis	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/canonical_correlation_analysis	https://github.com/galaxyproject/tools-devteam/tree/main/tools/canonical_correlation_analysis	1.0.0	R				0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1
-canu	13021.0	533.0	canu	Canu is a hierarchical assembly pipeline designed for high-noise single-molecule sequencing (such as the PacBio RS II/Sequel or Oxford Nanopore MinION).	canu	canu		CANU	De-novo assembly tool for long read chemistry like Nanopore data and PacBio data.	De-novo assembly	Genomics	Up-to-date	https://github.com/marbl/canu		canu	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/canu	https://github.com/bgruening/galaxytools/tree/master/tools/canu	2.2	canu	2.2	De-novo assembly	Genomics	0	1	1	1	0	1	1	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1
-categorize_elements_satisfying_criteria	40.0	1.0	categorize_elements_satisfying_criteria	Categorize Elements satisfying criteria.								To update		Statistics	categorize_elements_satisfying_criteria	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/categorize_elements_satisfying_criteria	https://github.com/galaxyproject/tools-devteam/tree/main/tools/categorize_elements_satisfying_criteria	1.0.0					0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1
-ccat	165.0	15.0	peakcalling_ccat	Control-based ChIP-seq Analysis Tool								To update		ChIP-seq	ccat	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/ccat	https://github.com/galaxyproject/tools-devteam/tree/main/tools/ccat	0.0.2	ccat	3.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1
-cd_hit_dup			cd_hit_dup	simple tool for removing duplicates from sequencing reads								To update		Metagenomics, Sequence Analysis	cd_hit_dup	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/cd_hit_dup	https://github.com/galaxyproject/tools-devteam/tree/main/tools/cd_hit_dup	0.0.1	cd-hit-auxtools	4.8.1			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-cellpose			cellpose	Cellpose is an anatomical segmentation algorithm								To update	https://github.com/MouseLand/cellpose	Imaging	cellpose	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/cellpose	https://github.com/bgruening/galaxytools/tree/master/tools/cellpose	3.0.8	cellpose				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-cellprofiler			cp_cellprofiler, cp_color_to_gray, cp_convert_objects_to_image, cp_display_data_on_image, cp_enhance_or_suppress_features, cp_export_to_spreadsheet, cp_gray_to_color, cp_identify_primary_objects, cp_image_math, cp_mask_image, cp_measure_granularity, cp_measure_image_area_occupied, cp_measure_image_intensity, cp_measure_image_quality, cp_measure_object_intensity, cp_measure_object_size_shape, cp_measure_texture, cp_overlay_outlines, cp_relate_objects, cp_save_images, cp_common, cp_tile, cp_track_objects	cellProfiler wrapper	CellProfiler	CellProfiler	cellprofiler	CellProfiler	Tool for quantifying data from biological images, particularly in high-throughput experiments.	Quantification, Image analysis, Parsing	Imaging, Microarray experiment, Genotype and phenotype	To update		Imaging	cellprofiler	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools	https://github.com/bgruening/galaxytools/tree/master/tools/cellprofiler				Quantification, Image analysis, Parsing	Imaging, Microarray experiment, Genotype and phenotype	0	23	23	19	0	23	23	19	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	19	23	19
-cellprofiler_v4			cp_cellprofiler4	cellProfiler4 wrapper								To update		Imaging	cellprofiler4	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools	https://github.com/bgruening/galaxytools/tree/master/tools/cellprofiler_v4	4.2.6					0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0
-change_case			ChangeCase	Convert column case.								To update		Text Manipulation	change_case	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/change_case	https://github.com/galaxyproject/tools-devteam/tree/main/tools/change_case	1.0.1	perl				1	1	1	1	1	1	1	1	0	1	1	1	1	0	1	0	1	1	1	1	0	1	1	1	1	1	1	1	0	0	0	1	0	0	1	0	1	1	0	1	1	1
-chipseeker	15690.0	418.0	chipseeker	A tool for ChIP peak annotation and visualization								To update	https://bioconductor.org/packages/release/bioc/html/ChIPseeker.html	ChIP-seq, Genome annotation	chipseeker	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/chipseeker	https://github.com/bgruening/galaxytools/tree/master/tools/chipseeker	1.32.0	bioconductor-chipseeker	1.38.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	1
-chromosome_diagram			chromosome_diagram	Chromosome Diagrams using Biopython								To update		Graphics, Sequence Analysis, Visualization	chromosome_diagram	peterjc		https://github.com/peterjc/pico_galaxy/tree/master/tools/chromosome_diagram	0.0.3	biopython	1.70			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-circexplorer	251.0	8.0	circexplorer	A combined strategy to identify circular RNAs (circRNAs and ciRNAs)								To update	https://github.com/YangLab/CIRCexplorer	Sequence Analysis, RNA	circexplorer	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/circexplorer	https://github.com/bgruening/galaxytools/tree/master/tools/circexplorer	1.1.9.0	circexplorer	1.1.10			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1
-clc_assembly_cell			clc_assembler, clc_mapper	Galaxy wrapper for the CLC Assembly Cell suite from CLCBio								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell	Assembly, Next Gen Mappers, SAM	clc_assembly_cell	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell	https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell	0.0.7	samtools	1.20			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-clinod			clinod	NoD: a Nucleolar localization sequence detector for eukaryotic and viral proteins	clinod	clinod		clinod	The command line NoD predictor (clinod) can be run from the command line to predict Nucleolar localization sequences (NoLSs) that are short targeting sequences responsible for the localization of proteins to the nucleolus.The predictor accepts a list of FASTA formatted sequences as an input and outputs the NOLS predictions as a result.Please note that currently, JPred secondary structure predictions are not supported by clinod. However, we are working on it.	Nucleic acid sequence analysis	Sequence analysis	To update	http://www.compbio.dundee.ac.uk/www-nod/	Sequence Analysis	clinod	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod	https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod	0.1.0	clinod	1.3	Nucleic acid sequence analysis	Sequence analysis	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-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	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/cluster	1.0.0	bx-python	0.11.0			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	1
-cmsearch_deoverlap	102.0	1.0	cmsearch_deoverlap	removes lower scoring overlaps from cmsearch results.	cmsearch-deoverlap	cmsearch-deoverlap		cmsearch-deoverlap	Removes lower scoring overlaps from cmsearch results.	Comparison, Alignment	Biology, Medicine	To update	https://github.com/EBI-Metagenomics/pipeline-v5/blob/master/tools/RNA_prediction/cmsearch-deoverlap/cmsearch-deoverlap.pl	RNA	cmsearch_deoverlap	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmsearch_deoverlap	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmsearch_deoverlap	0.08+galaxy2	perl		Comparison, Alignment	Biology, Medicine	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0
-cmv	70.0	1.0	cmcv, cmv, hmmcv, hmmv	cmv is a collection of tools for the visualisation of Hidden Markov Models and RNA-family models.								Up-to-date	https://github.com/eggzilla/cmv	RNA	cmv	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv	1.0.8	cmv	1.0.8			0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2
-cofold	342.0	8.0	cofold	Cofold predicts RNA secondary structures that takes co-transcriptional folding into account.								To update	http://www.e-rna.org/cofold/	RNA	cofold	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cofold	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cofold	2.0.4.0	cofold	2.0.4			0	0	1	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/column_arrange_by_header	0.2					1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1
-combine_metaphlan_humann			combine_metaphlan_humann	Combine MetaPhlAn2 and HUMAnN2 outputs to relate genus/species abundances and gene families/pathways abundances	combine_metaphlan_and_humann	combine_metaphlan_and_humann		Combine Metaphlan and HUMAnN	This tool combine MetaPhlAn outputs and HUMANnN outputs	Aggregation	Metagenomics, Molecular interactions, pathways and networks	To update		Metagenomics	combine_metaphlan2_humann2	bebatut	https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2	https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan_humann	0.3.0	python		Aggregation	Metagenomics, Molecular interactions, pathways and networks	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0
-compalignp	220.0		compalignp	Compute fractional identity between trusted alignment and test alignment								Up-to-date		RNA, Sequence Analysis	compalignp	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/compalignp/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/compalignp	1.0	compalignp	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1
-compare_humann2_output	332.0	10.0	compare_humann2_output	Compare outputs of HUMAnN2 for several samples and extract similar and specific information	compare_humann2_outputs	compare_humann2_outputs		Compare HUMAnN2 outputs	This tool compare HUMANnN2 outputs with gene families or pathways and their relative abundances between several samples	Comparison	Metagenomics, Gene and protein families	To update		Metagenomics	compare_humann2_output	bebatut	https://github.com/bgruening/galaxytools/tree/master/tools/compare_humann2_output	https://github.com/bgruening/galaxytools/tree/master/tools/compare_humann2_output	0.2.0			Comparison	Metagenomics, Gene and protein families	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/complement	1.0.0	bx-python	0.11.0			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	1
-compute_motif_frequencies_for_all_motifs	94.0	2.0	compute_motif_frequencies_for_all_motifs	Compute Motif Frequencies For All Motifs, motif by motif.								To update		Sequence Analysis, Statistics	compute_motif_frequencies_for_all_motifs	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_motif_frequencies_for_all_motifs	https://github.com/galaxyproject/tools-devteam/tree/main/tools/compute_motif_frequencies_for_all_motifs	1.0.0					0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1
-compute_motifs_frequency	65.0		compute_motifs_frequency	Compute Motif Frequencies in indel flanking regions.								To update		Sequence Analysis, Statistics	compute_motifs_frequency	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_motifs_frequency	https://github.com/galaxyproject/tools-devteam/tree/main/tools/compute_motifs_frequency	1.0.0					0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1
-compute_q_values	35.0		compute_q_values	Compute q-values based on multiple simultaneous tests p-values								To update		Statistics	compute_q_values	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_q_values	https://github.com/galaxyproject/tools-devteam/tree/main/tools/compute_q_values	1.0.1	R				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-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	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/concat	1.0.1	bx-python	0.11.0			1	1	1	1	1	1	1	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	1
-condense_characters			Condense characters1	Condense consecutive characters.								To update		Text Manipulation	condense_characters	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters	https://github.com/galaxyproject/tools-devteam/tree/main/tools/condense_characters	1.0.0					1	1	0	0	1	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-convert_characters			Convert characters1	Convert delimiters to tab.								To update		Text Manipulation	convert_characters	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters	https://github.com/galaxyproject/tools-devteam/tree/main/tools/convert_characters	1.0.1	python				1	1	1	1	1	1	1	1	0	1	1	1	1	0	1	1	1	1	1	1	0	1	1	1	1	1	1	0	0	0	0	1	0	0	1	0	1	1	0	1	1	1
-convert_solid_color2nuc			color2nuc	Convert Color Space to Nucleotides								To update		Fasta Manipulation	convert_solid_color2nuc	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_solid_color2nuc	https://github.com/galaxyproject/tools-devteam/tree/main/tools/convert_solid_color2nuc	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-coprarna			coprarna	Target prediction for prokaryotic trans-acting small RNAs								To update	https://github.com/PatrickRWright/CopraRNA	RNA, Sequence Analysis	coprarna	rnateam	https://github.com/PatrickRWright/CopraRNA	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/coprarna	2.1.1	coprarna	2.1.4			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-correlation	809.0	47.0	cor2	Correlation for numeric columns								To update		Statistics	correlation	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/correlation	https://github.com/galaxyproject/tools-devteam/tree/main/tools/correlation	1.0.0	rpy				0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1
-count_gff_features	271.0	49.0	count_gff_features	Count GFF Features								To update		Sequence Analysis	count_gff_features	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/count_gff_features	https://github.com/galaxyproject/tools-devteam/tree/main/tools/count_gff_features	0.2	galaxy-ops	1.1.0			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1
-count_roi_variants			count_roi_variants	Count sequence variants in region of interest in BAM file								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants	Assembly, SAM	count_roi_variants	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants	https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants	0.0.6	samtools	1.20			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-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	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/coverage	1.0.0	bx-python	0.11.0			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	1
-coverage_stats			coverage_stats	BAM coverage statistics using samtools idxstats and depth								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats	Assembly, SAM	coverage_stats	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats	https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats	0.1.0	samtools	1.20			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-cpat	134.0	21.0	cpat	Coding-potential assessment tool using an alignment-free logistic regression model.								Up-to-date	https://github.com/liguowang/cpat	Transcriptomics	cpat	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/cpat	https://github.com/bgruening/galaxytools/tree/master/tools/cpat	3.0.5	cpat	3.0.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0
-crt			crispr_recognition_tool	CRISPR Recognition Tool								To update		Sequence Analysis	crispr_recognition_tool	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/crt	https://github.com/bgruening/galaxytools/tree/master/tools/crt	1.2.0	crisper_recognition_tool	1.2			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1
-ctd_batch	203.0	13.0	ctdBatch_1	CTD analysis of chemicals, diseases, or genes								To update		Sequence Analysis	ctd_batch	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/ctd_batch	https://github.com/galaxyproject/tools-devteam/tree/main/tools/ctd_batch	1.0.0					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1
-cummerbund	1782.0	31.0	cummeRbund	Wrapper for the Bioconductor cummeRbund library								To update	https://bioconductor.org/packages/release/bioc/html/cummeRbund.html	RNA, Visualization	cummerbund	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund	https://github.com/galaxyproject/tools-devteam/tree/main/tools/cummerbund	2.16.0	fonts-conda-ecosystem				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1
-cummerbund_to_tabular	1204.0	13.0	cummerbund_to_cuffdiff	Regenerate the tabular files generated by cuffdiff from a cummeRbund SQLite database.								To update		Convert Formats, Next Gen Mappers	cummerbund_to_tabular	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund_to_tabular	https://github.com/galaxyproject/tools-devteam/tree/main/tools/cummerbund_to_tabular	1.0.1					1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1
-cut_columns			Cut1	Select columns from a dataset.								To update		Text Manipulation	cut_columns	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns	https://github.com/galaxyproject/tools-devteam/tree/main/tools/cut_columns	1.0.2					1	1	1	1	1	1	1	1	0	1	1	1	1	0	1	0	1	1	1	1	0	1	1	1	1	1	1	1	0	0	0	1	0	0	1	0	1	1	0	1	1	1
-delete_overlapping_indels	39.0	2.0	delete_overlapping_indels	Delete Overlapping Indels from a chromosome indels file								To update		Sequence Analysis	delete_overlapping_indels	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/delete_overlapping_indels	https://github.com/galaxyproject/tools-devteam/tree/main/tools/delete_overlapping_indels	1.0.0					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1
-dewseq	72.0	11.0	dewseq	DEWSeq is a sliding window based peak caller for eCLIP/iCLIP data								To update	https://github.com/EMBL-Hentze-group/DEWSeq_analysis_helpers	Sequence Analysis, RNA, CLIP-seq	dewseq	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq	0.1.0+galaxy0	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0
-dgidb_annotator	231.0	30.0	dgidb_annotate	Annotates a tabular file with information from the Drug-Gene Interaction Database (http://dgidb.genome.wustl.edu/)								To update		Systems Biology, Variant Analysis	dgidb_annotator	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/dgidb_annotator	https://github.com/galaxyproject/tools-devteam/tree/main/tools/dgidb_annotator	0.1					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1
-diff	235.0	30.0	diff	GNU diff tool that calculates the differences between two files.								To update	http://www.gnu.org/software/diffutils/	Text Manipulation	diff	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/diff	https://github.com/bgruening/galaxytools/tree/master/tools/diff	3.7	diffutils				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1
-diffbind	6264.0	250.0		Diffbind provides functions for  processing  ChIP-Seq  data.								To update	http://bioconductor.org/packages/release/bioc/html/DiffBind.html	ChIP-seq	diffbind	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/diffbind	https://github.com/bgruening/galaxytools/tree/master/tools/diffbind						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-divide_pg_snp	31.0		dividePgSnp	Separate pgSnp alleles into columns								To update		Sequence Analysis	divide_pg_snp	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/divide_pg_snp	https://github.com/galaxyproject/tools-devteam/tree/main/tools/divide_pg_snp	1.0.0					1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1
-dorina	1086.0	1.0	dorina_search	data source for RNA interactions in post-transcriptional regulation								To update		RNA, Data Source	dorina	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dorina/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dorina	1.0					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0
-dot2ct			rnastructure_dot2ct	Dot-Bracket to Connect Table (CT)								To update		Sequence Analysis, RNA	dot2ct	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dot2ct	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dot2ct	5.7.a	rnastructure	6.4			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-dotknot	83.0	1.0	dotknot	DotKnot is a heuristic method for pseudoknot prediction in a given RNA sequence								To update	http://dotknot.csse.uwa.edu.au/	RNA, Proteomics	dotknot	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dotknot	1.3.1	vienna_rna				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0
-draw_stacked_barplots	173.0	12.0	draw_stacked_barplots	Draw Stacked Bar Plots for different categories and different criteria								To update		Graphics, Statistics	draw_stacked_barplots	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/draw_stacked_barplots	https://github.com/galaxyproject/tools-devteam/tree/main/tools/draw_stacked_barplots	1.0.0	R				0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1
-dwt_cor_ava_perclass			compute_p-values_correlation_coefficients_feature_occurrences_between_two_datasets_using_discrete_wavelet_transfom	Compute P-values and Correlation Coefficients for Feature Occurrences								To update		Statistics	dwt_cor_ava_perclass	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass	https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_cor_ava_perclass	1.0.1	r-waveslim	1.7.5			0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-dwt_cor_avb_all			compute_p-values_correlation_coefficients_featureA_featureB_occurrences_between_two_datasets_using_discrete_wavelet_transfom	Compute P-values and Correlation Coefficients for Occurrences of Two Set of Features								To update		Statistics	dwt_cor_avb_all	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_avb_all	https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_cor_avb_all	1.0.1	r-waveslim	1.7.5			0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-dwt_ivc_all			compute_p-values_second_moments_feature_occurrences_between_two_datasets_using_discrete_wavelet_transfom	Compute P-values and Second Moments for Feature Occurrences								To update		Statistics	dwt_ivc_all	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_ivc_all	https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_ivc_all	1.0.1	r-waveslim	1.7.5			0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-dwt_var_perclass			compute_p-values_max_variances_feature_occurrences_in_one_dataset_using_discrete_wavelet_transfom	Compute P-values and Max Variances for Feature Occurrences								To update		Statistics	dwt_var_perclass	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perclass	https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_var_perclass	1.0.1	r-waveslim	1.7.5			0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-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	https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_var_perfeature	1.0.2	r-bitops				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1
-ear			make_ear	A tool to compile assembly reports and stastics from assembly pipeline								To update	https://github.com/ERGA-consortium/EARs/tree/main	Sequence Analysis, Assembly	erga_ear	iuc	https://github.com/ERGA-consortium/EARs/tree/main	https://github.com/bgruening/galaxytools/tree/master/tools/ear	1.0.0	reportlab				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-edta	484.0	58.0	edta	The EDTA package was designed to filter out false discoveries in raw TE candidates and generate a high-quality non-redundant TE library for whole-genome TE annotations. 	edta	edta		The Extensive de novo TE Annotator (EDTA)	The EDTA package was designed to filter out false discoveries in raw TE candidates and generate a high-quality non-redundant TE library for whole-genome TE annotations. Selection of initial search programs were based on benckmarkings on the annotation performance using a manually curated TE library in the rice genome.	De-novo assembly, Deisotoping, Genome annotation	Workflows, Mobile genetic elements, Plant biology, Transcription factors and regulatory sites, Model organisms	To update	https://github.com/oushujun/EDTA	Variant Analysis	edta	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/edta	https://github.com/bgruening/galaxytools/tree/master/tools/edta		edta	2.2.0	De-novo assembly, Deisotoping, Genome annotation	Workflows, Mobile genetic elements, Plant biology, Transcription factors and regulatory sites, Model organisms	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0
-effectiveT3			effectiveT3	Find bacterial type III effectors in protein sequences	effectivet3	effectivet3		EffectiveT3	Prediction of putative Type-III secreted proteins.	Sequence classification	Sequence analysis	To update	http://effectors.org	Sequence Analysis	effectivet3	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3	https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3	0.0.21	effectiveT3	1.0.1	Sequence classification	Sequence analysis	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-epicseg	245.0	5.0	epicseg_segment	EpiCSeg is a tool for conducting chromatin segmentation.								To update	https://github.com/lamortenera/epicseg	Epigenetics	epicseg	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/epicseg	https://github.com/bgruening/galaxytools/tree/master/tools/epicseg	@VERSION_STRING@	epicseg	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1
-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	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/exparna	1.0.1	exparna	1.0.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-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	https://github.com/galaxyproject/tools-devteam/tree/main/tools/express	1.1.1	eXpress	1.5.1			0	1	1	0	0	1	1	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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	https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_compute_length	1.0.3	python				1	1	1	1	1	1	1	1	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	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	https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_concatenate_by_species	0.0.1	bx-python	0.11.0			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1
-fasta_filter_by_id			fasta_filter_by_id	Filter FASTA sequences by ID (DEPRECATED)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id	Fasta Manipulation, Sequence Analysis, Text Manipulation	fasta_filter_by_id	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id	https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id	0.0.7	galaxy_sequence_utils	1.1.5			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-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	https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_filter_by_length	1.2	python				1	1	1	1	1	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	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	https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_to_tabular	1.1.1	python				1	1	1	1	1	1	1	1	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	1
-fastq_filter_by_id			fastq_filter_by_id	Filter FASTQ sequences by ID (DEPRECATED)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id	Fastq Manipulation, Sequence Analysis, Text Manipulation	fastq_filter_by_id	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id	0.0.7	galaxy_sequence_utils	1.1.5			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-fastq_info	5765.0	679.0	fastq_info	FASTQ info allows to validate single or paired fastq files								To update	https://github.com/nunofonseca/fastq_utils	Fastq Manipulation	fastq_info	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info	https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info	0.25.1	fastq_utils	0.25.2			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0
-fastq_pair_names			fastq_pair_names	Extract FASTQ paired read names								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names	Sequence Analysis	fastq_pair_names	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names	0.0.5	galaxy_sequence_utils	1.1.5			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-fastq_paired_unpaired			fastq_paired_unpaired	Divide FASTQ file into paired and unpaired reads								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired	Sequence Analysis, Text Manipulation	fastq_paired_unpaired	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired	0.1.5	galaxy_sequence_utils	1.1.5			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-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	https://github.com/galaxyproject/tools-devteam/tree/main/tools/fastq_trimmer_by_quality	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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	https://github.com/galaxyproject/tools-devteam/tree/main/tools/fastqsolexa_to_fasta_qual	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-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	https://github.com/galaxyproject/tools-devteam/tree/main/tools/featurecounter	2.0.0	bx-python	0.11.0			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1
-file_manipulation			bg_uniq	This tool returns all unique lines from a tab-separated file.								To update	https://github.com/bgruening/galaxytools/tree/master/tools/file_manipulation	Text Manipulation	unique	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/file_manipulation	https://github.com/bgruening/galaxytools/tree/master/tools/file_manipulation	0.4	python				0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0
-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	https://github.com/galaxyproject/tools-devteam/tree/main/tools/filter_transcripts_via_tracking	0.1					1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1
-find_diag_hits	69.0	5.0	find_diag_hits	Find diagnostic hits								To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	find_diag_hits	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/find_diag_hits	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/find_diag_hits	1.0.0	taxonomy	0.10.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1
-find_subsequences	763.0	31.0	bg_find_subsequences									To update			find_subsequences	bgruening		https://github.com/bgruening/galaxytools/tree/master/tools/find_subsequences	0.3	biopython	1.70			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/flanking_features	4.0.1	bx-python	0.11.0			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	1
-flye	20904.0	1499.0	flye	Assembly of long and error-prone reads.	Flye	Flye		Flye	Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The package represents a complete pipeline: it takes raw PB / ONT reads as input and outputs polished contigs.	Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly	Sequence assembly, Metagenomics, Whole genome sequencing, Genomics	To update	https://github.com/fenderglass/Flye/	Assembly	flye	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/flye	https://github.com/bgruening/galaxytools/tree/master/tools/flye	2.9.3	flye	2.9.4	Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly	Sequence assembly, Metagenomics, Whole genome sequencing	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	1
-footprint	57.0		footprint	Find transcription factor footprints								To update	https://ohlerlab.mdc-berlin.de/software/Reproducible_footprinting_139/	Epigenetics	footprint	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/footprint	https://github.com/bgruening/galaxytools/tree/master/tools/footprint	1.0.0	footprint	1.0.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1
-format_cd_hit_output	166.0	20.0	format_cd_hit_output	Format CD-hit output to rename representative sequences with cluster name and/or extract distribution inside clusters given a mapping file								To update		Fasta Manipulation	format_cd_hit_output	bebatut	https://github.com/bgruening/galaxytools/tree/master/tools/format_cd_hit_output/	https://github.com/bgruening/galaxytools/tree/master/tools/format_cd_hit_output	1.0.0+galaxy1					0	0	1	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1
-format_metaphlan2_output	5588.0	166.0	format_metaphlan2_output	Format MetaPhlAn2 output to extract abundance at different taxonomic levels	format_metaphlan2_output	format_metaphlan2_output		Format metaphlan2 output	This tool format output file of MetaPhlan2 containing community content (abundance) at all taxonomic levels (from kingdom to strains).	Formatting	Taxonomy, Metagenomics	To update		Metagenomics	format_metaphlan2_output	bebatut	https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/	https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output	0.2.0			Formatting	Taxonomy, Metagenomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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	https://github.com/galaxyproject/tools-devteam/tree/main/tools/generate_pc_lda_matrix	1.0.0					1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/get_flanks	1.0.0	bx-python	0.11.0			1	1	1	1	1	1	1	1	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1
-get_orfs_or_cdss	7.0		get_orfs_or_cdss	Search nucleotide sequences for open reading frames (ORFs), or coding sequences (CDSs)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss	Sequence Analysis	get_orfs_or_cdss	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss	https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss	0.2.3	biopython	1.70			0	1	1	1	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0
-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	https://github.com/galaxyproject/tools-devteam/tree/main/tools/getindelrates_3way	1.0.0	bx-python	0.11.0			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-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	https://github.com/galaxyproject/tools-devteam/tree/main/tools/getindels_2way	1.0.0	numpy				1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-gfastats	8159.0	418.0	gfastats	Tool for generating sequence statistics and simultaneous genome assembly file manipulation.	gfastats	gfastats		gfastats	gfastats is a single fast and exhaustive tool for summary statistics and simultaneous genome assembly file manipulation. gfastats also allows seamless fasta/fastq/gfa conversion.	Data handling	Computational biology	Up-to-date	https://github.com/vgl-hub/gfastats	Sequence Analysis	gfastats	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/gfastats	https://github.com/bgruening/galaxytools/tree/master/tools/gfastats	1.3.6	gfastats	1.3.6	Data handling	Computational biology	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0
-gi2taxonomy	660.0	27.0	Fetch Taxonomic Ranks	Fetch taxonomic representation	gi2taxonomy	gi2taxonomy		gi2taxonomy	The tool fetches taxonomic information for a list of sequence identifiers (i.e. GI numbers, as used by the National Center for Biotechnology Information (NCBI).	Database search, ID mapping	Taxonomy	To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	gi2taxonomy	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/gi2taxonomy	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/gi2taxonomy	1.1.1	taxonomy	0.10.0	Database search, ID mapping	Taxonomy	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0
-glimmer_hmm				GlimmerHMM is a new gene finder based on a Generalized Hidden Markov Model (GHMM)								To update	https://ccb.jhu.edu/software/glimmerhmm/	Sequence Analysis	glimmer_hmm	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm	https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-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	https://github.com/galaxyproject/tools-devteam/tree/main/tools/gmaj	2.0.1					1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1
-gotohscan	71.0	1.0	rbc_gotohscan	Find subsequences in db								To update		Sequence Analysis	gotohscan	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/gotohscan	https://github.com/bgruening/galaxytools/tree/master/tools/gotohscan	1.3.0	gotohscan	1.3			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1
-graph_converter			graph_converter	Convert between different graph formats								To update		Convert Formats	graph_converter	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/graph_converter	https://github.com/bgruening/galaxytools/tree/master/tools/graph_converter	0.1.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-graphclust	6.0		graphclust	GraphClust can be used for structural clustering of RNA sequences.								To update	http://www.bioinf.uni-freiburg.de/Software/GraphClust/	RNA	graphclust	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/graphclust	https://github.com/bgruening/galaxytools/tree/master/tools/graphclust	0.1	GraphClust				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-graphicsmagick			graphicsmagick_image_compare, graphicsmagick_image_convert, graphicsmagick_image_montage	Contains tools based on GraphicsMagick								To update	http://www.graphicsmagick.org	Imaging	graphicsmagick	bgruening	https://github.com/bgruening/galaxytools/new/gm/tools/image_processing/image_processing/	https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/graphicsmagick	1.3.43	graphicsmagick	1.3.26			1	0	3	0	1	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2
-graphmap			graphmap_align, graphmap_overlap	Mapper for long, error-prone reads.	graphmap	graphmap		graphmap	Splice-aware RNA-seq mapper for long reads | GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.html https://www.biorxiv.org/content/10.1101/720458v1	Sequence trimming, EST assembly, Read mapping	Gene transcripts, RNA-Seq, RNA splicing	To update	https://github.com/isovic/graphmap/	Assembly	graphmap	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/graphmap	https://github.com/bgruening/galaxytools/tree/master/tools/graphmap	0.5.2	graphmap	0.6.3	Sequence trimming, EST assembly, Read mapping	Gene transcripts, RNA-Seq, RNA splicing	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2
-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	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot	1.1.7+galaxy1	graphprot	1.1.7			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1
-hclust2			hclust2	Plots heatmaps								To update	https://bitbucket.org/nsegata/hclust2/	Data Visualization	hclust2	rnateam	https://github.com/yuanbit/galaxytools/tree/hclust2/tools/hclust2	https://github.com/bgruening/galaxytools/tree/master/tools/hclust2	0.99	hclust2	1.0.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-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	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/hgv/hgv_fundo	1.0.0					1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/hgv/hgv_hilbertvis	1.0.0	R				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1
-hictk			hictk	Convert cooler to juicebox_hic								Up-to-date	https://github.com/paulsengroup/hictk	Convert Formats, Epigenetics	hictk	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/hictk	https://github.com/bgruening/galaxytools/tree/master/tools/hictk	0.0.12	hictk	0.0.12			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-hicup			hicup2juicer, hicup_deduplicator, hicup_digester, hicup_filter, hicup_hicup, hicup_mapper, hicup_truncater	The HiCUP-Pipeline from the Bioinformatics Babraham Institute.								To update	https://www.bioinformatics.babraham.ac.uk/projects/hicup/read_the_docs/html/index.html	Epigenetics	hicup	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/hicup	https://github.com/bgruening/galaxytools/tree/master/tools/hicup	0.9.2					7	0	7	0	7	0	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	6
-hifiasm	1410.0	297.0	hifiasm	A fast haplotype-resolved de novo assembler								To update	https://github.com/chhylp123/hifiasm	Assembly	hifiasm	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm	https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm	0.19.8	hifiasm	0.19.9			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0
-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	https://github.com/galaxyproject/tools-devteam/tree/main/tools/hisat	1.0.3	hisat				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-histogram	2367.0	94.0	histogram_rpy	Histogram of a numeric column								To update		Graphics, Statistics	histogram	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/histogram	https://github.com/galaxyproject/tools-devteam/tree/main/tools/histogram	1.0.4	rpy2	2.7.8			1	1	1	1	1	1	1	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1
-homer				Software for motif discovery and next generation sequencing analysis.								To update	http://homer.salk.edu/homer/	Sequence Analysis	homer	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/homer	https://github.com/bgruening/galaxytools/tree/master/tools/homer						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-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	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip	0.1.0+galaxy0	htseq-clip	2.19.0b0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0
-illumina_methylation_analyser			illumina_methylation_analyser	Methylation analyzer for Illumina 450k DNA emthylation microarrays								To update	https://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyser	Sequence Analysis	illumina_methylation_analyser	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyser	https://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyser	0.1	Rscript				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-imagej2			imagej2_adjust_threshold_binary, imagej2_analyze_particles_binary, imagej2_analyze_skeleton, imagej2_binary_to_edm, imagej2_bunwarpj_adapt_transform, imagej2_bunwarpj_align, imagej2_bunwarpj_compare_elastic, imagej2_bunwarpj_compare_elastic_raw, imagej2_bunwarpj_compare_raw, imagej2_bunwarpj_compose_elastic, imagej2_bunwarpj_compose_raw, imagej2_bunwarpj_compose_raw_elastic, imagej2_bunwarpj_convert_to_raw, imagej2_bunwarpj_elastic_transform, imagej2_bunwarpj_raw_transform, imagej2_create_image, imagej2_enhance_contrast, imagej2_find_edges, imagej2_find_maxima, imagej2_make_binary, imagej2_math, imagej2_noise, imagej2_shadows, imagej2_sharpen, imagej2_skeletonize3d, imagej2_smooth, imagej2_watershed_binary	ImageJ2 is a new version of ImageJ for the next generation of multidimensionalimage data, with a focus on scientific imaging.	imagej	imagej	imagej2	ImageJ2	It is a public domain Java image processing program, which was designed with an open architecture. Custom acquisition, analysis and processing plugins can be developed using ImageJ’s built-in editor and a Java compiler. User-written plugins make it possible to solve many image processing and analysis problems, from three-dimensional live-cell imaging, to radiological image processing, multiple imaging system data comparisons to automated hematology systems.	Image analysis, Image annotation, Visualisation	Imaging	To update	http://fiji.sc	Imaging	imagej2	imgteam	https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2	https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2				Image analysis, Image annotation, Visualisation	Imaging	0	0	27	0	0	0	27	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	27	27
-improviser			proteomics_improviser	Visualisation of PepXML files								To update	http://www.improviser.uni-freiburg.de/	Proteomics	proteomics_improviser	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/proteomics/improviser	https://github.com/bgruening/galaxytools/tree/master/tools/proteomics/improviser	1.1.0.1					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-indels_3way	22.0		indels_3way	Fetch Indels from 3-way alignments								To update		Sequence Analysis	indels_3way	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/indels_3way	https://github.com/galaxyproject/tools-devteam/tree/main/tools/indels_3way	1.0.3					1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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	"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, Structural genomics	To update	http://infernal.janelia.org/	RNA	infernal	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/infernal	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/infernal	1.1.4	infernal	1.1.5	Nucleic acid feature detection	Sequence sites, features and motifs, Structural genomics	0	6	6	0	0	6	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/inforna						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-instagraal	139.0	14.0	instagraal	Large genome reassembly based on Hi-C data	instagraal	instagraal		instaGRAAL	Chromosome-level quality scaffolding of brown algal genomes using InstaGRAAL.Large genome reassembly based on Hi-C data, continuation of GRAAL.Large genome reassembly based on Hi-C data (continuation and partial rewrite of GRAAL) and post-scaffolding polishing libraries.This work is under continuous development/improvement - see GRAAL for information about the basic principles.sudo pip3 install -e git+https://github.com/koszullab/instagraal.git@master#egg=instagraal.Note to OS X users: There is currently no CUDA support on Mojave (10.14) and it is unclear when it is going to be added, if it is to be added at all. This means instaGRAAL (or indeed any CUDA-based application) will not work on Mojave. If you wish to run it on OS X, the only solution for now is to downgrade to High Sierra (10.13)	Genome assembly, Mapping assembly, Genetic mapping, Scaffolding	Sequence assembly, Mapping, Metagenomics, Statistics and probability, DNA binding sites	To update	https://github.com/koszullab/instaGRAAL	Assembly	instagraal	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/instagraal	https://github.com/bgruening/galaxytools/tree/master/tools/instagraal	0.1.6			Genome assembly, Mapping assembly, Genetic mapping, Scaffolding	Sequence assembly, Mapping, Metagenomics, Statistics and probability, DNA binding sites	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0
-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	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna	3.4.0	intarna	3.4.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/intersect	1.0.0	bx-python	0.11.0			1	1	1	1	1	1	1	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	1
-iprscan5				Interproscan queries the interpro database and provides annotations.								To update	http://www.ebi.ac.uk/Tools/pfa/iprscan5/	Sequence Analysis	iprscan5	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/iprscan5	https://github.com/bgruening/galaxytools/tree/master/tools/iprscan5						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-itsx	868.0	38.0	itsx	ITSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences.	ITSx	ITSx		ITSx	TSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences, which is commonly used as a molecular barcode for e.g. fungi. As the inclusion of parts of the neighbouring, very conserved, ribosomal genes (SSU, 5S and LSU rRNA sequences) in the sequence identification process can lead to severely misleading results, ITSx identifies and extracts only the ITS regions themselves.	Sequence feature detection	Functional, regulatory and non-coding RNA, Microbiology	Up-to-date	https://microbiology.se/software/itsx/	Metagenomics	itsx	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/itsx	https://github.com/bgruening/galaxytools/tree/master/tools/itsx	1.1.3	itsx	1.1.3	Sequence feature detection	Functional, regulatory and non-coding RNA, Microbiology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0
-jbrowse2			jbrowse2	JBrowse2 Genome Browser integrated as a Galaxy Tool	jbrowse2	jbrowse2						To update	https://jbrowse.org	Sequence Analysis	jbrowse2	fubar	https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2	https://github.com/bgruening/galaxytools/tree/master/tools/jbrowse2	2.11.1	jbrowse2	2.11.2			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-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	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/join	1.0.0	bx-python	0.11.0			1	1	1	1	1	1	1	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	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	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy	1.0.1	python				0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	1
-jupyter_job			run_jupyter_job	Run jupyter notebook script in Galaxy								To update		Machine Learning	run_jupyter_job	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job	https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job	0.0.1					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-kernel_canonical_correlation_analysis	69.0	2.0	kcca1	Kernel Canonical Correlation Analysis								To update		Statistics	kernel_canonical_correlation_analysis	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/kernel_canonical_correlation_analysis	https://github.com/galaxyproject/tools-devteam/tree/main/tools/kernel_canonical_correlation_analysis	1.0.0	rpy				1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1
-kernel_principal_component_analysis	155.0	13.0	kpca1	Kernel Principal Component Analysis								To update		Statistics	kernel_principal_component_analysis	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/kernel_principal_component_analysis	https://github.com/galaxyproject/tools-devteam/tree/main/tools/kernel_principal_component_analysis	1.0.0	rpy				1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/kinwalker						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-kraken2tax	14683.0	481.0	Kraken2Tax	Convert Kraken output to Galaxy taxonomy data.								To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	kraken2tax	devteam	https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/taxonomy/kraken2tax/	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/kraken2tax	1.2+galaxy0	gawk				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	1
-labels			bg_labels	remaps and annotates alignments								To update	https://github.com/bgruening/galaxytools/tree/master/tools/labels	Sequence Analysis	labels	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/labels	https://github.com/bgruening/galaxytools/tree/master/tools/labels	1.0.5.0	labels				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-lastz_paired_reads	9.0	1.0	lastz_paired_reads_wrapper	Galaxy wrapper for the Lastz alignment tool on paired reads								To update		Next Gen Mappers	lastz_paired_reads	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads	https://github.com/galaxyproject/tools-devteam/tree/main/tools/lastz_paired_reads	1.1.1	lastz	1.04.22			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1
-lca_wrapper	137.0	2.0	lca1	Find lowest diagnostic rank								To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	lca_wrapper	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/lca_wrapper	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/lca_wrapper	1.0.1	taxonomy	0.10.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1
-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	https://github.com/galaxyproject/tools-devteam/tree/main/tools/lda_analysis	1.0.1	R				1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1
-lighter	152.0	9.0	lighter	Lighter is a kmer-based error correction method for whole genome sequencing data	lighter	lighter		Lighter	Kmer-based error correction method for whole genome sequencing data. Lighter uses sampling (rather than counting) to obtain a set of kmers that are likely from the genome. Using this information, Lighter can correct the reads containing sequence errors.	k-mer counting, Sequence read processing, Sequencing quality control, Sequencing error detection	Sequencing, Whole genome sequencing, DNA, Genomics	To update	https://github.com/mourisl/Lighter	Sequence Analysis, Fasta Manipulation	lighter	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/lighter	https://github.com/bgruening/galaxytools/tree/master/tools/lighter	1.0	lighter	1.1.3	k-mer counting, Sequence read processing, Sequencing quality control, Sequencing error detection	Whole genome sequencing, DNA, Genomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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	https://github.com/galaxyproject/tools-devteam/tree/main/tools/linear_regression	1.0.1	R				1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-locarna			locarna_exparnap, locarna_multiple, locarna_pairwise, locarna_pairwise_p, locarna_reliability_profile	LocARNA - A suite for multiple alignment and folding of RNAs								To update	http://www.bioinf.uni-freiburg.de/Software/LocARNA/	RNA	locarna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna	1.9.2.3	locarna	2.0.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	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	https://github.com/galaxyproject/tools-devteam/tree/main/tools/logistic_regression_vif	1.0.1	numpy				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-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	https://github.com/galaxyproject/tools-devteam/tree/main/tools/maf_cpg_filter	1.0.0	bx-python	0.11.0			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-mafft	143045.0	817.0	rbc_mafft_add, rbc_mafft	Multiple alignment program for amino acid or nucleotide sequences	MAFFT	MAFFT		MAFFT	MAFFT (Multiple Alignment using Fast Fourier Transform) is a high speed multiple sequence alignment program.	Multiple sequence alignment	Sequence analysis	To update	https://mafft.cbrc.jp/alignment/software/	RNA	mafft	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/mafft	https://github.com/bgruening/galaxytools/tree/master/tools/mafft	7.520	mafft	7.525	Multiple sequence alignment	Sequence analysis	2	2	2	2	2	2	2	2	0	0	0	1	0	0	2	0	0	0	0	0	0	0	1	0	2	0	0	2	0	0	0	2	0	0	0	0	0	0	0	2	2	2
-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	https://github.com/galaxyproject/tools-devteam/tree/main/tools/mapping_to_ucsc	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-mavedb			mavedb_importer	data source for MaveDB								To update		Data Source	mavedb_importer	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/mave_tools/mavedb/	https://github.com/bgruening/galaxytools/tree/master/tools/mave_tools/mavedb	0.9					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-mea	85.0	3.0	mea	Maximum expected accuracy prediction								To update	http://www.bioinf.uni-leipzig.de/Software/mea	RNA	mea	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mea	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mea	0.6.4.1	mea	0.6.4			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	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	https://github.com/galaxyproject/tools-devteam/tree/main/tools/megablast_xml_parser	1.0.1	python				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/merge	1.0.0	bx-python	0.11.0			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	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	https://github.com/galaxyproject/tools-devteam/tree/main/tools/merge_cols	1.0.3	python				1	1	1	1	1	1	1	1	0	1	1	1	1	0	1	0	1	1	1	1	0	1	1	1	1	1	1	0	0	0	0	1	0	0	1	0	1	1	0	1	1	1
-methtools			methtools_calling, r_correlation_matrix, methtools_destrand, methtools_dmr, methtools_filter, methtools_plot, smooth_running_window, methtools_tiling	tools for methylation analysis								To update	https://github.com/bgruening/galaxytools/tree/master/tools/methtools	Sequence Analysis	methtools	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/methtools	https://github.com/bgruening/galaxytools/tree/master/tools/methtools	0.1.1	methtools				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-methyldackel			pileometh	A tool for processing bisulfite sequencing alignments								To update	https://github.com/dpryan79/MethylDackel	Sequence Analysis	pileometh	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel	https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel	0.5.2	methyldackel	0.6.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	1
-methylkit			methylkit	A method for DNA methylation analysis and annotation from high-throughput bisulfite sequencing.								To update	http://bioconductor.org/packages/release/bioc/html/methylKit.html	Epigenetics	methylkit	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/methylkit	https://github.com/bgruening/galaxytools/tree/master/tools/methylkit	0.99.2	bioconductor-methylkit	1.28.0			0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-metilene	3966.0	103.0	metilene	Differential DNA methylation calling								To update		RNA, Statistics	metilene	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/metilene	https://github.com/bgruening/galaxytools/tree/master/tools/metilene	0.2.6.1	metilene	0.2.8			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	1
-mgnify_seqprep			mgnify_seqprep	A modifiied vesion of SeqPrep. Made for use with the MGnify pipelines.	seqprep	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	To update	https://github.com/jstjohn/SeqPrep	Fastq Manipulation, Sequence Analysis	mgnify_seqprep	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/mgnify_seqprep	https://github.com/bgruening/galaxytools/tree/master/tools/mgnify_seqprep	1.2			Nucleic acid design	Genomics, Sequence assembly, Sequencing, Probes and primers	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-miclip			mi_clip	Identification of binding sites in CLIP-Seq data.								To update	https://cran.r-project.org/src/contrib/Archive/MiClip/	Sequence Analysis	miclip	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/miclip	https://github.com/bgruening/galaxytools/tree/master/tools/miclip	1.2.0	Rscript				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-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	https://github.com/galaxyproject/tools-devteam/tree/main/tools/microsatellite_birthdeath	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-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	https://github.com/galaxyproject/tools-devteam/tree/main/tools/microsats_alignment_level	1.0.0	sputnik				1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-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	https://github.com/galaxyproject/tools-devteam/tree/main/tools/microsats_mutability	1.1.0	bx-python	0.11.0			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-minced	895.0	53.0	minced	MinCED - Mining CRISPRs in Environmental Datasets								To update	http://bioweb2.pasteur.fr/docs/modules/minced/0.1.5/_README	Sequence Analysis	minced	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/minced	https://github.com/bgruening/galaxytools/tree/master/tools/minced	0.2.0	minced	0.4.2			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	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	https://github.com/galaxyproject/tools-devteam/tree/main/tools/mine	0.0.1	MINE				1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1
-minipolish	185.0	21.0	minipolish	Polishing miniasm assemblies	minipolish	minipolish		minipolish	A tool that bridges the output of miniasm (long-read assembly) and racon (assembly polishing) together to polish a draft assembly. It also provides read depth information in contigs.	Localised reassembly, Read depth analysis	Sequence assembly, Sequencing	Up-to-date	https://github.com/rrwick/Minipolish	Sequence Analysis	minipolish	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/minipolish	https://github.com/bgruening/galaxytools/tree/master/tools/minipolish	0.1.3	minipolish	0.1.3	Localised reassembly, Read depth analysis	Sequence assembly, Sequencing	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0
-mitohifi	613.0	56.0	mitohifi	Assembly mitogenomes from Pacbio HiFi read.								To update	https://github.com/marcelauliano/MitoHiFi/tree/mitohifi_v2	Assembly	mitohifi	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi	https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi	3					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0
-molecule2gspan			bg_mol2gspan	converter								To update	https://github.com/bgruening/galaxytools/tree/master/tools/molecule2gspan	Convert Formats	molecule_to_gspan	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/molecule2gspan	https://github.com/bgruening/galaxytools/tree/master/tools/molecule2gspan	0.2	openbabel	2.3.90dev7d621d9			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-mqc	76.0	5.0	mqc	Ribosome profiling mapping quality control tool								To update	https://github.com/Biobix/mQC	Sequence Analysis	mqc	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mqc/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mqc	1.9	mqc	1.10			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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	https://github.com/galaxyproject/tools-devteam/tree/main/tools/multispecies_orthologous_microsats	1.0.0	bx-sputnik				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-mummer	652.0	83.0	mummerplot_wrapper	Draw dotplots using mummer, mucmer, or promer with mummerplot								To update	http://mummer.sourceforge.net/	Graphics, Sequence Analysis, Visualization	mummer	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/mummer	https://github.com/peterjc/pico_galaxy/tree/master/tools/mummer	0.0.8	ghostscript	9.18			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1
-music_deconvolution	530.0	67.0	music_construct_eset, music_inspect_eset, music_manipulate_eset, music_compare, music_deconvolution	Multi-subject Single Cell deconvolution (MuSiC)								Up-to-date	https://github.com/xuranw/MuSiC	Transcriptomics	music	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/	https://github.com/bgruening/galaxytools/tree/master/tools/music_deconvolution	0.1.1	music-deconvolution	0.1.1			5	5	4	0	5	5	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0
-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	https://github.com/galaxyproject/tools-devteam/tree/main/tools/mutate_snp_codon	1.0.0					1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1
-nanopolish			nanopolish_eventalign, nanopolish_methylation, nanopolish_polya, nanopolish_variants	Nanopolish software package for signal-level analysis of Oxford Nanopore sequencing data.								Up-to-date	https://github.com/jts/nanopolish		nanopolish	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish	https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish	0.14.0	nanopolish	0.14.0			0	4	4	4	0	4	4	4	0	0	0	0	0	0	3	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	4
-nastiseq	40.0		nastiseq	A method to identify cis-NATs using ssRNA-seq								Up-to-date	https://ohlerlab.mdc-berlin.de/software/NASTIseq_104/	RNA	nastiseq	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/nastiseq	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/nastiseq	1.0	r-nastiseq	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1
-netboxr	11.0	5.0	netboxr	netboxr enables automated discovery of biological process modules by network analysis								To update		Systems Biology	netboxr	bgruening		https://github.com/bgruening/galaxytools/tree/master/tools/netboxr	1.6.0	bioconductor-netboxr	1.9.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0
-nextdenovo	268.0	84.0	nextdenovo	String graph-based de novo assembler for long reads	nextdenovo	nextdenovo		NextDenovo	"NextDenovo is a string graph-based de novo assembler for long reads (CLR, HiFi and ONT). It uses a ""correct-then-assemble"" strategy similar to canu (no correction step for PacBio Hifi reads), but requires significantly less computing resources and storages."	De-novo assembly, Genome assembly	Sequencing, Sequence assembly	To update	https://github.com/Nextomics/NextDenovo	Assembly	nextdenovo	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo	https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo	2.5.0	nextdenovo	2.5.2	De-novo assembly, Genome assembly	Sequencing, Sequence assembly	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0
-nlstradamus			nlstradamus	Find nuclear localization signals (NLSs) in protein sequences								To update	http://www.moseslab.csb.utoronto.ca/NLStradamus	Fasta Manipulation, Sequence Analysis	nlstradamus	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/nlstradamus	https://github.com/peterjc/pico_galaxy/tree/master/tools/nlstradamus	0.0.11	NLStradamus	1.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-nucleosome_prediction	861.0	2.0	Nucleosome	Prediction of Nucleosomes Positions on the Genome	nucleosome_prediction	nucleosome_prediction		nucleosome_prediction	Prediction of Nucleosomes Positions on the Genome	Prediction and recognition, Nucleosome position prediction, Sequence analysis	Structural genomics, Nucleic acid sites, features and motifs	Up-to-date	https://genie.weizmann.ac.il/software/nucleo_exe.html	Sequence Analysis	nucleosome_prediction	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/nucleosome_prediction	https://github.com/bgruening/galaxytools/tree/master/tools/nucleosome_prediction	3.0	nucleosome_prediction	3.0	Prediction and recognition, Nucleosome position prediction, Sequence analysis	Structural genomics, Nucleic acid sites, features and motifs	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1
-numeric_clustering	486.0		numeric_clustering	Clustering tool for numberic values								To update	http://scikit-learn.org/stable/index.html	Statistics	numeric_clustering	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering	https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering	0.9	anaconda				0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0
-openms			AccurateMassSearch, AdditiveSeries, BaselineFilter, CVInspector, CompNovo, CompNovoCID, ConsensusID, ConsensusMapNormalizer, ConvertTSVToTraML, ConvertTraMLToTSV, DTAExtractor, DeMeanderize, Decharger, DecoyDatabase, Digestor, DigestorMotif, EICExtractor, ERPairFinder, ExternalCalibration, FFEval, FalseDiscoveryRate, FeatureFinderCentroided, FeatureFinderIdentification, FeatureFinderIsotopeWavelet, FeatureFinderMRM, FeatureFinderMetabo, FeatureFinderMultiplex, FeatureFinderSuperHirn, FeatureLinkerLabeled, FeatureLinkerUnlabeled, FeatureLinkerUnlabeledQT, FidoAdapter, FileConverter, FileFilter, FileInfo, FileMerger, FuzzyDiff, HighResPrecursorMassCorrector, IDConflictResolver, IDDecoyProbability, IDExtractor, IDFileConverter, IDFilter, IDMapper, IDMassAccuracy, IDMerger, IDPosteriorErrorProbability, IDRTCalibration, IDRipper, IDScoreSwitcher, IDSplitter, ITRAQAnalyzer, InclusionExclusionListCreator, InspectAdapter, InternalCalibration, IsobaricAnalyzer, LabeledEval, LowMemPeakPickerHiRes, LowMemPeakPickerHiRes_RandomAccess, LuciphorAdapter, MRMMapper, MRMPairFinder, MRMTransitionGroupPicker, MSGFPlusAdapter, MSSimulator, MapAlignmentEvaluation, MapNormalizer, MapRTTransformer, MapStatistics, MascotAdapter, MascotAdapterOnline, MassCalculator, MassTraceExtractor, MetaProSIP, MetaboliteSpectralMatcher, MultiplexResolver, MzMLSplitter, MzTabExporter, NoiseFilterGaussian, NoiseFilterSGolay, OpenSwathAnalyzer, OpenSwathAssayGenerator, OpenSwathChromatogramExtractor, OpenSwathConfidenceScoring, OpenSwathDIAPreScoring, OpenSwathDecoyGenerator, OpenSwathFeatureXMLToTSV, OpenSwathFileSplitter, OpenSwathMzMLFileCacher, OpenSwathRTNormalizer, OpenSwathRewriteToFeatureXML, OpenSwathWorkflow, PTModel, PTPredict, PeakPickerHiRes, PeakPickerIterative, PeakPickerWavelet, PepNovoAdapter, PeptideIndexer, PhosphoScoring, PrecursorIonSelector, PrecursorMassCorrector, ProteinInference, ProteinQuantifier, ProteinResolver, QCCalculator, QCEmbedder, QCExporter, QCExtractor, QCImporter, QCMerger, QCShrinker, RNPxl, RNPxlXICFilter, RTEvaluation, RTModel, RTPredict, SemanticValidator, SequenceCoverageCalculator, SimpleSearchEngine, SpecLibCreator, SpectraFilterBernNorm, SpectraFilterMarkerMower, SpectraFilterNLargest, SpectraFilterNormalizer, SpectraFilterParentPeakMower, SpectraFilterScaler, SpectraFilterSqrtMower, SpectraFilterThresholdMower, SpectraFilterWindowMower, SpectraMerger, SvmTheoreticalSpectrumGeneratorTrainer, TICCalculator, TMTAnalyzer, TOFCalibration, TextExporter, TopPerc, TransformationEvaluation, XMLValidator, XTandemAdapter	OpenMS in version 2.1.								To update		Proteomics	openms	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/openms	https://github.com/bgruening/galaxytools/tree/master/tools/openms	2.1.0	openms	3.1.0			7	34	135	0	7	34	135	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	19	135	134
-pandas_rolling_window	269.0	7.0	pandas_rolling_window	Rolling window calculations								To update	https://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.DataFrame.rolling.html	Statistics	pandas_rolling_window	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/pandas_rolling_window	https://github.com/bgruening/galaxytools/tree/master/tools/pandas_rolling_window	0.1	numpy				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1
-paralyzer	299.0	7.0	paralyzer	A method to generate a high resolution map of interaction sites between RNA-binding proteins and their targets.								Up-to-date	https://ohlerlab.mdc-berlin.de/software/PARalyzer_85/	RNA	paralyzer	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer	1.5	paralyzer	1.5			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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	https://github.com/galaxyproject/tools-devteam/tree/main/tools/partialr_square	1.0.0	R				1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-peakachu	3109.0	78.0	peakachu	PEAKachu is a peak-caller for CLIP- and RIP-Seq data								To update		Sequence Analysis, RNA	peakachu	rnateam	https://github.com/tbischler/PEAKachu	https://github.com/bgruening/galaxytools/tree/master/tools/peakachu	0.2.0+galaxy1	peakachu	0.2.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	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	https://github.com/galaxyproject/tools-devteam/tree/main/tools/pearson_correlation	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-perf			stats_perf_tool	suitable for boolean classification problems								To update	http://osmot.cs.cornell.edu/kddcup/software.html		stats_perf_tool	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/perf	https://github.com/bgruening/galaxytools/tree/master/tools/perf	5.11.0	perf				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-pfamscan	165.0	19.0	pfamscan	Search a FASTA sequence against a library of Pfam HMM.	pfamscan	pfamscan		PfamScan	This tool is used to search a FASTA sequence against a library of Pfam HMM.	Protein sequence analysis	Sequence analysis	Up-to-date	http://ftp.ebi.ac.uk/pub/databases/Pfam/Tools/	Sequence Analysis	pfamscan	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/pfamscan	https://github.com/bgruening/galaxytools/tree/master/tools/pfamscan	1.6	pfam_scan	1.6	Protein sequence analysis	Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0
-pg_tools			pg_dump, pg_import, pg_query	tool suite for dealing with Postgresql databases from Galaxy's history								To update	https://www.postgresql.org	Data Export, Data Source	pgtools	bgruening	https://github.com/bgruening/galaxytools/tools/pgtools	https://github.com/bgruening/galaxytools/tree/master/tools/pg_tools		postgresql				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-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	https://github.com/galaxyproject/tools-devteam/tree/main/tools/pgsnp2gd_snp	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-pharmcat	82.0	14.0	pharmcat	Pharmacogenomics Clinical Annotation Tool								To update	https://pharmcat.org/	Variant Analysis	pharmcat	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat	https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat						1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0
-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	https://github.com/galaxyproject/tools-devteam/tree/main/tools/pileup_interval	1.0.3	bx-python	0.11.0			1	1	1	1	1	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	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	https://github.com/galaxyproject/tools-devteam/tree/main/tools/pileup_parser	1.0.2	perl				1	1	1	1	1	1	1	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	1
-pipmir	275.0	21.0	pipmir	A method to identify novel plant miRNA.								To update	https://ohlerlab.mdc-berlin.de/software/Pipeline_for_the_Identification_of_Plant_miRNAs_84/	RNA	pipmir	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir	0.1.0	pipmir	1.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1
-piranha	1809.0	39.0	piranha	Piranha is a peak-caller for CLIP- and RIP-Seq data								To update		Sequence Analysis, RNA	piranha	rnateam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/piranha	https://github.com/bgruening/galaxytools/tree/master/tools/piranha	1.2.1.0	piranha	1.2.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1
-platypus			bg_platypus	efficient and accurate variant-detection in high-throughput sequencing data								To update	http://www.well.ox.ac.uk/platypus	Sequence Analysis	platypus	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/platypus	https://github.com/bgruening/galaxytools/tree/master/tools/platypus	0.0.11	platypus				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-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	https://github.com/galaxyproject/tools-devteam/tree/main/tools/plot_from_lda	1.0.1	R				1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1
-plotly_ml_performance_plots	1323.0	71.0	plotly_ml_performance_plots	performance plots for machine learning problems								To update	http://scikit-learn.org/stable/modules/classes.html#module-sklearn.metrics	Visualization	plotly_ml_performance_plots	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots	https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots	0.3	galaxy-ml	0.10.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1
-plotly_parallel_coordinates_plot	652.0	37.0	plotly_parallel_coordinates_plot	parallel coordinates plot produced with plotly								To update	https://plot.ly/python/parallel-coordinates-plot/	Visualization	plotly_parallel_coordinates_plot	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot	https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot	0.2	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1
-plotly_regression_performance_plots	843.0	79.0	plotly_regression_performance_plots	performance plots for regression problems								To update	http://scikit-learn.org/stable/supervised_learning.html#supervised-learning	Visualization	plotly_regression_performance_plots	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots	https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots	0.1	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1
-poisson2test	116.0	6.0	poisson2test	Poisson two-sample test								To update	https://bitbucket.org/natefoo/taxonomy	Statistics, Metagenomics	poisson2test	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/poisson2test	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/poisson2test	1.0.0	taxonomy	0.10.0			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1
-predictnls			predictnls	Python reimplementation of predictNLS for Galaxy								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/predictnls	Sequence Analysis	predictnls	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/predictnls	https://github.com/peterjc/pico_galaxy/tree/master/tools/predictnls	0.0.10					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-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	https://github.com/galaxyproject/tools-devteam/tree/main/tools/principal_component_analysis	1.0.2	rpy				1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1
-protease_prediction	149.0	4.0	eden_protease_prediction	This tool can learn the cleavage specificity of a given class of proteases.								To update	https://github.com/fabriziocosta/eden	Sequence Analysis, Proteomics	protease_prediction	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/protease_prediction	https://github.com/bgruening/galaxytools/tree/master/tools/protease_prediction	0.9	eden	2.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1
-protein_analysis			promoter2, Psortb, rxlr_motifs, signalp3, tmhmm2, wolf_psort	TMHMM, SignalP, Promoter, RXLR motifs, WoLF PSORT and PSORTb								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysis	Sequence Analysis	tmhmm_and_signalp	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysis	https://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysis	0.0.13	promoter				0	0	6	0	0	0	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	6	6
-protein_properties	256.0	15.0	bg_protein_properties	Calculation of various properties from given protein sequences								To update		Sequence Analysis	protein_properties	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/protein_properties	https://github.com/bgruening/galaxytools/tree/master/tools/protein_properties	0.2.0	biopython	1.70			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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	https://github.com/galaxyproject/tools-devteam/tree/main/tools/quality_filter	1.0.1	bx-python	0.11.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-rRNA			meta_rna	Identification of ribosomal RNA genes in metagenomic fragments.								To update	http://weizhong-lab.ucsd.edu/meta_rna/	RNA	rrna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rRNA	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rRNA	0.1	hmmsearch3.0				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-racon	21353.0	309.0	racon	Consensus module for raw de novo DNA assembly of long uncorrected reads.	Racon	Racon		Racon	Consensus module for raw de novo DNA assembly of long uncorrected readsRacon is intended as a standalone consensus module to correct raw contigs generated by rapid assembly methods which do not include a consensus step. The goal of Racon is to generate genomic consensus which is of similar or better quality compared to the output generated by assembly methods which employ both error correction and consensus steps, while providing a speedup of several times compared to those methods. It supports data produced by both Pacific Biosciences and Oxford Nanopore Technologies.	Genome assembly, Mapping assembly	Whole genome sequencing, Sequence assembly	Up-to-date	https://github.com/isovic/racon	Sequence Analysis	racon	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/racon	https://github.com/bgruening/galaxytools/tree/master/tools/racon	1.5.0	racon	1.5.0	Genome assembly, Mapping assembly	Whole genome sequencing, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1
-rbpbench	36.0		rbpbench	Evaluate CLIP-seq and other genomic region data using a comprehensive collection of RBP binding motifs	rbpbench	rbpbench		RBPBench	Evaluate CLIP-seq and other genomic region data using a comprehensive collection of RBP binding motifs		RNA, Protein interactions, RNA immunoprecipitation, Bioinformatics, Sequence analysis	To update	https://github.com/michauhl/RBPBench	Sequence Analysis, RNA, CLIP-seq	rbpbench	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rbpbench	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rbpbench	0.8.1	rbpbench	0.9		RNA, Protein interactions, RNA immunoprecipitation, Bioinformatics, Sequence analysis	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-rcas	1226.0	38.0	rcas	RCAS (RNA Centric Annotation System) for functional analysis of transcriptome-wide regions detected by high-throughput experiments								To update	https://github.com/BIMSBbioinfo/RCAS	RNA	rcas	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rcas/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rcas	1.5.4	bioconductor-rcas	1.28.2			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1
-rcve			rcve1	Compute RCVE								To update		Sequence Analysis, Variant Analysis	rcve	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/rcve	https://github.com/galaxyproject/tools-devteam/tree/main/tools/rcve	1.0.0	R				1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-reago			reago	Reago is tool to assembly 16S ribosomal RNA recovery from metagenomic data.	reago	reago		REAGO	This is an assembly tool for 16S ribosomal RNA recovery from metagenomic data.	Sequence assembly	Sequence assembly, RNA, Metagenomics, Microbiology	Up-to-date	https://github.com/chengyuan/reago-1.1	Metagenomics, RNA	reago	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago	1.1	reago	1.1	Sequence assembly	Sequence assembly, RNA, Metagenomics, Microbiology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-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	https://github.com/galaxyproject/tools-devteam/tree/main/tools/remove_beginning	1.0.0					1	1	1	1	1	1	1	1	0	1	1	1	1	0	1	0	1	1	1	1	0	1	1	1	1	1	1	0	0	0	0	1	0	0	1	0	1	1	0	1	1	1
-remurna	42.0	2.0	remurna	remuRNA - Measurement of Single Nucleotide Polymorphism induced Changes of RNA Conformation								To update	https://www.ncbi.nlm.nih.gov/CBBresearch/Przytycka/index.cgi#remurna	RNA	remurna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/remurna	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/remurna	1.0.0	remurna	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1
-repeat_masker	3750.0	248.0	repeatmasker_wrapper	RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.								To update	http://www.repeatmasker.org/	Sequence Analysis	repeat_masker	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker	https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker	0.1.2	RepeatMasker	4.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1
-replaceColumn			replace_column_with_key_value_file	A tool to replace all column entries of a file given by values of a key-value file.								To update		Text Manipulation	replace_column_by_key_value_file	bgruening	https://github.com/bgruening/galaxytools/tree/replaceColumn/tools/replaceColumn	https://github.com/bgruening/galaxytools/tree/master/tools/replaceColumn	0.2					1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	1	0	0	0	0	0	0	0	1	1	1
-rest_tool			pubchem_rest_tool	This tool fetches data from pubchem via the PubChem REST API.								To update	https://pubchem.ncbi.nlm.nih.gov/pug_rest/PUG_REST.html	Data Source	pubchem_rest_tool	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/rest_tool	https://github.com/bgruening/galaxytools/tree/master/tools/rest_tool	0.1.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-ribotaper	628.0	44.0	ribotaper_create_annotation, ribotaper_create_metaplots, ribotaper_ribosome_profiling	A method for defining traslated ORFs using Ribosome Profiling data.	ribotaper	ribotaper		RiboTaper	New analysis pipeline for Ribosome Profiling (Ribo-seq) experiments, which exploits the triplet periodicity of ribosomal footprints to call translated regions.	Gene expression profiling	Functional genomics	To update	https://ohlerlab.mdc-berlin.de/software/RiboTaper_126/	RNA	ribotaper	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper	1.3.1a	ribotaper	1.3.1	Gene expression profiling	Functional genomics	0	0	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3
-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	https://github.com/galaxyproject/tools-devteam/tree/main/tools/rmap	1.0.0	rmap	2.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-rmapq			rmapq_wrapper	RMAPQ for Solexa Short Reads Alignment with Quality Scores								To update		Next Gen Mappers	rmapq	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/rmapq	https://github.com/galaxyproject/tools-devteam/tree/main/tools/rmapq	1.0.0	rmap	2.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-rna_shapes			RNAshapes	Compute secondary structures of RNA								To update		RNA	rnashapes	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rna_shapes	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rna_shapes	3.3.0	@EXECUTABLE@				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1
-rnabob	164.0	3.0	rbc_rnabob	Fast pattern searching for RNA structural motifs								To update	http://eddylab.org/software.html	RNA	rnabob	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnabob	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnabob	2.2.1.0	rnabob	2.2.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1
-rnacode	1358.0	5.0	rbc_rnacode	Analyze the protein coding potential in MSA								To update		RNA	rnacode	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode	0.3.2	rnacode	0.3			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1
-rnacommender	1074.0	6.0	rbc_rnacommender	RNAcommender is a tool for genome-wide recommendation of RNA-protein interactions.								To update	https://github.com/gianlucacorrado/RNAcommender	RNA	rnacommender	rnateam	https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacommender	0.1.1	sam	3.5			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1
-rnalien	33.0	4.0	RNAlien	RNAlien unsupervized RNA family model construction								To update	http://rna.tbi.univie.ac.at/rnalien/	RNA, Sequence Analysis	rnalien	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnalien	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnalien	1.3.6	rnalien	1.8.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1
-rnasnp	86.0	5.0	rnasnp	RNAsnp Efficient detection of local RNA secondary structure changes induced by SNPs								To update	http://rth.dk/resources/rnasnp/	RNA	rnasnp	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rnasnp	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnasnp	1.2.0	rnasnp	1.2			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1
-rnaz	42965.0	14.0	rnaz, rnaz_annotate, rnaz_cluster, rnaz_randomize_aln, rnaz_select_seqs, rnaz_window	RNAz is a program for predicting structurally conserved and thermodynamically stable RNA secondary structures in multiple sequence alignments.								Up-to-date	https://www.tbi.univie.ac.at/~wash/RNAz/	RNA	rnaz	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaz	2.1.1	rnaz	2.1.1			0	0	6	0	0	0	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	6
-sailfish	4024.0	55.0	sailfish	Sailfish is a tool for transcript quantification from RNA-seq data								To update	http://www.cs.cmu.edu/~ckingsf/software/sailfish/	Sequence Analysis, RNA	sailfish	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/sailfish	https://github.com/bgruening/galaxytools/tree/master/tools/sailfish	0.10.1.1	bzip2				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	1
-salmon	55161.0	746.0	alevin, salmon, salmonquantmerge	Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq and single-cell data.	salmon	salmon		Salmon	A tool for transcript expression quantification from RNA-seq data	Sequence composition calculation, RNA-Seq quantification, Gene expression analysis	RNA-Seq, Gene expression, Transcriptomics	To update	https://github.com/COMBINE-lab/salmon	Sequence Analysis, RNA, Transcriptomics		bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/salmon	https://github.com/bgruening/galaxytools/tree/master/tools/salmon	1.10.1	salmon	1.10.3	Sequence composition calculation, RNA-Seq quantification, Gene expression analysis	RNA-Seq, Transcriptomics	2	1	3	1	2	1	3	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	1	0	0	1	0	0	0	1	0	0	0	0	0	0	0	3	3	3
-sam2interval	1189.0	20.0	sam2interval	Convert SAM to interval.								To update		SAM	sam2interval	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/sam2interval	https://github.com/galaxyproject/tools-devteam/tree/main/tools/sam2interval	1.0.2	python				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1
-sam_bitwise_flag_filter	261.0	1.0	sam_bw_filter	Filter SAM on bitwise flag values								To update		SAM	sam_bitwise_flag_filter	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/sam_bitwise_flag_filter	https://github.com/galaxyproject/tools-devteam/tree/main/tools/sam_bitwise_flag_filter	1.0.1	python				1	1	0	1	1	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1
-sambamba			sambamba_flagstat, sambamba_markdup, sambamba_merge, sambamba_sort	Sambamba: process your BAM data faster!								Up-to-date	https://github.com/biod/sambamba	SAM	sambamba	bgruening	https://github.com/biod/sambamba	https://github.com/bgruening/galaxytools/tree/master/tools/sambamba	1.0.1	sambamba	1.0.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-sample_seqs	3765.0	149.0	sample_seqs	Sub-sample sequences files (e.g. to reduce coverage)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs	Assembly, Fasta Manipulation, Fastq Manipulation, Sequence Analysis	sample_seqs	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs	https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs	0.2.6	biopython	1.70			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1
-samtools_depad			samtools_depad	Re-align a SAM/BAM file with a padded reference (using samtools depad)								To update	http://www.htslib.org/	Assembly, SAM, Sequence Analysis	samtools_depad	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad	0.0.5	samtools	1.20			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-samtools_depth	4948.0	296.0	samtools_depth	Coverage depth via samtools								To update	http://www.htslib.org/	Assembly, Sequence Analysis, SAM	samtools_depth	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth	0.0.3	samtools	1.20			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	1
-samtools_idxstats	48426.0	1450.0	samtools_idxstats	BAM mapping statistics (using samtools idxstats)								To update	http://www.htslib.org/	Assembly, Next Gen Mappers, SAM	samtools_idxstats	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats	0.0.6	samtools	1.20			1	1	1	1	1	1	1	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	0	0	1	1	1
-scatterplot	1637.0	61.0	scatterplot_rpy	Scatterplot of two numeric columns								To update		Graphics, Statistics	scatterplot	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot	https://github.com/galaxyproject/tools-devteam/tree/main/tools/scatterplot	1.0.3	numpy				1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1
-sed			sed_stream_editor	Manipulate your data with the sed command line tool.								To update	https://github.com/bgruening/galaxytools/tree/master/tools/sed	Text Manipulation	sed_wrapper	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/sed	https://github.com/bgruening/galaxytools/tree/master/tools/sed	0.0.1	sed				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-segemehl	1276.0	30.0	segemehl	segemehl - short read mapping with gaps								To update	http://www.bioinf.uni-leipzig.de/Software/segemehl/	Next Gen Mappers	segemehl	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/segemehl	https://github.com/bgruening/galaxytools/tree/master/tools/segemehl	0.2.0.4	segemehl	0.3.4			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1
-selectsequencesfrommsa	457.0	27.0	selectsequencesfrommsa	SelectSequences - selects representative entries from a multiple sequence alignment in clustal format								Up-to-date	https://github.com/eggzilla/SelectSequences	RNA, Sequence Analysis	selectsequencesfrommsa	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa	1.0.5	selectsequencesfrommsa	1.0.5			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1
-seq_composition	874.0	71.0	seq_composition	Sequence composition								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_composition	Sequence Analysis	seq_composition	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_composition	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_composition	0.0.5	biopython	1.70			1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1
-seq_filter_by_id	25302.0	306.0	seq_filter_by_id	Filter sequences by ID								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id	Fasta Manipulation, Sequence Analysis, Text Manipulation	seq_filter_by_id	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id	0.2.9	biopython	1.70			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1
-seq_filter_by_mapping	3784.0	82.0	seq_filter_by_mapping	Filter sequencing reads using SAM/BAM mapping files								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping	Assembly, Fasta Manipulation, Fastq Manipulation, SAM, Sequence Analysis	seq_filter_by_mapping	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping	0.0.8	biopython	1.70			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1
-seq_length			seq_length	Compute sequence length (from FASTA, QUAL, FASTQ, SFF, etc)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length	Fasta Manipulation, Fastq Manipulation, Sequence Analysis	seq_length	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length	0.0.5	biopython	1.70			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-seq_primer_clip			seq_primer_clip	Trim off 5' or 3' primers								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip	Assembly, Fasta Manipulation, Text Manipulation	seq_primer_clip	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip	0.0.18	galaxy_sequence_utils	1.1.5			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-seq_rename			seq_rename	Rename sequences with ID mapping from a tabular file								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename	Fasta Manipulation, Sequence Analysis, Text Manipulation	seq_rename	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename	0.0.10	galaxy_sequence_utils	1.1.5			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1
-seq_select_by_id			seq_select_by_id	Select sequences by ID								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id	Fasta Manipulation, Sequence Analysis, Text Manipulation	seq_select_by_id	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id	0.0.15	biopython	1.70			0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-short_reads_figure_high_quality_length			hist_high_quality_score	Histogram of high quality score reads								To update		Sequence Analysis, Graphics	short_reads_figure_high_quality_length	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_figure_high_quality_length	https://github.com/galaxyproject/tools-devteam/tree/main/tools/short_reads_figure_high_quality_length	1.0.0	rpy				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-short_reads_figure_score	163.0	13.0	quality_score_distribution	Build base quality distribution								To update		Sequence Analysis, Graphics	short_reads_figure_score	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_figure_score	https://github.com/galaxyproject/tools-devteam/tree/main/tools/short_reads_figure_score	1.0.2	fontconfig				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1
-short_reads_trim_seq	220.0	21.0	trim_reads	Select high quality segments								To update		Fastq Manipulation	short_reads_trim_seq	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_trim_seq	https://github.com/galaxyproject/tools-devteam/tree/main/tools/short_reads_trim_seq	1.0.0					1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1
-show_beginning			Show beginning1	Select lines from the beginning of a file.								To update		Text Manipulation	show_beginning	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/show_beginning	https://github.com/galaxyproject/tools-devteam/tree/main/tools/show_beginning	1.0.0					1	1	1	1	1	1	1	1	0	1	1	1	1	0	1	0	1	1	1	1	0	1	1	1	0	1	1	0	0	0	0	1	0	0	1	0	1	1	0	1	1	1
-show_tail			Show tail1	Select lines from the end of a file.								To update		Text Manipulation	show_tail	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/show_tail	https://github.com/galaxyproject/tools-devteam/tree/main/tools/show_tail	1.0.0					1	1	1	1	1	1	1	1	0	1	1	0	1	0	1	0	1	1	1	1	0	1	1	1	0	1	1	0	0	0	0	1	0	0	1	0	1	1	0	1	1	1
-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	https://github.com/galaxyproject/tools-devteam/tree/main/tools/sicer	1.1	SICER	1.1			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	1
-sklearn			sklearn_mlxtend_association_rules, sklearn_clf_metrics, sklearn_discriminant_classifier, sklearn_ensemble, sklearn_estimator_attributes, sklearn_feature_selection, sklearn_fitted_model_eval, sklearn_generalized_linear, keras_batch_models, keras_model_builder, keras_model_config, keras_train_and_eval, sklearn_label_encoder, sklearn_lightgbm, ml_visualization_ex, model_prediction, sklearn_model_validation, sklearn_nn_classifier, sklearn_numeric_clustering, sklearn_pairwise_metrics, sklearn_pca, sklearn_build_pipeline, sklearn_data_preprocess, sklearn_regression_metrics, sklearn_sample_generator, sklearn_searchcv, sklearn_model_fit, scipy_sparse, stacking_ensemble_models, sklearn_svm_classifier, sklearn_to_categorical, sklearn_train_test_eval, sklearn_train_test_split	Machine Learning tool suite from Scikit-learn								To update	http://scikit-learn.org	Machine Learning, Statistics	sklearn	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/sklearn	https://github.com/bgruening/galaxytools/tree/master/tools/sklearn	1.0.11.0					30	14	31	16	30	14	31	16	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	29	31	27
-snpfreq	37.0	7.0	hgv_snpFreq	snpFreq significant SNPs in case-control data								To update		Variant Analysis, Statistics	snpfreq	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/snpfreq	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/hgv/snpfreq	1.0.1	R				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1
-sortmerna	18504.0	376.0	bg_sortmerna	SortMeRNA is a software designed to rapidly filter ribosomal RNA fragments from metatransriptomic data produced by next-generation sequencers.	sortmerna	sortmerna		SortMeRNA	Sequence analysis tool for filtering, mapping and OTU-picking NGS reads.	Sequence similarity search, Sequence comparison, Sequence alignment analysis	Metatranscriptomics, Metagenomics	To update	http://bioinfo.lifl.fr/RNA/sortmerna/	RNA	sortmerna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna	4.3.6	sortmerna	4.3.7	Sequence similarity search, Sequence alignment analysis	Metatranscriptomics, Metagenomics	1	1	1	1	1	1	1	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1
-split_file_on_column	5507.0	159.0	tp_split_on_column	Split a file on a specific column.								To update		Text Manipulation	split_file_on_column	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_on_column	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_on_column	0.6	gawk				1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1
-split_file_to_collection	15358.0	412.0	split_file_to_collection	Split tabular, MGF, FASTA, or FASTQ files to a dataset collection.								To update	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection	Text Manipulation	split_file_to_collection	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection	0.5.2	python				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	1	0	0	0	0	0	0	0	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	https://github.com/galaxyproject/tools-devteam/tree/main/tools/split_paired_reads	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-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	https://github.com/bgruening/galaxytools/tree/master/tools/splitfasta	0.4.0	biopython	1.70			1	0	1	0	1	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1
-sshmm	223.0	5.0	sshmm	ssHMM is an RNA sequence-structure motif finder for RNA-binding protein data, such as CLIP-Seq data								Up-to-date	https://github.molgen.mpg.de/heller/ssHMM	Sequence Analysis, RNA	sshmm	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm	1.0.7	sshmm	1.0.7			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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	https://github.com/bgruening/galaxytools/tree/master/tools/statistics	0.3	numpy				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0
-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	https://github.com/bgruening/galaxytools/tree/master/tools/stress_ng	0.12.04	stress-ng				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-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	https://github.com/galaxyproject/tools-devteam/tree/main/tools/substitution_rates	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-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	https://github.com/galaxyproject/tools-devteam/tree/main/tools/substitutions	1.0.1	bx-python	0.11.0			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-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	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/subtract	1.0.0	bx-python	0.11.0			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	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	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/subtract_query	0.1	bx-python	0.11.0			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1
-t2ps	457.0	31.0	Draw_phylogram	Draw phylogeny	t2ps	t2ps		Draw phylogeny	"""Given taxonomy representation (produced by *Fetch taxonomic representation* tool) this utility produces a graphical representations of phylogenetic tree in PDF format."" - Galaxy tool wrapper"	Phylogenetic tree visualisation	Phylogenomics	To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	t2ps	devteam	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2ps	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2ps	1.0.0	taxonomy	0.10.0	Phylogenetic tree visualisation	Phylogenomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1
-t2t_report	947.0	26.0	t2t_report	Summarize taxonomy								To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	t2t_report	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/t2t_report	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2t_report	1.0.0	taxonomy	0.10.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	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	https://github.com/galaxyproject/tools-devteam/tree/main/tools/t_test_two_samples	1.0.1	R				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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	https://github.com/galaxyproject/tools-devteam/tree/main/tools/table_annovar	0.2	annovar				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-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	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/tables_arithmetic_operations	1.0.0	perl				0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	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	https://github.com/galaxyproject/tools-devteam/tree/main/tools/tabular_to_fasta	1.1.1	python				1	1	1	1	1	1	1	1	0	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	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	https://github.com/bgruening/galaxytools/tree/master/tools/tapscan	4.76+galaxy0	hmmer	3.4			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-targetfinder	713.0	37.0	targetfinder	Plant small RNA target prediction tool								Up-to-date	https://github.com/carringtonlab/TargetFinder.git	RNA	targetfinder	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder	1.7	targetfinder	1.7			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1
-text_processing	3864895.0	15048.0	tp_awk_tool, tp_cat, tp_cut_tool, tp_easyjoin_tool, tp_find_and_replace, tp_grep_tool, tp_head_tool, tp_multijoin_tool, nl, tp_text_file_with_recurring_lines, tp_replace_in_column, tp_replace_in_line, tp_sed_tool, tp_sort_header_tool, tp_sort_rows, tp_uniq_tool, tp_tac, tp_tail_tool, tp_unfold_column_tool, tp_sorted_uniq	High performance text processing tools using the GNU coreutils, sed, awk and friends.								To update	https://www.gnu.org/software/	Text Manipulation	text_processing	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing	9.3	coreutils	8.25			20	20	20	20	20	20	20	20	0	0	0	0	0	0	0	0	0	0	0	0	0	0	19	1	19	0	0	19	0	0	0	20	0	0	0	0	0	0	0	19	19	19
-tgsgapcloser	460.0	36.0	tgsgapcloser	TGS-GapCloser uses error-prone long reads or preassembled contigs to fill N-gap in the genome assembly.	TGS-GapCloser	TGS-GapCloser		TGS-GapCloser	TGS-GapCloser is a fast and accurately passing through the Bermuda in large genome using error-prone third-generation long reads.	Genome assembly, Read mapping, Scaffolding, Localised reassembly	Sequencing, Sequence assembly, Phylogeny, Transcription factors and regulatory sites, Mapping	To update	https://github.com/BGI-Qingdao/TGS-GapCloser	Assembly	tgsgapcloser	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser	https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser	1.0.3	tgsgapcloser	1.2.1	Genome assembly, Read mapping, Scaffolding, Localised reassembly	Sequencing, Sequence assembly, Phylogeny, Transcription factors and regulatory sites, Mapping	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0
-tiara			tiara	Tool for identification of eukaryotic sequences in the metagenomic datasets.	Tiara	Tiara		TIARA	Total Integrated Archive of Short-Read and Array (TIARA) database, contains personal genomic information obtained from next generation sequencing (NGS) techniques and ultra-high-resolution comparative genomic hybridization (CGH) arrays. This database improves the accuracy of detecting personal genomic variations, such as SNPs, short indels and structural variants (SVs).	Genome comparison, Data retrieval, Variant calling, Genome visualisation, Structural variation detection	Sequencing, Genomics, DNA polymorphism, DNA structural variation	To update	https://github.com/ibe-uw/tiara	Metagenomics, Sequence Analysis	tiara	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/tiara	https://github.com/bgruening/galaxytools/tree/master/tools/tiara	1.0.3	tiara		Genome comparison, Data retrieval, Variant calling, Genome visualisation, Structural variation detection	Sequencing, Genomics, DNA polymorphism	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-tool_recommendation_model			create_tool_recommendation_model	Create model to recommend tools								To update	https://github.com/bgruening/galaxytools	Machine Learning	create_tool_recommendation_model	bgruening	https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model	https://github.com/bgruening/galaxytools/tree/master/tools/tool_recommendation_model	0.0.5	python				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1
-tophat	1.0		tophat	Tophat for Illumina								To update		RNA, Next Gen Mappers	tophat	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat	https://github.com/galaxyproject/tools-devteam/tree/main/tools/tophat	1.5.0	samtools	1.20			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0
-tophat2	24167.0	312.0	tophat2	Tophat - fast splice junction mapper for RNA-Seq reads								To update	http://ccb.jhu.edu/software/tophat/index.shtml	RNA, Next Gen Mappers	tophat2	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat2	https://github.com/galaxyproject/tools-devteam/tree/main/tools/tophat2	2.1.1	bowtie2	2.5.4			1	1	1	0	1	1	1	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	1	0	0	0	0	1	1	1
-tophat_fusion_post	216.0	15.0	tophat_fusion_post	Wrapper for Tophat-Fusion post step								To update		Transcriptomics	tophat_fusion_post	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat_fusion_post	https://github.com/galaxyproject/tools-devteam/tree/main/tools/tophat_fusion_post	0.1	blast+				0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1
-trim_galore	238699.0	2334.0	trim_galore	Trim Galore adaptive quality and adapter trimmer	trim_galore	trim_galore		Trim Galore	A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files, with some extra functionality for MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries.	Sequence trimming, Primer removal, Read pre-processing	Sequence analysis	To update	http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/	Sequence Analysis, Fastq Manipulation	trim_galore	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore	https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore	0.6.7	trim-galore	0.6.10	Sequence trimming, Primer removal, Read pre-processing	Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	1
-trimmer	6058.0	188.0	trimmer	Trim leading or trailing characters.								To update		Text Manipulation	trimmer	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer	https://github.com/galaxyproject/tools-devteam/tree/main/tools/trimmer	0.0.1					1	1	1	1	1	1	1	1	0	1	1	1	1	0	1	0	1	1	1	1	0	1	1	1	1	1	1	0	0	0	0	1	0	0	1	0	1	1	0	1	1	1
-trna_prediction	2935.0	236.0	aragorn_trna, trnascan	Aragorn predicts tRNA and tmRNA in nucleotide sequences.								To update	http://mbioserv2.mbioekol.lu.se/ARAGORN/	RNA	trna_prediction	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction	0.6	aragorn	1.2.41			0	2	2	0	0	2	2	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	2	2
-ucsc_custom_track	393.0	45.0	build_ucsc_custom_track_1	Build custom track for UCSC genome browser								To update		Sequence Analysis	ucsc_custom_track	devteam	https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track	https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track	1.0.1	python				1	0	1	0	1	0	1	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1
-uniprot_rest_interface	2406.0	132.0	uniprot	UniProt ID mapping and sequence retrieval								To update	https://github.com/jdrudolph/uniprot	Proteomics, Sequence Analysis	uniprot_rest_interface	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface	https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface	0.5	requests				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1
-varscan_version_2	5191.0	246.0	varscan	VarScan wrapper								To update	https://dkoboldt.github.io/varscan/	Variant Analysis	varscan_version_2	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/varscan_version_2	https://github.com/galaxyproject/tools-devteam/tree/main/tools/varscan_version_2	2.4.2	varscan	2.4.6			1	1	1	1	1	1	1	1	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1
-vcf2pgsnp	206.0	15.0	vcf2pgSnp	VCF to pgSnp								To update		Variant Analysis	vcf2pgsnp	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf2pgsnp	https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf2pgsnp	1.0.0					1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1
-vcf_annotate	1.0		vcf_annotate	Annotate a VCF file (dbSNP, hapmap)								To update		Variant Analysis	vcf_annotate	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_annotate	https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf_annotate	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-vcf_extract			vcf_extract	Extract reads from a specified region								To update		Variant Analysis	vcf_extract	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_extract	https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf_extract	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-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	https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf_filter	1.0.0					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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	https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf_intersect	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-vcftools_annotate	171.0	24.0	vcftools_annotate	Annotate VCF using custom/user-defined annotations								To update	https://vcftools.github.io/	Variant Analysis	vcftools_annotate	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_annotate	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_annotate	0.1	echo				1	0	1	1	1	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1
-vcftools_compare	531.0	34.0	vcftools_compare	Compare VCF files to get overlap and uniqueness statistics								To update	https://vcftools.github.io/	Variant Analysis	vcftools_compare	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_compare	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_compare	0.1	tabix	1.11			0	0	1	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1
-vcftools_consensus			vcftools_consensus	Apply VCF variants to a fasta file to create consensus sequence								To update	https://vcftools.github.io/	Variant Analysis	vcftools_consensus	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_consensus	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_consensus	0.1.11	samtools	1.20			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-vcftools_isec	498.0	35.0	vcftools_isec	Intersect multiple VCF datasets								To update	https://vcftools.github.io/	Variant Analysis	vcftools_isec	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_isec	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_isec	0.1.1	tabix	1.11			0	1	1	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1
-vcftools_merge	953.0	68.0	vcftools_merge	Merge multiple VCF datasets into a single dataset								To update	https://vcftools.github.io/	Variant Analysis	vcftools_merge	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_merge	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_merge	0.1.11	tabix	1.11			0	1	1	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1
-vcftools_slice	411.0	24.0	vcftools_slice	Subset VCF dataset by genomic regions								To update	https://vcftools.github.io/	Variant Analysis	vcftools_slice	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_slice	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_slice	0.1	echo				1	0	1	1	1	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1
-vcftools_subset	137.0	17.0	vcftools_subset	Select samples from a VCF dataset								To update	https://vcftools.github.io/	Variant Analysis	vcftools_subset	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_subset	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_subset	0.1	tabix	1.11			0	0	1	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1
-venn_list	5067.0	248.0	venn_list	Draw Venn Diagram (PDF) from lists, FASTA files, etc								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list	Graphics, Sequence Analysis, Visualization	venn_list	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list	https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list	0.1.2	galaxy_sequence_utils	1.1.5			1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	1
-vienna_rna	799.0		viennarna_kinfold, viennarna_kinwalker, viennarna_rna2dfold, viennarna_rnaaliduplex, viennarna_rnaalifold, viennarna_rnacofold, viennarna_rnadistance, viennarna_rnaduplex, viennarna_rnaeval, viennarna_rnafold, viennarna_rnaheat, viennarna_rnainverse, viennarna_rnalalifold, viennarna_rnalfold, viennarna_rnapaln, viennarna_rnadpdist, viennarna_rnapkplex, viennarna_rnaplex, viennarna_rnaplfold, viennarna_rnaplot, viennarna_rnasnoop, viennarna_rnasubopt, viennarna_rnaup	ViennaRNA - Prediction and comparison of RNA secondary structures								To update	http://www.tbi.univie.ac.at/RNA/	RNA	viennarna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna	2.2.10	viennarna	2.6.4			0	0	21	0	0	0	21	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	21	21
-vt			vt_@BINARY@, vt_@BINARY@	A tool set for short variant discovery in genetic sequence data.								To update		Sequence Analysis, Variant Analysis	vt	bgruening	https://github.com/atks/vt	https://github.com/bgruening/galaxytools/tree/master/tools/vt	0.2	vt	2015.11.10			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-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	https://github.com/galaxyproject/tools-devteam/tree/main/tools/weightedaverage	1.0.1	galaxy-ops	1.1.0			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-whisper			whisper	Transcribe audio or video files to text using the OpenAI Whisper.								To update	https://github.com/bgruening/galaxytools/tree/master/tools/whisper	Machine Learning	whisper	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/whisper	https://github.com/bgruening/galaxytools/tree/master/tools/whisper	20231117					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-windowsplitter			winSplitter	Make windows								To update		Sequence Analysis, Variant Analysis	windowsplitter	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter	https://github.com/galaxyproject/tools-devteam/tree/main/tools/windowsplitter	1.0.1	bx-python	0.11.0			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-woundhealing			woundhealing_scratch_assay	Tool to automate quantification of wound healing in high-throughput microscopy scratch assays								Up-to-date	https://git.embl.de/grp-cba/wound-healing-htm-screen	Imaging	Wound healing scratch assay image analysis	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools	https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/woundhealing	1.6.1	fiji-morpholibj	1.6.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
-wtdbg	1660.0	116.0	wtdbg	WTDBG is a fuzzy Bruijn graph (FBG) approach to long noisy reads assembly.	wtdbg2	wtdbg2		wtdbg2	Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output. Wtdbg2 is able to assemble the human and even the 32Gb Axolotl genome at a speed tens of times faster than CANU and FALCON while producing contigs of comparable base accuracy.	Genome assembly, De-novo assembly	Sequence assembly, Sequencing	Up-to-date	https://github.com/ruanjue/wtdbg2	Assembly	wtdbg	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg	https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg	2.5	wtdbg	2.5	Genome assembly, De-novo assembly	Sequence assembly, Sequencing	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	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	https://github.com/galaxyproject/tools-devteam/tree/main/tools/xy_plot	1.0.2	r-base				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1
+Galaxy wrapper id	Galaxy tool ids	Description	bio.tool id	bio.tool ids	biii	bio.tool name	bio.tool description	EDAM operation	EDAM topic	Status	Source	ToolShed categories	ToolShed id	Galaxy wrapper owner	Galaxy wrapper source	Galaxy wrapper parsed folder	Galaxy wrapper version	Conda id	Conda version	EDAM operation (no superclasses)	EDAM topic (no superclasses)	Available on UseGalaxy.org (Main)	Available on UseGalaxy.org.au	Available on UseGalaxy.eu	Available on UseGalaxy.fr	Tools available on UseGalaxy.org (Main)	Tools available on UseGalaxy.org.au	Tools available on UseGalaxy.eu	Tools available on UseGalaxy.fr	Tools available on ANASTASIA	Tools available on APOSTL	Tools available on ARGs-OAP	Tools available on BF2I-MAP	Tools available on BioBix	Tools available on CIRM-CFBP	Tools available on Center for Phage Technology (CPT)	Tools available on ChemFlow	Tools available on Coloc-stats	Tools available on CorGAT	Tools available on CropGalaxy	Tools available on Dintor	Tools available on FreeBioinfo	Tools available on GASLINI	Tools available on Galaxy@AuBi	Tools available on Galaxy@Pasteur	Tools available on GalaxyTrakr	Tools available on Genomic Hyperbrowser	Tools available on GigaGalaxy	Tools available on HyPhy HIV NGS Tools	Tools available on IPK Galaxy Blast Suite	Tools available on ImmPort Galaxy	Tools available on InteractoMIX	Tools available on MISSISSIPPI	Tools available on Mandoiu Lab	Tools available on MiModD NacreousMap	Tools available on Oqtans	Tools available on Palfinder	Tools available on PepSimili	Tools available on PhagePromotor	Tools available on Protologger	Tools available on UseGalaxy.be	Tools available on UseGalaxy.cz	Tools available on UseGalaxy.no	No. of tool users (2022-2023) (usegalaxy.eu)	Total tool usage (usegalaxy.eu)
+10x_bamtofastq	10x_bamtofastq	Converts 10x Genomics BAM to FASTQ								Up-to-date	https://github.com/10XGenomics/bamtofastq	Convert Formats	10x_bamtofastq	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq	https://github.com/bgruening/galaxytools/tree/master/tools/10x_bamtofastq	1.4.1	10x_bamtofastq	1.4.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	46	228
+AggregateAlignments	graphclust_aggregate_alignments	Aggregate and filter alignment metrics of individual clusters, like the output of graphclust_align_cluster.								Up-to-date		RNA	graphclust_aggregate_alignments	rnateam	https://github.com/bgruening/galaxytools/tools/GraphClust/AggregateAlignments	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/AggregateAlignments	0.6.0	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	6	116
+AlignCluster	graphclust_align_cluster	Align predicted clusters of glob_report_no_align step with locarna and conservation analysis and visualizations.								To update		RNA	graphclust_align_cluster	rnateam	https://github.com/bgruening/galaxytools/tools/GraphClust/AlignCluster	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/AlignCluster	0.1	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	10	3060
+CMFinder	cmFinder	Determines consensus motives for sequences.								To update		RNA	graphclust_cmfinder	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CMFinder	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CMFinder	0.4	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	14	45191
+CollectResults	glob_report	Post-processing. Redundant clusters are merged and instances that belong to multiple clusters are assigned unambiguously. For every pair of clusters, the relative overlap (i.e. the fraction of instances that occur in both clusters) is computed and clusters are merged if the overlap exceeds 50%. instances that occur in both clusters) is computed and clusters are merged if the overlap exceeds 50%.								To update		RNA	graphclust_postprocessing	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResults	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResults	0.5	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	14	1961
+CollectResultsNoAlign	graphclust_glob_report_no_align	Redundant GraphClust clusters are merged and instances that belong to multiple clusters are assigned unambiguously.								To update		RNA	graphclust_postprocessing_no_align	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign	0.5	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	108
+GSPAN	gspan	Second step of GraphClust								To update		RNA	graphclust_fasta_to_gspan	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/GSPAN	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/GSPAN	0.4	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	4	133
+LocARNAGraphClust	locarna_best_subtree	MLocARNA computes a multiple sequence-structure alignment of RNA sequences.								To update		RNA	graphclust_mlocarna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/LocARNAGraphClust	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/LocARNAGraphClust	0.4	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	13	45325
+NSPDK	NSPDK_candidateClust, nspdk_sparse	Produces an explicit sparse feature encoding and copmutes global feature index and returns top dense sets.								To update		RNA	graphclust_nspdk	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/NSPDK	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/NSPDK	9.2.3.1	graphclust-wrappers	0.6.0			0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	28	62388
+Plotting	motifFinderPlot	Plotting results for GraphClust								To update		RNA	graphclust_motif_finder_plot	rnateam	https://github.com/eteriSokhoyan/galaxytools/tree/master/tools/GraphClust/Plotting	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/Plotting	0.4	seaborn				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	3	68
+PrepareForMlocarna	preMloc	This tool prepares files for locarna step.								To update		RNA	graphclust_prepocessing_for_mlocarna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/PrepareForMlocarna	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/PrepareForMlocarna	0.4	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	15	1932
+Preprocessing	preproc	Preprocessing input for GraphClust								To update		RNA	graphclust_preprocessing	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/Preprocessing	0.5	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	18	1758
+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	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/Structure_GSPAN	0.4	graphclust-wrappers	0.6.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	16	2925
+add_line_to_file	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	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/add_line_to_file	0.1.0	coreutils	8.25			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	193	14480
+add_value	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	https://github.com/galaxyproject/tools-devteam/tree/main/tools/add_value	1.0.1	perl				1	1	1	1	1	1	1	1	0	1	1	1	1	0	1	0	1	1	1	1	0	1	1	1	1	1	1	0	0	0	0	1	0	0	1	0	1	1	0	1	1	1	591	367167
+agat	agat	GTF/GFF analysis toolkit	agat	agat		AGAT	Another Gff Analysis Toolkit (AGAT)Suite of tools to handle gene annotations in any GTF/GFF format.	Data handling, Genome annotation	Genomics	To update	https://github.com/NBISweden/AGAT	Convert Formats, Statistics, Fasta Manipulation	agat	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/agat	https://github.com/bgruening/galaxytools/tree/master/tools/agat	1.2.0	agat	1.4.0	Data handling, Genome annotation	Genomics	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	42	481
+align_back_trans	align_back_trans	Thread nucleotides onto a protein alignment (back-translation)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans	Fasta Manipulation, Sequence Analysis	align_back_trans	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans	https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans	0.0.10	biopython	1.70			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	11	329
+annotation_profiler	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	https://github.com/galaxyproject/tools-devteam/tree/main/tools/annotation_profiler	1.0.0	bx-python	0.11.0			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	2
+antarna	antarna	antaRNA uses ant colony optimization to solve the inverse folding problem in RNA research .								To update		RNA	antarna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna	1.1	antarna	2.0.1.2			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	2	52
+antismash	antismash	Antismash allows the genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters	antismash	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	https://github.com/bgruening/galaxytools/tree/master/tools/antismash	6.1.1	antismash	7.1.0	Sequence clustering, Gene prediction, Differential gene expression analysis	Molecular interactions, pathways and networks, Gene and protein families	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	279	14596
+aresite2	AREsite2_REST	AREsite2 REST Interface								To update	http://rna.tbi.univie.ac.at/AREsite	RNA, Data Source, Sequence Analysis	aresite2	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2	0.1.2	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	4	65
+atactk_trim_adapters	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	https://github.com/bgruening/galaxytools/tree/master/tools/atactk_trim_adapters	0.1.6	atactk	0.1.9			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	26	257
+augustus	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	https://github.com/bgruening/galaxytools/tree/master/tools/augustus	3.1.0	augustus	3.5.0			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	516	8864
+bamhash	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	https://github.com/bgruening/galaxytools/tree/master/tools/bamhash	1.1	bamhash	1.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	15	169
+barcode_collapse	barcode_collapse	Paired End randomer aware duplicate removal algorithm								To update	https://github.com/YeoLab/gscripts	RNA, Sequence Analysis	barcode_collapse	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse	https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse	0.1.0	pysam	0.22.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+basecoverage	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	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/basecoverage	1.0.0	bx-python	0.11.0			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	1	2	308
+best_regression_subsets	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	https://github.com/galaxyproject/tools-devteam/tree/main/tools/best_regression_subsets	1.0.0	numpy				1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	3
+bia-ftplinks	bia_download	Tool to query ftp links for study from bioimage archive								To update		Imaging	bia_download	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools	https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/bia-ftplinks	0.1.0	wget				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2
+bigwig_to_bedgraph	bigwig_to_bedgraph	Convert from bigWig to bedGraph format								To update		Convert Formats	bigwig_to_bedgraph	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/bigwig_to_bedgraph	https://github.com/bgruening/galaxytools/tree/master/tools/bigwig_to_bedgraph	0.1.0	ucsc_tools				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	200	5749
+biomodelsML	biomodels_biomd0000001066, biomodels_biomd0000001076	Wrappers for tools to bring BioModels AI models into Galaxy.								To update	https://www.ebi.ac.uk/biomodels/	Machine Learning	biomodels	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools	https://github.com/bgruening/galaxytools/tree/master/tools/biomodelsML	1.1					0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	13
+bionano	bionano_scaffold	Bionano Solve is a set of tools for analyzing Bionano data								To update	https://bionanogenomics.com/	Assembly	bionano	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/bionano	https://github.com/bgruening/galaxytools/tree/master/tools/bionano	3.7.0					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	112	531
+bismark	bismark_pretty_report, bismark_bowtie2, bismark_deduplicate, bismark_methylation_extractor	A tool to map bisulfite converted sequence reads and determine cytosine methylation states								To update	https://www.bioinformatics.babraham.ac.uk/projects/bismark/	Sequence Analysis, Next Gen Mappers	bismark	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/bismark	https://github.com/bgruening/galaxytools/tree/master/tools/bismark	0.22.1	bismark	0.24.2			0	4	4	4	0	4	4	4	0	0	0	4	0	0	0	0	0	0	0	0	0	0	4	0	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	4	4	4	332	12876
+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	https://github.com/galaxyproject/tools-devteam/tree/main/tools/blat_coverage_report	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+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	https://github.com/galaxyproject/tools-devteam/tree/main/tools/blat_mapping	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+blobtoolkit	blobtoolkit	Identification and isolation non-target data in draft and publicly available genome assemblies.								To update	https://blobtoolkit.genomehubs.org/	Sequence Analysis, Assembly	blobtoolkit	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit	https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit	4.0.7					0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	21	685
+blockbuster	blockbuster	Blockbuster detects blocks of overlapping reads using a gaussian-distribution approach.								To update	http://hoffmann.bioinf.uni-leipzig.de/LIFE/blockbuster.html	RNA, Sequence Analysis	blockbuster	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster	https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster	0.1.2	blockbuster	0.0.1.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	1	34	3009
+blockclust	blockclust	BlockClust detects transcripts with similar processing patterns.								Up-to-date	https://github.com/bgruening/galaxytools/tree/master/workflows/blockclust	RNA	blockclust	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/blockclust	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/blockclust	1.1.1	blockclust	1.1.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	1	15	1478
+bowtie_wrappers	bowtie_wrapper	Galaxy wrappers for the Bowtie short read mapping tools.								To update	http://bowtie-bio.sourceforge.net/	Next Gen Mappers	bowtie_wrappers	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers	https://github.com/galaxyproject/tools-devteam/tree/main/tools/bowtie_wrappers	1.2.0	bowtie	1.3.1			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	1	506	22988
+canonical_correlation_analysis	cca1	Canonical Correlation Analysis								To update		Statistics	canonical_correlation_analysis	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/canonical_correlation_analysis	https://github.com/galaxyproject/tools-devteam/tree/main/tools/canonical_correlation_analysis	1.0.0	R				0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	10	74
+canu	canu	Canu is a hierarchical assembly pipeline designed for high-noise single-molecule sequencing (such as the PacBio RS II/Sequel or Oxford Nanopore MinION).	canu	canu		CANU	De-novo assembly tool for long read chemistry like Nanopore data and PacBio data.	De-novo assembly	Genomics	Up-to-date	https://github.com/marbl/canu		canu	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/canu	https://github.com/bgruening/galaxytools/tree/master/tools/canu	2.2	canu	2.2	De-novo assembly	Genomics	0	1	1	1	0	1	1	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	533	13021
+categorize_elements_satisfying_criteria	categorize_elements_satisfying_criteria	Categorize Elements satisfying criteria.								To update		Statistics	categorize_elements_satisfying_criteria	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/categorize_elements_satisfying_criteria	https://github.com/galaxyproject/tools-devteam/tree/main/tools/categorize_elements_satisfying_criteria	1.0.0					0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	1	40
+ccat	peakcalling_ccat	Control-based ChIP-seq Analysis Tool								To update		ChIP-seq	ccat	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/ccat	https://github.com/galaxyproject/tools-devteam/tree/main/tools/ccat	0.0.2	ccat	3.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	15	173
+cd_hit_dup	cd_hit_dup	simple tool for removing duplicates from sequencing reads								To update		Metagenomics, Sequence Analysis	cd_hit_dup	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/cd_hit_dup	https://github.com/galaxyproject/tools-devteam/tree/main/tools/cd_hit_dup	0.0.1	cd-hit-auxtools	4.8.1			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+cellpose	cellpose	Cellpose is an anatomical segmentation algorithm								To update	https://github.com/MouseLand/cellpose	Imaging	cellpose	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/cellpose	https://github.com/bgruening/galaxytools/tree/master/tools/cellpose	3.0.8	cellpose				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+cellprofiler	cp_cellprofiler, cp_color_to_gray, cp_convert_objects_to_image, cp_display_data_on_image, cp_enhance_or_suppress_features, cp_export_to_spreadsheet, cp_gray_to_color, cp_identify_primary_objects, cp_image_math, cp_mask_image, cp_measure_granularity, cp_measure_image_area_occupied, cp_measure_image_intensity, cp_measure_image_quality, cp_measure_object_intensity, cp_measure_object_size_shape, cp_measure_texture, cp_overlay_outlines, cp_relate_objects, cp_save_images, cp_common, cp_tile, cp_track_objects	cellProfiler wrapper	CellProfiler	CellProfiler	cellprofiler	CellProfiler	Tool for quantifying data from biological images, particularly in high-throughput experiments.	Quantification, Image analysis, Parsing	Imaging, Microarray experiment, Genotype and phenotype	To update		Imaging	cellprofiler	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools	https://github.com/bgruening/galaxytools/tree/master/tools/cellprofiler				Quantification, Image analysis, Parsing	Imaging, Microarray experiment, Genotype and phenotype	0	23	23	19	0	23	23	19	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	19	23	19	178	4614
+cellprofiler_v4	cp_cellprofiler4	cellProfiler4 wrapper								To update		Imaging	cellprofiler4	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools	https://github.com/bgruening/galaxytools/tree/master/tools/cellprofiler_v4	4.2.6					0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	8	43
+change_case	ChangeCase	Convert column case.								To update		Text Manipulation	change_case	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/change_case	https://github.com/galaxyproject/tools-devteam/tree/main/tools/change_case	1.0.1	perl				1	1	1	1	1	1	1	1	0	1	1	1	1	0	1	0	1	1	1	1	0	1	1	1	1	1	1	1	0	0	0	1	0	0	1	0	1	1	0	1	1	1	931	10965
+chipseeker	chipseeker	A tool for ChIP peak annotation and visualization								To update	https://bioconductor.org/packages/release/bioc/html/ChIPseeker.html	ChIP-seq, Genome annotation	chipseeker	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/chipseeker	https://github.com/bgruening/galaxytools/tree/master/tools/chipseeker	1.32.0	bioconductor-chipseeker	1.38.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	1	418	15690
+chromosome_diagram	chromosome_diagram	Chromosome Diagrams using Biopython								To update		Graphics, Sequence Analysis, Visualization	chromosome_diagram	peterjc		https://github.com/peterjc/pico_galaxy/tree/master/tools/chromosome_diagram	0.0.3	biopython	1.70			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+circexplorer	circexplorer	A combined strategy to identify circular RNAs (circRNAs and ciRNAs)								To update	https://github.com/YangLab/CIRCexplorer	Sequence Analysis, RNA	circexplorer	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/circexplorer	https://github.com/bgruening/galaxytools/tree/master/tools/circexplorer	1.1.9.0	circexplorer	1.1.10			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	8	251
+clc_assembly_cell	clc_assembler, clc_mapper	Galaxy wrapper for the CLC Assembly Cell suite from CLCBio								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell	Assembly, Next Gen Mappers, SAM	clc_assembly_cell	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell	https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell	0.0.7	samtools	1.20			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+clinod	clinod	NoD: a Nucleolar localization sequence detector for eukaryotic and viral proteins	clinod	clinod		clinod	The command line NoD predictor (clinod) can be run from the command line to predict Nucleolar localization sequences (NoLSs) that are short targeting sequences responsible for the localization of proteins to the nucleolus.The predictor accepts a list of FASTA formatted sequences as an input and outputs the NOLS predictions as a result.Please note that currently, JPred secondary structure predictions are not supported by clinod. However, we are working on it.	Nucleic acid sequence analysis	Sequence analysis	To update	http://www.compbio.dundee.ac.uk/www-nod/	Sequence Analysis	clinod	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod	https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod	0.1.0	clinod	1.3	Nucleic acid sequence analysis	Sequence analysis	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+cluster	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	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/cluster	1.0.0	bx-python	0.11.0			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	1	1	801
+cmsearch_deoverlap	cmsearch_deoverlap	removes lower scoring overlaps from cmsearch results.	cmsearch-deoverlap	cmsearch-deoverlap		cmsearch-deoverlap	Removes lower scoring overlaps from cmsearch results.	Comparison, Alignment	Biology, Medicine	To update	https://github.com/EBI-Metagenomics/pipeline-v5/blob/master/tools/RNA_prediction/cmsearch-deoverlap/cmsearch-deoverlap.pl	RNA	cmsearch_deoverlap	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmsearch_deoverlap	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmsearch_deoverlap	0.08+galaxy2	perl		Comparison, Alignment	Biology, Medicine	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	102
+cmv	cmcv, cmv, hmmcv, hmmv	cmv is a collection of tools for the visualisation of Hidden Markov Models and RNA-family models.								Up-to-date	https://github.com/eggzilla/cmv	RNA	cmv	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv	1.0.8	cmv	1.0.8			0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	1	108
+cofold	cofold	Cofold predicts RNA secondary structures that takes co-transcriptional folding into account.								To update	http://www.e-rna.org/cofold/	RNA	cofold	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cofold	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cofold	2.0.4.0	cofold	2.0.4			0	0	1	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	8	342
+column_arrange_by_header	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	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/column_arrange_by_header	0.2					1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	179	3781
+combine_metaphlan_humann	combine_metaphlan_humann	Combine MetaPhlAn2 and HUMAnN2 outputs to relate genus/species abundances and gene families/pathways abundances	combine_metaphlan_and_humann	combine_metaphlan_and_humann		Combine Metaphlan and HUMAnN	This tool combine MetaPhlAn outputs and HUMANnN outputs	Aggregation	Metagenomics, Molecular interactions, pathways and networks	To update		Metagenomics	combine_metaphlan2_humann2	bebatut	https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2	https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan_humann	0.3.0	python		Aggregation	Metagenomics, Molecular interactions, pathways and networks	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	9	147
+compalignp	compalignp	Compute fractional identity between trusted alignment and test alignment								Up-to-date		RNA, Sequence Analysis	compalignp	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/compalignp/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/compalignp	1.0	compalignp	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	220
+compare_humann2_output	compare_humann2_output	Compare outputs of HUMAnN2 for several samples and extract similar and specific information	compare_humann2_outputs	compare_humann2_outputs		Compare HUMAnN2 outputs	This tool compare HUMANnN2 outputs with gene families or pathways and their relative abundances between several samples	Comparison	Metagenomics, Gene and protein families	To update		Metagenomics	compare_humann2_output	bebatut	https://github.com/bgruening/galaxytools/tree/master/tools/compare_humann2_output	https://github.com/bgruening/galaxytools/tree/master/tools/compare_humann2_output	0.2.0			Comparison	Metagenomics, Gene and protein families	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	10	332
+complement	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	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/complement	1.0.0	bx-python	0.11.0			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	1	1	233
+compute_motif_frequencies_for_all_motifs	compute_motif_frequencies_for_all_motifs	Compute Motif Frequencies For All Motifs, motif by motif.								To update		Sequence Analysis, Statistics	compute_motif_frequencies_for_all_motifs	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_motif_frequencies_for_all_motifs	https://github.com/galaxyproject/tools-devteam/tree/main/tools/compute_motif_frequencies_for_all_motifs	1.0.0					0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	2	94
+compute_motifs_frequency	compute_motifs_frequency	Compute Motif Frequencies in indel flanking regions.								To update		Sequence Analysis, Statistics	compute_motifs_frequency	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_motifs_frequency	https://github.com/galaxyproject/tools-devteam/tree/main/tools/compute_motifs_frequency	1.0.0					0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	65
+compute_q_values	compute_q_values	Compute q-values based on multiple simultaneous tests p-values								To update		Statistics	compute_q_values	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_q_values	https://github.com/galaxyproject/tools-devteam/tree/main/tools/compute_q_values	1.0.1	R				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	35
+concat	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	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/concat	1.0.1	bx-python	0.11.0			1	1	1	1	1	1	1	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	1	309	564900
+condense_characters	Condense characters1	Condense consecutive characters.								To update		Text Manipulation	condense_characters	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters	https://github.com/galaxyproject/tools-devteam/tree/main/tools/condense_characters	1.0.0					1	1	0	0	1	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+convert_characters	Convert characters1	Convert delimiters to tab.								To update		Text Manipulation	convert_characters	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters	https://github.com/galaxyproject/tools-devteam/tree/main/tools/convert_characters	1.0.1	python				1	1	1	1	1	1	1	1	0	1	1	1	1	0	1	1	1	1	1	1	0	1	1	1	1	1	1	0	0	0	0	1	0	0	1	0	1	1	0	1	1	1	475	23829
+convert_solid_color2nuc	color2nuc	Convert Color Space to Nucleotides								To update		Fasta Manipulation	convert_solid_color2nuc	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_solid_color2nuc	https://github.com/galaxyproject/tools-devteam/tree/main/tools/convert_solid_color2nuc	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+coprarna	coprarna	Target prediction for prokaryotic trans-acting small RNAs								To update	https://github.com/PatrickRWright/CopraRNA	RNA, Sequence Analysis	coprarna	rnateam	https://github.com/PatrickRWright/CopraRNA	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/coprarna	2.1.1	coprarna	2.1.4			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+correlation	cor2	Correlation for numeric columns								To update		Statistics	correlation	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/correlation	https://github.com/galaxyproject/tools-devteam/tree/main/tools/correlation	1.0.0	rpy				0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	47	837
+count_gff_features	count_gff_features	Count GFF Features								To update		Sequence Analysis	count_gff_features	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/count_gff_features	https://github.com/galaxyproject/tools-devteam/tree/main/tools/count_gff_features	0.2	galaxy-ops	1.1.0			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	49	271
+count_roi_variants	count_roi_variants	Count sequence variants in region of interest in BAM file								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants	Assembly, SAM	count_roi_variants	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants	https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants	0.0.6	samtools	1.20			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+coverage	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	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/coverage	1.0.0	bx-python	0.11.0			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	1	17	1502
+coverage_stats	coverage_stats	BAM coverage statistics using samtools idxstats and depth								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats	Assembly, SAM	coverage_stats	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats	https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats	0.1.0	samtools	1.20			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+cpat	cpat	Coding-potential assessment tool using an alignment-free logistic regression model.								Up-to-date	https://github.com/liguowang/cpat	Transcriptomics	cpat	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/cpat	https://github.com/bgruening/galaxytools/tree/master/tools/cpat	3.0.5	cpat	3.0.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	21	134
+crt	crispr_recognition_tool	CRISPR Recognition Tool								To update		Sequence Analysis	crispr_recognition_tool	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/crt	https://github.com/bgruening/galaxytools/tree/master/tools/crt	1.2.0	crisper_recognition_tool	1.2			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	74	3389
+ctd_batch	ctdBatch_1	CTD analysis of chemicals, diseases, or genes								To update		Sequence Analysis	ctd_batch	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/ctd_batch	https://github.com/galaxyproject/tools-devteam/tree/main/tools/ctd_batch	1.0.0					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	13	203
+cummerbund	cummeRbund	Wrapper for the Bioconductor cummeRbund library								To update	https://bioconductor.org/packages/release/bioc/html/cummeRbund.html	RNA, Visualization	cummerbund	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund	https://github.com/galaxyproject/tools-devteam/tree/main/tools/cummerbund	2.16.0	fonts-conda-ecosystem				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	31	1782
+cummerbund_to_tabular	cummerbund_to_cuffdiff	Regenerate the tabular files generated by cuffdiff from a cummeRbund SQLite database.								To update		Convert Formats, Next Gen Mappers	cummerbund_to_tabular	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund_to_tabular	https://github.com/galaxyproject/tools-devteam/tree/main/tools/cummerbund_to_tabular	1.0.1					1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	13	1204
+cut_columns	Cut1	Select columns from a dataset.								To update		Text Manipulation	cut_columns	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns	https://github.com/galaxyproject/tools-devteam/tree/main/tools/cut_columns	1.0.2					1	1	1	1	1	1	1	1	0	1	1	1	1	0	1	0	1	1	1	1	0	1	1	1	1	1	1	1	0	0	0	1	0	0	1	0	1	1	0	1	1	1	5064	1957541
+delete_overlapping_indels	delete_overlapping_indels	Delete Overlapping Indels from a chromosome indels file								To update		Sequence Analysis	delete_overlapping_indels	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/delete_overlapping_indels	https://github.com/galaxyproject/tools-devteam/tree/main/tools/delete_overlapping_indels	1.0.0					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	2	39
+dewseq	dewseq	DEWSeq is a sliding window based peak caller for eCLIP/iCLIP data								To update	https://github.com/EMBL-Hentze-group/DEWSeq_analysis_helpers	Sequence Analysis, RNA, CLIP-seq	dewseq	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq	0.1.0+galaxy0	python				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	11	72
+dgidb_annotator	dgidb_annotate	Annotates a tabular file with information from the Drug-Gene Interaction Database (http://dgidb.genome.wustl.edu/)								To update		Systems Biology, Variant Analysis	dgidb_annotator	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/dgidb_annotator	https://github.com/galaxyproject/tools-devteam/tree/main/tools/dgidb_annotator	0.1					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	7	65
+diff	diff	GNU diff tool that calculates the differences between two files.								To update	http://www.gnu.org/software/diffutils/	Text Manipulation	diff	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/diff	https://github.com/bgruening/galaxytools/tree/master/tools/diff	3.7	diffutils				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	30	235
+diffbind		Diffbind provides functions for  processing  ChIP-Seq  data.								To update	http://bioconductor.org/packages/release/bioc/html/DiffBind.html	ChIP-seq	diffbind	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/diffbind	https://github.com/bgruening/galaxytools/tree/master/tools/diffbind						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+divide_pg_snp	dividePgSnp	Separate pgSnp alleles into columns								To update		Sequence Analysis	divide_pg_snp	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/divide_pg_snp	https://github.com/galaxyproject/tools-devteam/tree/main/tools/divide_pg_snp	1.0.0					1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	32
+dorina	dorina_search	data source for RNA interactions in post-transcriptional regulation								To update		RNA, Data Source	dorina	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dorina/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dorina	1.0					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	1576
+dot2ct	rnastructure_dot2ct	Dot-Bracket to Connect Table (CT)								To update		Sequence Analysis, RNA	dot2ct	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dot2ct	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dot2ct	5.7.a	rnastructure	6.4			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+dotknot	dotknot	DotKnot is a heuristic method for pseudoknot prediction in a given RNA sequence								To update	http://dotknot.csse.uwa.edu.au/	RNA, Proteomics	dotknot	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dotknot	1.3.1	vienna_rna				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	83
+draw_stacked_barplots	draw_stacked_barplots	Draw Stacked Bar Plots for different categories and different criteria								To update		Graphics, Statistics	draw_stacked_barplots	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/draw_stacked_barplots	https://github.com/galaxyproject/tools-devteam/tree/main/tools/draw_stacked_barplots	1.0.0	R				0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	12	173
+dwt_cor_ava_perclass	compute_p-values_correlation_coefficients_feature_occurrences_between_two_datasets_using_discrete_wavelet_transfom	Compute P-values and Correlation Coefficients for Feature Occurrences								To update		Statistics	dwt_cor_ava_perclass	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_ava_perclass	https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_cor_ava_perclass	1.0.1	r-waveslim	1.7.5			0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+dwt_cor_avb_all	compute_p-values_correlation_coefficients_featureA_featureB_occurrences_between_two_datasets_using_discrete_wavelet_transfom	Compute P-values and Correlation Coefficients for Occurrences of Two Set of Features								To update		Statistics	dwt_cor_avb_all	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_cor_avb_all	https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_cor_avb_all	1.0.1	r-waveslim	1.7.5			0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+dwt_ivc_all	compute_p-values_second_moments_feature_occurrences_between_two_datasets_using_discrete_wavelet_transfom	Compute P-values and Second Moments for Feature Occurrences								To update		Statistics	dwt_ivc_all	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_ivc_all	https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_ivc_all	1.0.1	r-waveslim	1.7.5			0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+dwt_var_perclass	compute_p-values_max_variances_feature_occurrences_in_one_dataset_using_discrete_wavelet_transfom	Compute P-values and Max Variances for Feature Occurrences								To update		Statistics	dwt_var_perclass	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perclass	https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_var_perclass	1.0.1	r-waveslim	1.7.5			0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+dwt_var_perfeature	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	https://github.com/galaxyproject/tools-devteam/tree/main/tools/dwt_var_perfeature	1.0.2	r-bitops				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	36
+ear	make_ear	A tool to compile assembly reports and stastics from assembly pipeline								To update	https://github.com/ERGA-consortium/EARs/tree/main	Sequence Analysis, Assembly	erga_ear	iuc	https://github.com/ERGA-consortium/EARs/tree/main	https://github.com/bgruening/galaxytools/tree/master/tools/ear	1.0.0	reportlab				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+edta	edta	The EDTA package was designed to filter out false discoveries in raw TE candidates and generate a high-quality non-redundant TE library for whole-genome TE annotations. 	edta	edta		The Extensive de novo TE Annotator (EDTA)	The EDTA package was designed to filter out false discoveries in raw TE candidates and generate a high-quality non-redundant TE library for whole-genome TE annotations. Selection of initial search programs were based on benckmarkings on the annotation performance using a manually curated TE library in the rice genome.	De-novo assembly, Deisotoping, Genome annotation	Workflows, Mobile genetic elements, Plant biology, Transcription factors and regulatory sites, Model organisms	To update	https://github.com/oushujun/EDTA	Variant Analysis	edta	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/edta	https://github.com/bgruening/galaxytools/tree/master/tools/edta		edta	2.2.0	De-novo assembly, Deisotoping, Genome annotation	Workflows, Mobile genetic elements, Plant biology, Transcription factors and regulatory sites, Model organisms	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	58	484
+effectiveT3	effectiveT3	Find bacterial type III effectors in protein sequences	effectivet3	effectivet3		EffectiveT3	Prediction of putative Type-III secreted proteins.	Sequence classification	Sequence analysis	To update	http://effectors.org	Sequence Analysis	effectivet3	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3	https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3	0.0.21	effectiveT3	1.0.1	Sequence classification	Sequence analysis	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+epicseg	epicseg_segment	EpiCSeg is a tool for conducting chromatin segmentation.								To update	https://github.com/lamortenera/epicseg	Epigenetics	epicseg	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/epicseg	https://github.com/bgruening/galaxytools/tree/master/tools/epicseg	@VERSION_STRING@	epicseg	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	5	245
+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	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/exparna	1.0.1	exparna	1.0.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+express	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	https://github.com/galaxyproject/tools-devteam/tree/main/tools/express	1.1.1	eXpress	1.5.1			0	1	1	0	0	1	1	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	12	325
+fasta_compute_length	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	https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_compute_length	1.0.3	python				1	1	1	1	1	1	1	1	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	1	380	7758
+fasta_concatenate_by_species	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	https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_concatenate_by_species	0.0.1	bx-python	0.11.0			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	88	35793
+fasta_filter_by_id	fasta_filter_by_id	Filter FASTA sequences by ID (DEPRECATED)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id	Fasta Manipulation, Sequence Analysis, Text Manipulation	fasta_filter_by_id	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id	https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id	0.0.7	galaxy_sequence_utils	1.1.5			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+fasta_filter_by_length	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	https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_filter_by_length	1.2	python				1	1	1	1	1	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	1	350	48649
+fasta_to_tabular	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	https://github.com/galaxyproject/tools-devteam/tree/main/tools/fasta_to_tabular	1.1.1	python				1	1	1	1	1	1	1	1	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	1	622	105935
+fastq_filter_by_id	fastq_filter_by_id	Filter FASTQ sequences by ID (DEPRECATED)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id	Fastq Manipulation, Sequence Analysis, Text Manipulation	fastq_filter_by_id	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id	0.0.7	galaxy_sequence_utils	1.1.5			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+fastq_info	fastq_info	FASTQ info allows to validate single or paired fastq files								To update	https://github.com/nunofonseca/fastq_utils	Fastq Manipulation	fastq_info	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info	https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info	0.25.1	fastq_utils	0.25.2			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	679	5765
+fastq_pair_names	fastq_pair_names	Extract FASTQ paired read names								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names	Sequence Analysis	fastq_pair_names	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names	0.0.5	galaxy_sequence_utils	1.1.5			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+fastq_paired_unpaired	fastq_paired_unpaired	Divide FASTQ file into paired and unpaired reads								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired	Sequence Analysis, Text Manipulation	fastq_paired_unpaired	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired	0.1.5	galaxy_sequence_utils	1.1.5			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+fastq_trimmer_by_quality	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	https://github.com/galaxyproject/tools-devteam/tree/main/tools/fastq_trimmer_by_quality	1.1.5	galaxy_sequence_utils	1.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	459	5676
+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	https://github.com/galaxyproject/tools-devteam/tree/main/tools/fastqsolexa_to_fasta_qual	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+featurecounter	featureCoverage1	Feature coverage								To update		Sequence Analysis, Variant Analysis	featurecounter	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/featurecounter	https://github.com/galaxyproject/tools-devteam/tree/main/tools/featurecounter	2.0.0	bx-python	0.11.0			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	6	22385
+file_manipulation	bg_uniq	This tool returns all unique lines from a tab-separated file.								To update	https://github.com/bgruening/galaxytools/tree/master/tools/file_manipulation	Text Manipulation	unique	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/file_manipulation	https://github.com/bgruening/galaxytools/tree/master/tools/file_manipulation	0.4	python				0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	176	8496
+filter_transcripts_via_tracking	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	https://github.com/galaxyproject/tools-devteam/tree/main/tools/filter_transcripts_via_tracking	0.1					1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	1	20
+find_diag_hits	find_diag_hits	Find diagnostic hits								To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	find_diag_hits	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/find_diag_hits	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/find_diag_hits	1.0.0	taxonomy	0.10.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	5	69
+find_subsequences	bg_find_subsequences									To update			find_subsequences	bgruening		https://github.com/bgruening/galaxytools/tree/master/tools/find_subsequences	0.3	biopython	1.70			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	31	763
+flanking_features	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	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/flanking_features	4.0.1	bx-python	0.11.0			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	1	20	671
+flye	flye	Assembly of long and error-prone reads.	Flye	Flye		Flye	Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The package represents a complete pipeline: it takes raw PB / ONT reads as input and outputs polished contigs.	Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly	Sequence assembly, Metagenomics, Whole genome sequencing, Genomics	To update	https://github.com/fenderglass/Flye/	Assembly	flye	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/flye	https://github.com/bgruening/galaxytools/tree/master/tools/flye	2.9.3	flye	2.9.4	Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly	Sequence assembly, Metagenomics, Whole genome sequencing	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	1	1499	20904
+footprint	footprint	Find transcription factor footprints								To update	https://ohlerlab.mdc-berlin.de/software/Reproducible_footprinting_139/	Epigenetics	footprint	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/footprint	https://github.com/bgruening/galaxytools/tree/master/tools/footprint	1.0.0	footprint	1.0.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	57
+format_cd_hit_output	format_cd_hit_output	Format CD-hit output to rename representative sequences with cluster name and/or extract distribution inside clusters given a mapping file								To update		Fasta Manipulation	format_cd_hit_output	bebatut	https://github.com/bgruening/galaxytools/tree/master/tools/format_cd_hit_output/	https://github.com/bgruening/galaxytools/tree/master/tools/format_cd_hit_output	1.0.0+galaxy1					0	0	1	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	20	166
+format_metaphlan2_output	format_metaphlan2_output	Format MetaPhlAn2 output to extract abundance at different taxonomic levels	format_metaphlan2_output	format_metaphlan2_output		Format metaphlan2 output	This tool format output file of MetaPhlan2 containing community content (abundance) at all taxonomic levels (from kingdom to strains).	Formatting	Taxonomy, Metagenomics	To update		Metagenomics	format_metaphlan2_output	bebatut	https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/	https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output	0.2.0			Formatting	Taxonomy, Metagenomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	166	5588
+generate_pc_lda_matrix	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	https://github.com/galaxyproject/tools-devteam/tree/main/tools/generate_pc_lda_matrix	1.0.0					1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	12	119
+get_flanks	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	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/get_flanks	1.0.0	bx-python	0.11.0			1	1	1	1	1	1	1	1	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	555	324598
+get_orfs_or_cdss	get_orfs_or_cdss	Search nucleotide sequences for open reading frames (ORFs), or coding sequences (CDSs)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss	Sequence Analysis	get_orfs_or_cdss	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss	https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss	0.2.3	biopython	1.70			0	1	1	1	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	15	186
+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	https://github.com/galaxyproject/tools-devteam/tree/main/tools/getindelrates_3way	1.0.0	bx-python	0.11.0			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+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	https://github.com/galaxyproject/tools-devteam/tree/main/tools/getindels_2way	1.0.0	numpy				1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+gfastats	gfastats	Tool for generating sequence statistics and simultaneous genome assembly file manipulation.	gfastats	gfastats		gfastats	gfastats is a single fast and exhaustive tool for summary statistics and simultaneous genome assembly file manipulation. gfastats also allows seamless fasta/fastq/gfa conversion.	Data handling	Computational biology	Up-to-date	https://github.com/vgl-hub/gfastats	Sequence Analysis	gfastats	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/gfastats	https://github.com/bgruening/galaxytools/tree/master/tools/gfastats	1.3.6	gfastats	1.3.6	Data handling	Computational biology	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	418	8159
+gi2taxonomy	Fetch Taxonomic Ranks	Fetch taxonomic representation	gi2taxonomy	gi2taxonomy		gi2taxonomy	The tool fetches taxonomic information for a list of sequence identifiers (i.e. GI numbers, as used by the National Center for Biotechnology Information (NCBI).	Database search, ID mapping	Taxonomy	To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	gi2taxonomy	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/gi2taxonomy	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/gi2taxonomy	1.1.1	taxonomy	0.10.0	Database search, ID mapping	Taxonomy	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	27	660
+glimmer_hmm		GlimmerHMM is a new gene finder based on a Generalized Hidden Markov Model (GHMM)								To update	https://ccb.jhu.edu/software/glimmerhmm/	Sequence Analysis	glimmer_hmm	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm	https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+gmaj	gmaj_1	GMAJ Multiple Alignment Viewer								To update		Visualization	gmaj	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/gmaj	https://github.com/galaxyproject/tools-devteam/tree/main/tools/gmaj	2.0.1					1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	4	11
+gotohscan	rbc_gotohscan	Find subsequences in db								To update		Sequence Analysis	gotohscan	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/gotohscan	https://github.com/bgruening/galaxytools/tree/master/tools/gotohscan	1.3.0	gotohscan	1.3			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	71
+graph_converter	graph_converter	Convert between different graph formats								To update		Convert Formats	graph_converter	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/graph_converter	https://github.com/bgruening/galaxytools/tree/master/tools/graph_converter	0.1.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+graphclust	graphclust	GraphClust can be used for structural clustering of RNA sequences.								To update	http://www.bioinf.uni-freiburg.de/Software/GraphClust/	RNA	graphclust	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/graphclust	https://github.com/bgruening/galaxytools/tree/master/tools/graphclust	0.1	GraphClust				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6
+graphicsmagick	graphicsmagick_image_compare, graphicsmagick_image_convert, graphicsmagick_image_montage	Contains tools based on GraphicsMagick								To update	http://www.graphicsmagick.org	Imaging	graphicsmagick	bgruening	https://github.com/bgruening/galaxytools/new/gm/tools/image_processing/image_processing/	https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/graphicsmagick	1.3.43	graphicsmagick	1.3.26			1	0	3	0	1	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	43	2605
+graphmap	graphmap_align, graphmap_overlap	Mapper for long, error-prone reads.	graphmap	graphmap		graphmap	Splice-aware RNA-seq mapper for long reads | GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.html https://www.biorxiv.org/content/10.1101/720458v1	Sequence trimming, EST assembly, Read mapping	Gene transcripts, RNA-Seq, RNA splicing	To update	https://github.com/isovic/graphmap/	Assembly	graphmap	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/graphmap	https://github.com/bgruening/galaxytools/tree/master/tools/graphmap	0.5.2	graphmap	0.6.3	Sequence trimming, EST assembly, Read mapping	Gene transcripts, RNA-Seq, RNA splicing	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2	2	136	6651
+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	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot	1.1.7+galaxy1	graphprot	1.1.7			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	6	474
+hclust2	hclust2	Plots heatmaps								To update	https://bitbucket.org/nsegata/hclust2/	Data Visualization	hclust2	rnateam	https://github.com/yuanbit/galaxytools/tree/hclust2/tools/hclust2	https://github.com/bgruening/galaxytools/tree/master/tools/hclust2	0.99	hclust2	1.0.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+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	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/hgv/hgv_fundo	1.0.0					1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0
+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	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/hgv/hgv_hilbertvis	1.0.0	R				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0
+hictk	hictk	Convert cooler to juicebox_hic								Up-to-date	https://github.com/paulsengroup/hictk	Convert Formats, Epigenetics	hictk	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/hictk	https://github.com/bgruening/galaxytools/tree/master/tools/hictk	0.0.12	hictk	0.0.12			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+hicup	hicup2juicer, hicup_deduplicator, hicup_digester, hicup_filter, hicup_hicup, hicup_mapper, hicup_truncater	The HiCUP-Pipeline from the Bioinformatics Babraham Institute.								To update	https://www.bioinformatics.babraham.ac.uk/projects/hicup/read_the_docs/html/index.html	Epigenetics	hicup	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/hicup	https://github.com/bgruening/galaxytools/tree/master/tools/hicup	0.9.2					7	0	7	0	7	0	7	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	7	6	76	921
+hifiasm	hifiasm	A fast haplotype-resolved de novo assembler								To update	https://github.com/chhylp123/hifiasm	Assembly	hifiasm	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm	https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm	0.19.8	hifiasm	0.19.9			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	297	1410
+hisat	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	https://github.com/galaxyproject/tools-devteam/tree/main/tools/hisat	1.0.3	hisat				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	228
+histogram	histogram_rpy	Histogram of a numeric column								To update		Graphics, Statistics	histogram	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/histogram	https://github.com/galaxyproject/tools-devteam/tree/main/tools/histogram	1.0.4	rpy2	2.7.8			1	1	1	1	1	1	1	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	242	4350
+homer		Software for motif discovery and next generation sequencing analysis.								To update	http://homer.salk.edu/homer/	Sequence Analysis	homer	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/homer	https://github.com/bgruening/galaxytools/tree/master/tools/homer						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+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	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip	0.1.0+galaxy0	htseq-clip	2.19.0b0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	15	77
+illumina_methylation_analyser	illumina_methylation_analyser	Methylation analyzer for Illumina 450k DNA emthylation microarrays								To update	https://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyser	Sequence Analysis	illumina_methylation_analyser	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyser	https://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyser	0.1	Rscript				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+imagej2	imagej2_adjust_threshold_binary, imagej2_analyze_particles_binary, imagej2_analyze_skeleton, imagej2_binary_to_edm, imagej2_bunwarpj_adapt_transform, imagej2_bunwarpj_align, imagej2_bunwarpj_compare_elastic, imagej2_bunwarpj_compare_elastic_raw, imagej2_bunwarpj_compare_raw, imagej2_bunwarpj_compose_elastic, imagej2_bunwarpj_compose_raw, imagej2_bunwarpj_compose_raw_elastic, imagej2_bunwarpj_convert_to_raw, imagej2_bunwarpj_elastic_transform, imagej2_bunwarpj_raw_transform, imagej2_create_image, imagej2_enhance_contrast, imagej2_find_edges, imagej2_find_maxima, imagej2_make_binary, imagej2_math, imagej2_noise, imagej2_shadows, imagej2_sharpen, imagej2_skeletonize3d, imagej2_smooth, imagej2_watershed_binary	ImageJ2 is a new version of ImageJ for the next generation of multidimensionalimage data, with a focus on scientific imaging.	imagej	imagej	imagej2	ImageJ2	It is a public domain Java image processing program, which was designed with an open architecture. Custom acquisition, analysis and processing plugins can be developed using ImageJ’s built-in editor and a Java compiler. User-written plugins make it possible to solve many image processing and analysis problems, from three-dimensional live-cell imaging, to radiological image processing, multiple imaging system data comparisons to automated hematology systems.	Image analysis, Image annotation, Visualisation	Imaging	To update	http://fiji.sc	Imaging	imagej2	imgteam	https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2	https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2				Image analysis, Image annotation, Visualisation	Imaging	0	0	27	0	0	0	27	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	27	27	26	1537
+improviser	proteomics_improviser	Visualisation of PepXML files								To update	http://www.improviser.uni-freiburg.de/	Proteomics	proteomics_improviser	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/proteomics/improviser	https://github.com/bgruening/galaxytools/tree/master/tools/proteomics/improviser	1.1.0.1					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+indels_3way	indels_3way	Fetch Indels from 3-way alignments								To update		Sequence Analysis	indels_3way	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/indels_3way	https://github.com/galaxyproject/tools-devteam/tree/main/tools/indels_3way	1.0.3					1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	22
+infernal	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	"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, Structural genomics	To update	http://infernal.janelia.org/	RNA	infernal	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/infernal	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/infernal	1.1.4	infernal	1.1.5	Nucleic acid feature detection	Sequence sites, features and motifs, Structural genomics	0	6	6	0	0	6	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	6	67	100294
+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	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/inforna						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+instagraal	instagraal	Large genome reassembly based on Hi-C data	instagraal	instagraal		instaGRAAL	Chromosome-level quality scaffolding of brown algal genomes using InstaGRAAL.Large genome reassembly based on Hi-C data, continuation of GRAAL.Large genome reassembly based on Hi-C data (continuation and partial rewrite of GRAAL) and post-scaffolding polishing libraries.This work is under continuous development/improvement - see GRAAL for information about the basic principles.sudo pip3 install -e git+https://github.com/koszullab/instagraal.git@master#egg=instagraal.Note to OS X users: There is currently no CUDA support on Mojave (10.14) and it is unclear when it is going to be added, if it is to be added at all. This means instaGRAAL (or indeed any CUDA-based application) will not work on Mojave. If you wish to run it on OS X, the only solution for now is to downgrade to High Sierra (10.13)	Genome assembly, Mapping assembly, Genetic mapping, Scaffolding	Sequence assembly, Mapping, Metagenomics, Statistics and probability, DNA binding sites	To update	https://github.com/koszullab/instaGRAAL	Assembly	instagraal	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/instagraal	https://github.com/bgruening/galaxytools/tree/master/tools/instagraal	0.1.6			Genome assembly, Mapping assembly, Genetic mapping, Scaffolding	Sequence assembly, Mapping, Metagenomics, Statistics and probability, DNA binding sites	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	14	139
+intarna	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	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna	3.4.0	intarna	3.4.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	23	7569
+intersect	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	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/intersect	1.0.0	bx-python	0.11.0			1	1	1	1	1	1	1	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	1	1003	348449
+iprscan5		Interproscan queries the interpro database and provides annotations.								To update	http://www.ebi.ac.uk/Tools/pfa/iprscan5/	Sequence Analysis	iprscan5	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/iprscan5	https://github.com/bgruening/galaxytools/tree/master/tools/iprscan5						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+itsx	itsx	ITSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences.	ITSx	ITSx		ITSx	TSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences, which is commonly used as a molecular barcode for e.g. fungi. As the inclusion of parts of the neighbouring, very conserved, ribosomal genes (SSU, 5S and LSU rRNA sequences) in the sequence identification process can lead to severely misleading results, ITSx identifies and extracts only the ITS regions themselves.	Sequence feature detection	Functional, regulatory and non-coding RNA, Microbiology	Up-to-date	https://microbiology.se/software/itsx/	Metagenomics	itsx	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/itsx	https://github.com/bgruening/galaxytools/tree/master/tools/itsx	1.1.3	itsx	1.1.3	Sequence feature detection	Functional, regulatory and non-coding RNA, Microbiology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	38	868
+jbrowse2	jbrowse2	JBrowse2 Genome Browser integrated as a Galaxy Tool	jbrowse2	jbrowse2						To update	https://jbrowse.org	Sequence Analysis	jbrowse2	fubar	https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2	https://github.com/bgruening/galaxytools/tree/master/tools/jbrowse2	2.11.1	jbrowse2	2.11.2			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+join	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	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/join	1.0.0	bx-python	0.11.0			1	1	1	1	1	1	1	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	1	284	329556
+join_files_on_column_fuzzy	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	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/join_files_on_column_fuzzy	1.0.1	python				0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	1	117	2448
+jupyter_job	run_jupyter_job	Run jupyter notebook script in Galaxy								To update		Machine Learning	run_jupyter_job	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job	https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job	0.0.1					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	30
+kernel_canonical_correlation_analysis	kcca1	Kernel Canonical Correlation Analysis								To update		Statistics	kernel_canonical_correlation_analysis	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/kernel_canonical_correlation_analysis	https://github.com/galaxyproject/tools-devteam/tree/main/tools/kernel_canonical_correlation_analysis	1.0.0	rpy				1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	2	69
+kernel_principal_component_analysis	kpca1	Kernel Principal Component Analysis								To update		Statistics	kernel_principal_component_analysis	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/kernel_principal_component_analysis	https://github.com/galaxyproject/tools-devteam/tree/main/tools/kernel_principal_component_analysis	1.0.0	rpy				1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	13	156
+kinwalker		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	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/kinwalker						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+kraken2tax	Kraken2Tax	Convert Kraken output to Galaxy taxonomy data.								To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	kraken2tax	devteam	https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/taxonomy/kraken2tax/	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/kraken2tax	1.2+galaxy0	gawk				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	1	481	14683
+labels	bg_labels	remaps and annotates alignments								To update	https://github.com/bgruening/galaxytools/tree/master/tools/labels	Sequence Analysis	labels	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/labels	https://github.com/bgruening/galaxytools/tree/master/tools/labels	1.0.5.0	labels				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+lastz_paired_reads	lastz_paired_reads_wrapper	Galaxy wrapper for the Lastz alignment tool on paired reads								To update		Next Gen Mappers	lastz_paired_reads	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads	https://github.com/galaxyproject/tools-devteam/tree/main/tools/lastz_paired_reads	1.1.1	lastz	1.04.22			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	1	9
+lca_wrapper	lca1	Find lowest diagnostic rank								To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	lca_wrapper	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/lca_wrapper	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/lca_wrapper	1.0.1	taxonomy	0.10.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	2	137
+lda_analysis	lda_analy1	Perform Linear Discriminant Analysis								To update		Graphics, Statistics	lda_analysis	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/lda_analysis	https://github.com/galaxyproject/tools-devteam/tree/main/tools/lda_analysis	1.0.1	R				1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	18	148
+lighter	lighter	Lighter is a kmer-based error correction method for whole genome sequencing data	lighter	lighter		Lighter	Kmer-based error correction method for whole genome sequencing data. Lighter uses sampling (rather than counting) to obtain a set of kmers that are likely from the genome. Using this information, Lighter can correct the reads containing sequence errors.	k-mer counting, Sequence read processing, Sequencing quality control, Sequencing error detection	Sequencing, Whole genome sequencing, DNA, Genomics	To update	https://github.com/mourisl/Lighter	Sequence Analysis, Fasta Manipulation	lighter	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/lighter	https://github.com/bgruening/galaxytools/tree/master/tools/lighter	1.0	lighter	1.1.3	k-mer counting, Sequence read processing, Sequencing quality control, Sequencing error detection	Whole genome sequencing, DNA, Genomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	9	152
+linear_regression	LinearRegression1	Perform Linear Regression								To update		Statistics	linear_regression	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/linear_regression	https://github.com/galaxyproject/tools-devteam/tree/main/tools/linear_regression	1.0.1	R				1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+locarna	locarna_exparnap, locarna_multiple, locarna_pairwise, locarna_pairwise_p, locarna_reliability_profile	LocARNA - A suite for multiple alignment and folding of RNAs								To update	http://www.bioinf.uni-freiburg.de/Software/LocARNA/	RNA	locarna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna	1.9.2.3	locarna	2.0.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	11	339
+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	https://github.com/galaxyproject/tools-devteam/tree/main/tools/logistic_regression_vif	1.0.1	numpy				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+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	https://github.com/galaxyproject/tools-devteam/tree/main/tools/maf_cpg_filter	1.0.0	bx-python	0.11.0			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+mafft	rbc_mafft_add, rbc_mafft	Multiple alignment program for amino acid or nucleotide sequences	MAFFT	MAFFT		MAFFT	MAFFT (Multiple Alignment using Fast Fourier Transform) is a high speed multiple sequence alignment program.	Multiple sequence alignment	Sequence analysis	To update	https://mafft.cbrc.jp/alignment/software/	RNA	mafft	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/mafft	https://github.com/bgruening/galaxytools/tree/master/tools/mafft	7.520	mafft	7.525	Multiple sequence alignment	Sequence analysis	2	2	2	2	2	2	2	2	0	0	0	1	0	0	2	0	0	0	0	0	0	0	1	0	2	0	0	2	0	0	0	2	0	0	0	0	0	0	0	2	2	2	817	143045
+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	https://github.com/galaxyproject/tools-devteam/tree/main/tools/mapping_to_ucsc	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+mavedb	mavedb_importer	data source for MaveDB								To update		Data Source	mavedb_importer	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/mave_tools/mavedb/	https://github.com/bgruening/galaxytools/tree/master/tools/mave_tools/mavedb	0.9					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+mea	mea	Maximum expected accuracy prediction								To update	http://www.bioinf.uni-leipzig.de/Software/mea	RNA	mea	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mea	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mea	0.6.4.1	mea	0.6.4			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	3	85
+megablast_xml_parser	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	https://github.com/galaxyproject/tools-devteam/tree/main/tools/megablast_xml_parser	1.0.1	python				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	36	338
+merge	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	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/merge	1.0.0	bx-python	0.11.0			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	1	193	563676
+merge_cols	mergeCols1	Merge columns together.								To update		Text Manipulation	merge_cols	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols	https://github.com/galaxyproject/tools-devteam/tree/main/tools/merge_cols	1.0.3	python				1	1	1	1	1	1	1	1	0	1	1	1	1	0	1	0	1	1	1	1	0	1	1	1	1	1	1	0	0	0	0	1	0	0	1	0	1	1	0	1	1	1	542	28593
+methtools	methtools_calling, r_correlation_matrix, methtools_destrand, methtools_dmr, methtools_filter, methtools_plot, smooth_running_window, methtools_tiling	tools for methylation analysis								To update	https://github.com/bgruening/galaxytools/tree/master/tools/methtools	Sequence Analysis	methtools	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/methtools	https://github.com/bgruening/galaxytools/tree/master/tools/methtools	0.1.1	methtools				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5461
+methyldackel	pileometh	A tool for processing bisulfite sequencing alignments								To update	https://github.com/dpryan79/MethylDackel	Sequence Analysis	pileometh	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel	https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel	0.5.2	methyldackel	0.6.1			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	1	200	16573
+methylkit	methylkit	A method for DNA methylation analysis and annotation from high-throughput bisulfite sequencing.								To update	http://bioconductor.org/packages/release/bioc/html/methylKit.html	Epigenetics	methylkit	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/methylkit	https://github.com/bgruening/galaxytools/tree/master/tools/methylkit	0.99.2	bioconductor-methylkit	1.28.0			0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+metilene	metilene	Differential DNA methylation calling								To update		RNA, Statistics	metilene	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/metilene	https://github.com/bgruening/galaxytools/tree/master/tools/metilene	0.2.6.1	metilene	0.2.8			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	1	103	3966
+mgnify_seqprep	mgnify_seqprep	A modifiied vesion of SeqPrep. Made for use with the MGnify pipelines.	seqprep	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	To update	https://github.com/jstjohn/SeqPrep	Fastq Manipulation, Sequence Analysis	mgnify_seqprep	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/mgnify_seqprep	https://github.com/bgruening/galaxytools/tree/master/tools/mgnify_seqprep	1.2			Nucleic acid design	Genomics, Sequence assembly, Sequencing, Probes and primers	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+miclip	mi_clip	Identification of binding sites in CLIP-Seq data.								To update	https://cran.r-project.org/src/contrib/Archive/MiClip/	Sequence Analysis	miclip	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/miclip	https://github.com/bgruening/galaxytools/tree/master/tools/miclip	1.2.0	Rscript				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+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	https://github.com/galaxyproject/tools-devteam/tree/main/tools/microsatellite_birthdeath	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+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	https://github.com/galaxyproject/tools-devteam/tree/main/tools/microsats_alignment_level	1.0.0	sputnik				1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+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	https://github.com/galaxyproject/tools-devteam/tree/main/tools/microsats_mutability	1.1.0	bx-python	0.11.0			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+minced	minced	MinCED - Mining CRISPRs in Environmental Datasets								To update	http://bioweb2.pasteur.fr/docs/modules/minced/0.1.5/_README	Sequence Analysis	minced	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/minced	https://github.com/bgruening/galaxytools/tree/master/tools/minced	0.2.0	minced	0.4.2			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	53	895
+mine	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	https://github.com/galaxyproject/tools-devteam/tree/main/tools/mine	0.0.1	MINE				1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	2	11
+minipolish	minipolish	Polishing miniasm assemblies	minipolish	minipolish		minipolish	A tool that bridges the output of miniasm (long-read assembly) and racon (assembly polishing) together to polish a draft assembly. It also provides read depth information in contigs.	Localised reassembly, Read depth analysis	Sequence assembly, Sequencing	Up-to-date	https://github.com/rrwick/Minipolish	Sequence Analysis	minipolish	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/minipolish	https://github.com/bgruening/galaxytools/tree/master/tools/minipolish	0.1.3	minipolish	0.1.3	Localised reassembly, Read depth analysis	Sequence assembly, Sequencing	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	21	185
+mitohifi	mitohifi	Assembly mitogenomes from Pacbio HiFi read.								To update	https://github.com/marcelauliano/MitoHiFi/tree/mitohifi_v2	Assembly	mitohifi	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi	https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi	3					1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	56	613
+molecule2gspan	bg_mol2gspan	converter								To update	https://github.com/bgruening/galaxytools/tree/master/tools/molecule2gspan	Convert Formats	molecule_to_gspan	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/molecule2gspan	https://github.com/bgruening/galaxytools/tree/master/tools/molecule2gspan	0.2	openbabel	2.3.90dev7d621d9			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+mqc	mqc	Ribosome profiling mapping quality control tool								To update	https://github.com/Biobix/mQC	Sequence Analysis	mqc	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mqc/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mqc	1.9	mqc	1.10			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	5	76
+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	https://github.com/galaxyproject/tools-devteam/tree/main/tools/multispecies_orthologous_microsats	1.0.0	bx-sputnik				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+mummer	mummerplot_wrapper	Draw dotplots using mummer, mucmer, or promer with mummerplot								To update	http://mummer.sourceforge.net/	Graphics, Sequence Analysis, Visualization	mummer	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/mummer	https://github.com/peterjc/pico_galaxy/tree/master/tools/mummer	0.0.8	ghostscript	9.18			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	83	652
+music_deconvolution	music_construct_eset, music_inspect_eset, music_manipulate_eset, music_compare, music_deconvolution	Multi-subject Single Cell deconvolution (MuSiC)								Up-to-date	https://github.com/xuranw/MuSiC	Transcriptomics	music	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/	https://github.com/bgruening/galaxytools/tree/master/tools/music_deconvolution	0.1.1	music-deconvolution	0.1.1			5	5	4	0	5	5	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	240	1872
+mutate_snp_codon	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	https://github.com/galaxyproject/tools-devteam/tree/main/tools/mutate_snp_codon	1.0.0					1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	47
+nanopolish	nanopolish_eventalign, nanopolish_methylation, nanopolish_polya, nanopolish_variants	Nanopolish software package for signal-level analysis of Oxford Nanopore sequencing data.								Up-to-date	https://github.com/jts/nanopolish		nanopolish	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish	https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish	0.14.0	nanopolish	0.14.0			0	4	4	4	0	4	4	4	0	0	0	0	0	0	3	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	4	4	4	78	8366
+nastiseq	nastiseq	A method to identify cis-NATs using ssRNA-seq								Up-to-date	https://ohlerlab.mdc-berlin.de/software/NASTIseq_104/	RNA	nastiseq	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/nastiseq	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/nastiseq	1.0	r-nastiseq	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	40
+netboxr	netboxr	netboxr enables automated discovery of biological process modules by network analysis								To update		Systems Biology	netboxr	bgruening		https://github.com/bgruening/galaxytools/tree/master/tools/netboxr	1.6.0	bioconductor-netboxr	1.9.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	5	11
+nextdenovo	nextdenovo	String graph-based de novo assembler for long reads	nextdenovo	nextdenovo		NextDenovo	"NextDenovo is a string graph-based de novo assembler for long reads (CLR, HiFi and ONT). It uses a ""correct-then-assemble"" strategy similar to canu (no correction step for PacBio Hifi reads), but requires significantly less computing resources and storages."	De-novo assembly, Genome assembly	Sequencing, Sequence assembly	To update	https://github.com/Nextomics/NextDenovo	Assembly	nextdenovo	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo	https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo	2.5.0	nextdenovo	2.5.2	De-novo assembly, Genome assembly	Sequencing, Sequence assembly	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	84	268
+nlstradamus	nlstradamus	Find nuclear localization signals (NLSs) in protein sequences								To update	http://www.moseslab.csb.utoronto.ca/NLStradamus	Fasta Manipulation, Sequence Analysis	nlstradamus	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/nlstradamus	https://github.com/peterjc/pico_galaxy/tree/master/tools/nlstradamus	0.0.11	NLStradamus	1.8			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+nucleosome_prediction	Nucleosome	Prediction of Nucleosomes Positions on the Genome	nucleosome_prediction	nucleosome_prediction		nucleosome_prediction	Prediction of Nucleosomes Positions on the Genome	Prediction and recognition, Nucleosome position prediction, Sequence analysis	Structural genomics, Nucleic acid sites, features and motifs	Up-to-date	https://genie.weizmann.ac.il/software/nucleo_exe.html	Sequence Analysis	nucleosome_prediction	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/nucleosome_prediction	https://github.com/bgruening/galaxytools/tree/master/tools/nucleosome_prediction	3.0	nucleosome_prediction	3.0	Prediction and recognition, Nucleosome position prediction, Sequence analysis	Structural genomics, Nucleic acid sites, features and motifs	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	2	861
+numeric_clustering	numeric_clustering	Clustering tool for numberic values								To update	http://scikit-learn.org/stable/index.html	Statistics	numeric_clustering	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering	https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering	0.9	anaconda				0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	486
+openms	AccurateMassSearch, AdditiveSeries, BaselineFilter, CVInspector, CompNovo, CompNovoCID, ConsensusID, ConsensusMapNormalizer, ConvertTSVToTraML, ConvertTraMLToTSV, DTAExtractor, DeMeanderize, Decharger, DecoyDatabase, Digestor, DigestorMotif, EICExtractor, ERPairFinder, ExternalCalibration, FFEval, FalseDiscoveryRate, FeatureFinderCentroided, FeatureFinderIdentification, FeatureFinderIsotopeWavelet, FeatureFinderMRM, FeatureFinderMetabo, FeatureFinderMultiplex, FeatureFinderSuperHirn, FeatureLinkerLabeled, FeatureLinkerUnlabeled, FeatureLinkerUnlabeledQT, FidoAdapter, FileConverter, FileFilter, FileInfo, FileMerger, FuzzyDiff, HighResPrecursorMassCorrector, IDConflictResolver, IDDecoyProbability, IDExtractor, IDFileConverter, IDFilter, IDMapper, IDMassAccuracy, IDMerger, IDPosteriorErrorProbability, IDRTCalibration, IDRipper, IDScoreSwitcher, IDSplitter, ITRAQAnalyzer, InclusionExclusionListCreator, InspectAdapter, InternalCalibration, IsobaricAnalyzer, LabeledEval, LowMemPeakPickerHiRes, LowMemPeakPickerHiRes_RandomAccess, LuciphorAdapter, MRMMapper, MRMPairFinder, MRMTransitionGroupPicker, MSGFPlusAdapter, MSSimulator, MapAlignmentEvaluation, MapNormalizer, MapRTTransformer, MapStatistics, MascotAdapter, MascotAdapterOnline, MassCalculator, MassTraceExtractor, MetaProSIP, MetaboliteSpectralMatcher, MultiplexResolver, MzMLSplitter, MzTabExporter, NoiseFilterGaussian, NoiseFilterSGolay, OpenSwathAnalyzer, OpenSwathAssayGenerator, OpenSwathChromatogramExtractor, OpenSwathConfidenceScoring, OpenSwathDIAPreScoring, OpenSwathDecoyGenerator, OpenSwathFeatureXMLToTSV, OpenSwathFileSplitter, OpenSwathMzMLFileCacher, OpenSwathRTNormalizer, OpenSwathRewriteToFeatureXML, OpenSwathWorkflow, PTModel, PTPredict, PeakPickerHiRes, PeakPickerIterative, PeakPickerWavelet, PepNovoAdapter, PeptideIndexer, PhosphoScoring, PrecursorIonSelector, PrecursorMassCorrector, ProteinInference, ProteinQuantifier, ProteinResolver, QCCalculator, QCEmbedder, QCExporter, QCExtractor, QCImporter, QCMerger, QCShrinker, RNPxl, RNPxlXICFilter, RTEvaluation, RTModel, RTPredict, SemanticValidator, SequenceCoverageCalculator, SimpleSearchEngine, SpecLibCreator, SpectraFilterBernNorm, SpectraFilterMarkerMower, SpectraFilterNLargest, SpectraFilterNormalizer, SpectraFilterParentPeakMower, SpectraFilterScaler, SpectraFilterSqrtMower, SpectraFilterThresholdMower, SpectraFilterWindowMower, SpectraMerger, SvmTheoreticalSpectrumGeneratorTrainer, TICCalculator, TMTAnalyzer, TOFCalibration, TextExporter, TopPerc, TransformationEvaluation, XMLValidator, XTandemAdapter	OpenMS in version 2.1.								To update		Proteomics	openms	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/openms	https://github.com/bgruening/galaxytools/tree/master/tools/openms	2.1.0	openms	3.1.0			7	34	135	0	7	34	135	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	19	135	134	916	105743
+pandas_rolling_window	pandas_rolling_window	Rolling window calculations								To update	https://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.DataFrame.rolling.html	Statistics	pandas_rolling_window	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/pandas_rolling_window	https://github.com/bgruening/galaxytools/tree/master/tools/pandas_rolling_window	0.1	numpy				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	7	269
+paralyzer	paralyzer	A method to generate a high resolution map of interaction sites between RNA-binding proteins and their targets.								Up-to-date	https://ohlerlab.mdc-berlin.de/software/PARalyzer_85/	RNA	paralyzer	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer	1.5	paralyzer	1.5			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	7	299
+partialr_square	partialRsq	Compute partial R square								To update		Statistics	partialr_square	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/partialr_square	https://github.com/galaxyproject/tools-devteam/tree/main/tools/partialr_square	1.0.0	R				1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+peakachu	peakachu	PEAKachu is a peak-caller for CLIP- and RIP-Seq data								To update		Sequence Analysis, RNA	peakachu	rnateam	https://github.com/tbischler/PEAKachu	https://github.com/bgruening/galaxytools/tree/master/tools/peakachu	0.2.0+galaxy1	peakachu	0.2.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	78	3109
+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	https://github.com/galaxyproject/tools-devteam/tree/main/tools/pearson_correlation	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+perf	stats_perf_tool	suitable for boolean classification problems								To update	http://osmot.cs.cornell.edu/kddcup/software.html		stats_perf_tool	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/perf	https://github.com/bgruening/galaxytools/tree/master/tools/perf	5.11.0	perf				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+pfamscan	pfamscan	Search a FASTA sequence against a library of Pfam HMM.	pfamscan	pfamscan		PfamScan	This tool is used to search a FASTA sequence against a library of Pfam HMM.	Protein sequence analysis	Sequence analysis	Up-to-date	http://ftp.ebi.ac.uk/pub/databases/Pfam/Tools/	Sequence Analysis	pfamscan	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/pfamscan	https://github.com/bgruening/galaxytools/tree/master/tools/pfamscan	1.6	pfam_scan	1.6	Protein sequence analysis	Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	19	165
+pg_tools	pg_dump, pg_import, pg_query	tool suite for dealing with Postgresql databases from Galaxy's history								To update	https://www.postgresql.org	Data Export, Data Source	pgtools	bgruening	https://github.com/bgruening/galaxytools/tools/pgtools	https://github.com/bgruening/galaxytools/tree/master/tools/pg_tools		postgresql				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+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	https://github.com/galaxyproject/tools-devteam/tree/main/tools/pgsnp2gd_snp	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+pharmcat	pharmcat	Pharmacogenomics Clinical Annotation Tool								To update	https://pharmcat.org/	Variant Analysis	pharmcat	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat	https://github.com/bgruening/galaxytools/tree/master/tools/pharmcat						1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	14	82
+pileup_interval	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	https://github.com/galaxyproject/tools-devteam/tree/main/tools/pileup_interval	1.0.3	bx-python	0.11.0			1	1	1	1	1	1	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	1	15	632
+pileup_parser	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	https://github.com/galaxyproject/tools-devteam/tree/main/tools/pileup_parser	1.0.2	perl				1	1	1	1	1	1	1	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	1	169	3158
+pipmir	pipmir	A method to identify novel plant miRNA.								To update	https://ohlerlab.mdc-berlin.de/software/Pipeline_for_the_Identification_of_Plant_miRNAs_84/	RNA	pipmir	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir	0.1.0	pipmir	1.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	21	275
+piranha	piranha	Piranha is a peak-caller for CLIP- and RIP-Seq data								To update		Sequence Analysis, RNA	piranha	rnateam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/piranha	https://github.com/bgruening/galaxytools/tree/master/tools/piranha	1.2.1.0	piranha	1.2.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	39	1809
+platypus	bg_platypus	efficient and accurate variant-detection in high-throughput sequencing data								To update	http://www.well.ox.ac.uk/platypus	Sequence Analysis	platypus	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/platypus	https://github.com/bgruening/galaxytools/tree/master/tools/platypus	0.0.11	platypus				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+plot_from_lda	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	https://github.com/galaxyproject/tools-devteam/tree/main/tools/plot_from_lda	1.0.1	R				1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	9	73
+plotly_ml_performance_plots	plotly_ml_performance_plots	performance plots for machine learning problems								To update	http://scikit-learn.org/stable/modules/classes.html#module-sklearn.metrics	Visualization	plotly_ml_performance_plots	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots	https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots	0.3	galaxy-ml	0.10.0			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	71	1323
+plotly_parallel_coordinates_plot	plotly_parallel_coordinates_plot	parallel coordinates plot produced with plotly								To update	https://plot.ly/python/parallel-coordinates-plot/	Visualization	plotly_parallel_coordinates_plot	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot	https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot	0.2	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	37	652
+plotly_regression_performance_plots	plotly_regression_performance_plots	performance plots for regression problems								To update	http://scikit-learn.org/stable/supervised_learning.html#supervised-learning	Visualization	plotly_regression_performance_plots	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots	https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots	0.1	python				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	79	843
+poisson2test	poisson2test	Poisson two-sample test								To update	https://bitbucket.org/natefoo/taxonomy	Statistics, Metagenomics	poisson2test	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/poisson2test	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/poisson2test	1.0.0	taxonomy	0.10.0			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	6	116
+predictnls	predictnls	Python reimplementation of predictNLS for Galaxy								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/predictnls	Sequence Analysis	predictnls	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/predictnls	https://github.com/peterjc/pico_galaxy/tree/master/tools/predictnls	0.0.10					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+principal_component_analysis	pca1	Principal Component Analysis								To update		Statistics	principal_component_analysis	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/principal_component_analysis	https://github.com/galaxyproject/tools-devteam/tree/main/tools/principal_component_analysis	1.0.2	rpy				1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	88	9989
+protease_prediction	eden_protease_prediction	This tool can learn the cleavage specificity of a given class of proteases.								To update	https://github.com/fabriziocosta/eden	Sequence Analysis, Proteomics	protease_prediction	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/protease_prediction	https://github.com/bgruening/galaxytools/tree/master/tools/protease_prediction	0.9	eden	2.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	7	154
+protein_analysis	promoter2, Psortb, rxlr_motifs, signalp3, tmhmm2, wolf_psort	TMHMM, SignalP, Promoter, RXLR motifs, WoLF PSORT and PSORTb								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysis	Sequence Analysis	tmhmm_and_signalp	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysis	https://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysis	0.0.13	promoter				0	0	6	0	0	0	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	6	6	451	6428
+protein_properties	bg_protein_properties	Calculation of various properties from given protein sequences								To update		Sequence Analysis	protein_properties	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/protein_properties	https://github.com/bgruening/galaxytools/tree/master/tools/protein_properties	0.2.0	biopython	1.70			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	30	604
+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	https://github.com/galaxyproject/tools-devteam/tree/main/tools/quality_filter	1.0.1	bx-python	0.11.0			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+rRNA	meta_rna	Identification of ribosomal RNA genes in metagenomic fragments.								To update	http://weizhong-lab.ucsd.edu/meta_rna/	RNA	rrna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rRNA	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rRNA	0.1	hmmsearch3.0				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+racon	racon	Consensus module for raw de novo DNA assembly of long uncorrected reads.	Racon	Racon		Racon	Consensus module for raw de novo DNA assembly of long uncorrected readsRacon is intended as a standalone consensus module to correct raw contigs generated by rapid assembly methods which do not include a consensus step. The goal of Racon is to generate genomic consensus which is of similar or better quality compared to the output generated by assembly methods which employ both error correction and consensus steps, while providing a speedup of several times compared to those methods. It supports data produced by both Pacific Biosciences and Oxford Nanopore Technologies.	Genome assembly, Mapping assembly	Whole genome sequencing, Sequence assembly	Up-to-date	https://github.com/isovic/racon	Sequence Analysis	racon	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/racon	https://github.com/bgruening/galaxytools/tree/master/tools/racon	1.5.0	racon	1.5.0	Genome assembly, Mapping assembly	Whole genome sequencing, Sequence assembly	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	309	21353
+rbpbench	rbpbench	Evaluate CLIP-seq and other genomic region data using a comprehensive collection of RBP binding motifs	rbpbench	rbpbench		RBPBench	Evaluate CLIP-seq and other genomic region data using a comprehensive collection of RBP binding motifs		RNA, Protein interactions, RNA immunoprecipitation, Bioinformatics, Sequence analysis	To update	https://github.com/michauhl/RBPBench	Sequence Analysis, RNA, CLIP-seq	rbpbench	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rbpbench	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rbpbench	0.8.1	rbpbench	0.9		RNA, Protein interactions, RNA immunoprecipitation, Bioinformatics, Sequence analysis	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	36
+rcas	rcas	RCAS (RNA Centric Annotation System) for functional analysis of transcriptome-wide regions detected by high-throughput experiments								To update	https://github.com/BIMSBbioinfo/RCAS	RNA	rcas	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rcas/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rcas	1.5.4	bioconductor-rcas	1.28.2			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	38	1226
+rcve	rcve1	Compute RCVE								To update		Sequence Analysis, Variant Analysis	rcve	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/rcve	https://github.com/galaxyproject/tools-devteam/tree/main/tools/rcve	1.0.0	R				1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+reago	reago	Reago is tool to assembly 16S ribosomal RNA recovery from metagenomic data.	reago	reago		REAGO	This is an assembly tool for 16S ribosomal RNA recovery from metagenomic data.	Sequence assembly	Sequence assembly, RNA, Metagenomics, Microbiology	Up-to-date	https://github.com/chengyuan/reago-1.1	Metagenomics, RNA	reago	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago	1.1	reago	1.1	Sequence assembly	Sequence assembly, RNA, Metagenomics, Microbiology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+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	https://github.com/galaxyproject/tools-devteam/tree/main/tools/remove_beginning	1.0.0					1	1	1	1	1	1	1	1	0	1	1	1	1	0	1	0	1	1	1	1	0	1	1	1	1	1	1	0	0	0	0	1	0	0	1	0	1	1	0	1	1	1	1409	137310
+remurna	remurna	remuRNA - Measurement of Single Nucleotide Polymorphism induced Changes of RNA Conformation								To update	https://www.ncbi.nlm.nih.gov/CBBresearch/Przytycka/index.cgi#remurna	RNA	remurna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/remurna	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/remurna	1.0.0	remurna	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	2	42
+repeat_masker	repeatmasker_wrapper	RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.								To update	http://www.repeatmasker.org/	Sequence Analysis	repeat_masker	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker	https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker	0.1.2	RepeatMasker	4.1.5			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	248	3750
+replaceColumn	replace_column_with_key_value_file	A tool to replace all column entries of a file given by values of a key-value file.								To update		Text Manipulation	replace_column_by_key_value_file	bgruening	https://github.com/bgruening/galaxytools/tree/replaceColumn/tools/replaceColumn	https://github.com/bgruening/galaxytools/tree/master/tools/replaceColumn	0.2					1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	1	0	0	0	0	0	0	0	1	1	1	189	576111
+rest_tool	pubchem_rest_tool	This tool fetches data from pubchem via the PubChem REST API.								To update	https://pubchem.ncbi.nlm.nih.gov/pug_rest/PUG_REST.html	Data Source	pubchem_rest_tool	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/rest_tool	https://github.com/bgruening/galaxytools/tree/master/tools/rest_tool	0.1.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+ribotaper	ribotaper_create_annotation, ribotaper_create_metaplots, ribotaper_ribosome_profiling	A method for defining traslated ORFs using Ribosome Profiling data.	ribotaper	ribotaper		RiboTaper	New analysis pipeline for Ribosome Profiling (Ribo-seq) experiments, which exploits the triplet periodicity of ribosomal footprints to call translated regions.	Gene expression profiling	Functional genomics	To update	https://ohlerlab.mdc-berlin.de/software/RiboTaper_126/	RNA	ribotaper	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper	1.3.1a	ribotaper	1.3.1	Gene expression profiling	Functional genomics	0	0	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	3	44	628
+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	https://github.com/galaxyproject/tools-devteam/tree/main/tools/rmap	1.0.0	rmap	2.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+rmapq	rmapq_wrapper	RMAPQ for Solexa Short Reads Alignment with Quality Scores								To update		Next Gen Mappers	rmapq	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/rmapq	https://github.com/galaxyproject/tools-devteam/tree/main/tools/rmapq	1.0.0	rmap	2.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+rna_shapes	RNAshapes	Compute secondary structures of RNA								To update		RNA	rnashapes	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rna_shapes	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rna_shapes	3.3.0	@EXECUTABLE@				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	11	129
+rnabob	rbc_rnabob	Fast pattern searching for RNA structural motifs								To update	http://eddylab.org/software.html	RNA	rnabob	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnabob	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnabob	2.2.1.0	rnabob	2.2.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	3	164
+rnacode	rbc_rnacode	Analyze the protein coding potential in MSA								To update		RNA	rnacode	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode	0.3.2	rnacode	0.3			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	5	1358
+rnacommender	rbc_rnacommender	RNAcommender is a tool for genome-wide recommendation of RNA-protein interactions.								To update	https://github.com/gianlucacorrado/RNAcommender	RNA	rnacommender	rnateam	https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacommender	0.1.1	sam	3.5			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	6	1074
+rnalien	RNAlien	RNAlien unsupervized RNA family model construction								To update	http://rna.tbi.univie.ac.at/rnalien/	RNA, Sequence Analysis	rnalien	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnalien	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnalien	1.3.6	rnalien	1.8.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	4	33
+rnasnp	rnasnp	RNAsnp Efficient detection of local RNA secondary structure changes induced by SNPs								To update	http://rth.dk/resources/rnasnp/	RNA	rnasnp	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rnasnp	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnasnp	1.2.0	rnasnp	1.2			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	5	86
+rnaz	rnaz, rnaz_annotate, rnaz_cluster, rnaz_randomize_aln, rnaz_select_seqs, rnaz_window	RNAz is a program for predicting structurally conserved and thermodynamically stable RNA secondary structures in multiple sequence alignments.								Up-to-date	https://www.tbi.univie.ac.at/~wash/RNAz/	RNA	rnaz	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaz	2.1.1	rnaz	2.1.1			0	0	6	0	0	0	6	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	6	28	43279
+sailfish	sailfish	Sailfish is a tool for transcript quantification from RNA-seq data								To update	http://www.cs.cmu.edu/~ckingsf/software/sailfish/	Sequence Analysis, RNA	sailfish	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/sailfish	https://github.com/bgruening/galaxytools/tree/master/tools/sailfish	0.10.1.1	bzip2				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	1	55	4024
+salmon	alevin, salmon, salmonquantmerge	Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq and single-cell data.	salmon	salmon		Salmon	A tool for transcript expression quantification from RNA-seq data	Sequence composition calculation, RNA-Seq quantification, Gene expression analysis	RNA-Seq, Gene expression, Transcriptomics	To update	https://github.com/COMBINE-lab/salmon	Sequence Analysis, RNA, Transcriptomics		bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/salmon	https://github.com/bgruening/galaxytools/tree/master/tools/salmon	1.10.1	salmon	1.10.3	Sequence composition calculation, RNA-Seq quantification, Gene expression analysis	RNA-Seq, Transcriptomics	2	1	3	1	2	1	3	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	1	0	0	1	0	0	0	1	0	0	0	0	0	0	0	3	3	3	969	61937
+sam2interval	sam2interval	Convert SAM to interval.								To update		SAM	sam2interval	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/sam2interval	https://github.com/galaxyproject/tools-devteam/tree/main/tools/sam2interval	1.0.2	python				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	20	1189
+sam_bitwise_flag_filter	sam_bw_filter	Filter SAM on bitwise flag values								To update		SAM	sam_bitwise_flag_filter	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/sam_bitwise_flag_filter	https://github.com/galaxyproject/tools-devteam/tree/main/tools/sam_bitwise_flag_filter	1.0.1	python				1	1	0	1	1	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	1	278
+sambamba	sambamba_flagstat, sambamba_markdup, sambamba_merge, sambamba_sort	Sambamba: process your BAM data faster!								Up-to-date	https://github.com/biod/sambamba	SAM	sambamba	bgruening	https://github.com/biod/sambamba	https://github.com/bgruening/galaxytools/tree/master/tools/sambamba	1.0.1	sambamba	1.0.1			0	0	4	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+sample_seqs	sample_seqs	Sub-sample sequences files (e.g. to reduce coverage)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs	Assembly, Fasta Manipulation, Fastq Manipulation, Sequence Analysis	sample_seqs	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs	https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs	0.2.6	biopython	1.70			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	149	3765
+samtools_depad	samtools_depad	Re-align a SAM/BAM file with a padded reference (using samtools depad)								To update	http://www.htslib.org/	Assembly, SAM, Sequence Analysis	samtools_depad	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad	0.0.5	samtools	1.20			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+samtools_depth	samtools_depth	Coverage depth via samtools								To update	http://www.htslib.org/	Assembly, Sequence Analysis, SAM	samtools_depth	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth	0.0.3	samtools	1.20			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	1	296	4948
+samtools_idxstats	samtools_idxstats	BAM mapping statistics (using samtools idxstats)								To update	http://www.htslib.org/	Assembly, Next Gen Mappers, SAM	samtools_idxstats	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats	0.0.6	samtools	1.20			1	1	1	1	1	1	1	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	1	0	0	0	1	0	0	0	0	0	0	0	1	1	1	1450	48426
+scatterplot	scatterplot_rpy	Scatterplot of two numeric columns								To update		Graphics, Statistics	scatterplot	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot	https://github.com/galaxyproject/tools-devteam/tree/main/tools/scatterplot	1.0.3	numpy				1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	61	1677
+sed	sed_stream_editor	Manipulate your data with the sed command line tool.								To update	https://github.com/bgruening/galaxytools/tree/master/tools/sed	Text Manipulation	sed_wrapper	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/sed	https://github.com/bgruening/galaxytools/tree/master/tools/sed	0.0.1	sed				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	2276
+segemehl	segemehl	segemehl - short read mapping with gaps								To update	http://www.bioinf.uni-leipzig.de/Software/segemehl/	Next Gen Mappers	segemehl	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/segemehl	https://github.com/bgruening/galaxytools/tree/master/tools/segemehl	0.2.0.4	segemehl	0.3.4			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	30	1276
+selectsequencesfrommsa	selectsequencesfrommsa	SelectSequences - selects representative entries from a multiple sequence alignment in clustal format								Up-to-date	https://github.com/eggzilla/SelectSequences	RNA, Sequence Analysis	selectsequencesfrommsa	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa	1.0.5	selectsequencesfrommsa	1.0.5			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	27	457
+seq_composition	seq_composition	Sequence composition								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_composition	Sequence Analysis	seq_composition	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_composition	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_composition	0.0.5	biopython	1.70			1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	71	874
+seq_filter_by_id	seq_filter_by_id	Filter sequences by ID								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id	Fasta Manipulation, Sequence Analysis, Text Manipulation	seq_filter_by_id	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id	0.2.9	biopython	1.70			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	306	25302
+seq_filter_by_mapping	seq_filter_by_mapping	Filter sequencing reads using SAM/BAM mapping files								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping	Assembly, Fasta Manipulation, Fastq Manipulation, SAM, Sequence Analysis	seq_filter_by_mapping	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping	0.0.8	biopython	1.70			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	82	3784
+seq_length	seq_length	Compute sequence length (from FASTA, QUAL, FASTQ, SFF, etc)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length	Fasta Manipulation, Fastq Manipulation, Sequence Analysis	seq_length	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length	0.0.5	biopython	1.70			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+seq_primer_clip	seq_primer_clip	Trim off 5' or 3' primers								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip	Assembly, Fasta Manipulation, Text Manipulation	seq_primer_clip	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip	0.0.18	galaxy_sequence_utils	1.1.5			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+seq_rename	seq_rename	Rename sequences with ID mapping from a tabular file								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename	Fasta Manipulation, Sequence Analysis, Text Manipulation	seq_rename	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename	0.0.10	galaxy_sequence_utils	1.1.5			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0
+seq_select_by_id	seq_select_by_id	Select sequences by ID								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id	Fasta Manipulation, Sequence Analysis, Text Manipulation	seq_select_by_id	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id	0.0.15	biopython	1.70			0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+short_reads_figure_high_quality_length	hist_high_quality_score	Histogram of high quality score reads								To update		Sequence Analysis, Graphics	short_reads_figure_high_quality_length	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_figure_high_quality_length	https://github.com/galaxyproject/tools-devteam/tree/main/tools/short_reads_figure_high_quality_length	1.0.0	rpy				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+short_reads_figure_score	quality_score_distribution	Build base quality distribution								To update		Sequence Analysis, Graphics	short_reads_figure_score	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_figure_score	https://github.com/galaxyproject/tools-devteam/tree/main/tools/short_reads_figure_score	1.0.2	fontconfig				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	13	163
+short_reads_trim_seq	trim_reads	Select high quality segments								To update		Fastq Manipulation	short_reads_trim_seq	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_trim_seq	https://github.com/galaxyproject/tools-devteam/tree/main/tools/short_reads_trim_seq	1.0.0					1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	21	220
+show_beginning	Show beginning1	Select lines from the beginning of a file.								To update		Text Manipulation	show_beginning	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/show_beginning	https://github.com/galaxyproject/tools-devteam/tree/main/tools/show_beginning	1.0.0					1	1	1	1	1	1	1	1	0	1	1	1	1	0	1	0	1	1	1	1	0	1	1	1	0	1	1	0	0	0	0	1	0	0	1	0	1	1	0	1	1	1	704	32112
+show_tail	Show tail1	Select lines from the end of a file.								To update		Text Manipulation	show_tail	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/show_tail	https://github.com/galaxyproject/tools-devteam/tree/main/tools/show_tail	1.0.0					1	1	1	1	1	1	1	1	0	1	1	0	1	0	1	0	1	1	1	1	0	1	1	1	0	1	1	0	0	0	0	1	0	0	1	0	1	1	0	1	1	1	128	2513
+sicer	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	https://github.com/galaxyproject/tools-devteam/tree/main/tools/sicer	1.1	SICER	1.1			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	1	5	374
+sklearn	sklearn_mlxtend_association_rules, sklearn_clf_metrics, sklearn_discriminant_classifier, sklearn_ensemble, sklearn_estimator_attributes, sklearn_feature_selection, sklearn_fitted_model_eval, sklearn_generalized_linear, keras_batch_models, keras_model_builder, keras_model_config, keras_train_and_eval, sklearn_label_encoder, sklearn_lightgbm, ml_visualization_ex, model_prediction, sklearn_model_validation, sklearn_nn_classifier, sklearn_numeric_clustering, sklearn_pairwise_metrics, sklearn_pca, sklearn_build_pipeline, sklearn_data_preprocess, sklearn_regression_metrics, sklearn_sample_generator, sklearn_searchcv, sklearn_model_fit, scipy_sparse, stacking_ensemble_models, sklearn_svm_classifier, sklearn_to_categorical, sklearn_train_test_eval, sklearn_train_test_split	Machine Learning tool suite from Scikit-learn								To update	http://scikit-learn.org	Machine Learning, Statistics	sklearn	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/sklearn	https://github.com/bgruening/galaxytools/tree/master/tools/sklearn	1.0.11.0					30	14	31	16	30	14	31	16	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	29	31	27	958	113932
+snpfreq	hgv_snpFreq	snpFreq significant SNPs in case-control data								To update		Variant Analysis, Statistics	snpfreq	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/snpfreq	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/hgv/snpfreq	1.0.1	R				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	7	37
+sortmerna	bg_sortmerna	SortMeRNA is a software designed to rapidly filter ribosomal RNA fragments from metatransriptomic data produced by next-generation sequencers.	sortmerna	sortmerna		SortMeRNA	Sequence analysis tool for filtering, mapping and OTU-picking NGS reads.	Sequence similarity search, Sequence comparison, Sequence alignment analysis	Metatranscriptomics, Metagenomics	To update	http://bioinfo.lifl.fr/RNA/sortmerna/	RNA	sortmerna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna	4.3.6	sortmerna	4.3.7	Sequence similarity search, Sequence alignment analysis	Metatranscriptomics, Metagenomics	1	1	1	1	1	1	1	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	376	18183
+split_file_on_column	tp_split_on_column	Split a file on a specific column.								To update		Text Manipulation	split_file_on_column	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_on_column	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_on_column	0.6	gawk				1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	159	5507
+split_file_to_collection	split_file_to_collection	Split tabular, MGF, FASTA, or FASTQ files to a dataset collection.								To update	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection	Text Manipulation	split_file_to_collection	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection	0.5.2	python				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	1	0	0	0	0	0	0	0	1	1	1	412	15358
+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	https://github.com/galaxyproject/tools-devteam/tree/main/tools/split_paired_reads	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+splitfasta	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	https://github.com/bgruening/galaxytools/tree/master/tools/splitfasta	0.4.0	biopython	1.70			1	0	1	0	1	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	96	1295
+sshmm	sshmm	ssHMM is an RNA sequence-structure motif finder for RNA-binding protein data, such as CLIP-Seq data								Up-to-date	https://github.molgen.mpg.de/heller/ssHMM	Sequence Analysis, RNA	sshmm	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm	1.0.7	sshmm	1.0.7			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	5	223
+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	https://github.com/bgruening/galaxytools/tree/master/tools/statistics	0.3	numpy				0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	21	304
+stress_ng	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	https://github.com/bgruening/galaxytools/tree/master/tools/stress_ng	0.12.04	stress-ng				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	47
+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	https://github.com/galaxyproject/tools-devteam/tree/main/tools/substitution_rates	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+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	https://github.com/galaxyproject/tools-devteam/tree/main/tools/substitutions	1.0.1	bx-python	0.11.0			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+subtract	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	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/subtract	1.0.0	bx-python	0.11.0			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	1	182	564229
+subtract_query	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	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/subtract_query	0.1	bx-python	0.11.0			1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	55	1019
+t2ps	Draw_phylogram	Draw phylogeny	t2ps	t2ps		Draw phylogeny	"""Given taxonomy representation (produced by *Fetch taxonomic representation* tool) this utility produces a graphical representations of phylogenetic tree in PDF format."" - Galaxy tool wrapper"	Phylogenetic tree visualisation	Phylogenomics	To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	t2ps	devteam	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2ps	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2ps	1.0.0	taxonomy	0.10.0	Phylogenetic tree visualisation	Phylogenomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	31	457
+t2t_report	t2t_report	Summarize taxonomy								To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	t2t_report	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/t2t_report	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2t_report	1.0.0	taxonomy	0.10.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	26	947
+t_test_two_samples	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	https://github.com/galaxyproject/tools-devteam/tree/main/tools/t_test_two_samples	1.0.1	R				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	6	210
+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	https://github.com/galaxyproject/tools-devteam/tree/main/tools/table_annovar	0.2	annovar				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+tables_arithmetic_operations	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	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/gops/tables_arithmetic_operations	1.0.0	perl				0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	1	14	2207
+tabular_to_fasta	tab2fasta	Tabular-to-FASTA								To update		Convert Formats	tabular_to_fasta	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/tabular_to_fasta	https://github.com/galaxyproject/tools-devteam/tree/main/tools/tabular_to_fasta	1.1.1	python				1	1	1	1	1	1	1	1	0	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	1	601	319334
+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	https://github.com/bgruening/galaxytools/tree/master/tools/tapscan	4.76+galaxy0	hmmer	3.4			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+targetfinder	targetfinder	Plant small RNA target prediction tool								Up-to-date	https://github.com/carringtonlab/TargetFinder.git	RNA	targetfinder	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder	1.7	targetfinder	1.7			1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	37	713
+text_processing	tp_awk_tool, tp_cat, tp_cut_tool, tp_easyjoin_tool, tp_find_and_replace, tp_grep_tool, tp_head_tool, tp_multijoin_tool, nl, tp_text_file_with_recurring_lines, tp_replace_in_column, tp_replace_in_line, tp_sed_tool, tp_sort_header_tool, tp_sort_rows, tp_uniq_tool, tp_tac, tp_tail_tool, tp_unfold_column_tool, tp_sorted_uniq	High performance text processing tools using the GNU coreutils, sed, awk and friends.								To update	https://www.gnu.org/software/	Text Manipulation	text_processing	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing	https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing	9.3	coreutils	8.25			20	20	20	20	20	20	20	20	0	0	0	0	0	0	0	0	0	0	0	0	0	0	19	1	19	0	0	19	0	0	0	20	0	0	0	0	0	0	0	19	19	19	15048	3864895
+tgsgapcloser	tgsgapcloser	TGS-GapCloser uses error-prone long reads or preassembled contigs to fill N-gap in the genome assembly.	TGS-GapCloser	TGS-GapCloser		TGS-GapCloser	TGS-GapCloser is a fast and accurately passing through the Bermuda in large genome using error-prone third-generation long reads.	Genome assembly, Read mapping, Scaffolding, Localised reassembly	Sequencing, Sequence assembly, Phylogeny, Transcription factors and regulatory sites, Mapping	To update	https://github.com/BGI-Qingdao/TGS-GapCloser	Assembly	tgsgapcloser	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser	https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser	1.0.3	tgsgapcloser	1.2.1	Genome assembly, Read mapping, Scaffolding, Localised reassembly	Sequencing, Sequence assembly, Phylogeny, Transcription factors and regulatory sites, Mapping	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	36	460
+tiara	tiara	Tool for identification of eukaryotic sequences in the metagenomic datasets.	Tiara	Tiara		TIARA	Total Integrated Archive of Short-Read and Array (TIARA) database, contains personal genomic information obtained from next generation sequencing (NGS) techniques and ultra-high-resolution comparative genomic hybridization (CGH) arrays. This database improves the accuracy of detecting personal genomic variations, such as SNPs, short indels and structural variants (SVs).	Genome comparison, Data retrieval, Variant calling, Genome visualisation, Structural variation detection	Sequencing, Genomics, DNA polymorphism, DNA structural variation	To update	https://github.com/ibe-uw/tiara	Metagenomics, Sequence Analysis	tiara	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/tiara	https://github.com/bgruening/galaxytools/tree/master/tools/tiara	1.0.3	tiara		Genome comparison, Data retrieval, Variant calling, Genome visualisation, Structural variation detection	Sequencing, Genomics, DNA polymorphism	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+tool_recommendation_model	create_tool_recommendation_model	Create model to recommend tools								To update	https://github.com/bgruening/galaxytools	Machine Learning	create_tool_recommendation_model	bgruening	https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model	https://github.com/bgruening/galaxytools/tree/master/tools/tool_recommendation_model	0.0.5	python				1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	15	445
+tophat	tophat	Tophat for Illumina								To update		RNA, Next Gen Mappers	tophat	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat	https://github.com/galaxyproject/tools-devteam/tree/main/tools/tophat	1.5.0	samtools	1.20			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1
+tophat2	tophat2	Tophat - fast splice junction mapper for RNA-Seq reads								To update	http://ccb.jhu.edu/software/tophat/index.shtml	RNA, Next Gen Mappers	tophat2	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat2	https://github.com/galaxyproject/tools-devteam/tree/main/tools/tophat2	2.1.1	bowtie2	2.5.4			1	1	1	0	1	1	1	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	1	0	0	1	0	0	0	0	1	1	1	312	24167
+tophat_fusion_post	tophat_fusion_post	Wrapper for Tophat-Fusion post step								To update		Transcriptomics	tophat_fusion_post	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat_fusion_post	https://github.com/galaxyproject/tools-devteam/tree/main/tools/tophat_fusion_post	0.1	blast+				0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	15	216
+trim_galore	trim_galore	Trim Galore adaptive quality and adapter trimmer	trim_galore	trim_galore		Trim Galore	A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files, with some extra functionality for MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries.	Sequence trimming, Primer removal, Read pre-processing	Sequence analysis	To update	http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/	Sequence Analysis, Fastq Manipulation	trim_galore	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore	https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore	0.6.7	trim-galore	0.6.10	Sequence trimming, Primer removal, Read pre-processing	Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	1	2334	238699
+trimmer	trimmer	Trim leading or trailing characters.								To update		Text Manipulation	trimmer	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer	https://github.com/galaxyproject/tools-devteam/tree/main/tools/trimmer	0.0.1					1	1	1	1	1	1	1	1	0	1	1	1	1	0	1	0	1	1	1	1	0	1	1	1	1	1	1	0	0	0	0	1	0	0	1	0	1	1	0	1	1	1	188	6058
+trna_prediction	aragorn_trna, trnascan	Aragorn predicts tRNA and tmRNA in nucleotide sequences.								To update	http://mbioserv2.mbioekol.lu.se/ARAGORN/	RNA	trna_prediction	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction	0.6	aragorn	1.2.41			0	2	2	0	0	2	2	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	2	2	236	2935
+ucsc_custom_track	build_ucsc_custom_track_1	Build custom track for UCSC genome browser								To update		Sequence Analysis	ucsc_custom_track	devteam	https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track	https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track	1.0.1	python				1	0	1	0	1	0	1	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	45	394
+uniprot_rest_interface	uniprot	UniProt ID mapping and sequence retrieval								To update	https://github.com/jdrudolph/uniprot	Proteomics, Sequence Analysis	uniprot_rest_interface	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface	https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface	0.5	requests				1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	132	2406
+varscan_version_2	varscan	VarScan wrapper								To update	https://dkoboldt.github.io/varscan/	Variant Analysis	varscan_version_2	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/varscan_version_2	https://github.com/galaxyproject/tools-devteam/tree/main/tools/varscan_version_2	2.4.2	varscan	2.4.6			1	1	1	1	1	1	1	1	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	246	5191
+vcf2pgsnp	vcf2pgSnp	VCF to pgSnp								To update		Variant Analysis	vcf2pgsnp	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf2pgsnp	https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf2pgsnp	1.0.0					1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	15	206
+vcf_annotate	vcf_annotate	Annotate a VCF file (dbSNP, hapmap)								To update		Variant Analysis	vcf_annotate	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_annotate	https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf_annotate	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1
+vcf_extract	vcf_extract	Extract reads from a specified region								To update		Variant Analysis	vcf_extract	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_extract	https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf_extract	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+vcf_filter	vcf_filter	Filter a VCF file								To update		Variant Analysis	vcf_filter	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_filter	https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf_filter	1.0.0					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	63	388
+vcf_intersect	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	https://github.com/galaxyproject/tools-devteam/tree/main/tools/vcf_intersect	1.0.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	19
+vcftools_annotate	vcftools_annotate	Annotate VCF using custom/user-defined annotations								To update	https://vcftools.github.io/	Variant Analysis	vcftools_annotate	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_annotate	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_annotate	0.1	echo				1	0	1	1	1	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	24	171
+vcftools_compare	vcftools_compare	Compare VCF files to get overlap and uniqueness statistics								To update	https://vcftools.github.io/	Variant Analysis	vcftools_compare	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_compare	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_compare	0.1	tabix	1.11			0	0	1	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	34	531
+vcftools_consensus	vcftools_consensus	Apply VCF variants to a fasta file to create consensus sequence								To update	https://vcftools.github.io/	Variant Analysis	vcftools_consensus	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_consensus	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_consensus	0.1.11	samtools	1.20			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+vcftools_isec	vcftools_isec	Intersect multiple VCF datasets								To update	https://vcftools.github.io/	Variant Analysis	vcftools_isec	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_isec	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_isec	0.1.1	tabix	1.11			0	1	1	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	35	498
+vcftools_merge	vcftools_merge	Merge multiple VCF datasets into a single dataset								To update	https://vcftools.github.io/	Variant Analysis	vcftools_merge	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_merge	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_merge	0.1.11	tabix	1.11			0	1	1	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	68	953
+vcftools_slice	vcftools_slice	Subset VCF dataset by genomic regions								To update	https://vcftools.github.io/	Variant Analysis	vcftools_slice	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_slice	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_slice	0.1	echo				1	0	1	1	1	0	1	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	24	411
+vcftools_subset	vcftools_subset	Select samples from a VCF dataset								To update	https://vcftools.github.io/	Variant Analysis	vcftools_subset	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_subset	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/vcftools/vcftools_subset	0.1	tabix	1.11			0	0	1	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	17	137
+venn_list	venn_list	Draw Venn Diagram (PDF) from lists, FASTA files, etc								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list	Graphics, Sequence Analysis, Visualization	venn_list	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list	https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list	0.1.2	galaxy_sequence_utils	1.1.5			1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	1	248	5067
+vienna_rna	viennarna_kinfold, viennarna_kinwalker, viennarna_rna2dfold, viennarna_rnaaliduplex, viennarna_rnaalifold, viennarna_rnacofold, viennarna_rnadistance, viennarna_rnaduplex, viennarna_rnaeval, viennarna_rnafold, viennarna_rnaheat, viennarna_rnainverse, viennarna_rnalalifold, viennarna_rnalfold, viennarna_rnapaln, viennarna_rnadpdist, viennarna_rnapkplex, viennarna_rnaplex, viennarna_rnaplfold, viennarna_rnaplot, viennarna_rnasnoop, viennarna_rnasubopt, viennarna_rnaup	ViennaRNA - Prediction and comparison of RNA secondary structures								To update	http://www.tbi.univie.ac.at/RNA/	RNA	viennarna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna	2.2.10	viennarna	2.6.4			0	0	21	0	0	0	21	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	21	21	123	7864
+vt	vt_@BINARY@, vt_@BINARY@	A tool set for short variant discovery in genetic sequence data.								To update		Sequence Analysis, Variant Analysis	vt	bgruening	https://github.com/atks/vt	https://github.com/bgruening/galaxytools/tree/master/tools/vt	0.2	vt	2015.11.10			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+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	https://github.com/galaxyproject/tools-devteam/tree/main/tools/weightedaverage	1.0.1	galaxy-ops	1.1.0			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+whisper	whisper	Transcribe audio or video files to text using the OpenAI Whisper.								To update	https://github.com/bgruening/galaxytools/tree/master/tools/whisper	Machine Learning	whisper	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/whisper	https://github.com/bgruening/galaxytools/tree/master/tools/whisper	20231117					0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+windowsplitter	winSplitter	Make windows								To update		Sequence Analysis, Variant Analysis	windowsplitter	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter	https://github.com/galaxyproject/tools-devteam/tree/main/tools/windowsplitter	1.0.1	bx-python	0.11.0			1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	11
+woundhealing	woundhealing_scratch_assay	Tool to automate quantification of wound healing in high-throughput microscopy scratch assays								Up-to-date	https://git.embl.de/grp-cba/wound-healing-htm-screen	Imaging	Wound healing scratch assay image analysis	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools	https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/woundhealing	1.6.1	fiji-morpholibj	1.6.1			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+wtdbg	wtdbg	WTDBG is a fuzzy Bruijn graph (FBG) approach to long noisy reads assembly.	wtdbg2	wtdbg2		wtdbg2	Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output. Wtdbg2 is able to assemble the human and even the 32Gb Axolotl genome at a speed tens of times faster than CANU and FALCON while producing contigs of comparable base accuracy.	Genome assembly, De-novo assembly	Sequence assembly, Sequencing	Up-to-date	https://github.com/ruanjue/wtdbg2	Assembly	wtdbg	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg	https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg	2.5	wtdbg	2.5	Genome assembly, De-novo assembly	Sequence assembly, Sequencing	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	116	1660
+xy_plot	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	https://github.com/galaxyproject/tools-devteam/tree/main/tools/xy_plot	1.0.2	r-base				1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	344	5892