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toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicplottads/hicexplorer_hicplottads/2.1.4.0	2019-02-01	284
toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0.2	2019-02-01	279
CONVERTER_fastq_to_fqtoc0	2019-02-01	277
Grouping1	2019-02-01	273
toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/1.3.4	2019-02-01	250
toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.2.0	2019-02-01	248
CONVERTER_interval_to_bed_0	2019-02-01	238
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0	2019-02-01	237
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtobam/2.27.0.0	2019-02-01	228
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toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.4.1	2019-02-01	226
toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.7.0	2019-02-01	226
toolshed.g2.bx.psu.edu/repos/devteam/varscan_version_2/varscan/2.4.2	2019-02-01	221
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.1	2019-02-01	218
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicplotmatrix/hicexplorer_hicplotmatrix/2.1.4.0	2019-02-01	215
toolshed.g2.bx.psu.edu/repos/crs4/bwa_mem/bwa_mem/0.8.0	2019-02-01	208
toolshed.g2.bx.psu.edu/repos/devteam/samtools_flagstat/samtools_flagstat/2.0.2	2019-02-01	206
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_compare/deeptools_bam_compare/3.0.2.0	2019-02-01	192
toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/0.5.3.2	2019-02-01	191
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.27.0.2	2019-02-01	191
toolshed.g2.bx.psu.edu/repos/devteam/fastqtofasta/fastq_to_fasta_python/1.1.1	2019-02-01	189
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toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.6	2019-02-01	184
toolshed.g2.bx.psu.edu/repos/iuc/gemini_query/gemini_query/0.20.1	2019-02-01	182
toolshed.g2.bx.psu.edu/repos/devteam/fastx_reverse_complement/cshl_fastx_reverse_complement/1.0.2	2019-02-01	181
toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.5	2019-02-01	175
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/1.1.0	2019-02-01	171
toolshed.g2.bx.psu.edu/repos/devteam/intersect/gops_intersect_1/1.0.0	2019-02-01	168
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toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_correlation/deeptools_plot_correlation/3.0.2.0	2019-02-01	161
toolshed.g2.bx.psu.edu/repos/galaxyp/maldi_quant_preprocessing/maldi_quant_preprocessing/1.18.0.2	2019-02-01	160
toolshed.g2.bx.psu.edu/repos/devteam/fastqtofasta/fastq_to_fasta_python/1.0.0	2019-02-01	159
ucsc_table_direct1	2019-02-01	158
toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.2	2019-02-01	157
toolshed.g2.bx.psu.edu/repos/devteam/bowtie_wrappers/bowtie_wrapper/1.2.0	2019-02-01	157
toolshed.g2.bx.psu.edu/repos/iuc/qiime_multiple_join_paired_ends/qiime_multiple_join_paired_ends/1.9.1.0	2019-02-01	154
toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_infer_experiment/2.6.4.1	2019-02-01	150
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hiccorrectmatrix/hicexplorer_hiccorrectmatrix/2.1.4.0	2019-02-01	150
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.27.0.0	2019-02-01	147
toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0	2019-02-01	147
toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1.1	2019-02-01	144
toolshed.g2.bx.psu.edu/repos/devteam/samtool_filter2/samtool_filter2/1.8	2019-02-01	142
toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/1.6.2	2019-02-01	141
toolshed.g2.bx.psu.edu/repos/devteam/picard/PicardASMetrics/1.56.0	2019-02-01	138
toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_fastq/mothur_make_fastq/1.36.1.0	2019-02-01	138
toolshed.g2.bx.psu.edu/repos/devteam/tophat2/tophat2/2.1.1	2019-02-01	136
toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.1.0	2019-02-01	136
toolshed.g2.bx.psu.edu/repos/bgruening/unique/bg_uniq/0.3	2019-02-01	132
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toolshed.g2.bx.psu.edu/repos/iuc/mothur_summary_qual/mothur_summary_qual/1.39.5.0	2019-02-01	132
toolshed.g2.bx.psu.edu/repos/devteam/fastq_to_tabular/fastq_to_tabular/1.1.1	2019-02-01	131
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtofastq/2.27.0.0	2019-02-01	130
toolshed.g2.bx.psu.edu/repos/iuc/abricate/abricate/0.8	2019-02-01	129
toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.67	2019-02-01	128
toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.3.0	2019-02-01	128
toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_preprocessing/cardinal_preprocessing/1.12.1.2	2019-02-01	127
toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.1.4	2019-02-01	126
wc_gnu	2019-02-01	124
toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.5.2b-2	2019-02-01	119
toolshed.g2.bx.psu.edu/repos/devteam/bam_to_sam/bam_to_sam/2.0.1	2019-02-01	116
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SortSam/2.18.2.1	2019-02-01	115
toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/2.2.1.2	2019-02-01	115
toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/search_gui/3.3.10.1	2019-02-01	113
toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/peptide_shaker/1.16.36.2	2019-02-01	112
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CASM/2.18.2.1	2019-02-01	111
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_multijoin_tool/1.1.1	2019-02-01	110
toolshed.g2.bx.psu.edu/repos/devteam/join/gops_join_1/1.0.0	2019-02-01	110
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectInsertSizeMetrics/2.18.2.1	2019-02-01	109
toolshed.g2.bx.psu.edu/repos/bgruening/pileometh/pileometh/0.3.0.1	2019-02-01	109
toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy1	2019-02-01	109
toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.5.2b-1	2019-02-01	107
toolshed.g2.bx.psu.edu/repos/devteam/fastx_trimmer/cshl_fastx_trimmer/1.0.2	2019-02-01	106
toolshed.g2.bx.psu.edu/repos/devteam/sam_merge/sam_merge2/1.2.0	2019-02-01	106
toolshed.g2.bx.psu.edu/repos/devteam/add_value/addValue/1.0.0	2019-02-01	106
toolshed.g2.bx.psu.edu/repos/nml/spades/spades/3.12.0+galaxy1	2019-02-01	105
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bam_summary/deeptools_multi_bam_summary/3.0.2.0	2019-02-01	104
toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_quality_report/cardinal_quality_report/1.12.1.2	2019-02-01	104
toolshed.g2.bx.psu.edu/repos/devteam/get_flanks/get_flanks1/1.0.0	2019-02-01	102
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.27.0.0	2019-02-01	101
toolshed.g2.bx.psu.edu/repos/galaxyp/fasta_merge_files_and_filter_unique_sequences/fasta_merge_files_and_filter_unique_sequences/1.2.0	2019-02-01	101
toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_heatmap2/ggplot2_heatmap2/2.2.1+galaxy1	2019-02-01	100
toolshed.g2.bx.psu.edu/repos/lparsons/fastq_join/fastq_join/1.1.2-806	2019-02-01	99
toolshed.g2.bx.psu.edu/repos/devteam/fastq_to_fasta/cshl_fastq_to_fasta/1.0.0	2019-02-01	99
CONVERTER_bedgraph_to_bigwig	2019-02-01	99
toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/0.11.2	2019-02-01	98
toolshed.g2.bx.psu.edu/repos/bgruening/interproscan5/interproscan/5.0.0	2019-02-01	97
toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/0.5.3.2	2019-02-01	97
toolshed.g2.bx.psu.edu/repos/iuc/extract_genomic_dna/Extract genomic DNA 1/3.0.3	2019-02-01	96
toolshed.g2.bx.psu.edu/repos/simon-gladman/velvetoptimiser/velvetoptimiser/2.2.6	2019-02-01	96
CONVERTER_bam_to_coodinate_sorted_bam	2019-02-01	93
toolshed.g2.bx.psu.edu/repos/iuc/ngsutils_bam_filter/ngsutils_bam_filter/0.5.9	2019-02-01	93
toolshed.g2.bx.psu.edu/repos/jjohnson/query_tabular/query_tabular/3.0.0	2019-02-01	92
toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.4.0	2019-02-01	92
toolshed.g2.bx.psu.edu/repos/iuc/pilon/pilon/1.20.1	2019-02-01	92
toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_quality_report/cardinal_quality_report/1.12.1.1	2019-02-01	91
toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.4.3.0	2019-02-01	90
toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.3.1	2019-02-01	90
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_mergebed/2.27.0.0	2019-02-01	89
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicbuildmatrix/hicexplorer_hicbuildmatrix/2.1.4.0	2019-02-01	88
toolshed.g2.bx.psu.edu/repos/iuc/qiime_pick_closed_reference_otus/qiime_pick_closed_reference_otus/1.9.1.0	2019-02-01	86
toolshed.g2.bx.psu.edu/repos/iuc/fraggenescan/fraggenescan/1.30.0	2019-02-01	85
toolshed.g2.bx.psu.edu/repos/iuc/gatk2/gatk2_unified_genotyper/2.8.0	2019-02-01	85
toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/0.0.2	2019-02-01	82
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.27.1	2019-02-01	82
ChangeCase	2019-02-01	82
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_mergebed/2.27.1	2019-02-01	82
toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.0	2019-02-01	82
toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_filtering/cardinal_filtering/1.12.1.2	2019-02-01	81
toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.36.4	2019-02-01	81
toolshed.g2.bx.psu.edu/repos/iuc/bctools_merge_pcr_duplicates/bctools_merge_pcr_duplicates/0.2.2	2019-02-01	80
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_closestbed/2.27.1	2019-02-01	80
toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_mz_images/cardinal_mz_images/1.12.1.2	2019-02-01	79
toolshed.g2.bx.psu.edu/repos/galaxyp/filter_by_fasta_ids/filter_by_fasta_ids/2.1	2019-02-01	79
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtofastq/2.27.1	2019-02-01	78
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicfindtads/hicexplorer_hicfindtads/2.1.4.0	2019-02-01	77
toolshed.g2.bx.psu.edu/repos/devteam/merge_cols/mergeCols1/1.0.1	2019-02-01	76
toolshed.g2.bx.psu.edu/repos/devteam/fastq_trimmer/fastq_trimmer/1.1.1	2019-02-01	76
toolshed.g2.bx.psu.edu/repos/iuc/sickle/sickle/1.33.1	2019-02-01	75
sort1	2019-02-01	74
toolshed.g2.bx.psu.edu/repos/rnateam/mafft/rbc_mafft/7.221.3	2019-02-01	72
toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.12	2019-02-01	70
toolshed.g2.bx.psu.edu/repos/iuc/mothur_summary_seqs/mothur_summary_seqs/1.39.5.0	2019-02-01	69
toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_tblastn_wrapper/0.3.1	2019-02-01	67
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1	2019-02-01	67
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.1	2019-02-01	66
toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_filtering/cardinal_filtering/1.12.1.1	2019-02-01	66
toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.4	2019-02-01	66
toolshed.g2.bx.psu.edu/repos/iuc/charts/charts/1.0.1	2019-02-01	65
toolshed.g2.bx.psu.edu/repos/iuc/bctools_extract_alignment_ends/bctools_extract_alignment_ends/0.2.2	2019-02-01	65
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_fingerprint/deeptools_plot_fingerprint/3.0.2.0	2019-02-01	64
toolshed.g2.bx.psu.edu/repos/devteam/vcfvcfintersect/vcfvcfintersect/1.0.0_rc1+galaxy0	2019-02-01	64
toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/1.6.3	2019-02-01	63
toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.19.5	2019-02-01	63
mergeCols1	2019-02-01	62
toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_heatmap2/ggplot2_heatmap2/3.0.1	2019-02-01	62
toolshed.g2.bx.psu.edu/repos/bgruening/bigwig_to_bedgraph/bigwig_to_bedgraph/0.1.0	2019-02-01	62
toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_spectra_plots/cardinal_spectra_plots/1.12.1.2	2019-02-01	61
Grep1	2019-02-01	60
toolshed.g2.bx.psu.edu/repos/iuc/fgsea/fgsea/1.8.0	2019-02-01	60
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicmergematrixbins/hicexplorer_hicmergematrixbins/2.1.4.0	2019-02-01	60
toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.6.0	2019-02-01	60
CONVERTER_fasta_to_fai	2019-02-01	59
toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.7.0	2019-02-01	59
toolshed.g2.bx.psu.edu/repos/devteam/fasta_filter_by_length/fasta_filter_by_length/1.1	2019-02-01	57
toolshed.g2.bx.psu.edu/repos/iuc/metaphlan2/metaphlan2/2.6.0.0	2019-02-01	57
toolshed.g2.bx.psu.edu/repos/rnateam/peakachu/peakachu/0.1.0.2	2019-02-01	57
toolshed.g2.bx.psu.edu/repos/devteam/scatterplot/scatterplot_rpy/1.0.3	2019-02-01	56
toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_segmentations/cardinal_segmentations/1.12.1.2	2019-02-01	56
toolshed.g2.bx.psu.edu/repos/iuc/goseq/goseq/1.34.0	2019-02-01	56
toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_data_exporter/cardinal_data_exporter/1.12.1.1	2019-02-01	55
toolshed.g2.bx.psu.edu/repos/devteam/fastq_quality_filter/cshl_fastq_quality_filter/1.0.2	2019-02-01	54
viz_overlay_moving_and_fixed_image	2019-02-01	54
toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.3	2019-02-01	53
toolshed.g2.bx.psu.edu/repos/iuc/bwameth/bwameth/0.2.0.4	2019-02-01	53
toolshed.g2.bx.psu.edu/repos/devteam/merge/gops_merge_1/1.0.0	2019-02-01	53
CONVERTER_bam_to_bigwig_0	2019-02-01	53
toolshed.g2.bx.psu.edu/repos/iuc/stacks_procrad/stacks_procrad/1.46.0	2019-02-01	52
toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.0.2.29-1	2019-02-01	52
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectInsertSizeMetrics/2.7.1.0	2019-02-01	52
toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_preprocessing/cardinal_preprocessing/1.12.1.1	2019-02-01	51
toolshed.g2.bx.psu.edu/repos/ethevenot/multivariate/Multivariate/2.3.10	2019-02-01	50
toolshed.g2.bx.psu.edu/repos/galaxyp/maldi_quant_peak_detection/maldi_quant_peak_detection/1.18.0.3	2019-02-01	50
toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy1	2019-02-01	49
toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/peptide_shaker/1.16.26	2019-02-01	49
toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.1	2019-02-01	49
toolshed.g2.bx.psu.edu/repos/gbcs-embl-heidelberg/je_markdupes/je_markdupes/1.2.1	2019-02-01	49
toolshed.g2.bx.psu.edu/repos/rnateam/piranha/piranha/0.1.0	2019-02-01	49
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_shufflebed/2.27.1	2019-02-01	49
toolshed.g2.bx.psu.edu/repos/iuc/megahit/megahit/1.1.2.3	2019-02-01	49
toolshed.g2.bx.psu.edu/repos/bgruening/bismark/bismark_bowtie/0.7.12	2019-02-01	48
toolshed.g2.bx.psu.edu/repos/bgruening/bismark/bismark_pretty_report/0.20.0	2019-02-01	48
toolshed.g2.bx.psu.edu/repos/rnateam/segemehl/segemehl/0.2.0.3	2019-02-01	48
toolshed.g2.bx.psu.edu/repos/iuc/mothur_screen_seqs/mothur_screen_seqs/1.39.5.0	2019-02-01	47
toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.24.1	2019-02-01	47
toolshed.g2.bx.psu.edu/repos/iuc/gtftobed12/gtftobed12/357	2019-02-01	47
toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_segmentations/cardinal_segmentations/1.12.1.1	2019-02-01	46
toolshed.g2.bx.psu.edu/repos/devteam/fastx_barcode_splitter/cshl_fastx_barcode_splitter/1.0.1	2019-02-01	45
toolshed.g2.bx.psu.edu/repos/bgruening/bismark/bismark_methylation_extractor/0.20.0	2019-02-01	45
toolshed.g2.bx.psu.edu/repos/imgteam/coordinates_of_roi/ip_coordinates_of_roi/0.0.3	2019-02-01	44
Show tail1	2019-02-01	44
toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/1.0.1	2019-02-01	44
CONVERTER_bed_gff_or_vcf_to_bigwig_0	2019-02-01	43
CONVERTER_fasta_to_tabular	2019-02-01	43
CONVERTER_vcf_bgzip_to_tabix_0	2019-02-01	43
CONVERTER_vcf_to_vcf_bgzip_0	2019-02-01	42
toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_download/4.3+T.galaxy2	2019-02-01	42
toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/2.4.0	2019-02-01	42
toolshed.g2.bx.psu.edu/repos/devteam/vcfbedintersect/vcfbedintersect/0.0.3	2019-02-01	42
toolshed.g2.bx.psu.edu/repos/devteam/sam_pileup/sam_pileup/1.1.2	2019-02-01	42
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicpca/hicexplorer_hicpca/2.1.4.0	2019-02-01	42
CONVERTER_bed_to_gff_0	2019-02-01	42
toolshed.g2.bx.psu.edu/repos/imgteam/projective_transformation_points/ip_projective_transformation_points/0.0.2	2019-02-01	42
toolshed.g2.bx.psu.edu/repos/iuc/gemini_annotate/gemini_annotate/0.20.1+galaxy1	2019-02-01	41
toolshed.g2.bx.psu.edu/repos/iuc/shovill/shovill/1.0.4	2019-02-01	41
toolshed.g2.bx.psu.edu/repos/iuc/meme_chip/meme_chip/4.11.2	2019-02-01	41
toolshed.g2.bx.psu.edu/repos/iuc/mothur_unique_seqs/mothur_unique_seqs/1.39.5.0	2019-02-01	41
toolshed.g2.bx.psu.edu/repos/devteam/megablast_wrapper/megablast_wrapper/1.2.0	2019-02-01	41
toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_data_exporter/cardinal_data_exporter/1.12.1.0	2019-02-01	41
toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.38.3	2019-02-01	40
toolshed.g2.bx.psu.edu/repos/iuc/ncbi_eutils_esearch/ncbi_eutils_esearch/1.2	2019-02-01	40
toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_combine/cardinal_combine/1.12.1.2	2019-02-01	40
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bigwig_summary/deeptools_multi_bigwig_summary/3.0.2.0	2019-02-01	40
toolshed.g2.bx.psu.edu/repos/iuc/deg_annotate/deg_annotate/1.1.0	2019-02-01	40
toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_deinterlacer/fastq_paired_end_deinterlacer/1.1.2	2019-02-01	39
toolshed.g2.bx.psu.edu/repos/bgruening/bismark/bismark_bowtie2/0.20.0.1	2019-02-01	39
toolshed.g2.bx.psu.edu/repos/rnateam/metilene/metilene/0.2.6.1	2019-02-01	39
toolshed.g2.bx.psu.edu/repos/devteam/pileup_parser/pileup_parser/1.0.2	2019-02-01	38
toolshed.g2.bx.psu.edu/repos/devteam/clustalw/clustalw/2.1	2019-02-01	38
toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_spectra_plots/cardinal_spectra_plots/1.12.1.1	2019-02-01	38
toolshed.g2.bx.psu.edu/repos/iuc/goenrichment/goenrichment/2.0.1	2019-02-01	38
toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.1.0+galaxy3	2019-02-01	38
toolshed.g2.bx.psu.edu/repos/gbcs-embl-heidelberg/je_demultiplex/je_demultiplex/1.2.1	2019-02-01	38
toolshed.g2.bx.psu.edu/repos/devteam/fastx_reverse_complement/cshl_fastx_reverse_complement/1.0.0	2019-02-01	38
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2	2019-02-01	38
toolshed.g2.bx.psu.edu/repos/devteam/fastq_stats/fastq_stats/1.1.1	2019-02-01	37
toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_mz_images/cardinal_mz_images/1.12.1.1	2019-02-01	37
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toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.27.1	2019-02-01	37
random_lines1	2019-02-01	37
toolshed.g2.bx.psu.edu/repos/peterjc/blast_rbh/blast_reciprocal_best_hits/0.1.11	2019-02-01	37
toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.36.0	2019-02-01	36
toolshed.g2.bx.psu.edu/repos/bgruening/column_arrange_by_header/bg_column_arrange_by_header/0.2	2019-02-01	36
toolshed.g2.bx.psu.edu/repos/rnateam/graphclust_nspdk/nspdk_sparse/9.2.3	2019-02-01	36
toolshed.g2.bx.psu.edu/repos/galaxyp/proteomics_moff/proteomics_moff/1.2.1.1	2019-02-01	36
toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.0	2019-02-01	36
toolshed.g2.bx.psu.edu/repos/rnateam/selectsequencesfrommsa/selectsequencesfrommsa/1.0.2	2019-02-01	35
toolshed.g2.bx.psu.edu/repos/iuc/extract_genomic_dna/Extract genomic DNA 1/3.0.0	2019-02-01	35
toolshed.g2.bx.psu.edu/repos/engineson/multiqc/multiqc/1.0.0.0	2019-02-01	35
toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/2.9.1.4	2019-02-01	35
toolshed.g2.bx.psu.edu/repos/mvdbeek/add_input_name_as_column/addName/0.1.1	2019-02-01	35
toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/search_gui/3.2.13	2019-02-01	35
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.7.1.2	2019-02-01	35
toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/1.6.0.2	2019-02-01	35
toolshed.g2.bx.psu.edu/repos/iuc/roary/roary/3.10.2	2019-02-01	35
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicplotviewpoint/hicexplorer_hicplotviewpoint/2.1.4.0	2019-02-01	34
toolshed.g2.bx.psu.edu/repos/crs4/muscle/muscle/0.0.11	2019-02-01	34
toolshed.g2.bx.psu.edu/repos/bgruening/augustus/augustus/3.2.3	2019-02-01	34
toolshed.g2.bx.psu.edu/repos/galaxyp/msgfplus/msgfplus/0.5	2019-02-01	34
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_falsediscoveryrate/FalseDiscoveryRate/2.3.0	2019-02-01	34
toolshed.g2.bx.psu.edu/repos/devteam/fastq_filter/fastq_filter/1.1.1	2019-02-01	34
CONVERTER_gff_to_bed_0	2019-02-01	34
toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.0.6	2019-02-01	33
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.0.0	2019-02-01	33
toolshed.g2.bx.psu.edu/repos/galaxyp/dbbuilder/dbbuilder/0.3.0	2019-02-01	33
toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/3.2+galaxy1	2019-02-01	33
toolshed.g2.bx.psu.edu/repos/iuc/gemini_load/gemini_load/0.20.1+galaxy1	2019-02-01	33
toolshed.g2.bx.psu.edu/repos/iuc/bctools_extract_crosslinked_nucleotides/bctools_extract_crosslinked_nucleotides/@VERSION+galaxy1	2019-02-01	33
toolshed.g2.bx.psu.edu/repos/devteam/bam_to_sam/bam_to_sam/2.0	2019-02-01	33
toolshed.g2.bx.psu.edu/repos/devteam/concat/gops_concat_1/1.0.1	2019-02-01	33
toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/search_gui/3.3.3.0	2019-02-01	33
toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_RPKM_count/2.4	2019-02-01	32
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicbuildmatrix/hicexplorer_hicbuildmatrix/2.1.2.0	2019-02-01	32
toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.6	2019-02-01	32
toolshed.g2.bx.psu.edu/repos/devteam/samtools_flagstat/samtools_flagstat/2.0.1	2019-02-01	32
CONVERTER_fasta_to_bowtie_base_index	2019-02-01	31
CONVERTER_bam_to_qname_sorted_bam	2019-02-01	31
toolshed.g2.bx.psu.edu/repos/devteam/fastq_to_fasta/cshl_fastq_to_fasta/1.0.2	2019-02-01	31
toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.0.2	2019-02-01	31
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_slopbed/2.27.0.0	2019-02-01	31
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_proteinquantifier/ProteinQuantifier/2.3.0	2019-02-01	30
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed/2.27.1	2019-02-01	30
toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/peptide_shaker/1.16.4	2019-02-01	30
trimmer	2019-02-01	30
toolshed.g2.bx.psu.edu/repos/bgruening/diffbind/diffbind/2.6.6.4	2019-02-01	30
toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastp_wrapper/0.3.1	2019-02-01	30
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idconflictresolver/IDConflictResolver/2.3.0	2019-02-01	30
toolshed.g2.bx.psu.edu/repos/devteam/sam2interval/sam2interval/1.0.1	2019-02-01	29
toolshed.g2.bx.psu.edu/repos/iuc/prinseq/prinseq/0.20.4	2019-02-01	28
toolshed.g2.bx.psu.edu/repos/devteam/cuffdiff/cuffdiff/2.2.1.5	2019-02-01	28
toolshed.g2.bx.psu.edu/repos/iuc/varscan_somatic/varscan_somatic/2.4.3.3	2019-02-01	28
toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.13.0	2019-02-01	28
toolshed.g2.bx.psu.edu/repos/iuc/mothur_pre_cluster/mothur_pre_cluster/1.39.5.0	2019-02-01	27
toolshed.g2.bx.psu.edu/repos/iuc/trinity/trinity/2.8.4	2019-02-01	27
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectRnaSeqMetrics/2.18.2.1	2019-02-01	27
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bigwig_compare/deeptools_bigwig_compare/3.0.2.0	2019-02-01	27
bed2gff1	2019-02-01	27
toolshed.g2.bx.psu.edu/repos/rnateam/chipseeker/chipseeker/1.14.2	2019-02-01	26
toolshed.g2.bx.psu.edu/repos/iuc/mothur_filter_seqs/mothur_filter_seqs/1.39.5.0	2019-02-01	26
toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.4	2019-02-01	26
toolshed.g2.bx.psu.edu/repos/devteam/samtools_bedcov/samtools_bedcov/2.0.1	2019-02-01	26
toolshed.g2.bx.psu.edu/repos/devteam/samtools_slice_bam/samtools_slice_bam/2.0.1	2019-02-01	26
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_msgfplusadapter/MSGFPlusAdapter/2.3.0	2019-02-01	26
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.27.1	2019-02-01	25
toolshed.g2.bx.psu.edu/repos/rnateam/rcas/rcas/1.5.4	2019-02-01	25
toolshed.g2.bx.psu.edu/repos/bgruening/bismark/bismark_bowtie2/0.20.0	2019-02-01	25
toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_bam2wig/2.6.4	2019-02-01	25
toolshed.g2.bx.psu.edu/repos/bgruening/bismark/bismark_deduplicate/0.20.0	2019-02-01	24
toolshed.g2.bx.psu.edu/repos/galaxyp/reactome_pathwaymatcher/reactome_pathwaymatcher/1.8.1.2	2019-02-01	24
toolshed.g2.bx.psu.edu/repos/galaxyp/maldi_quant_peak_detection/maldi_quant_peak_detection/1.18.0.2	2019-02-01	24
toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.65	2019-02-01	24
toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.36.5	2019-02-01	24
toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_bdgpeakcall/2.1.1.20160309.0	2019-02-01	24
toolshed.g2.bx.psu.edu/repos/iuc/qiime_extract_barcodes/qiime_extract_barcodes/1.9.1.0	2019-02-01	24
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1	2019-02-01	24
toolshed.g2.bx.psu.edu/repos/iuc/gatk2/gatk2_variant_select/2.8.0	2019-02-01	24
toolshed.g2.bx.psu.edu/repos/iuc/gatk2/gatk2_variant_filtration/2.8.0	2019-02-01	24
toolshed.g2.bx.psu.edu/repos/iuc/transdecoder/transdecoder/3.0.1	2019-02-01	24
toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastx_wrapper/0.3.1	2019-02-01	23
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_peptideindexer/PeptideIndexer/2.3.0	2019-02-01	23
__MERGE_COLLECTION__	2019-02-01	23
toolshed.g2.bx.psu.edu/repos/bgruening/graphicsmagick_image_convert/graphicsmagick_image_convert/1.3.26	2019-02-01	23
CONVERTER_fasta_to_len	2019-02-01	23
toolshed.g2.bx.psu.edu/repos/devteam/macs/peakcalling_macs/1.0.1	2019-02-01	23
toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.2.6	2019-02-01	22
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.27.0.0	2019-02-01	22
toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3+t.galaxy0	2019-02-01	22
toolshed.g2.bx.psu.edu/repos/peterjc/blastxml_to_top_descr/blastxml_to_top_descr/0.1.1	2019-02-01	22
toolshed.g2.bx.psu.edu/repos/iuc/mothur_count_seqs/mothur_count_seqs/1.39.5.0	2019-02-01	22
toolshed.g2.bx.psu.edu/repos/devteam/fastx_artifacts_filter/cshl_fastx_artifacts_filter/1.0.1	2019-02-01	22
toolshed.g2.bx.psu.edu/repos/devteam/subtract/gops_subtract_1/1.0.0	2019-02-01	22
toolshed.g2.bx.psu.edu/repos/rnateam/locarna_multiple/locarna_multiple/1.9.0.1	2019-02-01	22
toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_classification/cardinal_classification/1.12.1.2	2019-02-01	22
toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.22.5	2019-02-01	22
CONVERTER_len_to_linecount	2019-02-01	22
Summary_Statistics1	2019-02-01	22
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_pca/deeptools_plot_pca/3.1.2.0.0	2019-02-01	21
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicsummatrices/hicexplorer_hicsummatrices/2.1.4.0	2019-02-01	21
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_fingerprint/deeptools_plot_fingerprint/2.5.7.0	2019-02-01	21
toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie_merge/1.3.4	2019-02-01	21
ia_coordinates_of_roi	2019-02-01	21
toolshed.g2.bx.psu.edu/repos/iuc/dexseq/dexseq_count/1.26.0.0	2019-02-01	21
toolshed.g2.bx.psu.edu/repos/iuc/mothur_align_seqs/mothur_align_seqs/1.39.5.0	2019-02-01	21
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_makewindowsbed/2.27.1	2019-02-01	21
toolshed.g2.bx.psu.edu/repos/iuc/pear/iuc_pear/0.9.6.1	2019-02-01	21
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_fileinfo/FileInfo/2.3.0	2019-02-01	21
toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_annotate/4.3+t.galaxy1	2019-02-01	21
toolshed.g2.bx.psu.edu/repos/bgruening/join_files_on_column_fuzzy/join_files_on_column_fuzzy/1.0.1	2019-02-01	21
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_correlation/deeptools_plot_correlation/2.5.7.0	2019-02-01	21
toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_makeblastdb/0.3.1	2019-02-01	21
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toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bam_summary/deeptools_multi_bam_summary/2.5.7.0	2019-02-01	21
toolshed.g2.bx.psu.edu/repos/rnateam/viennarna_rnafold/viennarna_rnafold/2.2.10.4	2019-02-01	21
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeSamFiles/2.18.2.1	2019-02-01	20
toolshed.g2.bx.psu.edu/repos/iuc/humann2/humann2/0.11.1.0	2019-02-01	20
toolshed.g2.bx.psu.edu/repos/iuc/metaphlan2krona/metaphlan2krona/2.6.0.0	2019-02-01	20
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtobam/2.27.1	2019-02-01	20
toolshed.g2.bx.psu.edu/repos/bebatut/format_metaphlan2_output/format_metaphlan2_output/0.1.0	2019-02-01	20
toolshed.g2.bx.psu.edu/repos/iuc/gatk2/gatk2_depth_of_coverage/2.8.0	2019-02-01	20
toolshed.g2.bx.psu.edu/repos/devteam/cuffmerge/cuffmerge/2.2.1.1	2019-02-01	20
toolshed.g2.bx.psu.edu/repos/bgruening/column_arrange_by_header/bg_column_arrange_by_header/0.1	2019-02-01	20
toolshed.g2.bx.psu.edu/repos/bgruening/canu/canu/1.7	2019-02-01	20
toolshed.g2.bx.psu.edu/repos/peterjc/mira_assembler/mira_assembler/0.0.11	2019-02-01	20
toolshed.g2.bx.psu.edu/repos/iuc/mummer_nucmer/mummer_nucmer/4.0.0beta2	2019-02-01	20
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idposteriorerrorprobability/IDPosteriorErrorProbability/2.3.0	2019-02-01	20
toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_heatmap/ggplot2_heatmap/2.2.1	2019-02-01	19
toolshed.g2.bx.psu.edu/repos/iuc/samtools_sort/samtools_rmdup/1.0.1	2019-02-01	19
toolshed.g2.bx.psu.edu/repos/rnateam/graphclust_preprocessing/preproc/0.5	2019-02-01	19
toolshed.g2.bx.psu.edu/repos/galaxyp/thermo_raw_file_converter/thermo_raw_file_converter/0.0.1	2019-02-01	19
toolshed.g2.bx.psu.edu/repos/iuc/kallisto_quant/kallisto_quant/0.43.1.4	2019-02-01	19
toolshed.g2.bx.psu.edu/repos/rnateam/structure_to_gspan/structure_to_gspan/0.4	2019-02-01	19
toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/fasta_compute_length/1.0.1	2019-02-01	19
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_NormalizeFasta/2.18.2.1	2019-02-01	18
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed/2.27.0.0	2019-02-01	18
toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummer/mummer_mummer/4.0.0beta2	2019-02-01	18
toolshed.g2.bx.psu.edu/repos/rnateam/mirdeep2_quantifier/rbc_mirdeep2_quantifier/2.0.0	2019-02-01	18
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_fidoadapter/FidoAdapter/2.3.0	2019-02-01	18
toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.1+galaxy0	2019-02-01	18
toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.3	2019-02-01	18
toolshed.g2.bx.psu.edu/repos/galaxyp/msi_preprocessing/mass_spectrometry_imaging_preprocessing/1.10.0.7	2019-02-01	18
toolshed.g2.bx.psu.edu/repos/iuc/mothur_chimera_vsearch/mothur_chimera_vsearch/1.39.5.1	2019-02-01	18
toolshed.g2.bx.psu.edu/repos/devteam/fastx_barcode_splitter/cshl_fastx_barcode_splitter/1.0.0	2019-02-01	18
toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_histogram/ggplot2_histogram/2.2.1+galaxy0	2019-02-01	18
re_he_maldi_image_registration	2019-02-01	18
toolshed.g2.bx.psu.edu/repos/iuc/trinity_align_and_estimate_abundance/trinity_align_and_estimate_abundance/2.8.4	2019-02-01	18
toolshed.g2.bx.psu.edu/repos/devteam/cummerbund/cummeRbund/2.16.0	2019-02-01	18
toolshed.g2.bx.psu.edu/repos/imgteam/overlay_moving_and_fixed_image/ip_viz_overlay_moving_and_fixed_image/0.0.1	2019-02-01	18
toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.4.2	2019-02-01	18
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idscoreswitcher/IDScoreSwitcher/2.3.0	2019-02-01	18
toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.0.2.29-3	2019-02-01	17
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toolshed.g2.bx.psu.edu/repos/bgruening/trna_prediction/aragorn_trna/0.6	2019-02-01	15
toolshed.g2.bx.psu.edu/repos/iuc/extract_genomic_dna/Extract genomic DNA 1/3.0.2	2019-02-01	15
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multiintersectbed/2.27.1	2019-02-01	15
toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.6.0	2019-02-01	15
toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/datamash_ops/1.0.6	2019-02-01	15
toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.5.0.1	2019-02-01	15
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toolshed.g2.bx.psu.edu/repos/iuc/meme_fimo/meme_fimo/4.11.2.0	2019-02-01	14
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toolshed.g2.bx.psu.edu/repos/iuc/mothur_dist_seqs/mothur_dist_seqs/1.39.5.0	2019-02-01	14
toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/0.8.1+galaxy0	2019-02-01	14
ip_projective_transformation_points	2019-02-01	14
toolshed.g2.bx.psu.edu/repos/iuc/dexseq/dexseq/1.26.0+galaxy1	2019-02-01	14
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toolshed.g2.bx.psu.edu/repos/iuc/hmmer3/hmmer_hmmscan/0.1.0	2019-02-01	14
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toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_shared/mothur_make_shared/1.39.5.0	2019-02-01	14
toolshed.g2.bx.psu.edu/repos/iuc/mothur_rarefaction_single/mothur_rarefaction_single/1.39.5.0	2019-02-01	14
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.0	2019-02-01	14
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.7.1.1	2019-02-01	14
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_uniq_tool/1.1.1	2019-02-01	14
toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_pca/ggplot2_pca/2.2.1	2019-02-01	13
toolshed.g2.bx.psu.edu/repos/iuc/mothur_remove_lineage/mothur_remove_lineage/1.39.5.0	2019-02-01	13
toolshed.g2.bx.psu.edu/repos/iuc/mothur_summary_single/mothur_summary_single/1.39.5.0	2019-02-01	13
toolshed.g2.bx.psu.edu/repos/iuc/mothur_cluster_split/mothur_cluster_split/1.39.5.0	2019-02-01	13
toolshed.g2.bx.psu.edu/repos/iuc/mothur_remove_seqs/mothur_remove_seqs/1.36.1.0	2019-02-01	13
toolshed.g2.bx.psu.edu/repos/iuc/gemini_stats/gemini_stats/0.20.1	2019-02-01	13
toolshed.g2.bx.psu.edu/repos/iuc/mothur_dist_shared/mothur_dist_shared/1.39.5.0	2019-02-01	13
toolshed.g2.bx.psu.edu/repos/nml/metaspades/metaspades/3.9.0	2019-02-01	13
toolshed.g2.bx.psu.edu/repos/rnateam/atactk_trim_adapters/atactk_trim_adapters/0.1.6	2019-02-01	13
toolshed.g2.bx.psu.edu/repos/iuc/qiime_assign_taxonomy/qiime_assign_taxonomy/1.9.1.0	2019-02-01	13
toolshed.g2.bx.psu.edu/repos/iuc/flash/flash/1.2.11.3	2019-02-01	13
toolshed.g2.bx.psu.edu/repos/ethevenot/univariate/Univariate/2.2.4	2019-02-01	13
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toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.4.0d-2	2019-02-01	13
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toolshed.g2.bx.psu.edu/repos/yhoogstrate/flaimapper/flaimapper/3.0.0-0	2019-02-01	13
toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/1.4.6.p5	2019-02-01	12
toolshed.g2.bx.psu.edu/repos/bebatut/cdhit/cd_hit_est/1.3	2019-02-01	12
toolshed.g2.bx.psu.edu/repos/devteam/fastq_manipulation/fastq_manipulation/1.0.1	2019-02-01	12
toolshed.g2.bx.psu.edu/repos/kellrott/regex_replace/regex_replace/1.0.0	2019-02-01	12
toolshed.g2.bx.psu.edu/repos/devteam/samtools_calmd/samtools_calmd/2.0.2	2019-02-01	12
toolshed.g2.bx.psu.edu/repos/iuc/megahit/megahit/1.1.3.4	2019-02-01	12
toolshed.g2.bx.psu.edu/repos/devteam/samtool_filter2/samtool_filter2/1.1.2	2019-02-01	12
toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_feature_selection/sklearn_feature_selection/0.9.1	2019-02-01	12
toolshed.g2.bx.psu.edu/repos/lparsons/htseq_count/htseq_count/0.6.1galaxy2	2019-02-01	12
toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_violin/ggplot2_violin/2.2.1+galaxy0	2019-02-01	12
toolshed.g2.bx.psu.edu/repos/iuc/mothur_heatmap_bin/mothur_heatmap_bin/1.39.5.0	2019-02-01	12
toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.0.3	2019-02-01	12
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtofastq/2.24.0	2019-02-01	12
dexseq_annotate	2019-02-01	12
toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: geecee41/5.0.0	2019-02-01	12
toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.4.1	2019-02-01	12
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wiggle2simple1	2019-02-01	12
toolshed.g2.bx.psu.edu/repos/iuc/mothur_get_oturep/mothur_get_oturep/1.39.5.0	2019-02-01	12
toolshed.g2.bx.psu.edu/repos/devteam/picard/rgPicFixMate/1.56.0	2019-02-01	12
toolshed.g2.bx.psu.edu/repos/miller-lab/genome_diversity/gd_raxml/1.0.0	2019-02-01	12
__IMPORT_HISTORY__	2019-02-01	12
toolshed.g2.bx.psu.edu/repos/iuc/fgsea/fgsea/1.6.0	2019-02-01	12
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toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_filtering/cardinal_filtering/1.12.1.0	2019-02-01	12
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toolshed.g2.bx.psu.edu/repos/bgruening/sailfish/sailfish/0.10.1.1	2019-02-01	12
toolshed.g2.bx.psu.edu/repos/iuc/dexseq/dexseq_count/1.20.1	2019-02-01	12
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.0.1.0	2019-02-01	11
toolshed.g2.bx.psu.edu/repos/ethevenot/checkformat/checkFormat/3.0.0	2019-02-01	11
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toolshed.g2.bx.psu.edu/repos/iuc/egsea/egsea/1.8.0	2019-02-01	11
toolshed.g2.bx.psu.edu/repos/devteam/t_test_two_samples/t_test_two_samples/1.0.1	2019-02-01	11
toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_heatmap2/ggplot2_heatmap2/2.2.1	2019-02-01	11
toolshed.g2.bx.psu.edu/repos/devteam/fastq_trimmer_by_quality/fastq_quality_trimmer/1.1.1	2019-02-01	11
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toolshed.g2.bx.psu.edu/repos/iuc/pygenometracks/pygenomeTracks/2.0.1	2019-02-01	11
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_xtandemadapter/XTandemAdapter/2.3.0	2019-02-01	11
toolshed.g2.bx.psu.edu/repos/bgruening/rnaz/rnaz/2.1.1	2019-02-01	11
toolshed.g2.bx.psu.edu/repos/wolma/mimodd_main/mimodd_info/0.1.8_1	2019-02-01	10
toolshed.g2.bx.psu.edu/repos/galaxyp/msi_filtering/mass_spectrometry_imaging_filtering/1.10.0.6	2019-02-01	10
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toolshed.g2.bx.psu.edu/repos/iuc/ruvseq/ruvseq/1.12.0	2019-02-01	10
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Sff_extractor	2019-02-01	10
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toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.38.3+galaxy1	2019-02-01	10
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toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multiintersectbed/2.27.0.0	2019-02-01	10
toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.0	2019-02-01	10
toolshed.g2.bx.psu.edu/repos/iuc/gemini_actionable_mutations/gemini_actionable_mutations/0.20.1	2019-02-01	10
toolshed.g2.bx.psu.edu/repos/peterjc/mummer/mummerplot_wrapper/0.0.7	2019-02-01	10
toolshed.g2.bx.psu.edu/repos/rnateam/chipseeker/chipseeker/1.14.2.1	2019-02-01	10
toolshed.g2.bx.psu.edu/repos/devteam/flanking_features/flanking_features_1/4.0.1	2019-02-01	10
toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.2	2019-02-01	9
toolshed.g2.bx.psu.edu/repos/iuc/gemini_load/gemini_load/0.20.1	2019-02-01	9
toolshed.g2.bx.psu.edu/repos/rnateam/cmv/cmv/1.0.8	2019-02-01	9
toolshed.g2.bx.psu.edu/repos/devteam/picard/rgPicardMarkDups/1.56.0	2019-02-01	9
toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.3	2019-02-01	9
toolshed.g2.bx.psu.edu/repos/devteam/correlation/cor2/1.0.0	2019-02-01	9
toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy3	2019-02-01	9
toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_searchcv/sklearn_searchcv/1.0	2019-02-01	9
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toolshed.g2.bx.psu.edu/repos/iuc/gatk2/gatk2_print_reads/2.8.0	2019-02-01	9
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toolshed.g2.bx.psu.edu/repos/devteam/cuffnorm/cuffnorm/2.2.1.2	2019-02-01	9
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toolshed.g2.bx.psu.edu/repos/rnateam/rnacode/rbc_rnacode/0.3.0	2019-02-01	9
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_profile/deeptools_plot_profile/3.0.2.0	2019-02-01	8
toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread/2.2.1.1	2019-02-01	8
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toolshed.g2.bx.psu.edu/repos/ethevenot/heatmap/Heatmap/2.2.2	2019-02-01	8
toolshed.g2.bx.psu.edu/repos/iuc/gatk2/gatk2_haplotype_caller/2.8.0	2019-02-01	8
toolshed.g2.bx.psu.edu/repos/bgruening/circexplorer/circexplorer/1.1.9.0	2019-02-01	8
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toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/column_remove_by_header/0.0.1	2019-02-01	8
sklearn_ensemble	2019-02-01	8
toolshed.g2.bx.psu.edu/repos/iuc/gemini_db_info/gemini_db_info/0.20.1	2019-02-01	8
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CONVERTER_vcf_to_bgzip_0	2019-02-01	8
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_subtractbed/2.27.0.0	2019-02-01	8
toolshed.g2.bx.psu.edu/repos/iuc/gffcompare/gffcompare/0.10.6	2019-02-01	8
toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.1.1.20160309.4	2019-02-01	8
toolshed.g2.bx.psu.edu/repos/iuc/gffcompare/gffcompare/0.9.8+galaxy1	2019-02-01	8
CONVERTER_bed_to_fli_0	2019-02-01	7
CONVERTER_gff_to_interval_index_0	2019-02-01	7
toolshed.g2.bx.psu.edu/repos/iuc/humann2_genefamilies_genus_level/humann2_genefamilies_genus_level/0.11.1.0	2019-02-01	7
toolshed.g2.bx.psu.edu/repos/iuc/meme_meme/meme_meme/4.11.2.0	2019-02-01	7
toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_mergefa/1.3.1	2019-02-01	7
toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3r.1	2019-02-01	7
toolshed.g2.bx.psu.edu/repos/iuc/export2graphlan/export2graphlan/0.19	2019-02-01	7
toolshed.g2.bx.psu.edu/repos/bgruening/antismash/antismash/4.1	2019-02-01	7
toolshed.g2.bx.psu.edu/repos/iuc/gffcompare/gffcompare/0.9.8	2019-02-01	7
toolshed.g2.bx.psu.edu/repos/iuc/migmap/migmap/1.0.2.2	2019-02-01	7
toolshed.g2.bx.psu.edu/repos/iuc/fasttree/fasttree/2.1.10	2019-02-01	7
toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_ensemble/sklearn_ensemble/1.0	2019-02-01	7
toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.6.1	2019-02-01	7
toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.4.0	2019-02-01	7
CONVERTER_bed_to_bgzip_0	2019-02-01	7
toolshed.g2.bx.psu.edu/repos/iuc/gatk2/gatk2_realigner_target_creator/2.8.0	2019-02-01	7
toolshed.g2.bx.psu.edu/repos/iuc/graphlan/graphlan/1.0.0.0	2019-02-01	7
toolshed.g2.bx.psu.edu/repos/devteam/fastq_filter/fastq_filter/1.0.0	2019-02-01	7
toolshed.g2.bx.psu.edu/repos/iuc/vt_variant_tools/vt_normalize/0.1.0	2019-02-01	7
toolshed.g2.bx.psu.edu/repos/devteam/count_covariates/gatk_count_covariates/0.0.5	2019-02-01	7
toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_combine/cardinal_combine/1.12.1.0	2019-02-01	7
toolshed.g2.bx.psu.edu/repos/devteam/xy_plot/XY_Plot_1/1.0.2	2019-02-01	7
toolshed.g2.bx.psu.edu/repos/bgruening/crispr_recognition_tool/crispr_recognition_tool/1.2.0	2019-02-01	7
toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.2.6.2	2019-02-01	7
toolshed.g2.bx.psu.edu/repos/devteam/vcfcombine/vcfcombine/1.0.0_rc1+galaxy0	2019-02-01	7
toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.5.0	2019-02-01	7
toolshed.g2.bx.psu.edu/repos/iuc/graphlan_annotate/graphlan_annotate/1.0.0.0	2019-02-01	7
toolshed.g2.bx.psu.edu/repos/devteam/fastq_quality_boxplot/cshl_fastq_quality_boxplot/1.0.0	2019-02-01	6
toolshed.g2.bx.psu.edu/repos/rnateam/rnacode/rbc_rnacode/0.3.1	2019-02-01	6
toolshed.g2.bx.psu.edu/repos/bgruening/infernal/infernal_cmbuild/1.1.0.2	2019-02-01	6
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toolshed.g2.bx.psu.edu/repos/iuc/scpipe/scpipe/1.0.0+galaxy1	2019-02-01	6
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddOrReplaceReadGroups/1.136.0	2019-02-01	6
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_subtractbed/2.27.1	2019-02-01	6
toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_junction_saturation/2.6.4.1	2019-02-01	6
toolshed.g2.bx.psu.edu/repos/devteam/gi2taxonomy/Fetch Taxonomic Ranks/1.1.0	2019-02-01	6
toolshed.g2.bx.psu.edu/repos/bgruening/nn_classifier/nn_classifier/0.9	2019-02-01	6
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_flankbed/2.27.1	2019-02-01	6
gene2exon1	2019-02-01	6
toolshed.g2.bx.psu.edu/repos/earlhaminst/ensembl_get_sequences/get_sequences/0.1.2	2019-02-01	6
toolshed.g2.bx.psu.edu/repos/bonsai/sortmerna/merged_paired_reads_wrapper/1.0	2019-02-01	6
toolshed.g2.bx.psu.edu/repos/peterjc/tmhmm_and_signalp/signalp3/0.0.19	2019-02-01	6
toolshed.g2.bx.psu.edu/repos/iuc/mothur_heatmap_sim/mothur_heatmap_sim/1.39.5.0	2019-02-01	6
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toolshed.g2.bx.psu.edu/repos/bgruening/infernal/infernal_cmstat/1.1.0.1	2019-02-01	6
toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_nn_classifier/sklearn_nn_classifier/0.9	2019-02-01	6
toolshed.g2.bx.psu.edu/repos/iuc/mothur_tree_shared/mothur_tree_shared/1.39.5.0	2019-02-01	6
toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0	2019-02-01	6
toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: fuzzpro38/5.0.0	2019-02-01	6
toolshed.g2.bx.psu.edu/repos/galaxyp/msi_spectra_plot/mass_spectrometry_imaging_mzplots/1.10.0.6	2019-02-01	6
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_mergebedgraph/2.19.0	2019-02-01	6
toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_download/4.3r.1	2019-02-01	6
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_groupbybed/2.27.1	2019-02-01	6
toolshed.g2.bx.psu.edu/repos/bgruening/infernal/infernal_cmsearch/1.1.0.2	2019-02-01	6
CONVERTER_vcf_to_tabix_0	2019-02-01	6
toolshed.g2.bx.psu.edu/repos/imgteam/landmark_registration/ip_landmark_registration/0.0.2	2019-02-01	6
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toolshed.g2.bx.psu.edu/repos/bgruening/nanopolish_variants/nanopolish_variants/0.1.0	2019-02-01	5
toolshed.g2.bx.psu.edu/repos/peterjc/tmhmm_and_signalp/tmhmm2/0.0.14	2019-02-01	5
toolshed.g2.bx.psu.edu/repos/peterjc/blast2go/blast2go/0.0.9	2019-02-01	5
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.27.0.1	2019-02-01	5
toolshed.g2.bx.psu.edu/repos/iuc/spaln/spaln/2.3.2+galaxy0	2019-02-01	5
toolshed.g2.bx.psu.edu/repos/peterjc/tmhmm_and_signalp/tmhmm2/0.0.16	2019-02-01	5
toolshed.g2.bx.psu.edu/repos/iuc/kobas/kobas_annotate/0.4	2019-02-01	5
toolshed.g2.bx.psu.edu/repos/iuc/dexseq/plotdexseq/1.26.0.0	2019-02-01	5
toolshed.g2.bx.psu.edu/repos/iuc/gatk2/gatk2_indel_realigner/2.8.0	2019-02-01	5
toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: getorf42/5.0.0.1	2019-02-01	5
gff2bed1	2019-02-01	5
toolshed.g2.bx.psu.edu/repos/iuc/filtlong/filtlong/0.2.0	2019-02-01	5
velveth	2019-02-01	5
velvetg	2019-02-01	5
hgv_david	2019-02-01	5
toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_comp/1.3.1	2019-02-01	5
toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.3	2019-02-01	5
toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie_merge/1.3.3	2019-02-01	5
toolshed.g2.bx.psu.edu/repos/iuc/vsearch/vsearch_dereplication/1.9.7.0	2019-02-01	5
toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpSift_annotate/3.4	2019-02-01	5
biomart	2019-02-01	5
toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.3.7	2019-02-01	5
toolshed.g2.bx.psu.edu/repos/iuc/poretools_qualdist/poretools_qualdist/0.6.1a1.0	2019-02-01	5
toolshed.g2.bx.psu.edu/repos/bgruening/rnaz/rnaz/2.1.0	2019-02-01	5
toolshed.g2.bx.psu.edu/repos/imgteam/curl_post/curl_post/0.0.2	2019-02-01	5
toolshed.g2.bx.psu.edu/repos/bgruening/svm_classifier/svm_classifier/0.9	2019-02-01	5
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_complementbed/2.27.1	2019-02-01	5
toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.16.1+galaxy0	2019-02-01	5
toolshed.g2.bx.psu.edu/repos/jjohnson/cdhit/cd_hit_protein/1.2	2019-02-01	5
toolshed.g2.bx.psu.edu/repos/iuc/ncbi_eutils_esummary/ncbi_eutils_esummary/1.2	2019-02-01	5
toolshed.g2.bx.psu.edu/repos/rnateam/rcas/rcas/1.1.1	2019-02-01	5
toolshed.g2.bx.psu.edu/repos/iuc/pick_closed_reference_otus/pick_closed_reference_otus/1.9.1.0	2019-02-01	5
toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.1	2019-02-01	4
toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_rpsblast_wrapper/0.1.01	2019-02-01	4
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed_histogram/2.19.0	2019-02-01	4
toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_bdgcmp/2.1.1.20160309.0	2019-02-01	4
toolshed.g2.bx.psu.edu/repos/bgruening/glimmer3/glimmer_not-knowlegde-based/0.2	2019-02-01	4
toolshed.g2.bx.psu.edu/repos/devteam/principal_component_analysis/pca1/1.0.2	2019-02-01	4
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_QualityScoreDistribution/2.18.2.1	2019-02-01	4
toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_databases/4.3+T.galaxy1	2019-02-01	4
toolshed.g2.bx.psu.edu/repos/bjoern-gruening/sed_wrapper/sed_stream_editor/0.0.1	2019-02-01	4
toolshed.g2.bx.psu.edu/repos/ethevenot/biosigner/biosigner/2.2.7	2019-02-01	4
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_shufflebed/2.27.0.0	2019-02-01	4
toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_build_pipeline/sklearn_build_pipeline/1.0	2019-02-01	4
toolshed.g2.bx.psu.edu/repos/bgruening/plotly_parallel_coordinates_plot/plotly_parallel_coordinates_plot/0.1	2019-02-01	4
toolshed.g2.bx.psu.edu/repos/devteam/histogram/histogram_rpy/1.0.3	2019-02-01	4
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_closestbed/2.27.0.0	2019-02-01	4
toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: etandem33/5.0.0.1	2019-02-01	4
toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.68	2019-02-01	4
toolshed.g2.bx.psu.edu/repos/fcaramia/varscan/varscan_mpileup/2.3.5	2019-02-01	4
toolshed.g2.bx.psu.edu/repos/devteam/cuffmerge/cuffmerge/0.0.6	2019-02-01	4
toolshed.g2.bx.psu.edu/repos/galaxyp/unipept/unipept/4.0.0	2019-02-01	4
toolshed.g2.bx.psu.edu/repos/devteam/fastq_combiner/fastq_combiner/1.1.1	2019-02-01	4
toolshed.g2.bx.psu.edu/repos/iuc/enasearch_retrieve_data/enasearch_retrieve_data/0.1.1.0	2019-02-01	4
toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.4.0	2019-02-01	4
toolshed.g2.bx.psu.edu/repos/galaxyp/mass_spectrometry_imaging_segmentations/mass_spectrometry_imaging_segmentations/1.10.0.4	2019-02-01	4
toolshed.g2.bx.psu.edu/repos/tgac/miranda/miranda/3.3a	2019-02-01	4
toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_group/mothur_make_group/1.39.5.0	2019-02-01	4
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MeanQualityByCycle/2.18.2.1	2019-02-01	4
toolshed.g2.bx.psu.edu/repos/iuc/stacks_populations/stacks_populations/1.46.0	2019-02-01	4
r_correlation_matrix	2019-02-01	4
deeptools_bigwigCorrelate	2019-02-01	4
toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/4.6.3	2019-02-01	4
toolshed.g2.bx.psu.edu/repos/iuc/poretools_extract/poretools_extract/0.6.1a1.0	2019-02-01	4
toolshed.g2.bx.psu.edu/repos/iuc/stacks_denovomap/stacks_denovomap/1.46.0	2019-02-01	4
toolshed.g2.bx.psu.edu/repos/iuc/plasflow/PlasFlow/1.0	2019-02-01	4
cshl_find_and_replace	2019-02-01	4
toolshed.g2.bx.psu.edu/repos/iuc/raceid_inspectclusters/raceid_inspectclusters/3.0.2.1	2019-02-01	4
toolshed.g2.bx.psu.edu/repos/iuc/mothur_merge_files/mothur_merge_files/1.39.5.0	2019-02-01	4
toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.1.3	2019-02-01	4
toolshed.g2.bx.psu.edu/repos/bgruening/minced/minced/0.1.5	2019-02-01	4
toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/0.8.1+galaxy0	2019-02-01	4
toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastp_wrapper/0.1.01	2019-02-01	4
toolshed.g2.bx.psu.edu/repos/iuc/column_order_header_sort/column_order_header_sort/0.0.1	2019-02-01	4
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_peakpickerhires/PeakPickerHiRes/2.3.0	2019-02-01	3
toolshed.g2.bx.psu.edu/repos/iuc/gemini_load/gemini_load/0.18.1.0	2019-02-01	3
genomespace_exporter	2019-02-01	3
toolshed.g2.bx.psu.edu/repos/iuc/sqlite_to_tabular/sqlite_to_tabular/2.0.0	2019-02-01	3
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_featurefinderisotopewavelet/FeatureFinderIsotopeWavelet/2.3.0	2019-02-01	3
toolshed.g2.bx.psu.edu/repos/iuc/mummer_dnadiff/mummer_dnadiff/4.0.0beta2	2019-02-01	3
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_alignmentsieve/deeptools_alignmentsieve/3.0.2.0	2019-02-01	3
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_unionbedgraph/2.27.0.0	2019-02-01	3
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_consensusid/ConsensusID/2.3.0	2019-02-01	3
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_heatmap/deeptools_plot_heatmap/3.0.1.0	2019-02-01	3
toolshed.g2.bx.psu.edu/repos/bgruening/plotly_regression_performance_plots/plotly_regression_performance_plots/0.1	2019-02-01	3
toolshed.g2.bx.psu.edu/repos/iuc/raceid_clustering/raceid_clustering/3.0.2.1	2019-02-01	3
svm_classifier	2019-02-01	3
toolshed.g2.bx.psu.edu/repos/iuc/samtools_sort/samtools_sort/1.0.2	2019-02-01	3
toolshed.g2.bx.psu.edu/repos/iuc/crosscontamination_barcode_filter/crosscontamination_barcode_filter/0.1	2019-02-01	3
toolshed.g2.bx.psu.edu/repos/rnateam/rnalien/RNAlien/1.3.6	2019-02-01	3
toolshed.g2.bx.psu.edu/repos/devteam/cuffcompare/cuffcompare/2.2.1.1	2019-02-01	3
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddOrReplaceReadGroups/2.18.2.1	2019-02-01	3
toolshed.g2.bx.psu.edu/repos/iuc/enasearch_search_data/enasearch_search_data/0.1.1.0	2019-02-01	3
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_highresprecursormasscorrector/HighResPrecursorMassCorrector/2.3.0	2019-02-01	3
toolshed.g2.bx.psu.edu/repos/iuc/ucsc_fasplit/fasplit/357	2019-02-01	3
toolshed.g2.bx.psu.edu/repos/bgruening/rnaz_annotate/rnaz_annotate/2.1	2019-02-01	3
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicplotdistvscounts/hicexplorer_hicplotdistvscounts/2.1.4.0	2019-02-01	3
toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sra_pileup/2.9.1.2	2019-02-01	3
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bwtool-lift	2019-02-01	3
toolshed.g2.bx.psu.edu/repos/iuc/poretools_nucdist/poretools_nucdist/0.6.1a1.0	2019-02-01	3
toolshed.g2.bx.psu.edu/repos/bgruening/infernal/infernal_cmstat/1.1.2.0	2019-02-01	3
toolshed.g2.bx.psu.edu/repos/rnateam/viennarna_rnaplot/viennarna_rnaplot/2.2.10.0	2019-02-01	3
toolshed.g2.bx.psu.edu/repos/ethevenot/transformation/Transformation/2.2.0	2019-02-01	3
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_clusterbed/2.27.1	2019-02-01	3
toolshed.g2.bx.psu.edu/repos/iuc/ncbi_eutils_egquery/ncbi_eutils_egquery/1.2	2019-02-01	3
toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_svm_classifier/sklearn_svm_classifier/1.0	2019-02-01	3
toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.1	2019-02-01	3
toolshed.g2.bx.psu.edu/repos/devteam/samtool_filter2/samtool_filter2/1.1.1	2019-02-01	3
toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_tblastx_wrapper/0.3.1	2019-02-01	3
toolshed.g2.bx.psu.edu/repos/galaxyp/decoyfasta/decoyfasta/0.2.0	2019-02-01	3
toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/2.8.1.3	2019-02-01	3
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toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hiccorrelate/hicexplorer_hiccorrelate/2.1.4.0	2019-02-01	3
toolshed.g2.bx.psu.edu/repos/iuc/bctools_extract_barcodes/bctools_extract_barcodes/0.2.2	2019-02-01	3
toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummerplot/mummer_mummerplot/4.0.0beta2	2019-02-01	3
toolshed.g2.bx.psu.edu/repos/imgteam/2d_feature_extraction/ip_2d_feature_extraction/0.0.8	2019-02-01	3
toolshed.g2.bx.psu.edu/repos/iuc/dexseq/dexseq/1.20.1	2019-02-01	3
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idmerger/IDMerger/2.3.0	2019-02-01	3
toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/2.0.0	2019-02-01	3
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_rows/1.1.0	2019-02-01	3
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_pe_fragmentsize/deeptools_bam_pe_fragmentsize/3.0.2.0	2019-02-01	3
toolshed.g2.bx.psu.edu/repos/iuc/khmer_abundance_distribution_single/khmer_abundance_distribution_single/2.0.0	2019-02-01	3
toolshed.g2.bx.psu.edu/repos/devteam/vcffixup/vcffixup/1.0.0_rc1+galaxy0	2019-02-01	3
toolshed.g2.bx.psu.edu/repos/rnateam/peakachu/peakachu/0.1.0.1	2019-02-01	3
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeSamFiles/1.136.0	2019-02-01	3
toolshed.g2.bx.psu.edu/repos/iuc/trinity_analyze_diff_expr/trinity_analyze_diff_expr/2.8.4	2019-02-01	3
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicplotmatrix/hicexplorer_hicplotmatrix/2.1.2.0	2019-02-01	2
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_overlapbed/2.27.0.0	2019-02-01	2
toolshed.g2.bx.psu.edu/repos/devteam/fastq_quality_boxplot/cshl_fastq_quality_boxplot/1.0.1	2019-02-01	2
__BUILD_LIST__	2019-02-01	2
toolshed.g2.bx.psu.edu/repos/iuc/qiime_pick_rep_set/qiime_pick_rep_set/1.9.1.0	2019-02-01	2
ucsc_table_direct_archaea1	2019-02-01	2
toolshed.g2.bx.psu.edu/repos/iuc/qiime_pick_otus/qiime_pick_otus/1.9.1.0	2019-02-01	2
toolshed.g2.bx.psu.edu/repos/iuc/qiime_pick_open_reference_otus/qiime_pick_open_reference_otus/1.9.1.0	2019-02-01	2
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/deeptools_compute_matrix/3.0.1.0	2019-02-01	2
toolshed.g2.bx.psu.edu/repos/yhoogstrate/ega_download_streamer/ega_download_streamer/2.1.6.g0	2019-02-01	2
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_compare/deeptools_bam_compare/3.0.1.0	2019-02-01	2
CONVERTER_Bam_Bai_0	2019-02-01	2
toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.69	2019-02-01	2
toolshed.g2.bx.psu.edu/repos/iuc/deg_annotate/deg_annotate/1.0	2019-02-01	2
toolshed.g2.bx.psu.edu/repos/iuc/describe_samples/describe_samples/2.8.4	2019-02-01	2
toolshed.g2.bx.psu.edu/repos/iuc/qiime_align_seqs/qiime_align_seqs/1.9.1.0	2019-02-01	2
toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.38	2019-02-01	2
toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.64	2019-02-01	2
toolshed.g2.bx.psu.edu/repos/iuc/poretools_stats/poretools_stats/0.6.1a1.0	2019-02-01	2
toolshed.g2.bx.psu.edu/repos/iuc/seurat/seurat/2.3.4	2019-02-01	2
toolshed.g2.bx.psu.edu/repos/iuc/poretools_squiggle/poretools_squiggle/0.6.1a1.0	2019-02-01	2
toolshed.g2.bx.psu.edu/repos/rnateam/rnashapes/RNAshapes/3.3.0	2019-02-01	2
toolshed.g2.bx.psu.edu/repos/iuc/poretools_hist/poretools_hist/0.6.1a1.0	2019-02-01	2
toolshed.g2.bx.psu.edu/repos/devteam/featurecounter/featureCoverage1/2.0.0	2019-02-01	2
toolshed.g2.bx.psu.edu/repos/iuc/poretools_events/poretools_events/0.6.1a1.0	2019-02-01	2
toolshed.g2.bx.psu.edu/repos/earlhaminst/treebest_best/treebest_best_wrapper/1.9.2	2019-02-01	2
toolshed.g2.bx.psu.edu/repos/iuc/ebi_search_rest_results/ebi_search_rest_results/0.1.1	2019-02-01	2
toolshed.g2.bx.psu.edu/repos/rnateam/mlocarna/mlocarna/1.8.12.0	2019-02-01	2
toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/0.4.1	2019-02-01	2
toolshed.g2.bx.psu.edu/repos/galaxyp/lfq_protein_quant/lfq_protein_quant/1.0	2019-02-01	2
toolshed.g2.bx.psu.edu/repos/devteam/dgidb_annotator/dgidb_annotator/0.1	2019-02-01	2
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_flankbed/2.27.0.0	2019-02-01	2
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_coveragebed/2.27.1	2019-02-01	2
toolshed.g2.bx.psu.edu/repos/anton/vcfvcfintersect/vcfvcfintersect/0.0.1	2019-02-01	2
toolshed.g2.bx.psu.edu/repos/devteam/cuffmerge/cuffmerge/0.0.5	2019-02-01	2
toolshed.g2.bx.psu.edu/repos/bgruening/diamond/bg_diamond/0.8.24.1	2019-02-01	2
toolshed.g2.bx.psu.edu/repos/iuc/msaboot/msaboot/0.1.2	2019-02-01	2
CONVERTER_interval_to_bgzip_0	2019-02-01	2
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtoigv/2.27.1	2019-02-01	2
toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_get_chr_names/4.3+T.galaxy1	2019-02-01	2
toolshed.g2.bx.psu.edu/repos/bgruening/glimmer3/glimmer_knowlegde-based/0.2	2019-02-01	2
toolshed.g2.bx.psu.edu/repos/iuc/gemini_burden/gemini_burden/0.20.1	2019-02-01	2
toolshed.g2.bx.psu.edu/repos/iuc/gemini_comp_hets/gemini_comp_hets/0.18.1.0	2019-02-01	2
toolshed.g2.bx.psu.edu/repos/bgruening/graphmap_align/graphmap_align/0.5.2	2019-02-01	2
toolshed.g2.bx.psu.edu/repos/iuc/gemini_de_novo/gemini_de_novo/0.18.1.0	2019-02-01	2
toolshed.g2.bx.psu.edu/repos/iuc/mothur_taxonomy_to_krona/mothur_taxonomy_to_krona/1.0	2019-02-01	2
toolshed.g2.bx.psu.edu/repos/peterjc/tmhmm_and_signalp/wolf_psort/0.0.11	2019-02-01	2
toolshed.g2.bx.psu.edu/repos/devteam/vcfselectsamples/vcfselectsamples/1.0.0_rc1+galaxy0	2019-02-01	2
toolshed.g2.bx.psu.edu/repos/devteam/vcfleftalign/vcfleftalign/1.0.0_rc1+galaxy0	2019-02-01	2
toolshed.g2.bx.psu.edu/repos/peterjc/tmhmm_and_signalp/signalp3/0.0.12	2019-02-01	2
CONVERTER_sam_to_unsorted_bam	2019-02-01	2
bed_to_bigBed	2019-02-01	2
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_targetedfileconverter/TargetedFileConverter/2.3.0	2019-02-01	2
toolshed.g2.bx.psu.edu/repos/peterjc/tmhmm_and_signalp/promoter2/0.0.12	2019-02-01	2
toolshed.g2.bx.psu.edu/repos/peterjc/seq_filter_by_mapping/seq_filter_by_mapping/0.0.6	2019-02-01	2
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_fileinfo/FileInfo/2.2.0	2019-02-01	2
toolshed.g2.bx.psu.edu/repos/devteam/vcfgeno2haplo/vcfgeno2haplo/1.0.0_rc1+galaxy0	2019-02-01	2
toolshed.g2.bx.psu.edu/repos/iuc/gemini_load/gemini_load/0.18.1.1	2019-02-01	2
toolshed.g2.bx.psu.edu/repos/peterjc/seq_composition/seq_composition/0.0.5	2019-02-01	2
toolshed.g2.bx.psu.edu/repos/iuc/gemini_lof_sieve/gemini_lof_sieve/0.20.1	2019-02-01	2
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicfindtads/hicexplorer_hicfindtads/2.1.2.0	2019-02-01	2
toolshed.g2.bx.psu.edu/repos/iuc/gemini_recessive_and_dominant/gemini_recessive_and_dominant/0.18.1.0	2019-02-01	2
Count1	2019-02-01	2
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_xtandemadapter/XTandemAdapter/2.2.0.1	2019-02-01	2
toolshed.g2.bx.psu.edu/repos/devteam/kraken2tax/Kraken2Tax/1.2	2019-02-01	2
toolshed.g2.bx.psu.edu/repos/devteam/vcffilter/vcffilter2/0.0.3	2019-02-01	2
toolshed.g2.bx.psu.edu/repos/galaxyp/msconvert/msconvert_win/3.0.0	2019-02-01	2
__DATA_FETCH__	2019-02-01	2
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_annotatebed/2.27.0.0	2019-02-01	2
toolshed.g2.bx.psu.edu/repos/iuc/goseq/goseq/1.32.0	2019-02-01	2
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicplottads/hicexplorer_hicplottads/2.1.2.0	2019-02-01	2
toolshed.g2.bx.psu.edu/repos/iuc/goslimmer/goslimmer/1.0.1	2019-02-01	2
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/1.136.0	2019-02-01	2
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FilterSamReads/2.18.2.1	2019-02-01	2
toolshed.g2.bx.psu.edu/repos/crs4/edena/edena_ovl_wrapper/0.3	2019-02-01	2
toolshed.g2.bx.psu.edu/repos/bonsai/sortmerna/sortmerna_wrapper/1.0	2019-02-01	2
toolshed.g2.bx.psu.edu/repos/blankenberg/naive_variant_caller/naive_variant_caller/0.0.3	2019-02-01	2
toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_bam_stat/2.6.4	2019-02-01	2
toolshed.g2.bx.psu.edu/repos/blankenberg/naive_variant_caller/naive_variant_caller/0.0.1	2019-02-01	2
toolshed.g2.bx.psu.edu/repos/bgruening/wtdbg/wtdbg/1.2.8.1	2019-02-01	2
toolshed.g2.bx.psu.edu/repos/devteam/vcf2tsv/vcf2tsv/1.0.0_rc1+galaxy0	2019-02-01	2
toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/blastxml_to_tabular/0.3.1	2019-02-01	2
toolshed.g2.bx.psu.edu/repos/iuc/humann2_renorm_table/humann2_renorm_table/0.11.1.0	2019-02-01	2
toolshed.g2.bx.psu.edu/repos/iuc/idba_ud/idba_ud/1.1.3	2019-02-01	2
nn_classifier	2019-02-01	2
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_featurefindermrm/FeatureFinderMRM/2.3.0	2019-02-01	2
toolshed.g2.bx.psu.edu/repos/bgruening/openbabel/ctb_ob_genProp/1.0	2019-02-01	2
toolshed.g2.bx.psu.edu/repos/iuc/trinity_define_clusters_by_cutting_tree/trinity_define_clusters_by_cutting_tree/2.8.4	2019-02-01	2
toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_genprop/openbabel_genProp/2.4.1.0	2019-02-01	2
toolshed.g2.bx.psu.edu/repos/iuc/trinity_filter_low_expr_transcripts/trinity_filter_low_expr_transcripts/2.8.4	2019-02-01	2
toolshed.g2.bx.psu.edu/repos/iuc/mothur_get_groups/mothur_get_groups/1.39.5.0	2019-02-01	2
__EXTRACT_DATASET__	2019-02-01	2
Extract_features1	2019-02-01	2
toolshed.g2.bx.psu.edu/repos/imgteam/wsi_extract_top_view/ip_wsi_extract_top_view/0.1	2019-02-01	2
toolshed.g2.bx.psu.edu/repos/imgteam/split_labelmap/ip_split_labelmap/0.1	2019-02-01	2
toolshed.g2.bx.psu.edu/repos/iuc/trinity_run_de_analysis/trinity_run_de_analysis/2.8.4	2019-02-01	2
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toolshed.g2.bx.psu.edu/repos/iuc/trinity_samples_qccheck/trinity_samples_qccheck/2.8.4	2019-02-01	2
toolshed.g2.bx.psu.edu/repos/imgteam/mergeneighboursinlabelimage/ip_merge_neighbours_in_label/0.2	2019-02-01	2
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CleanSam/1.136.0	2019-02-01	2
toolshed.g2.bx.psu.edu/repos/galaxyp/quantp/quantp/1.1.2	2019-02-01	2
toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_predictd/2.1.1.20160309.0	2019-02-01	2
toolshed.g2.bx.psu.edu/repos/imgteam/binary2labelimage/ip_binary_to_labelimage/0.2	2019-02-01	2
toolshed.g2.bx.psu.edu/repos/imgteam/2d_simple_filter/ip_filter_standard/0.0.2	2019-02-01	2
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toolshed.g2.bx.psu.edu/repos/iuc/mageck_gsea/mageck_gsea/0.5.8	2019-02-01	2
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_falsediscoveryrate/FalseDiscoveryRate/2.2.0	2019-02-01	2
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toolshed.g2.bx.psu.edu/repos/guru-ananda/karyotype_plot/karyotype_Plot_1/1.0.0	2019-02-01	2
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.2	2019-02-01	2
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toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.0	2019-02-01	2
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toolshed.g2.bx.psu.edu/repos/jjohnson/cdhit/cd_hit_est/1.2	2019-02-01	2
toolshed.g2.bx.psu.edu/repos/iuc/vsearch/vsearch_sorting/2.8.3.0	2019-02-01	2
toolshed.g2.bx.psu.edu/repos/iuc/vsearch/vsearch_alignment/2.8.3.0	2019-02-01	2
toolshed.g2.bx.psu.edu/repos/galaxyp/unipept/unipept/2.0.1	2019-02-01	2
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toolshed.g2.bx.psu.edu/repos/iuc/disco/disco/1.2.0	2019-02-01	1
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toolshed.g2.bx.psu.edu/repos/iuc/heinz/heinz_scoring/1.0	2019-02-01	1
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toolshed.g2.bx.psu.edu/repos/iuc/heinz/heinz/1.0	2019-02-01	1
toolshed.g2.bx.psu.edu/repos/anton/vcfvcfintersect/vcfvcfintersect/0.0.2	2019-02-01	1
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toolshed.g2.bx.psu.edu/repos/devteam/basecoverage/gops_basecoverage_1/1.0.0	2019-02-01	1
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toolshed.g2.bx.psu.edu/repos/iuc/gemini_pathways/gemini_pathways/0.20.1	2019-02-01	1
toolshed.g2.bx.psu.edu/repos/peterjc/sample_seqs/sample_seqs/0.2.5	2019-02-01	1
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toolshed.g2.bx.psu.edu/repos/peterjc/blast2go/blast2go/0.0.8	2019-02-01	1
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_coverage/deeptools_plot_coverage/3.0.2.0	2019-02-01	1
toolshed.g2.bx.psu.edu/repos/iuc/stacks_refmap/stacks_refmap/1.46.0	2019-02-01	1
toolshed.g2.bx.psu.edu/repos/iuc/gemini_gene_wise/gemini_gene_wise/0.20.1	2019-02-01	1
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toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/search_gui/3.2.11	2019-02-01	1
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toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_filterdup/2.1.1.20160309.0	2019-02-01	1
toolshed.g2.bx.psu.edu/repos/devteam/vcf_filter/vcf_filter/1.0.0	2019-02-01	1
toolshed.g2.bx.psu.edu/repos/devteam/vcfcommonsamples/vcfcommonsamples/1.0.0_rc1+galaxy0	2019-02-01	1
toolshed.g2.bx.psu.edu/repos/iuc/mothur_remove_groups/mothur_remove_groups/1.39.5.0	2019-02-01	1
toolshed.g2.bx.psu.edu/repos/devteam/fasta_concatenate_by_species/fasta_concatenate0/0.0.0	2019-02-01	1
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toolshed.g2.bx.psu.edu/repos/devteam/vcfgenotypes/vcfgenotypes/1.0.0_rc1+galaxy0	2019-02-01	1
toolshed.g2.bx.psu.edu/repos/iuc/valet/valet/1.0.0	2019-02-01	1
toolshed.g2.bx.psu.edu/repos/devteam/bowtie_wrappers/bowtie_wrapper/1.1.3	2019-02-01	1
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toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/search_gui/3.2.13.1	2019-02-01	1
toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.16.5	2019-02-01	1
toolshed.g2.bx.psu.edu/repos/iuc/mageck_count/mageck_count/0.5.8.4	2019-02-01	1
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toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.20.7.0	2019-02-01	1
toolshed.g2.bx.psu.edu/repos/devteam/samtools_rmdup/samtools_rmdup/2.0	2019-02-01	1
toolshed.g2.bx.psu.edu/repos/devteam/fastq_trimmer/fastq_trimmer/1.0.0	2019-02-01	1
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toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fastq/tabular_to_fastq/1.1.1	2019-02-01	1
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toolshed.g2.bx.psu.edu/repos/iuc/gemini_fusions/gemini_fusions/0.20.1	2019-02-01	1
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toolshed.g2.bx.psu.edu/repos/devteam/join/gops_join_1/1.0.0	2019-01-01	242
toolshed.g2.bx.psu.edu/repos/rnateam/chipseeker/chipseeker/1.16.2	2019-01-01	215
toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.7	2019-01-01	209
toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_preprocessing/cardinal_preprocessing/1.12.1.1	2019-01-01	209
toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.36.0	2019-01-01	205
toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.6.0	2019-01-01	203
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.1	2019-01-01	200
toolshed.g2.bx.psu.edu/repos/devteam/merge/gops_merge_1/1.0.0	2019-01-01	187
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_fileinfo/FileInfo/2.3.0	2019-01-01	186
toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.1.0	2019-01-01	185
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/1.1.0	2019-01-01	177
CONVERTER_interval_to_bedstrict_0	2019-01-01	176
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_correlation/deeptools_plot_correlation/3.0.2.0	2019-01-01	174
toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/0.0.2	2019-01-01	172
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_falsediscoveryrate/FalseDiscoveryRate/2.3.0	2019-01-01	166
toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/4.6.3	2019-01-01	164
toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_bam2wig/2.6.4	2019-01-01	163
toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.2	2019-01-01	162
toolshed.g2.bx.psu.edu/repos/nml/spades/spades/3.12.0+galaxy1	2019-01-01	160
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_textexporter/TextExporter/2.3.0	2019-01-01	159
toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.1.0+galaxy4	2019-01-01	153
toolshed.g2.bx.psu.edu/repos/devteam/vcfallelicprimitives/vcfallelicprimitives/1.0.0_rc1+galaxy0	2019-01-01	152
CONVERTER_fastq_to_fqtoc0	2019-01-01	151
toolshed.g2.bx.psu.edu/repos/devteam/macs/peakcalling_macs/1.0.1	2019-01-01	149
wig_to_bigWig	2019-01-01	148
toolshed.g2.bx.psu.edu/repos/iuc/abricate/abricate/0.8	2019-01-01	147
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idfilter/IDFilter/2.3.0	2019-01-01	146
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_mztabexporter/MzTabExporter/2.3.0	2019-01-01	144
toolshed.g2.bx.psu.edu/repos/devteam/vcfbedintersect/vcfbedintersect/0.0.3	2019-01-01	144
Grouping1	2019-01-01	143
toolshed.g2.bx.psu.edu/repos/iuc/pilon/pilon/1.20.1	2019-01-01	143
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_peptideindexer/PeptideIndexer/2.3.0	2019-01-01	141
cat1	2019-01-01	140
toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.5	2019-01-01	134
toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_build_pipeline/sklearn_build_pipeline/1.0	2019-01-01	133
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_annotatebed/2.27.0.0	2019-01-01	130
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_xtandemadapter/XTandemAdapter/2.3.0	2019-01-01	128
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SortSam/2.18.2.1	2019-01-01	125
toolshed.g2.bx.psu.edu/repos/devteam/intersect/gops_intersect_1/1.0.0	2019-01-01	122
toolshed.g2.bx.psu.edu/repos/galaxyp/maldi_quant_peak_detection/maldi_quant_peak_detection/1.18.0.2	2019-01-01	121
toolshed.g2.bx.psu.edu/repos/devteam/get_flanks/get_flanks1/1.0.0	2019-01-01	121
toolshed.g2.bx.psu.edu/repos/iuc/filtlong/filtlong/0.2.0	2019-01-01	120
toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_infer_experiment/2.6.4.1	2019-01-01	120
toolshed.g2.bx.psu.edu/repos/crs4/bwa_mem/bwa_mem/0.8.0	2019-01-01	116
toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/1.5.3	2019-01-01	115
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectRnaSeqMetrics/2.18.2.1	2019-01-01	115
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/1.1.0	2019-01-01	114
toolshed.g2.bx.psu.edu/repos/iuc/gemini_query/gemini_query/0.20.1	2019-01-01	111
CONVERTER_bam_to_coodinate_sorted_bam	2019-01-01	110
comp1	2019-01-01	108
toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3r.1	2019-01-01	106
toolshed.g2.bx.psu.edu/repos/iuc/pygenometracks/pygenomeTracks/2.0.1	2019-01-01	106
toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_searchcv/sklearn_searchcv/0.9	2019-01-01	105
toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.22.5	2019-01-01	104
toolshed.g2.bx.psu.edu/repos/iuc/ngsutils_bam_filter/ngsutils_bam_filter/0.5.9	2019-01-01	103
barchart_gnuplot	2019-01-01	103
toolshed.g2.bx.psu.edu/repos/devteam/fastq_to_fasta/cshl_fastq_to_fasta/1.0.0	2019-01-01	100
__BUILD_LIST__	2019-01-01	100
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2	2019-01-01	98
toolshed.g2.bx.psu.edu/repos/iuc/prinseq/prinseq/0.20.4	2019-01-01	96
toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3+t.galaxy0	2019-01-01	95
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_mergebed/2.27.1	2019-01-01	94
toolshed.g2.bx.psu.edu/repos/simon-gladman/velvetoptimiser/velvetoptimiser/2.2.6	2019-01-01	93
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1	2019-01-01	89
toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_filtering/cardinal_filtering/1.12.1.1	2019-01-01	86
toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.3.1	2019-01-01	86
toolshed.g2.bx.psu.edu/repos/devteam/samtools_slice_bam/samtools_slice_bam/2.0.1	2019-01-01	85
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_mergebed/2.27.0.0	2019-01-01	83
toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.13.0	2019-01-01	83
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeSamFiles/2.18.2.1	2019-01-01	81
toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0.2	2019-01-01	80
toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/3.2+galaxy1	2019-01-01	79
toolshed.g2.bx.psu.edu/repos/devteam/vcffilter/vcffilter2/1.0.0_rc1+galaxy2	2019-01-01	78
toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_heatmap2/ggplot2_heatmap2/2.2.1+galaxy1	2019-01-01	77
toolshed.g2.bx.psu.edu/repos/devteam/tophat2/tophat2/2.1.1	2019-01-01	77
toolshed.g2.bx.psu.edu/repos/iuc/mothur_summary_seqs/mothur_summary_seqs/1.39.5.0	2019-01-01	76
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.27.0.0	2019-01-01	76
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toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.20.7.2	2019-01-01	74
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicplotmatrix/hicexplorer_hicplotmatrix/2.1.4.0	2019-01-01	74
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectInsertSizeMetrics/2.18.2.1	2019-01-01	74
toolshed.g2.bx.psu.edu/repos/iuc/roary/roary/3.10.2	2019-01-01	70
toolshed.g2.bx.psu.edu/repos/galaxyp/msi_filtering/mass_spectrometry_imaging_filtering/1.10.0.6	2019-01-01	66
toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_download/4.3r.1	2019-01-01	66
toolshed.g2.bx.psu.edu/repos/bgruening/pileometh/pileometh/0.3.0.1	2019-01-01	66
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed/2.27.1	2019-01-01	66
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_compare/deeptools_bam_compare/3.0.2.0	2019-01-01	65
toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/search_gui/3.3.3.0	2019-01-01	65
toolshed.g2.bx.psu.edu/repos/devteam/fastqtofasta/fastq_to_fasta_python/1.0.0	2019-01-01	64
toolshed.g2.bx.psu.edu/repos/iuc/gtftobed12/gtftobed12/357	2019-01-01	64
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CASM/2.18.2.1	2019-01-01	63
toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_annotate/4.3+t.galaxy0	2019-01-01	63
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bam_summary/deeptools_multi_bam_summary/3.0.2.0	2019-01-01	63
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bigwig_summary/deeptools_multi_bigwig_summary/3.0.2.0	2019-01-01	63
toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.3	2019-01-01	62
toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastp_wrapper/0.3.1	2019-01-01	60
toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_data_exporter/cardinal_data_exporter/1.12.1.0	2019-01-01	60
toolshed.g2.bx.psu.edu/repos/devteam/fastq_quality_filter/cshl_fastq_quality_filter/1.0.2	2019-01-01	60
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.27.0.1	2019-01-01	59
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.27.0.0	2019-01-01	57
toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/0.11.2	2019-01-01	57
toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.69	2019-01-01	56
toolshed.g2.bx.psu.edu/repos/iuc/metaphlan2/metaphlan2/2.6.0.0	2019-01-01	54
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/1.1.0	2019-01-01	54
toolshed.g2.bx.psu.edu/repos/peterjc/seq_filter_by_id/seq_filter_by_id/0.2.7	2019-01-01	53
toolshed.g2.bx.psu.edu/repos/devteam/fastx_trimmer/cshl_fastx_trimmer/1.0.2	2019-01-01	53
toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy1	2019-01-01	53
toolshed.g2.bx.psu.edu/repos/devteam/bam_to_sam/bam_to_sam/2.0.1	2019-01-01	53
toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.0.2	2019-01-01	53
toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.0	2019-01-01	52
toolshed.g2.bx.psu.edu/repos/devteam/sam_merge/sam_merge2/1.2.0	2019-01-01	52
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.7.1.1	2019-01-01	52
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.0	2019-01-01	51
toolshed.g2.bx.psu.edu/repos/iuc/mothur_screen_seqs/mothur_screen_seqs/1.39.5.0	2019-01-01	51
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toolshed.g2.bx.psu.edu/repos/iuc/hmmer3/hmmer_hmmbuild/0.1.0	2019-01-01	49
toolshed.g2.bx.psu.edu/repos/iuc/hmmer3/hmmer_hmmsearch/0.1.0	2019-01-01	48
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.0	2019-01-01	48
toolshed.g2.bx.psu.edu/repos/iuc/goseq/goseq/1.30.1	2019-01-01	48
toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_makeblastdb/0.3.1	2019-01-01	48
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.0	2019-01-01	48
toolshed.g2.bx.psu.edu/repos/iuc/mothur_unique_seqs/mothur_unique_seqs/1.39.5.0	2019-01-01	47
toolshed.g2.bx.psu.edu/repos/devteam/add_value/addValue/1.0.0	2019-01-01	47
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bigwig_compare/deeptools_bigwig_compare/3.0.2.0	2019-01-01	46
toolshed.g2.bx.psu.edu/repos/iuc/deg_annotate/deg_annotate/1.0	2019-01-01	45
toolshed.g2.bx.psu.edu/repos/devteam/fasta_filter_by_length/fasta_filter_by_length/1.1	2019-01-01	45
toolshed.g2.bx.psu.edu/repos/iuc/trinity_align_and_estimate_abundance/trinity_align_and_estimate_abundance/2.8.4	2019-01-01	45
toolshed.g2.bx.psu.edu/repos/iuc/varscan_somatic/varscan_somatic/2.4.3.3	2019-01-01	45
Grep1	2019-01-01	44
CONVERTER_bed_gff_or_vcf_to_bigwig_0	2019-01-01	43
toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_filtering/cardinal_filtering/1.12.1.0	2019-01-01	43
toolshed.g2.bx.psu.edu/repos/wolma/mimodd_main/mimodd_vcf_filter/0.1.8_1	2019-01-01	43
toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/0.5.3.2	2019-01-01	43
CONVERTER_fasta_to_tabular	2019-01-01	42
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.2	2019-01-01	42
toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_combine/cardinal_combine/1.12.1.0	2019-01-01	42
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toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicplottads/hicexplorer_hicplottads/2.1.4.0	2019-01-01	41
toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/peptide_shaker/1.16.26	2019-01-01	41
toolshed.g2.bx.psu.edu/repos/iuc/mothur_filter_seqs/mothur_filter_seqs/1.39.5.0	2019-01-01	41
toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.1	2019-01-01	41
ia_coordinates_of_roi	2019-01-01	41
toolshed.g2.bx.psu.edu/repos/devteam/samtools_bedcov/samtools_bedcov/2.0.1	2019-01-01	40
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_uniq_tool/1.1.1	2019-01-01	39
toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/1.6.2	2019-01-01	39
toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.5.0.1	2019-01-01	39
toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.1.4	2019-01-01	39
toolshed.g2.bx.psu.edu/repos/devteam/picard/rgPicardMarkDups/1.56.0	2019-01-01	39
toolshed.g2.bx.psu.edu/repos/iuc/gemini_load/gemini_load/0.20.1	2019-01-01	39
toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.39	2019-01-01	38
toolshed.g2.bx.psu.edu/repos/devteam/fastq_filter/fastq_filter/1.1.1	2019-01-01	37
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mergeCols1	2019-01-01	36
toolshed.g2.bx.psu.edu/repos/galaxyp/fasta_merge_files_and_filter_unique_sequences/fasta_merge_files_and_filter_unique_sequences/1.2.0	2019-01-01	36
toolshed.g2.bx.psu.edu/repos/devteam/fastx_artifacts_filter/cshl_fastx_artifacts_filter/1.0.0	2019-01-01	36
toolshed.g2.bx.psu.edu/repos/jjohnson/samtools_filter/samtools_filter/1.1.1	2019-01-01	36
toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.0	2019-01-01	36
toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.1.0	2019-01-01	36
toolshed.g2.bx.psu.edu/repos/rnateam/metilene/metilene/0.2.6.1	2019-01-01	35
toolshed.g2.bx.psu.edu/repos/iuc/qiime_core_diversity/qiime_core_diversity/1.9.1.0	2019-01-01	35
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toolshed.g2.bx.psu.edu/repos/iuc/transdecoder/transdecoder/3.0.1	2019-01-01	35
toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_mz_images/cardinal_mz_images/1.12.1.1	2019-01-01	35
toolshed.g2.bx.psu.edu/repos/iuc/mothur_cluster_split/mothur_cluster_split/1.39.5.0	2019-01-01	35
toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie_merge/1.3.4	2019-01-01	35
toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_segmentations/cardinal_segmentations/1.12.1.1	2019-01-01	34
toolshed.g2.bx.psu.edu/repos/iuc/gatk2/gatk2_realigner_target_creator/2.8.0	2019-01-01	33
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toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.19.5	2019-01-01	33
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toolshed.g2.bx.psu.edu/repos/iuc/qiime_assign_taxonomy/qiime_assign_taxonomy/1.9.1.0	2019-01-01	32
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_groupbybed/2.27.1	2019-01-01	32
toolshed.g2.bx.psu.edu/repos/devteam/samtools_calmd/samtools_calmd/2.0.2	2019-01-01	32
toolshed.g2.bx.psu.edu/repos/devteam/sam2interval/sam2interval/1.0.1	2019-01-01	32
toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.0.0	2019-01-01	32
toolshed.g2.bx.psu.edu/repos/iuc/qiime_split_libraries_fastq/qiime_split_libraries_fastq/1.9.1.0	2019-01-01	32
toolshed.g2.bx.psu.edu/repos/bgruening/bigwig_to_bedgraph/bigwig_to_bedgraph/0.1.0	2019-01-01	32
toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_shared/mothur_make_shared/1.39.5.0	2019-01-01	31
aggregate_scores_in_intervals2	2019-01-01	31
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_profile/deeptools_plot_profile/3.0.2.0	2019-01-01	31
toolshed.g2.bx.psu.edu/repos/devteam/xy_plot/XY_Plot_1/1.0.2	2019-01-01	31
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hiccorrectmatrix/hicexplorer_hiccorrectmatrix/2.1.4.0	2019-01-01	31
toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.1.3	2019-01-01	30
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.1	2019-01-01	30
toolshed.g2.bx.psu.edu/repos/bebatut/combine_metaphlan2_humann2/combine_metaphlan2_humann2/0.1.0	2019-01-01	30
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddOrReplaceReadGroups/2.18.2.1	2019-01-01	30
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectWgsMetrics/2.18.2.1	2019-01-01	30
toolshed.g2.bx.psu.edu/repos/bgruening/unique/bg_uniq/0.3	2019-01-01	30
toolshed.g2.bx.psu.edu/repos/iuc/mothur_align_seqs/mothur_align_seqs/1.39.5.0	2019-01-01	30
toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_spectra_plots/cardinal_spectra_plots/1.12.1.1	2019-01-01	30
toolshed.g2.bx.psu.edu/repos/bgruening/plotly_regression_performance_plots/plotly_regression_performance_plots/0.1	2019-01-01	29
toolshed.g2.bx.psu.edu/repos/galaxyp/thermo_raw_file_converter/thermo_raw_file_converter/0.0.1	2019-01-01	29
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_msgfplusadapter/MSGFPlusAdapter/2.3.0	2019-01-01	29
toolshed.g2.bx.psu.edu/repos/bgruening/graphicsmagick_image_convert/graphicsmagick_image_convert/1.3.26	2019-01-01	29
toolshed.g2.bx.psu.edu/repos/devteam/merge_cols/mergeCols1/1.0.1	2019-01-01	29
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1	2019-01-01	29
ip_projective_transformation_points	2019-01-01	29
toolshed.g2.bx.psu.edu/repos/iuc/mothur_classify_otu/mothur_classify_otu/1.39.5.0	2019-01-01	28
toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.12.5+galaxy2	2019-01-01	28
toolshed.g2.bx.psu.edu/repos/devteam/picard/rgPicFixMate/1.56.0	2019-01-01	28
toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.0.2.29-1	2019-01-01	28
toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_joiner/fastq_paired_end_joiner/2.0.1.1	2019-01-01	27
toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/2.2.1.2	2019-01-01	27
toolshed.g2.bx.psu.edu/repos/iuc/tsne/tsne/0.0.2	2019-01-01	27
__MERGE_COLLECTION__	2019-01-01	27
toolshed.g2.bx.psu.edu/repos/iuc/extract_genomic_dna/Extract genomic DNA 1/3.0.3	2019-01-01	27
toolshed.g2.bx.psu.edu/repos/devteam/varscan_version_2/varscan/2.4.2	2019-01-01	27
toolshed.g2.bx.psu.edu/repos/iuc/mothur_count_seqs/mothur_count_seqs/1.39.5.0	2019-01-01	27
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicbuildmatrix/hicexplorer_hicbuildmatrix/2.1.4.0	2019-01-01	26
toolshed.g2.bx.psu.edu/repos/iuc/qiime_pick_open_reference_otus/qiime_pick_open_reference_otus/1.9.1.0	2019-01-01	26
toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.0	2019-01-01	26
toolshed.g2.bx.psu.edu/repos/devteam/cluster/gops_cluster_1/1.0.0	2019-01-01	26
toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/0.5.3.2	2019-01-01	26
toolshed.g2.bx.psu.edu/repos/bgruening/plotly_parallel_coordinates_plot/plotly_parallel_coordinates_plot/0.1	2019-01-01	26
toolshed.g2.bx.psu.edu/repos/devteam/subtract/gops_subtract_1/1.0.0	2019-01-01	26
toolshed.g2.bx.psu.edu/repos/iuc/gatk2/gatk2_indel_realigner/2.8.0	2019-01-01	26
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_multijoin_tool/1.1.1	2019-01-01	25
CONVERTER_bedgraph_to_bigwig	2019-01-01	25
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idmerger/IDMerger/2.3.0	2019-01-01	25
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed_bedgraph/2.19.0	2019-01-01	25
toolshed.g2.bx.psu.edu/repos/galaxyp/msi_qualitycontrol/mass_spectrometry_imaging_qc/1.10.0.7	2019-01-01	25
toolshed.g2.bx.psu.edu/repos/bgruening/antismash/antismash/4.1	2019-01-01	25
toolshed.g2.bx.psu.edu/repos/iuc/humann2/humann2/0.11.1.0	2019-01-01	25
toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_heatmap/ggplot2_heatmap/2.2.1	2019-01-01	24
toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.65	2019-01-01	24
toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.6	2019-01-01	24
toolshed.g2.bx.psu.edu/repos/iuc/mothur_pre_cluster/mothur_pre_cluster/1.39.5.0	2019-01-01	24
toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.2	2019-01-01	24
CONVERTER_bed_to_gff_0	2019-01-01	24
toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.36.4	2019-01-01	24
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix_operations/deeptools_compute_matrix_operations/3.0.2.0	2019-01-01	24
toolshed.g2.bx.psu.edu/repos/iuc/mothur_remove_lineage/mothur_remove_lineage/1.39.5.0	2019-01-01	24
scale_image	2019-01-01	24
viz_overlay_moving_and_fixed_image	2019-01-01	24
__UNZIP_COLLECTION__	2019-01-01	23
toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.5.2b-1	2019-01-01	23
toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0	2019-01-01	23
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_pe_fragmentsize/deeptools_bam_pe_fragmentsize/3.0.2.0	2019-01-01	23
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtofastq/2.27.0.0	2019-01-01	23
toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.6.1.1	2019-01-01	23
toolshed.g2.bx.psu.edu/repos/nml/metaspades/metaspades/3.9.0	2019-01-01	22
toolshed.g2.bx.psu.edu/repos/wolma/mimodd_main/mimodd_varreport/0.1.8_1	2019-01-01	22
toolshed.g2.bx.psu.edu/repos/iuc/gemini_inheritance/gemini_inheritance/0.20.1	2019-01-01	22
CONVERTER_fasta_to_fai	2019-01-01	22
toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/2.0.0	2019-01-01	21
toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/1.0.1	2019-01-01	21
toolshed.g2.bx.psu.edu/repos/devteam/vcfcombine/vcfcombine/1.0.0_rc1+galaxy0	2019-01-01	21
toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.4.2	2019-01-01	21
toolshed.g2.bx.psu.edu/repos/iuc/mothur_classify_seqs/mothur_classify_seqs/1.39.5.0	2019-01-01	21
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_fidoadapter/FidoAdapter/2.3.0	2019-01-01	21
toolshed.g2.bx.psu.edu/repos/bebatut/format_metaphlan2_output/format_metaphlan2_output/0.1.0	2019-01-01	21
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idscoreswitcher/IDScoreSwitcher/2.3.0	2019-01-01	21
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idposteriorerrorprobability/IDPosteriorErrorProbability/2.3.0	2019-01-01	21
toolshed.g2.bx.psu.edu/repos/iuc/metaphlan2krona/metaphlan2krona/2.6.0.0	2019-01-01	20
toolshed.g2.bx.psu.edu/repos/iuc/gemini_db_info/gemini_db_info/0.20.1	2019-01-01	20
toolshed.g2.bx.psu.edu/repos/devteam/scatterplot/scatterplot_rpy/1.0.3	2019-01-01	20
Convert characters1	2019-01-01	20
toolshed.g2.bx.psu.edu/repos/rnateam/blockclust/blockclust/1.1.0	2019-01-01	20
toolshed.g2.bx.psu.edu/repos/iuc/charts/charts/1.0.1	2019-01-01	20
toolshed.g2.bx.psu.edu/repos/iuc/trinity/trinity/2.8.4	2019-01-01	20
toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.5.2b-2	2019-01-01	20
toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastx_wrapper/0.3.1	2019-01-01	20
toolshed.g2.bx.psu.edu/repos/bgruening/interproscan5/interproscan/5.0.0	2019-01-01	20
toolshed.g2.bx.psu.edu/repos/iuc/mothur_rarefaction_single/mothur_rarefaction_single/1.39.5.0	2019-01-01	19
toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpSift_annotate/3.4	2019-01-01	19
toolshed.g2.bx.psu.edu/repos/iuc/raceid_inspectclusters/raceid_inspectclusters/3.0.2.1	2019-01-01	19
toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_violin/ggplot2_violin/2.2.1+galaxy0	2019-01-01	19
toolshed.g2.bx.psu.edu/repos/iuc/bwameth/bwameth/0.2.0.4	2019-01-01	19
toolshed.g2.bx.psu.edu/repos/galaxyp/filter_by_fasta_ids/filter_by_fasta_ids/2.0	2019-01-01	19
toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.34.9.9	2019-01-01	18
toolshed.g2.bx.psu.edu/repos/bgruening/join_files_on_column_fuzzy/join_files_on_column_fuzzy/1.0.1	2019-01-01	18
toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_splitter/fastq_paired_end_splitter/1.1.1	2019-01-01	18
CONVERTER_ref_to_seq_taxomony	2019-01-01	18
toolshed.g2.bx.psu.edu/repos/bgruening/canu/canu/1.7	2019-01-01	18
toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_interlacer/fastq_paired_end_interlacer/1.2.0.1	2019-01-01	18
toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.1.1.20160309.4	2019-01-01	18
toolshed.g2.bx.psu.edu/repos/iuc/mothur_chimera_vsearch/mothur_chimera_vsearch/1.39.5.1	2019-01-01	18
toolshed.g2.bx.psu.edu/repos/peterjc/mira_assembler/mira_assembler/0.0.11	2019-01-01	18
toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_generalized_linear/sklearn_generalized_linear/1.0	2019-01-01	18
toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy1	2019-01-01	18
toolshed.g2.bx.psu.edu/repos/peterjc/blast_rbh/blast_reciprocal_best_hits/0.1.11	2019-01-01	18
toolshed.g2.bx.psu.edu/repos/bebatut/cdhit/cd_hit_est/1.3	2019-01-01	18
toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/2.2.1+galaxy0	2019-01-01	18
toolshed.g2.bx.psu.edu/repos/kellrott/regex_replace/regex_replace/1.0.0	2019-01-01	18
toolshed.g2.bx.psu.edu/repos/devteam/fastx_quality_statistics/cshl_fastx_quality_statistics/1.0.0	2019-01-01	18
toolshed.g2.bx.psu.edu/repos/iuc/shovill/shovill/1.0.4	2019-01-01	17
toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.36.5	2019-01-01	17
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SamToFastq/2.18.2.1	2019-01-01	17
toolshed.g2.bx.psu.edu/repos/devteam/bowtie_wrappers/bowtie_wrapper/1.2.0	2019-01-01	17
toolshed.g2.bx.psu.edu/repos/bgruening/diamond/bg_diamond/0.8.24.1	2019-01-01	17
toolshed.g2.bx.psu.edu/repos/bgruening/graphmap_align/graphmap_align/0.5.2	2019-01-01	17
toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_RPKM_count/2.4	2019-01-01	17
toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/2.4.0	2019-01-01	17
toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_get_chr_names/4.3+T.galaxy1	2019-01-01	17
toolshed.g2.bx.psu.edu/repos/iuc/raceid_clustering/raceid_clustering/3.0.2.1	2019-01-01	17
toolshed.g2.bx.psu.edu/repos/iuc/mothur_remove_seqs/mothur_remove_seqs/1.36.1.0	2019-01-01	17
toolshed.g2.bx.psu.edu/repos/iuc/mageck_mle/mageck_mle/0.5.8.1	2019-01-01	16
toolshed.g2.bx.psu.edu/repos/devteam/fastq_to_fasta/cshl_fastq_to_fasta/1.0.2	2019-01-01	16
toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.0.3	2019-01-01	16
toolshed.g2.bx.psu.edu/repos/iuc/qiime_pick_closed_reference_otus/qiime_pick_closed_reference_otus/1.9.1.0	2019-01-01	16
toolshed.g2.bx.psu.edu/repos/iuc/mothur_taxonomy_to_krona/mothur_taxonomy_to_krona/1.0	2019-01-01	16
toolshed.g2.bx.psu.edu/repos/iuc/mothur_dist_seqs/mothur_dist_seqs/1.39.5.0	2019-01-01	16
random_lines1	2019-01-01	16
toolshed.g2.bx.psu.edu/repos/bebatut/group_humann2_uniref_abundances_to_go/group_humann2_uniref_abundances_to_go/1.2.0	2019-01-01	16
ChangeCase	2019-01-01	15
toolshed.g2.bx.psu.edu/repos/iuc/qiime_pick_otus/qiime_pick_otus/1.9.1.0	2019-01-01	15
toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.1.0	2019-01-01	15
toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2	2019-01-01	15
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicfindtads/hicexplorer_hicfindtads/2.1.4.0	2019-01-01	15
toolshed.g2.bx.psu.edu/repos/iuc/scpipe/scpipe/1.0.0	2019-01-01	15
toolshed.g2.bx.psu.edu/repos/devteam/histogram/histogram_rpy/1.0.3	2019-01-01	15
toolshed.g2.bx.psu.edu/repos/iuc/gemini_actionable_mutations/gemini_actionable_mutations/0.20.1	2019-01-01	15
toolshed.g2.bx.psu.edu/repos/iuc/humann2_genefamilies_genus_level/humann2_genefamilies_genus_level/0.11.1.0	2019-01-01	15
toolshed.g2.bx.psu.edu/repos/iuc/samtools_sort/samtools_sort/1.0.2	2019-01-01	15
wc_gnu	2019-01-01	15
toolshed.g2.bx.psu.edu/repos/iuc/megahit/megahit/1.1.2.3	2019-01-01	15
toolshed.g2.bx.psu.edu/repos/iuc/qiime_split_libraries/qiime_split_libraries/1.9.1.0	2019-01-01	15
toolshed.g2.bx.psu.edu/repos/peterjc/blastxml_to_top_descr/blastxml_to_top_descr/0.1.1	2019-01-01	14
toolshed.g2.bx.psu.edu/repos/peterjc/venn_list/venn_list/0.0.11	2019-01-01	14
toolshed.g2.bx.psu.edu/repos/bgruening/join_files_on_column_fuzzy/join_files_on_column_fuzzy/1.0.0	2019-01-01	14
re_he_maldi_image_registration	2019-01-01	14
toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_geneBody_coverage/2.6.4.3	2019-01-01	14
toolshed.g2.bx.psu.edu/repos/iuc/graphlan/graphlan/1.0.0.0	2019-01-01	14
toolshed.g2.bx.psu.edu/repos/iuc/fraggenescan/fraggenescan/1.30.0	2019-01-01	14
toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/2.8.1.3	2019-01-01	14
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_enrichment/deeptools_plot_enrichment/3.0.2.0	2019-01-01	14
toolshed.g2.bx.psu.edu/repos/iuc/raceid_filtnormconf/raceid_filtnormconf/3.0.2.1	2019-01-01	14
trimmer	2019-01-01	14
toolshed.g2.bx.psu.edu/repos/devteam/picard/PicardHsMetrics/1.56.0	2019-01-01	14
toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.6.1	2019-01-01	13
CONVERTER_bz2_to_uncompressed	2019-01-01	13
toolshed.g2.bx.psu.edu/repos/devteam/dna_filtering/histogram_rpy/1.0.3	2019-01-01	13
raceid_main	2019-01-01	13
toolshed.g2.bx.psu.edu/repos/galaxyp/dbbuilder/dbbuilder/0.3.0	2019-01-01	13
toolshed.g2.bx.psu.edu/repos/iuc/vt_variant_tools/vt_normalize/0.1.0	2019-01-01	13
toolshed.g2.bx.psu.edu/repos/iuc/vsearch/vsearch_dereplication/1.9.7.0	2019-01-01	13
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.1	2019-01-01	13
toolshed.g2.bx.psu.edu/repos/devteam/megablast_xml_parser/megablast_xml_parser/1.0.0	2019-01-01	13
toolshed.g2.bx.psu.edu/repos/iuc/export2graphlan/export2graphlan/0.19	2019-01-01	13
toolshed.g2.bx.psu.edu/repos/devteam/picard/PicardInsertSize/1.56.0	2019-01-01	13
toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_distribution/2.6.4.1	2019-01-01	13
toolshed.g2.bx.psu.edu/repos/iuc/graphlan_annotate/graphlan_annotate/1.0.0.0	2019-01-01	13
toolshed.g2.bx.psu.edu/repos/iuc/trinity_run_de_analysis/trinity_run_de_analysis/2.8.4	2019-01-01	12
toolshed.g2.bx.psu.edu/repos/iuc/mothur_count_groups/mothur_count_groups/1.39.5.0	2019-01-01	12
toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_bdgdiff/2.1.1.20160309.1	2019-01-01	12
toolshed.g2.bx.psu.edu/repos/devteam/fastq_quality_boxplot/cshl_fastq_quality_boxplot/1.0.0	2019-01-01	12
CONVERTER_bed_to_fli_0	2019-01-01	12
toolshed.g2.bx.psu.edu/repos/iuc/gemini_annotate/gemini_annotate/0.20.1	2019-01-01	12
toolshed.g2.bx.psu.edu/repos/iuc/mothur_summary_single/mothur_summary_single/1.39.5.0	2019-01-01	12
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicbuildmatrix/hicexplorer_hicbuildmatrix/2.1.2.0	2019-01-01	12
toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_ensemble/sklearn_ensemble/1.0	2019-01-01	12
toolshed.g2.bx.psu.edu/repos/iuc/mothur_sub_sample/mothur_sub_sample/1.39.5.0	2019-01-01	12
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeBamAlignment/2.18.2.1	2019-01-01	12
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtofastq/2.24.0	2019-01-01	12
toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.2.6.2	2019-01-01	12
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicmergematrixbins/hicexplorer_hicmergematrixbins/2.1.2.0	2019-01-01	12
toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/1.6.0.2	2019-01-01	12
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicplotmatrix/hicexplorer_hicplotmatrix/2.1.2.0	2019-01-01	12
toolshed.g2.bx.psu.edu/repos/devteam/samtool_filter2/samtool_filter2/1.1.2	2019-01-01	12
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicsummatrices/hicexplorer_hicsummatrices/2.1.4.0	2019-01-01	12
toolshed.g2.bx.psu.edu/repos/devteam/fastq_manipulation/fastq_manipulation/1.0.1	2019-01-01	12
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toolshed.g2.bx.psu.edu/repos/iuc/mothur_dist_shared/mothur_dist_shared/1.39.5.0	2019-01-01	12
toolshed.g2.bx.psu.edu/repos/iuc/qiime_pick_rep_set/qiime_pick_rep_set/1.9.1.0	2019-01-01	12
toolshed.g2.bx.psu.edu/repos/chemteam/gmx_nvt/gmx_nvt/2018.2	2019-01-01	11
toolshed.g2.bx.psu.edu/repos/chemteam/gmx_em/gmx_em/2018.2	2019-01-01	11
toolshed.g2.bx.psu.edu/repos/bgruening/augustus/augustus/3.2.3	2019-01-01	11
toolshed.g2.bx.psu.edu/repos/chemteam/gmx_solvate/gmx_solvate/2018.2	2019-01-01	11
toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_download/4.0.0	2019-01-01	11
toolshed.g2.bx.psu.edu/repos/iuc/trinity_abundance_estimates_to_matrix/trinity_abundance_estimates_to_matrix/2.8.4	2019-01-01	11
toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_dedup/umi_tools_dedup/0.5.3.0	2019-01-01	11
toolshed.g2.bx.psu.edu/repos/wolma/mimodd_main/mimodd_info/0.1.8_1	2019-01-01	11
toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sra_pileup/2.9.1.2	2019-01-01	11
toolshed.g2.bx.psu.edu/repos/miller-lab/genome_diversity/gd_raxml/1.0.0	2019-01-01	11
CONVERTER_vcf_to_bgzip_0	2019-01-01	11
CONVERTER_vcf_bgzip_to_tabix_0	2019-01-01	11
CONVERTER_bed_to_bgzip_0	2019-01-01	11
toolshed.g2.bx.psu.edu/repos/lparsons/fastq_join/fastq_join/1.1.2-806	2019-01-01	11
toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_annotate/4.3.0	2019-01-01	11
toolshed.g2.bx.psu.edu/repos/rnateam/atactk_trim_adapters/atactk_trim_adapters/0.1.6	2019-01-01	11
toolshed.g2.bx.psu.edu/repos/iuc/varscan_mpileup/varscan_mpileup/2.4.3.1	2019-01-01	11
toolshed.g2.bx.psu.edu/repos/chemteam/gmx_setup/gmx_setup/2018.2	2019-01-01	11
toolshed.g2.bx.psu.edu/repos/devteam/fastx_clipper/cshl_fastx_clipper/1.0.3	2019-01-01	10
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_makewindowsbed/2.27.1	2019-01-01	10
toolshed.g2.bx.psu.edu/repos/peterjc/blast2go/blast2go/0.0.9	2019-01-01	10
toolshed.g2.bx.psu.edu/repos/iuc/circos/circgraph/0.9-RC2	2019-01-01	10
CONVERTER_vcf_to_vcf_bgzip_0	2019-01-01	10
toolshed.g2.bx.psu.edu/repos/devteam/sam_pileup/sam_pileup/1.1.2	2019-01-01	10
toolshed.g2.bx.psu.edu/repos/devteam/fastq_manipulation/fastq_manipulation/1.1.1	2019-01-01	10
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_estimatereadfiltering/deeptools_estimatereadfiltering/3.0.2.0	2019-01-01	10
toolshed.g2.bx.psu.edu/repos/iuc/seurat/seurat/2.3.4	2019-01-01	10
toolshed.g2.bx.psu.edu/repos/devteam/fastq_trimmer/fastq_trimmer/1.1.1	2019-01-01	10
Paste1	2019-01-01	10
toolshed.g2.bx.psu.edu/repos/iuc/gatk2/gatk2_unified_genotyper/2.8.0	2019-01-01	10
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_fingerprint/deeptools_plot_fingerprint/3.0.2.0	2019-01-01	10
CONVERTER_bam_to_qname_sorted_bam	2019-01-01	10
toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/2.9.1.4	2019-01-01	10
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idmapper/IDMapper/2.3.0	2019-01-01	10
toolshed.g2.bx.psu.edu/repos/devteam/vcfannotate/vcfannotate/1.0.0_rc1+galaxy0	2019-01-01	9
toolshed.g2.bx.psu.edu/repos/bgruening/bismark/bismark_bowtie2/0.20.0	2019-01-01	9
toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/fasta_compute_length/1.0.1	2019-01-01	9
CONVERTER_bed_to_tabix_0	2019-01-01	9
toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1.1	2019-01-01	9
toolshed.g2.bx.psu.edu/repos/iuc/egsea/egsea/1.6.0.1	2019-01-01	9
toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.4.0	2019-01-01	9
toolshed.g2.bx.psu.edu/repos/galaxyp/unipept/unipept/2.0.1	2019-01-01	9
toolshed.g2.bx.psu.edu/repos/iuc/mothur_get_oturep/mothur_get_oturep/1.39.5.0	2019-01-01	9
toolshed.g2.bx.psu.edu/repos/iuc/mothur_heatmap_bin/mothur_heatmap_bin/1.39.5.0	2019-01-01	9
toolshed.g2.bx.psu.edu/repos/devteam/fastqtofasta/fastq_to_fasta_python/1.1.1	2019-01-01	9
toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_deinterlacer/fastq_paired_end_deinterlacer/1.1.2	2019-01-01	9
toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/0.8.1+galaxy0	2019-01-01	9
toolshed.g2.bx.psu.edu/repos/bgruening/split_file_on_column/tp_split_on_column/0.2	2019-01-01	9
toolshed.g2.bx.psu.edu/repos/chemteam/gmx_md/gmx_md/2018.2	2019-01-01	9
toolshed.g2.bx.psu.edu/repos/chemteam/gmx_npt/gmx_npt/2018.2	2019-01-01	9
toolshed.g2.bx.psu.edu/repos/devteam/picard/PicardASMetrics/1.56.0	2019-01-01	9
toolshed.g2.bx.psu.edu/repos/crs4/muscle/muscle/0.0.11	2019-01-01	9
toolshed.g2.bx.psu.edu/repos/wolma/mimodd_main/mimodd_varcall/0.1.8_1	2019-01-01	9
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.27.1	2019-01-01	9
toolshed.g2.bx.psu.edu/repos/iuc/gemini_query/gemini_query/0.18.1.0	2019-01-01	9
toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.68	2019-01-01	9
toolshed.g2.bx.psu.edu/repos/iuc/sqlite_to_tabular/sqlite_to_tabular/2.0.0	2019-01-01	9
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.0	2019-01-01	9
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.27.1	2019-01-01	9
toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.3.7	2019-01-01	9
toolshed.g2.bx.psu.edu/repos/iuc/meme_chip/meme_chip/4.11.2+galaxy1	2019-01-01	9
toolshed.g2.bx.psu.edu/repos/iuc/gatk2/gatk2_depth_of_coverage/2.8.0	2019-01-01	9
toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread/2.2.1.1	2019-01-01	9
toolshed.g2.bx.psu.edu/repos/rnateam/sortmerna/bg_sortmerna/2.1b.5	2019-01-01	9
toolshed.g2.bx.psu.edu/repos/iuc/qiime_extract_barcodes/qiime_extract_barcodes/1.9.1.0	2019-01-01	8
toolshed.g2.bx.psu.edu/repos/iuc/qiime_validate_mapping_file/qiime_validate_mapping_file/1.9.1.0	2019-01-01	8
toolshed.g2.bx.psu.edu/repos/gbcs-embl-heidelberg/je_demultiplex_illu/je_demultiplex_illu/1.2.1	2019-01-01	8
toolshed.g2.bx.psu.edu/repos/iuc/gemini_load/gemini_load/0.18.1.0	2019-01-01	8
toolshed.g2.bx.psu.edu/repos/iuc/qiime_make_otu_heatmap/qiime_make_otu_heatmap/1.9.1.0	2019-01-01	8
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicpca/hicexplorer_hicpca/2.1.4.0	2019-01-01	8
toolshed.g2.bx.psu.edu/repos/iuc/gemini_query/gemini_query/0.18.1.1	2019-01-01	8
CONVERTER_interval_to_bed12_0	2019-01-01	8
toolshed.g2.bx.psu.edu/repos/rnateam/peakachu/peakachu/0.1.0.2	2019-01-01	8
Count1	2019-01-01	8
toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.3	2019-01-01	8
toolshed.g2.bx.psu.edu/repos/iuc/ucsc_twobittofa/ucsc-twobittofa/357	2019-01-01	8
toolshed.g2.bx.psu.edu/repos/iuc/varscan_somatic/varscan_somatic/2.4.3.2	2019-01-01	8
toolshed.g2.bx.psu.edu/repos/iuc/raceid_trajectory/raceid_trajectory/3.0.2.1	2019-01-01	8
toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_ensemble/sklearn_ensemble/0.9	2019-01-01	8
toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_tblastx_wrapper/0.3.1	2019-01-01	8
toolshed.g2.bx.psu.edu/repos/iuc/gemini_load/gemini_load/0.18.1.1	2019-01-01	8
toolshed.g2.bx.psu.edu/repos/iuc/gemini_dump/gemini_dump/0.18.1.1	2019-01-01	8
CONVERTER_fasta_to_len	2019-01-01	8
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multiintersectbed/2.27.0.0	2019-01-01	8
toolshed.g2.bx.psu.edu/repos/devteam/concat/gops_concat_1/1.0.1	2019-01-01	8
CONVERTER_len_to_linecount	2019-01-01	8
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_pca/deeptools_plot_pca/3.1.2.0.0	2019-01-01	8
toolshed.g2.bx.psu.edu/repos/iuc/qiime_make_otu_table/qiime_make_otu_table/1.9.1.0	2019-01-01	8
toolshed.g2.bx.psu.edu/repos/devteam/cummerbund/cummeRbund/2.16.0	2019-01-01	8
toolshed.g2.bx.psu.edu/repos/devteam/vcfvcfintersect/vcfvcfintersect/1.0.0_rc1+galaxy0	2019-01-01	8
toolshed.g2.bx.psu.edu/repos/devteam/count_covariates/gatk_count_covariates/0.0.5	2019-01-01	7
toolshed.g2.bx.psu.edu/repos/iuc/bctools_extract_alignment_ends/bctools_extract_alignment_ends/0.2.2	2019-01-01	7
toolshed.g2.bx.psu.edu/repos/iuc/extract_genomic_dna/Extract genomic DNA 1/3.0.0	2019-01-01	7
toolshed.g2.bx.psu.edu/repos/iuc/trinity_analyze_diff_expr/trinity_analyze_diff_expr/2.8.4	2019-01-01	7
toolshed.g2.bx.psu.edu/repos/iuc/ncbi_eutils_esearch/ncbi_eutils_esearch/1.2	2019-01-01	7
toolshed.g2.bx.psu.edu/repos/iuc/mothur_venn/mothur_venn/1.39.5.0	2019-01-01	7
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_unfold_column_tool/1.1.1	2019-01-01	7
toolshed.g2.bx.psu.edu/repos/devteam/freebayes_wrapper/freebayes_wrapper/0.5.0	2019-01-01	7
toolshed.g2.bx.psu.edu/repos/iuc/qiime_count_seqs/qiime_count_seqs/1.9.1.0	2019-01-01	7
toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.5.0	2019-01-01	7
toolshed.g2.bx.psu.edu/repos/iuc/rnaspades/rnaspades/3.9.0.1	2019-01-01	7
toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_histogram/ggplot2_histogram/2.2.1+galaxy0	2019-01-01	7
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_coverage/deeptools_plot_coverage/3.0.2.0	2019-01-01	7
toolshed.g2.bx.psu.edu/repos/iuc/samtools_sort/samtools_rmdup/1.0.1	2019-01-01	7
toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_pca/ggplot2_pca/2.2.1	2019-01-01	7
toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.1.1	2019-01-01	7
CONVERTER_fasta_to_2bit	2019-01-01	7
toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_build_pipeline/sklearn_build_pipeline/0.9	2019-01-01	7
toolshed.g2.bx.psu.edu/repos/iuc/mageck_count/mageck_count/0.5.8.4	2019-01-01	7
toolshed.g2.bx.psu.edu/repos/iuc/qiime_multiple_join_paired_ends/qiime_multiple_join_paired_ends/1.9.1.0	2019-01-01	7
toolshed.g2.bx.psu.edu/repos/rnateam/dorina/dorina_search/1.0.0	2019-01-01	7
toolshed.g2.bx.psu.edu/repos/iuc/raceid_inspecttrajectory/raceid_inspecttrajectory/3.0.2.1	2019-01-01	7
toolshed.g2.bx.psu.edu/repos/rnateam/peakachu/peakachu/0.1.0.1	2019-01-01	7
toolshed.g2.bx.psu.edu/repos/wolma/mimodd_main/mimodd_map/0.1.8_1	2019-01-01	7
toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/datamash_ops/1.0.6	2019-01-01	7
toolshed.g2.bx.psu.edu/repos/devteam/correlation/cor2/1.0.0	2019-01-01	7
toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_RNA_fragment_size/2.6.4.1	2019-01-01	7
toolshed.g2.bx.psu.edu/repos/bgruening/infernal/infernal_cmbuild/1.1.2.0	2019-01-01	6
toolshed.g2.bx.psu.edu/repos/iuc/mothur_heatmap_sim/mothur_heatmap_sim/1.39.5.0	2019-01-01	6
toolshed.g2.bx.psu.edu/repos/rnateam/sortmerna/bg_sortmerna/2.1b.4	2019-01-01	6
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_fileinfo/FileInfo/2.2.0	2019-01-01	6
toolshed.g2.bx.psu.edu/repos/rnateam/graphclust_mlocarna/locarna_best_subtree/0.3	2019-01-01	6
toolshed.g2.bx.psu.edu/repos/iuc/deg_annotate/deg_annotate/1.1.0	2019-01-01	6
toolshed.g2.bx.psu.edu/repos/wolma/mimodd_main/mimodd_varextract/0.1.8_1	2019-01-01	6
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_falsediscoveryrate/FalseDiscoveryRate/2.2.0	2019-01-01	6
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_alignmentsieve/deeptools_alignmentsieve/3.0.2.0	2019-01-01	6
toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3k.0	2019-01-01	6
toolshed.g2.bx.psu.edu/repos/bgruening/bismark/bismark_bowtie/0.7.12	2019-01-01	6
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_proteinquantifier/ProteinQuantifier/2.3.0	2019-01-01	6
toolshed.g2.bx.psu.edu/repos/wolma/mimodd_main/mimodd_rebase/0.1.8_1	2019-01-01	6
toolshed.g2.bx.psu.edu/repos/iuc/mothur_merge_files/mothur_merge_files/1.39.5.0	2019-01-01	6
toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_bdgcmp/2.1.1.20160309.0	2019-01-01	6
toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_filterdup/2.1.1.20160309.0	2019-01-01	6
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/deeptools_compute_matrix/2.5.1.1.0	2019-01-01	6
toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/column_remove_by_header/0.0.1	2019-01-01	6
toolshed.g2.bx.psu.edu/repos/iuc/scpipe/scpipe/1.0.0+galaxy1	2019-01-01	6
toolshed.g2.bx.psu.edu/repos/iuc/xpath/xpath/1.0.0	2019-01-01	6
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_correlation/deeptools_plot_correlation/2.5.7.0	2019-01-01	6
toolshed.g2.bx.psu.edu/repos/iuc/mothur_screen_seqs/mothur_screen_seqs/1.36.1.0	2019-01-01	6
toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.1	2019-01-01	6
toolshed.g2.bx.psu.edu/repos/guru-ananda/karyotype_plot/karyotype_Plot_1/1.0.0	2019-01-01	6
toolshed.g2.bx.psu.edu/repos/earlhaminst/replace_chromosome_names/replace_chromosome_names/0.1	2019-01-01	6
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_decoydatabase/DecoyDatabase/2.3.0	2019-01-01	6
toolshed.g2.bx.psu.edu/repos/iuc/fasttree/fasttree/2.1.10	2019-01-01	6
toolshed.g2.bx.psu.edu/repos/rnateam/graphclust_cmfinder/cmFinder/0.3	2019-01-01	6
toolshed.g2.bx.psu.edu/repos/iuc/gemini_annotate/gemini_annotate/0.20.1+galaxy1	2019-01-01	6
toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/0.8.1+galaxy0	2019-01-01	6
toolshed.g2.bx.psu.edu/repos/devteam/samtools_phase/samtools_phase/2.0.1	2019-01-01	6
toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: cpgplot15/5.0.0	2019-01-01	6
toolshed.g2.bx.psu.edu/repos/iuc/mothur_tree_shared/mothur_tree_shared/1.39.5.0	2019-01-01	6
dexseq_annotate	2019-01-01	6
toolshed.g2.bx.psu.edu/repos/devteam/fastq_trimmer_by_quality/fastq_quality_trimmer/1.1.1	2019-01-01	6
toolshed.g2.bx.psu.edu/repos/iuc/qiime_align_seqs/qiime_align_seqs/1.9.1.0	2019-01-01	6
toolshed.g2.bx.psu.edu/repos/iuc/qiime_filter_alignment/qiime_filter_alignment/1.9.1.0	2019-01-01	6
__FLATTEN__	2019-01-01	6
toolshed.g2.bx.psu.edu/repos/bgruening/pileometh/pileometh/0.3.0	2019-01-01	6
toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.2.6	2019-01-01	6
toolshed.g2.bx.psu.edu/repos/iuc/describe_samples/describe_samples/2.8.4	2019-01-01	6
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_closestbed/2.27.1	2019-01-01	6
toolshed.g2.bx.psu.edu/repos/bgruening/infernal/infernal_cmsearch/1.1.2.0	2019-01-01	6
toolshed.g2.bx.psu.edu/repos/iuc/kallisto_quant/kallisto_quant/0.43.1.4	2019-01-01	6
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_slopbed/2.27.0.0	2019-01-01	6
toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_svm_classifier/sklearn_svm_classifier/0.9	2019-01-01	6
toolshed.g2.bx.psu.edu/repos/iuc/gffcompare/gffcompare/0.9.8+galaxy1	2019-01-01	6
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_isobaricanalyzer/IsobaricAnalyzer/2.3.0	2019-01-01	6
toolshed.g2.bx.psu.edu/repos/rnateam/viennarna_rnafold/viennarna_rnafold/2.2.10.4	2019-01-01	6
toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/0.7.0.3	2019-01-01	6
genomespace_importer	2019-01-01	6
toolshed.g2.bx.psu.edu/repos/devteam/fastq_quality_boxplot/cshl_fastq_quality_boxplot/1.0.1	2019-01-01	6
CONVERTER_gff_to_fli_0	2019-01-01	6
toolshed.g2.bx.psu.edu/repos/rnateam/paralyzer/paralyzer/1.5	2019-01-01	6
toolshed.g2.bx.psu.edu/repos/iuc/mothur_summary_seqs/mothur_summary_seqs/1.36.1.0	2019-01-01	6
gff2bed1	2019-01-01	5
toolshed.g2.bx.psu.edu/repos/iuc/bctools_extract_crosslinked_nucleotides/bctools_extract_crosslinked_nucleotides/@VERSION+galaxy1	2019-01-01	5
toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy_core/3.2	2019-01-01	5
__EXTRACT_DATASET__	2019-01-01	5
toolshed.g2.bx.psu.edu/repos/fgiacomoni/lipidmaps_textsearch/lipidmaps/2018-10-02	2019-01-01	5
toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_whitelist/umi_tools_whitelist/0.5.3.1	2019-01-01	5
toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.3.1	2019-01-01	5
toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_download/4.3+T.galaxy2	2019-01-01	5
toolshed.g2.bx.psu.edu/repos/iuc/dexseq/dexseq/1.26.0.0	2019-01-01	5
toolshed.g2.bx.psu.edu/repos/devteam/vcftools_slice/vcftools_slice/0.1	2019-01-01	5
toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.2	2019-01-01	5
toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_rpsblast_wrapper/0.3.1	2019-01-01	5
toolshed.g2.bx.psu.edu/repos/bgruening/glimmer3/glimmer_not-knowlegde-based/0.2	2019-01-01	5
toolshed.g2.bx.psu.edu/repos/bgruening/column_arrange_by_header/bg_column_arrange_by_header/0.1	2019-01-01	5
toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpSift_filter/3.4	2019-01-01	5
solid2fastq	2019-01-01	5
toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_data_preprocess/sklearn_data_preprocess/1.0	2019-01-01	5
toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_bam_stat/2.6.4	2019-01-01	5
toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.67	2019-01-01	5
toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_randsample/2.1.1.20160309.0	2019-01-01	5
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_closestbed/2.27.0.0	2019-01-01	5
toolshed.g2.bx.psu.edu/repos/iuc/dexseq/dexseq_count/1.26.0.0	2019-01-01	5
Extract_features1	2019-01-01	5
toolshed.g2.bx.psu.edu/repos/iuc/mothur_fastq_info/mothur_fastq_info/1.39.5.0	2019-01-01	5
CONVERTER_gff_to_interval_index_0	2019-01-01	5
toolshed.g2.bx.psu.edu/repos/rnateam/rcas/rcas/1.1.1	2019-01-01	5
toolshed.g2.bx.psu.edu/repos/iuc/ococo/ococo/0.1.2.6	2019-01-01	5
toolshed.g2.bx.psu.edu/repos/iuc/qiime_multiple_split_libraries_fastq/qiime_multiple_split_libraries_fastq/1.9.1.0	2019-01-01	5
toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_annotate/4.3+t.galaxy1	2019-01-01	5
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_fingerprint/deeptools_plot_fingerprint/2.5.7.0	2019-01-01	5
toolshed.g2.bx.psu.edu/repos/iuc/gemini_de_novo/gemini_de_novo/0.18.1.1	2019-01-01	5
velveth	2019-01-01	5
toolshed.g2.bx.psu.edu/repos/devteam/short_reads_figure_score/quality_score_distribution/1.0.2	2019-01-01	5
toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.4.0.0	2019-01-01	5
toolshed.g2.bx.psu.edu/repos/iuc/trinity_super_transcripts/trinity_super_transcripts/2.8.4	2019-01-01	5
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hiccomparematrices/hicexplorer_hiccomparematrices/2.1.4.0	2019-01-01	5
toolshed.g2.bx.psu.edu/repos/iuc/qiime_make_phylogeny/qiime_make_phylogeny/1.9.1.0	2019-01-01	5
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toolshed.g2.bx.psu.edu/repos/iuc/meme_chip/meme_chip/4.11.2	2019-01-01	5
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.27.1	2019-01-01	5
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bam_summary/deeptools_multi_bam_summary/2.5.7.0	2019-01-01	5
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.27.0.1	2019-01-01	5
toolshed.g2.bx.psu.edu/repos/devteam/vcfselectsamples/vcfselectsamples/1.0.0_rc1+galaxy0	2019-01-01	4
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectInsertSizeMetrics/2.7.1.0	2019-01-01	4
toolshed.g2.bx.psu.edu/repos/iuc/length_and_gc_content/length_and_gc_content/0.1.1	2019-01-01	4
toolshed.g2.bx.psu.edu/repos/iuc/qiime_summarize_taxa/qiime_summarize_taxa/1.9.1.0	2019-01-01	4
toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_predictd/2.1.1.20160309.0	2019-01-01	4
toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0.1	2019-01-01	4
toolshed.g2.bx.psu.edu/repos/iuc/iqtree/iqtree/1.5.5.1	2019-01-01	4
toolshed.g2.bx.psu.edu/repos/devteam/fastq_to_tabular/fastq_to_tabular/1.1.0	2019-01-01	4
toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: getorf42/5.0.0.1	2019-01-01	4
toolshed.g2.bx.psu.edu/repos/chemteam/bio3d_pca/bio3d_pca/2.3	2019-01-01	4
toolshed.g2.bx.psu.edu/repos/chemteam/bio3d_rmsd/bio3d_rmsd/2.3	2019-01-01	4
toolshed.g2.bx.psu.edu/repos/chemteam/bio3d_rmsf/bio3d_rmsf/2.3	2019-01-01	4
toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.1.0	2019-01-01	4
toolshed.g2.bx.psu.edu/repos/devteam/fastx_nucleotides_distribution/cshl_fastx_nucleotides_distribution/1.0.0	2019-01-01	4
toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_group/mothur_make_group/1.39.5.0	2019-01-01	4
toolshed.g2.bx.psu.edu/repos/devteam/dgidb_annotator/dgidb_annotator/0.1	2019-01-01	4
toolshed.g2.bx.psu.edu/repos/iuc/star_fusion/star_fusion/0.5.4-3	2019-01-01	4
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_heatmap/deeptools_plot_heatmap/3.0.0.0	2019-01-01	4
toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.2.0	2019-01-01	4
toolshed.g2.bx.psu.edu/repos/devteam/megablast_wrapper/megablast_wrapper/1.2.0	2019-01-01	4
toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_quality/2.6.4	2019-01-01	4
hgv_david	2019-01-01	4
toolshed.g2.bx.psu.edu/repos/iuc/varscan_somatic/varscan_somatic/2.4.3.1	2019-01-01	4
deeptools_bigwigCorrelate	2019-01-01	4
toolshed.g2.bx.psu.edu/repos/galaxyp/msi_preprocessing/mass_spectrometry_imaging_preprocessing/1.10.0.7	2019-01-01	4
toolshed.g2.bx.psu.edu/repos/iuc/mothur_remove_groups/mothur_remove_groups/1.39.5.0	2019-01-01	4
toolshed.g2.bx.psu.edu/repos/devteam/fastq_combiner/fastq_combiner/1.1.1	2019-01-01	4
toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_heatmap2/ggplot2_heatmap2/2.2.1	2019-01-01	4
toolshed.g2.bx.psu.edu/repos/iuc/gemini_recessive_and_dominant/gemini_recessive_and_dominant/0.18.1.1	2019-01-01	4
toolshed.g2.bx.psu.edu/repos/iuc/gemini_pathways/gemini_pathways/0.20.1	2019-01-01	4
CONVERTER_wig_to_bigwig	2019-01-01	4
toolshed.g2.bx.psu.edu/repos/jjohnson/query_tabular/query_tabular/3.0.0	2019-01-01	4
toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_sample/1.3.1	2019-01-01	4
toolshed.g2.bx.psu.edu/repos/iuc/mummer_dnadiff/mummer_dnadiff/4.0.0beta2	2019-01-01	4
toolshed.g2.bx.psu.edu/repos/peterjc/tmhmm_and_signalp/Psortb/0.0.9	2019-01-01	4
toolshed.g2.bx.psu.edu/repos/jjohnson/sqlite_to_tabular/sqlite_to_tabular/0.0.1	2019-01-01	4
toolshed.g2.bx.psu.edu/repos/rnateam/rcas/rcas/1.5.4	2019-01-01	4
CONVERTER_picard_interval_list_to_bed6	2019-01-01	4
bed_to_bigBed	2019-01-01	4
toolshed.g2.bx.psu.edu/repos/iuc/meme_fimo/meme_fimo/4.11.2.0	2019-01-01	4
toolshed.g2.bx.psu.edu/repos/devteam/vcftools_compare/vcftools_compare/0.1	2019-01-01	4
toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.1.8.3	2019-01-01	4
toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_download/4.1.0	2019-01-01	4
toolshed.g2.bx.psu.edu/repos/rnateam/blockbuster/blockbuster/0.1.2	2019-01-01	4
toolshed.g2.bx.psu.edu/repos/iuc/trinity_samples_qccheck/trinity_samples_qccheck/2.8.4	2019-01-01	4
toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_bdgbroadcall/2.1.1.20160309.0	2019-01-01	4
toolshed.g2.bx.psu.edu/repos/bgruening/replace_column_by_key_value_file/replace_column_with_key_value_file/0.1	2019-01-01	4
toolshed.g2.bx.psu.edu/repos/lparsons/fastq_join/fastq_join/1.1.2-806.1	2019-01-01	4
toolshed.g2.bx.psu.edu/repos/anton/vcfcombine/vcfcombine/0.0.1	2019-01-01	3
toolshed.g2.bx.psu.edu/repos/crs4/prokka/prokka/1.12.0	2019-01-01	3
toolshed.g2.bx.psu.edu/repos/rnateam/graphclust_preprocessing/preproc/0.4	2019-01-01	3
toolshed.g2.bx.psu.edu/repos/iuc/mothur_merge_files/mothur_merge_files/1.36.1.0	2019-01-01	3
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toolshed.g2.bx.psu.edu/repos/devteam/vcfgeno2haplo/vcfgeno2haplo/1.0.0_rc1+galaxy0	2019-01-01	3
toolshed.g2.bx.psu.edu/repos/iuc/qiime_alpha_diversity/qiime_alpha_diversity/1.9.1.0	2019-01-01	3
toolshed.g2.bx.psu.edu/repos/crs4/edena/edena_ovl_wrapper/0.3	2019-01-01	3
toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_shared/mothur_make_shared/1.36.1.0	2019-01-01	3
velvetg	2019-01-01	3
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_fidoadapter/FidoAdapter/2.2.0.1	2019-01-01	3
toolshed.g2.bx.psu.edu/repos/iuc/gemini_fusions/gemini_fusions/0.20.1	2019-01-01	3
toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.4.0	2019-01-01	3
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_subtractbed/2.27.1	2019-01-01	3
toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_group/mothur_make_group/1.36.1.0	2019-01-01	3
toolshed.g2.bx.psu.edu/repos/peterjc/tmhmm_and_signalp/rxlr_motifs/0.0.14	2019-01-01	3
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idconflictresolver/IDConflictResolver/2.2.0	2019-01-01	3
toolshed.g2.bx.psu.edu/repos/iuc/picrust_predict_metagenomes/picrust_predict_metagenomes/1.1.1.0	2019-01-01	3
toolshed.g2.bx.psu.edu/repos/bgruening/diamond/bg_diamond_makedb/0.8.24	2019-01-01	3
toolshed.g2.bx.psu.edu/repos/rnateam/mafft/rbc_mafft/7.221.3	2019-01-01	3
toolshed.g2.bx.psu.edu/repos/iuc/mothur_cluster_split/mothur_cluster_split/1.36.1.0	2019-01-01	3
toolshed.g2.bx.psu.edu/repos/rnateam/cmv/cmv/1.0.8	2019-01-01	3
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_shufflebed/2.27.0.0	2019-01-01	3
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_DownsampleSam/2.18.2.1	2019-01-01	3
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_msgfplusadapter/MSGFPlusAdapter/2.2.0	2019-01-01	3
toolshed.g2.bx.psu.edu/repos/iuc/gemini_db_info/gemini_db_info/0.18.1.1	2019-01-01	3
toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_svm_classifier/sklearn_svm_classifier/1.0	2019-01-01	3
toolshed.g2.bx.psu.edu/repos/galaxyp/msi_combine/mass_spectrometry_imaging_combine/1.10.0.5	2019-01-01	3
toolshed.g2.bx.psu.edu/repos/iuc/gemini_db_info/gemini_db_info/0.18.1.0	2019-01-01	3
toolshed.g2.bx.psu.edu/repos/iuc/fgsea/fgsea/1.6.0	2019-01-01	3
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_BedToIntervalList/2.18.2.1	2019-01-01	3
toolshed.g2.bx.psu.edu/repos/iuc/mothur_unique_seqs/mothur_unique_seqs/1.36.1.0	2019-01-01	3
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_featurefindermultiplex/FeatureFinderMultiplex/2.3.0	2019-01-01	3
toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_biom/mothur_make_biom/1.39.5.0	2019-01-01	3
toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_bdgpeakcall/2.1.1.20160309.0	2019-01-01	3
toolshed.g2.bx.psu.edu/repos/iuc/mothur_filter_seqs/mothur_filter_seqs/1.36.1.0	2019-01-01	3
toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_biom/mothur_make_biom/1.36.1.0	2019-01-01	3
toolshed.g2.bx.psu.edu/repos/iuc/khmer_abundance_distribution_single/khmer_abundance_distribution_single/2.0.0	2019-01-01	3
toolshed.g2.bx.psu.edu/repos/iuc/meme_dreme/meme_dreme/4.11.2.0	2019-01-01	3
toolshed.g2.bx.psu.edu/repos/iuc/mothur_count_seqs/mothur_count_seqs/1.36.1.0	2019-01-01	3
toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.4.1	2019-01-01	3
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_peakpickerhires/PeakPickerHiRes/2.3.0	2019-01-01	3
toolshed.g2.bx.psu.edu/repos/iuc/gemini_amend/gemini_amend/0.20.1	2019-01-01	3
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_featurefindermultiplex/FeatureFinderMultiplex/2.2.0	2019-01-01	3
toolshed.g2.bx.psu.edu/repos/iuc/humann2_renorm_table/humann2_renorm_table/0.11.1.0	2019-01-01	3
toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.3	2019-01-01	3
toolshed.g2.bx.psu.edu/repos/iuc/gemini_actionable_mutations/gemini_actionable_mutations/0.18.1.0	2019-01-01	3
toolshed.g2.bx.psu.edu/repos/iuc/ucsc_fasplit/fasplit/357	2019-01-01	3
gene2exon1	2019-01-01	3
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idmapper/IDMapper/2.2.0	2019-01-01	3
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idfilter/IDFilter/2.2.0	2019-01-01	3
translate_nucleotides	2019-01-01	3
toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_databases/4.3r.1	2019-01-01	3
toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fastq/tabular_to_fastq/1.0.0	2019-01-01	3
toolshed.g2.bx.psu.edu/repos/devteam/vcf2pgsnp/vcf2pgSnp/1.0.0	2019-01-01	3
toolshed.g2.bx.psu.edu/repos/iuc/gatk2/gatk2_base_recalibrator/2.8.0	2019-01-01	3
toolshed.g2.bx.psu.edu/repos/bgruening/nanopolish_variants/nanopolish_variants/0.1.0	2019-01-01	3
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toolshed.g2.bx.psu.edu/repos/rnateam/structure_to_gspan/structure_to_gspan/0.3	2019-01-01	3
toolshed.g2.bx.psu.edu/repos/iuc/mothur_get_groups/mothur_get_groups/1.39.5.0	2019-01-01	3
srma_wrapper	2019-01-01	3
toolshed.g2.bx.psu.edu/repos/iuc/mothur_classify_otu/mothur_classify_otu/1.36.1.0	2019-01-01	3
toolshed.g2.bx.psu.edu/repos/devteam/ucsc_custom_track/build_ucsc_custom_track_1/1.0.0	2019-01-01	3
toolshed.g2.bx.psu.edu/repos/miller-lab/genome_diversity/gd_multiple_to_gd_genotype/1.0.0	2019-01-01	3
toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.12.5+galaxy3	2019-01-01	3
toolshed.g2.bx.psu.edu/repos/bgruening/diffbind/diffbind/2.6.6.4	2019-01-01	3
toolshed.g2.bx.psu.edu/repos/devteam/gi2taxonomy/Fetch Taxonomic Ranks/1.1.0	2019-01-01	3
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_highresprecursormasscorrector/HighResPrecursorMassCorrector/2.2.0	2019-01-01	3
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_proteinquantifier/ProteinQuantifier/2.2.0	2019-01-01	3
toolshed.g2.bx.psu.edu/repos/iuc/goseq/goseq/1.26.0	2019-01-01	3
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_peptideindexer/PeptideIndexer/2.2.0	2019-01-01	3
toolshed.g2.bx.psu.edu/repos/iuc/mothur_cluster/mothur_cluster/1.39.5.0	2019-01-01	3
toolshed.g2.bx.psu.edu/repos/iuc/stacks_denovomap/stacks_denovomap/1.46.0	2019-01-01	3
toolshed.g2.bx.psu.edu/repos/rnateam/graphclust_nspdk/nspdk_sparse/9.2.2	2019-01-01	3
toolshed.g2.bx.psu.edu/repos/devteam/samtools_flagstat/samtools_flagstat/2.0.1	2019-01-01	3
toolshed.g2.bx.psu.edu/repos/iuc/mothur_align_seqs/mothur_align_seqs/1.36.1.0	2019-01-01	3
toolshed.g2.bx.psu.edu/repos/iuc/migmap/migmap/1.0.2.2	2019-01-01	3
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicplotdistvscounts/hicexplorer_hicplotdistvscounts/2.1.4.0	2019-01-01	3
toolshed.g2.bx.psu.edu/repos/devteam/fastq_stats/fastq_stats/1.0.0	2019-01-01	3
toolshed.g2.bx.psu.edu/repos/iuc/mothur_pre_cluster/mothur_pre_cluster/1.36.1.0	2019-01-01	3
toolshed.g2.bx.psu.edu/repos/wolma/mimodd_main/mimodd_convert/0.1.8_1	2019-01-01	3
toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.19.3.3	2019-01-01	3
toolshed.g2.bx.psu.edu/repos/devteam/varscan_version_2/varscan/0.1	2019-01-01	3
toolshed.g2.bx.psu.edu/repos/bgruening/plotly_ml_performance_plots/plotly_ml_performance_plots/0.1	2019-01-01	3
toolshed.g2.bx.psu.edu/repos/iuc/mothur_remove_rare/mothur_remove_rare/1.39.5.0	2019-01-01	3
toolshed.g2.bx.psu.edu/repos/devteam/cuffnorm/cuffnorm/2.2.1.2	2019-01-01	3
toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.1	2019-01-01	3
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_subtractbed/2.27.0.0	2019-01-01	3
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicmergematrixbins/hicexplorer_hicmergematrixbins/2.1.4.0	2019-01-01	3
toolshed.g2.bx.psu.edu/repos/rnateam/graphclust_nspdk/NSPDK_candidateClust/9.2.2	2019-01-01	3
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/1.136.0	2019-01-01	3
toolshed.g2.bx.psu.edu/repos/devteam/fastx_nucleotides_distribution/cshl_fastx_nucleotides_distribution/1.0.1	2019-01-01	3
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toolshed.g2.bx.psu.edu/repos/iuc/trinity_contig_exn50_statistic/trinity_contig_exn50_statistic/2.8.4	2019-01-01	3
toolshed.g2.bx.psu.edu/repos/rnateam/graphclust_postprocessing/glob_report/0.4	2019-01-01	3
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicatesWithMateCigar/2.18.2.1	2019-01-01	3
toolshed.g2.bx.psu.edu/repos/iuc/mothur_classify_seqs/mothur_classify_seqs/1.36.1.0	2019-01-01	3
toolshed.g2.bx.psu.edu/repos/devteam/cummerbund_to_tabular/cummerbund_to_cuffdiff/1.0.1	2019-01-01	3
toolshed.g2.bx.psu.edu/repos/iuc/sickle/sickle/1.33.1	2019-01-01	3
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idposteriorerrorprobability/IDPosteriorErrorProbability/2.2.0	2019-01-01	3
toolshed.g2.bx.psu.edu/repos/rnateam/graphclust_prepocessing_for_mlocarna/preMloc/0.3	2019-01-01	3
toolshed.g2.bx.psu.edu/repos/saskia-hiltemann/krona_text/krona-text/1	2019-01-01	3
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_filefilter/FileFilter/2.2.0	2019-01-01	3
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idscoreswitcher/IDScoreSwitcher/2.2.0	2019-01-01	3
toolshed.g2.bx.psu.edu/repos/iuc/mothur_seq_error/mothur_seq_error/1.39.5.0	2019-01-01	3
toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: water107/5.0.0.1	2019-01-01	3
toolshed.g2.bx.psu.edu/repos/iuc/bwameth/bwameth/0.2.0.3	2019-01-01	3
toolshed.g2.bx.psu.edu/repos/iuc/gubbins/gubbins/0.1.0	2019-01-01	3
toolshed.g2.bx.psu.edu/repos/devteam/fastx_quality_statistics/cshl_fastx_quality_statistics/1.0.1	2019-01-01	3
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_profile/deeptools_plot_profile/2.5.1.1.0	2019-01-01	3
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_filefilter/FileFilter/2.3.0	2019-01-01	3
toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: transeq101/5.0.0	2019-01-01	3
toolshed.g2.bx.psu.edu/repos/gbcs-embl-heidelberg/je_demultiplex/je_demultiplex/1.2.1	2019-01-01	2
gtf_filter_by_attribute_values_list	2019-01-01	2
toolshed.g2.bx.psu.edu/repos/anton/vcfannotate/vcfannotate/0.0.1	2019-01-01	2
toolshed.g2.bx.psu.edu/repos/peterjc/tmhmm_and_signalp/signalp3/0.0.19	2019-01-01	2
toolshed.g2.bx.psu.edu/repos/miller-lab/genome_diversity/gd_make_gd_file/1.0.0	2019-01-01	2
toolshed.g2.bx.psu.edu/repos/jjohnson/translate_bed_sequences/translate_bed_sequences/0.0.1	2019-01-01	2
toolshed.g2.bx.psu.edu/repos/bgruening/openbabel/ctb_ob_genProp/1.0	2019-01-01	2
qual_stats_boxplot	2019-01-01	2
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_annotatebed/2.27.1	2019-01-01	2
toolshed.g2.bx.psu.edu/repos/iuc/ebi_search_rest_results/ebi_search_rest_results/0.1.1	2019-01-01	2
toolshed.g2.bx.psu.edu/repos/iuc/gemini_roh/gemini_roh/0.20.1	2019-01-01	2
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_BamIndexStats/1.56.0	2019-01-01	2
toolshed.g2.bx.psu.edu/repos/bgruening/sailfish/sailfish/0.10.1.1	2019-01-01	2
toolshed.g2.bx.psu.edu/repos/wolma/mimodd_main/mimodd_covstats/0.1.8_1	2019-01-01	2
toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_geneBody_coverage2/2.6.4.1	2019-01-01	2
toolshed.g2.bx.psu.edu/repos/iuc/qiime_summarize_taxa_through_plots/qiime_summarize_taxa_through_plots/1.9.1.0	2019-01-01	2
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.0.0	2019-01-01	2
toolshed.g2.bx.psu.edu/repos/galaxyp/uniprotxml_downloader/uniprotxml_downloader/2.0.0	2019-01-01	2
toolshed.g2.bx.psu.edu/repos/iuc/enasearch_search_data/enasearch_search_data/0.1.1.0	2019-01-01	2
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_fileconverter/FileConverter/2.3.0	2019-01-01	2
toolshed.g2.bx.psu.edu/repos/devteam/ctd_batch/ctdBatch_1/1.0.0	2019-01-01	2
toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.1	2019-01-01	2
toolshed.g2.bx.psu.edu/repos/anton/vcfvcfintersect/vcfvcfintersect/0.0.1	2019-01-01	2
toolshed.g2.bx.psu.edu/repos/iuc/merge_metaphlan_tables/merge_metaphlan_tables/2.6.0.0	2019-01-01	2
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_qccalculator/QCCalculator/2.3.0	2019-01-01	2
toolshed.g2.bx.psu.edu/repos/devteam/vcfbedintersect/vcfbedintersect/1.0.0_rc1+galaxy0	2019-01-01	2
toolshed.g2.bx.psu.edu/repos/iuc/metaphlan_hclust_heatmap/metaphlan_hclust_heatmap/2.6.0.0	2019-01-01	2
toolshed.g2.bx.psu.edu/repos/iuc/mummer_nucmer/mummer_nucmer/4.0.0beta2	2019-01-01	2
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_highresprecursormasscorrector/HighResPrecursorMassCorrector/2.3.0	2019-01-01	2
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed_histogram/2.19.0	2019-01-01	2
toolshed.g2.bx.psu.edu/repos/devteam/vcf_filter/vcf_filter/1.0.0	2019-01-01	2
toolshed.g2.bx.psu.edu/repos/iuc/gatk2/gatk2_haplotype_caller/2.8.0	2019-01-01	2
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_featurefindercentroided/FeatureFinderCentroided/2.3.0	2019-01-01	2
toolshed.g2.bx.psu.edu/repos/iuc/bcftools_call/bcftools_call/1.4.0	2019-01-01	2
toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummerplot/mummer_mummerplot/4.0.0beta2	2019-01-01	2
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hiccorrelate/hicexplorer_hiccorrelate/2.1.4.0	2019-01-01	2
toolshed.g2.bx.psu.edu/repos/iuc/goseq/goseq/1.32.0	2019-01-01	2
toolshed.g2.bx.psu.edu/repos/devteam/t2t_report/t2t_report/1.0.0	2019-01-01	2
toolshed.g2.bx.psu.edu/repos/iuc/enasearch_retrieve_data/enasearch_retrieve_data/0.1.1.0	2019-01-01	2
toolshed.g2.bx.psu.edu/repos/iuc/meme_meme/meme_meme/4.12.0.0	2019-01-01	2
toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_inner_distance/2.6.4.1	2019-01-01	2
toolshed.g2.bx.psu.edu/repos/jjohnson/rsem/extract_transcript_to_gene_map_from_trinity/1.1.17	2019-01-01	2
toolshed.g2.bx.psu.edu/repos/iuc/mothur_trim_flows/mothur_trim_flows/1.39.5.0	2019-01-01	2
toolshed.g2.bx.psu.edu/repos/iuc/mothur_sffinfo/mothur_sffinfo/1.39.5.0	2019-01-01	2
toolshed.g2.bx.psu.edu/repos/iuc/trinity_gene_to_trans_map/trinity_gene_to_trans_map/2.8.4	2019-01-01	2
toolshed.g2.bx.psu.edu/repos/peterjc/seq_composition/seq_composition/0.0.5	2019-01-01	2
toolshed.g2.bx.psu.edu/repos/devteam/vcffixup/vcffixup/1.0.0_rc1+galaxy0	2019-01-01	2
toolshed.g2.bx.psu.edu/repos/ethevenot/heatmap/Heatmap/2.2.2	2019-01-01	2
toolshed.g2.bx.psu.edu/repos/iuc/gemini_comp_hets/gemini_comp_hets/0.18.1.1	2019-01-01	2
toolshed.g2.bx.psu.edu/repos/galaxyp/lfq_protein_quant/lfq_protein_quant/1.0	2019-01-01	2
toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/2.7.0.1	2019-01-01	2
toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: geecee41/5.0.0	2019-01-01	2
toolshed.g2.bx.psu.edu/repos/iuc/qiime_plot_taxa_summary/qiime_plot_taxa_summary/1.9.1.0	2019-01-01	2
toolshed.g2.bx.psu.edu/repos/devteam/bam_to_sam/bam_to_sam/2.0	2019-01-01	2
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idconflictresolver/IDConflictResolver/2.3.0	2019-01-01	2
toolshed.g2.bx.psu.edu/repos/devteam/vcfflatten/vcfflatten2/1.0.0_rc1+galaxy0	2019-01-01	2
toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy3	2019-01-01	2
toolshed.g2.bx.psu.edu/repos/galaxyp/msi_spectra_plot/mass_spectrometry_imaging_mzplots/1.10.0.6	2019-01-01	2
toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummer/mummer_mummer/4.0.0beta2	2019-01-01	2
toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_download/4.3r.0	2019-01-01	2
toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_annotate/4.0.0	2019-01-01	2
toolshed.g2.bx.psu.edu/repos/bgruening/autodock_vina_prepare_receptor/prepare_receptor/0.1.0	2019-01-01	2
toolshed.g2.bx.psu.edu/repos/anton/vcfbedintersect/vcfbedintersect/0.0.1	2019-01-01	2
toolshed.g2.bx.psu.edu/repos/iuc/varscan_copynumber/varscan_copynumber/2.4.3.2	2019-01-01	2
toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_wrapper_2/1.3.2	2019-01-01	2
toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_get_chr_names/@wrapper_version@.galaxy1	2019-01-01	2
toolshed.g2.bx.psu.edu/repos/iuc/ruvseq/ruvseq/1.12.0	2019-01-01	2
toolshed.g2.bx.psu.edu/repos/devteam/bowtie_color_wrappers/bowtie_color_wrapper/1.1.2	2019-01-01	2
toolshed.g2.bx.psu.edu/repos/iuc/meme_meme/meme_meme/4.11.2.0	2019-01-01	2
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.0.0	2019-01-01	2
toolshed.g2.bx.psu.edu/repos/iuc/vsearch/vsearch_clustering/2.8.3.0	2019-01-01	2
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_groupbybed/2.27.0.0	2019-01-01	2
toolshed.g2.bx.psu.edu/repos/bgruening/crispr_recognition_tool/crispr_recognition_tool/1.2.0	2019-01-01	2
toolshed.g2.bx.psu.edu/repos/iuc/gemini/gemini_load/0.10.1.0	2019-01-01	2
toolshed.g2.bx.psu.edu/repos/earlhaminst/hcluster_sg/hcluster_sg/0.5.1.1	2019-01-01	2
toolshed.g2.bx.psu.edu/repos/devteam/vcfsort/vcfsort/1.0.0_rc1+galaxy0	2019-01-01	2
toolshed.g2.bx.psu.edu/repos/devteam/clustalw/clustalw/2.1	2019-01-01	2
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bigwig_summary/deeptools_multi_bigwig_summary/3.0.1.0	2019-01-01	2
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_slopbed/2.27.1	2019-01-01	2
toolshed.g2.bx.psu.edu/repos/galaxyp/msi_ion_images/mass_spectrometry_imaging_ion_images/1.10.0.5	2019-01-01	2
toolshed.g2.bx.psu.edu/repos/iuc/pear/iuc_pear/0.9.6.1	2019-01-01	2
toolshed.g2.bx.psu.edu/repos/iuc/plasflow/PlasFlow/1.0	2019-01-01	2
toolshed.g2.bx.psu.edu/repos/devteam/flanking_features/flanking_features_1/4.0.1	2019-01-01	1
toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.1.1	2019-01-01	1
toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.1	2019-01-01	1
gtf2bedgraph	2019-01-01	1
toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_rpstblastn_wrapper/0.3.1	2019-01-01	1
toolshed.g2.bx.psu.edu/repos/galaxyp/translate_bed/translate_bed/0.1.0	2019-01-01	1
toolshed.g2.bx.psu.edu/repos/bgruening/svm_classifier/svm_classifier/0.9	2019-01-01	1
toolshed.g2.bx.psu.edu/repos/gbcs-embl-heidelberg/je_clip/je_clip/1.2.1	2019-01-01	1
toolshed.g2.bx.psu.edu/repos/devteam/t2ps/Draw_phylogram/1.0.0	2019-01-01	1
toolshed.g2.bx.psu.edu/repos/iuc/vsearch/vsearch_dereplication/2.8.3.0	2019-01-01	1
intermine	2019-01-01	1
toolshed.g2.bx.psu.edu/repos/iuc/vsearch/vsearch_sorting/2.8.3.0	2019-01-01	1
toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_numeric_clustering/sklearn_numeric_clustering/1.0	2019-01-01	1
gff_filter_by_attribute	2019-01-01	1
toolshed.g2.bx.psu.edu/repos/iuc/zerone/zerone/1.0	2019-01-01	1
toolshed.g2.bx.psu.edu/repos/jjohnson/cdhit/cd_hit_est/1.2	2019-01-01	1
toolshed.g2.bx.psu.edu/repos/iuc/meme_fimo/meme_fimo/4.12.0.0	2019-01-01	1
toolshed.g2.bx.psu.edu/repos/gga/apollo_list_organism/list_organism/3.1	2019-01-01	1
toolshed.g2.bx.psu.edu/repos/jjohnson/rsem/rsem_prepare_reference/1.1.17	2019-01-01	1
toolshed.g2.bx.psu.edu/repos/galaxyp/msi_qualitycontrol/mass_spectrometry_imaging_qc/1.10.0.2	2019-01-01	1
toolshed.g2.bx.psu.edu/repos/iuc/megahit_contig2fastg/megahit_contig2fastg/1.1.3+galaxy1	2019-01-01	1
toolshed.g2.bx.psu.edu/repos/iuc/mageck_mle/mageck_mle/0.5.7.1	2019-01-01	1
toolshed.g2.bx.psu.edu/repos/lecorguille/anova/abims_anova/1.2.1	2019-01-01	1
toolshed.g2.bx.psu.edu/repos/galaxyp/reactome_pathwaymatcher/reactome_pathwaymatcher/1.8.1.2	2019-01-01	1
toolshed.g2.bx.psu.edu/repos/bgruening/rnaz/rnaz/2.1.1	2019-01-01	1
toolshed.g2.bx.psu.edu/repos/galaxyp/msi_preprocessing/mass_spectrometry_imaging_preprocessing/1.10.0.2	2019-01-01	1
toolshed.g2.bx.psu.edu/repos/bgruening/rnaz/rnaz/2.1.0	2019-01-01	1
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CleanSam/2.18.2.1	2019-01-01	1
toolshed.g2.bx.psu.edu/repos/galaxyp/proteomics_moff/proteomics_moff/1.2.1.1	2019-01-01	1
toolshed.g2.bx.psu.edu/repos/galaxyp/msi_filtering/mass_spectrometry_imaging_filtering/1.7.0.1	2019-01-01	1
toolshed.g2.bx.psu.edu/repos/devteam/samtools_split/samtools_split/1.3.1	2019-01-01	1
toolshed.g2.bx.psu.edu/repos/devteam/t_test_two_samples/t_test_two_samples/1.0.1	2019-01-01	1
toolshed.g2.bx.psu.edu/repos/lparsons/fastq_join/fastq_join/1.1.2-484	2019-01-01	1
toolshed.g2.bx.psu.edu/repos/bgruening/opsin/ctb_opsin/0.1	2019-01-01	1
toolshed.g2.bx.psu.edu/repos/iuc/jq/jq/1.0	2019-01-01	1
toolshed.g2.bx.psu.edu/repos/iuc/jcvi_gff_stats/jcvi_gff_stats/0.8.4	2019-01-01	1
toolshed.g2.bx.psu.edu/repos/bgruening/numeric_clustering/numeric_clustering/0.9	2019-01-01	1
toolshed.g2.bx.psu.edu/repos/miller-lab/genome_diversity/gd_cluster_kegg/1.0.0	2019-01-01	1
toolshed.g2.bx.psu.edu/repos/galaxyp/msi_filtering/mass_spectrometry_imaging_filtering/1.10.0.4	2019-01-01	1
toolshed.g2.bx.psu.edu/repos/bgruening/minced/minced/0.1.5	2019-01-01	1
toolshed.g2.bx.psu.edu/repos/iuc/bam_to_scidx/bam_to_scidx/1.0.1	2019-01-01	1
toolshed.g2.bx.psu.edu/repos/iuc/intervene/intervene_pairwise/0.6.4	2019-01-01	1
toolshed.g2.bx.psu.edu/repos/galaxyp/msi_combine/mass_spectrometry_imaging_combine/1.7.0.0	2019-01-01	1
toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/blastxml_to_tabular/0.3.1	2019-01-01	1
toolshed.g2.bx.psu.edu/repos/bgruening/uniprot_rest_interface/uniprot/0.2	2019-01-01	1
toolshed.g2.bx.psu.edu/repos/devteam/vcf2tsv/vcf2tsv/1.0.0_rc1+galaxy0	2019-01-01	1
toolshed.g2.bx.psu.edu/repos/iuc/mothur_list_otulabels/mothur_list_otulabels/1.39.5.0	2019-01-01	1
toolshed.g2.bx.psu.edu/repos/iuc/bcftools/bcftools_view/0.1.19.0	2019-01-01	1
toolshed.g2.bx.psu.edu/repos/bgruening/infernal/infernal_cmstat/1.1.2.0	2019-01-01	1
toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_clipping_profile/2.6.4	2019-01-01	1
toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_FPKM_count/2.6.4.1	2019-01-01	1
toolshed.g2.bx.psu.edu/repos/galaxyp/msi_combine/mass_spectrometry_imaging_combine/1.10.0.4	2019-01-01	1
toolshed.g2.bx.psu.edu/repos/galaxyp/msi_combine/mass_spectrometry_imaging_combine/1.10.0.2	2019-01-01	1
toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_design/mothur_make_design/1.39.5.0	2019-01-01	1
toolshed.g2.bx.psu.edu/repos/chemteam/mdanalysis_rdf/mdanalysis_rdf/0.18	2019-01-01	1
toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_geneBody_coverage/2.6.4.2	2019-01-01	1
toolshed.g2.bx.psu.edu/repos/iuc/bcftools_csq/bcftools_csq/1.4.0.0	2019-01-01	1
toolshed.g2.bx.psu.edu/repos/iuc/heinz/heinz_visualization/0.1.0	2019-01-01	1
echo_main_env	2019-01-01	1
toolshed.g2.bx.psu.edu/repos/bgruening/hicup_deduplicator/hicup_deduplicator/0.6.1.0	2019-01-01	1
toolshed.g2.bx.psu.edu/repos/crs4/sopra/sopra_wpc/0.1	2019-01-01	1
toolshed.g2.bx.psu.edu/repos/iuc/mothur_merge_groups/mothur_merge_groups/1.39.5.0	2019-01-01	1
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FixMateInformation/2.18.2.1	2019-01-01	1
toolshed.g2.bx.psu.edu/repos/iuc/stacks_ustacks/stacks_ustacks/1.46.0	2019-01-01	1
toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_junction_annotation/2.6.4.1	2019-01-01	1
toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_junction_saturation/2.6.4.1	2019-01-01	1
toolshed.g2.bx.psu.edu/repos/devteam/vcfbreakcreatemulti/vcfbreakcreatemulti/1.0.0_rc1+galaxy0	2019-01-01	1
toolshed.g2.bx.psu.edu/repos/devteam/vcfcheck/vcfcheck/1.0.0_rc1+galaxy0	2019-01-01	1
toolshed.g2.bx.psu.edu/repos/galaxyp/msconvert_nix/msconvert_nix/3.0.9992.0	2019-01-01	1
toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_tin/2.6.4.1	2019-01-01	1
toolshed.g2.bx.psu.edu/repos/iuc/goenrichment/goenrichment/2.0.1	2019-01-01	1
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toolshed.g2.bx.psu.edu/repos/galaxyp/msconvert/msconvert_win/3.0.0	2019-01-01	1
toolshed.g2.bx.psu.edu/repos/devteam/kraken_report/kraken-mpa-report/1.2.4	2019-01-01	1
toolshed.g2.bx.psu.edu/repos/galaxyp/msconvert/msconvert_nix/3.0.0	2019-01-01	1
toolshed.g2.bx.psu.edu/repos/iuc/gemini_recessive_and_dominant/gemini_recessive_and_dominant/0.18.1.0	2019-01-01	1
toolshed.g2.bx.psu.edu/repos/iuc/gemini_lof_sieve/gemini_lof_sieve/0.20.1	2019-01-01	1
CONVERTER_wiggle_to_interval_0	2019-01-01	1
toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/1.3.0	2019-01-01	1
toolshed.g2.bx.psu.edu/repos/iuc/gemini_interactions/gemini_interactions/0.20.1	2019-01-01	1
toolshed.g2.bx.psu.edu/repos/devteam/vcfgenotypes/vcfgenotypes/1.0.0_rc1+galaxy0	2019-01-01	1
toolshed.g2.bx.psu.edu/repos/devteam/bowtie_wrappers/bowtie_wrapper/1.1.5	2019-01-01	1
toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpsift_vartype/4.3.1	2019-01-01	1
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_simplesearchengine/SimpleSearchEngine/2.3.0	2019-01-01	1
CONVERTER_sam_to_unsorted_bam	2019-01-01	1
toolshed.g2.bx.psu.edu/repos/devteam/vcfhethom/vcfhethom/1.0.0_rc1+galaxy0	2019-01-01	1
CONVERTER_sam_to_bigwig_0	2019-01-01	1
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtoigv/2.27.0.0	2019-01-01	1
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toolshed.g2.bx.psu.edu/repos/iuc/gatk2/gatk2_variant_select/2.8.0	2019-01-01	1
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toolshed.g2.bx.psu.edu/repos/iuc/gatk2/gatk2_variant_annotator/2.8.0	2019-01-01	1
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toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_download/4.3k.0	2019-01-01	1
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toolshed.g2.bx.psu.edu/repos/earlhaminst/ensembl_get_sequences/get_sequences/0.1.2	2019-01-01	1
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toolshed.g2.bx.psu.edu/repos/iuc/ncbi_eutils_egquery/ncbi_eutils_egquery/1.1	2019-01-01	1
toolshed.g2.bx.psu.edu/repos/iuc/ncbi_eutils_egquery/ncbi_eutils_egquery/1.2	2019-01-01	1
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toolshed.g2.bx.psu.edu/repos/earlhaminst/hcluster_sg_parser/hcluster_sg_parser/0.2.0	2019-01-01	1
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toolshed.g2.bx.psu.edu/repos/iuc/pick_closed_reference_otus/pick_closed_reference_otus/1.9.1.0	2019-01-01	1
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toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: newcpgseek58/5.0.0.1	2019-01-01	1
toolshed.g2.bx.psu.edu/repos/devteam/pileup_parser/pileup_parser/1.0.2	2019-01-01	1
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toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: seqmatchall83/5.0.0.1	2019-01-01	1
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toolshed.g2.bx.psu.edu/repos/galaxyp/gffcompare_to_bed/gffcompare_to_bed/0.1.0	2019-01-01	1
toolshed.g2.bx.psu.edu/repos/devteam/principal_component_analysis/pca1/1.0.2	2019-01-01	1
toolshed.g2.bx.psu.edu/repos/bgruening/bamhash/bamhash/1.1	2019-01-01	1
toolshed.g2.bx.psu.edu/repos/earlhaminst/treebest_best/treebest_best/1.9.2.post0	2019-01-01	1
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toolshed.g2.bx.psu.edu/repos/iuc/ebi_metagenomics_run_downloader/ebi_metagenomics_run_downloader/0.1.0	2019-01-01	1
toolshed.g2.bx.psu.edu/repos/earlhaminst/treebest_best/treebest_best_wrapper/1.9.2	2019-01-01	1
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toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: wordcount109/5.0.0.1	2019-01-01	1
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toolshed.g2.bx.psu.edu/repos/rnateam/rnacode/rbc_rnacode/0.3.0	2019-01-01	1
toolshed.g2.bx.psu.edu/repos/rnateam/rnalien/RNAlien/1.3.6	2019-01-01	1
toolshed.g2.bx.psu.edu/repos/iuc/dexseq/dexseq_count/1.0	2019-01-01	1
toolshed.g2.bx.psu.edu/repos/rnateam/selectsequencesfrommsa/selectsequencesfrommsa/1.0.2	2019-01-01	1
toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.1.8.0	2019-01-01	1
toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_subseq/1.3.1	2019-01-01	1
toolshed.g2.bx.psu.edu/repos/devteam/fastx_reverse_complement/cshl_fastx_reverse_complement/1.0.2	2019-01-01	1
toolshed.g2.bx.psu.edu/repos/rnateam/splitfasta/rbc_splitfasta/0.2.0	2019-01-01	1
toolshed.g2.bx.psu.edu/repos/rnateam/sshmm/sshmm/1.0.7	2019-01-01	1
toolshed.g2.bx.psu.edu/repos/iuc/pureclip/pureclip/1.0.4	2019-01-01	1
toolshed.g2.bx.psu.edu/repos/bgruening/chemical_data_sources/ctb_pubchem_download_assays/1.0.0	2019-01-01	1
toolshed.g2.bx.psu.edu/repos/rnateam/viennarna_rnaalifold/viennarna_rnaalifold/2.2.10.1	2019-01-01	1
toolshed.g2.bx.psu.edu/repos/devteam/fastx_renamer/cshl_fastx_renamer/0.0.14+galaxy0	2019-01-01	1
toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.38	2019-01-01	1
toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_mergefa/1.3.1	2019-01-01	1
toolshed.g2.bx.psu.edu/repos/rnateam/viennarna_rnaplot/viennarna_rnaplot/2.2.10.0	2019-01-01	1
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toolshed.g2.bx.psu.edu/repos/galaxyp/openms_mapstatistics/MapStatistics/2.3.0	2019-01-01	1
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toolshed.g2.bx.psu.edu/repos/ethevenot/multivariate/Multivariate/2.3.10	2019-01-01	1
toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.0.0	2019-01-01	1
toolshed.g2.bx.psu.edu/repos/devteam/fastx_barcode_splitter/cshl_fastx_barcode_splitter/1.0.1	2019-01-01	1
toolshed.g2.bx.psu.edu/repos/iuc/bp_genbank2gff3/bp_genbank2gff3/1.0	2019-01-01	1
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toolshed.g2.bx.psu.edu/repos/ethevenot/univariate/Univariate/2.2.4	2019-01-01	1
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_windowbed/2.27.0.0	2019-01-01	1
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_map/2.27.0.0	2019-01-01	1
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_maskfastabed/2.27.0.0	2019-01-01	1
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idmassaccuracy/IDMassAccuracy/2.3.0	2019-01-01	1
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toolshed.g2.bx.psu.edu/repos/fcaramia/varscan/varscan_mpileup/2.3.5	2019-01-01	1
toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/4.1	2019-01-01	1
toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_quality_report/cardinal_quality_report/1.12.1.0	2019-01-01	1
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multicovtbed/2.27.1	2019-01-01	1
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_mergebedgraph/2.19.0	2019-01-01	1
toolshed.g2.bx.psu.edu/repos/iuc/valet/valet/1.0.0	2019-01-01	1
upload1	2018-12-01	11541
toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72	2018-12-01	8270
toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.6.0b-1	2018-12-01	3608
toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.71	2018-12-01	3406
toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.3	2018-12-01	3284
toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/1.6.3	2018-12-01	3231
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toolshed.g2.bx.psu.edu/repos/bgruening/infernal/infernal_cmsearch/1.1.2.0	2018-12-01	2061
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toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_infer_experiment/2.6.4.1	2018-12-01	2031
toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_deinterlacer/fastq_paired_end_deinterlacer/1.1.2	2018-12-01	1795
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toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.6	2018-12-01	1578
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toolshed.g2.bx.psu.edu/repos/rnateam/graphclust_cmfinder/cmFinder/0.3	2018-12-01	1575
toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/2.9.1.3	2018-12-01	1557
toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.36.5	2018-12-01	1481
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toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/1.3.4	2018-12-01	1143
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toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0	2018-12-01	896
toolshed.g2.bx.psu.edu/repos/devteam/join/gops_join_1/1.0.0	2018-12-01	865
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toolshed.g2.bx.psu.edu/repos/iuc/goseq/goseq/1.30.1	2018-12-01	802
toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.4	2018-12-01	752
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1	2018-12-01	713
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toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.4	2018-12-01	654
toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_wrapper_2/1.3.2	2018-12-01	654
toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1	2018-12-01	649
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toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.4.2	2018-12-01	619
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toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_heatmap2/ggplot2_heatmap2/2.2.1+galaxy1	2018-12-01	529
toolshed.g2.bx.psu.edu/repos/devteam/tophat2/tophat2/2.1.1	2018-12-01	527
toolshed.g2.bx.psu.edu/repos/lparsons/htseq_count/htseq_count/0.9.1	2018-12-01	519
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/deeptools_compute_matrix/3.0.2.0	2018-12-01	485
toolshed.g2.bx.psu.edu/repos/rnateam/graphclust_mlocarna/locarna_best_subtree/0.4	2018-12-01	485
toolshed.g2.bx.psu.edu/repos/rnateam/graphclust_cmfinder/cmFinder/0.4	2018-12-01	485
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toolshed.g2.bx.psu.edu/repos/devteam/vcffilter/vcffilter2/1.0.0_rc1+galaxy1	2018-12-01	471
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toolshed.g2.bx.psu.edu/repos/devteam/vcfallelicprimitives/vcfallelicprimitives/1.0.0_rc1+galaxy0	2018-12-01	430
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_heatmap/deeptools_plot_heatmap/3.0.2.0	2018-12-01	430
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.0.2.0	2018-12-01	410
toolshed.g2.bx.psu.edu/repos/iuc/gtftobed12/gtftobed12/357	2018-12-01	398
toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.2.0	2018-12-01	364
toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.1.0.46-0	2018-12-01	361
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toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.2	2018-12-01	326
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toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.1	2018-12-01	294
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toolshed.g2.bx.psu.edu/repos/galaxyp/openms_falsediscoveryrate/FalseDiscoveryRate/2.3.0	2018-12-01	219
toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/2.0.0	2018-12-01	218
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_correlation/deeptools_plot_correlation/3.0.2.0	2018-12-01	214
toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.1.1.20160309.5	2018-12-01	211
toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.1	2018-12-01	208
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toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/3.2	2018-12-01	195
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toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_profile/deeptools_plot_profile/3.1.2.0.0	2018-12-01	188
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/1.1.0	2018-12-01	188
toolshed.g2.bx.psu.edu/repos/devteam/samtools_flagstat/samtools_flagstat/2.0.2	2018-12-01	185
toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.3	2018-12-01	182
toolshed.g2.bx.psu.edu/repos/crs4/prokka/prokka/1.13	2018-12-01	178
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_compare/deeptools_bam_compare/3.0.2.0	2018-12-01	166
toolshed.g2.bx.psu.edu/repos/devteam/intersect/gops_intersect_1/1.0.0	2018-12-01	157
toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/1.6.2	2018-12-01	156
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.0	2018-12-01	155
toolshed.g2.bx.psu.edu/repos/devteam/fastq_manipulation/fastq_manipulation/1.1.1	2018-12-01	139
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_coveragebed/2.27.0.2	2018-12-01	137
toolshed.g2.bx.psu.edu/repos/rnateam/chipseeker/chipseeker/1.16.2	2018-12-01	135
toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastx_wrapper/0.3.1	2018-12-01	134
toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.5.0.1	2018-12-01	131
toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.36.0	2018-12-01	130
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicplottads/hicexplorer_hicplottads/2.1.4.0	2018-12-01	128
toolshed.g2.bx.psu.edu/repos/devteam/vcfallelicprimitives/vcfallelicprimitives/0.0.3	2018-12-01	118
toolshed.g2.bx.psu.edu/repos/iuc/sqlite_to_tabular/sqlite_to_tabular/2.0.0	2018-12-01	117
toolshed.g2.bx.psu.edu/repos/iuc/gemini_query/gemini_query/0.18.1.0	2018-12-01	117
CONVERTER_fastq_to_fqtoc0	2018-12-01	117
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_msgfplusadapter/MSGFPlusAdapter/2.3.0	2018-12-01	116
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idscoreswitcher/IDScoreSwitcher/2.3.0	2018-12-01	115
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_xtandemadapter/XTandemAdapter/2.3.0	2018-12-01	114
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_fileinfo/FileInfo/2.3.0	2018-12-01	112
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_peptideindexer/PeptideIndexer/2.3.0	2018-12-01	111
toolshed.g2.bx.psu.edu/repos/ethevenot/multivariate/Multivariate/2.3.10	2018-12-01	111
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idfilter/IDFilter/2.3.0	2018-12-01	110
toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.20.7.2	2018-12-01	110
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_proteinquantifier/ProteinQuantifier/2.3.0	2018-12-01	110
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_fidoadapter/FidoAdapter/2.3.0	2018-12-01	108
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_featurefindermultiplex/FeatureFinderMultiplex/2.3.0	2018-12-01	108
CONVERTER_interval_to_bed12_0	2018-12-01	107
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.1	2018-12-01	107
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_filefilter/FileFilter/2.3.0	2018-12-01	106
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idmapper/IDMapper/2.3.0	2018-12-01	104
toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.0.2.29-1	2018-12-01	104
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_consensusid/ConsensusID/2.3.0	2018-12-01	104
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/1.1.0	2018-12-01	103
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_mergebed/2.27.0.0	2018-12-01	103
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idconflictresolver/IDConflictResolver/2.3.0	2018-12-01	103
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idmerger/IDMerger/2.3.0	2018-12-01	102
toolshed.g2.bx.psu.edu/repos/devteam/samtool_filter2/samtool_filter2/1.8	2018-12-01	101
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_highresprecursormasscorrector/HighResPrecursorMassCorrector/2.3.0	2018-12-01	100
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bigwig_summary/deeptools_multi_bigwig_summary/3.0.2.0	2018-12-01	98
toolshed.g2.bx.psu.edu/repos/devteam/samtools_slice_bam/samtools_slice_bam/2.0.1	2018-12-01	97
toolshed.g2.bx.psu.edu/repos/devteam/samtools_rmdup/samtools_rmdup/2.0.1	2018-12-01	97
toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.2	2018-12-01	95
toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/0.11.2	2018-12-01	93
toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.67	2018-12-01	92
toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.69	2018-12-01	90
toolshed.g2.bx.psu.edu/repos/rnateam/graphclust_align_cluster/graphclust_align_cluster/0.1	2018-12-01	87
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_fingerprint/deeptools_plot_fingerprint/3.0.2.0	2018-12-01	87
toolshed.g2.bx.psu.edu/repos/bgruening/antismash/antismash/4.1	2018-12-01	84
toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_tblastn_wrapper/0.3.1	2018-12-01	83
Remove beginning1	2018-12-01	82
toolshed.g2.bx.psu.edu/repos/devteam/get_flanks/get_flanks1/1.0.0	2018-12-01	79
toolshed.g2.bx.psu.edu/repos/galaxyp/unipept/unipept/2.0.1	2018-12-01	78
toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.3	2018-12-01	78
toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.1.1.20160309.4	2018-12-01	77
toolshed.g2.bx.psu.edu/repos/crs4/bwa_mem/bwa_mem/0.8.0	2018-12-01	75
toolshed.g2.bx.psu.edu/repos/devteam/fasta_filter_by_length/fasta_filter_by_length/1.1	2018-12-01	75
toolshed.g2.bx.psu.edu/repos/rnateam/segemehl/segemehl/0.2.0.3	2018-12-01	74
toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_contigs/mothur_make_contigs/1.39.5.0	2018-12-01	74
toolshed.g2.bx.psu.edu/repos/iuc/gemini_load/gemini_load/0.18.1.0	2018-12-01	73
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_annotatebed/2.27.0.0	2018-12-01	73
toolshed.g2.bx.psu.edu/repos/rnateam/structure_to_gspan/structure_to_gspan/0.3	2018-12-01	73
toolshed.g2.bx.psu.edu/repos/devteam/fastqtofasta/fastq_to_fasta_python/1.0.0	2018-12-01	72
toolshed.g2.bx.psu.edu/repos/iuc/deg_annotate/deg_annotate/1.0	2018-12-01	72
toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.4.3.0	2018-12-01	71
toolshed.g2.bx.psu.edu/repos/devteam/merge/gops_merge_1/1.0.0	2018-12-01	71
Grep1	2018-12-01	69
toolshed.g2.bx.psu.edu/repos/rnateam/graphclust_nspdk/NSPDK_candidateClust/9.2.2	2018-12-01	69
toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3r.1	2018-12-01	69
toolshed.g2.bx.psu.edu/repos/rnateam/graphclust_prepocessing_for_mlocarna/preMloc/0.3	2018-12-01	69
toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.5.2b-1	2018-12-01	69
toolshed.g2.bx.psu.edu/repos/rnateam/graphclust_preprocessing/preproc/0.4	2018-12-01	69
toolshed.g2.bx.psu.edu/repos/devteam/cuffdiff/cuffdiff/2.2.1.5	2018-12-01	68
toolshed.g2.bx.psu.edu/repos/rnateam/graphclust_postprocessing/glob_report/0.4	2018-12-01	66
toolshed.g2.bx.psu.edu/repos/rnateam/graphclust_nspdk/nspdk_sparse/9.2.2	2018-12-01	66
toolshed.g2.bx.psu.edu/repos/rnateam/epicseg/epicseg_segment/1.0	2018-12-01	66
toolshed.g2.bx.psu.edu/repos/eschen42/w4mclassfilter/w4mclassfilter/0.98.11	2018-12-01	66
toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.65	2018-12-01	65
toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.2.6	2018-12-01	65
__EXPORT_HISTORY__	2018-12-01	65
toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1.1	2018-12-01	63
toolshed.g2.bx.psu.edu/repos/crs4/muscle/muscle/0.0.11	2018-12-01	62
toolshed.g2.bx.psu.edu/repos/rnateam/sortmerna/bg_sortmerna/2.1b.5	2018-12-01	62
toolshed.g2.bx.psu.edu/repos/devteam/fastq_to_fasta/cshl_fastq_to_fasta/1.0.0	2018-12-01	61
toolshed.g2.bx.psu.edu/repos/bgruening/bigwig_to_bedgraph/bigwig_to_bedgraph/0.1.0	2018-12-01	61
toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3+t.galaxy0	2018-12-01	61
toolshed.g2.bx.psu.edu/repos/iuc/ngsutils_bam_filter/ngsutils_bam_filter/0.5.9	2018-12-01	59
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bam_summary/deeptools_multi_bam_summary/3.0.2.0	2018-12-01	58
CONVERTER_bedgraph_to_bigwig	2018-12-01	57
toolshed.g2.bx.psu.edu/repos/earlhaminst/ete/species_tree_generator/3.0.0b35	2018-12-01	56
wig_to_bigWig	2018-12-01	56
CONVERTER_fasta_to_tabular	2018-12-01	56
toolshed.g2.bx.psu.edu/repos/mvdbeek/add_input_name_as_column/addName/0.1.1	2018-12-01	55
toolshed.g2.bx.psu.edu/repos/iuc/trinity_align_and_estimate_abundance/trinity_align_and_estimate_abundance/2.8.4	2018-12-01	54
toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/search_gui/3.3.3.0	2018-12-01	54
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_gc_bias/deeptools_compute_gc_bias/3.0.2.0	2018-12-01	53
toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.3.1	2018-12-01	53
toolshed.g2.bx.psu.edu/repos/devteam/fastq_trimmer/fastq_trimmer/1.1.1	2018-12-01	52
toolshed.g2.bx.psu.edu/repos/rnateam/viennarna_rnafold/viennarna_rnafold/2.2.10.4	2018-12-01	51
toolshed.g2.bx.psu.edu/repos/jjohnson/rsem/rsem_prepare_reference/1.1.17	2018-12-01	51
toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/peptide_shaker/1.16.26	2018-12-01	50
Convert characters1	2018-12-01	50
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1	2018-12-01	50
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeSamFiles/2.18.2.1	2018-12-01	50
toolshed.g2.bx.psu.edu/repos/lparsons/htseq_count/htseq_count/0.6.1galaxy2	2018-12-01	49
toolshed.g2.bx.psu.edu/repos/iuc/shovill/shovill/1.0.4	2018-12-01	49
CONVERTER_bed_gff_or_vcf_to_bigwig_0	2018-12-01	49
ip_projective_transformation_points	2018-12-01	48
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.27.0.0	2018-12-01	48
ia_coordinates_of_roi	2018-12-01	48
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.27.1	2018-12-01	48
toolshed.g2.bx.psu.edu/repos/devteam/subtract/gops_subtract_1/1.0.0	2018-12-01	47
toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_annotate/4.3+t.galaxy0	2018-12-01	46
toolshed.g2.bx.psu.edu/repos/rnateam/metilene/metilene/0.2.6.1	2018-12-01	46
toolshed.g2.bx.psu.edu/repos/lparsons/htseq_count/htseq_count/0.6.1galaxy3	2018-12-01	44
toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.0	2018-12-01	44
toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0.2	2018-12-01	43
toolshed.g2.bx.psu.edu/repos/nml/spades/spades/3.12.0	2018-12-01	43
mergeCols1	2018-12-01	42
toolshed.g2.bx.psu.edu/repos/devteam/add_value/addValue/1.0.0	2018-12-01	42
toolshed.g2.bx.psu.edu/repos/devteam/sicer/peakcalling_sicer/0.0.2	2018-12-01	41
toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_download/4.3r.1	2018-12-01	39
toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.2	2018-12-01	39
toolshed.g2.bx.psu.edu/repos/bgruening/pileometh/pileometh/0.3.0.1	2018-12-01	39
toolshed.g2.bx.psu.edu/repos/iuc/gemini_db_info/gemini_db_info/0.18.1.0	2018-12-01	39
wc_gnu	2018-12-01	38
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.27.0.0	2018-12-01	38
toolshed.g2.bx.psu.edu/repos/devteam/fastx_trimmer/cshl_fastx_trimmer/1.0.2	2018-12-01	37
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_pca/deeptools_plot_pca/3.1.2.0.0	2018-12-01	36
toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_geneBody_coverage/2.6.4.3	2018-12-01	36
toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.2.2	2018-12-01	36
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.1	2018-12-01	36
toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_distribution/2.6.4.1	2018-12-01	36
toolshed.g2.bx.psu.edu/repos/devteam/bowtie_wrappers/bowtie_wrapper/1.2.0	2018-12-01	34
toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_fastq/mothur_make_fastq/1.36.1.0	2018-12-01	34
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CASM/2.18.2.1	2018-12-01	34
toolshed.g2.bx.psu.edu/repos/iuc/roary/roary/3.10.2	2018-12-01	33
toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastp_wrapper/0.3.1	2018-12-01	33
addValue	2018-12-01	33
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.0	2018-12-01	33
toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/2.2.1.2	2018-12-01	32
CONVERTER_bed_to_gff_0	2018-12-01	32
toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.1	2018-12-01	32
toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.1	2018-12-01	32
toolshed.g2.bx.psu.edu/repos/bgruening/graphicsmagick_image_convert/graphicsmagick_image_convert/1.3.26	2018-12-01	32
toolshed.g2.bx.psu.edu/repos/iuc/mothur_summary_seqs/mothur_summary_seqs/1.39.5.0	2018-12-01	32
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SortSam/2.18.2.1	2018-12-01	31
toolshed.g2.bx.psu.edu/repos/devteam/weblogo3/rgweblogo3/3.5.0	2018-12-01	31
toolshed.g2.bx.psu.edu/repos/devteam/varscan_version_2/varscan/2.4.2	2018-12-01	31
__ZIP_COLLECTION__	2018-12-01	31
toolshed.g2.bx.psu.edu/repos/iuc/raceid_inspectclusters/raceid_inspectclusters/3.0.2.1	2018-12-01	31
toolshed.g2.bx.psu.edu/repos/devteam/coverage/gops_coverage_1/1.0.0	2018-12-01	31
toolshed.g2.bx.psu.edu/repos/devteam/correlation/cor2/1.0.0	2018-12-01	31
toolshed.g2.bx.psu.edu/repos/devteam/cuffmerge/cuffmerge/2.2.1.1	2018-12-01	30
toolshed.g2.bx.psu.edu/repos/earlhaminst/t_coffee/t_coffee/11.0.8	2018-12-01	30
toolshed.g2.bx.psu.edu/repos/iuc/raceid_trajectory/raceid_trajectory/3.0.2.1	2018-12-01	30
toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.34.9.9	2018-12-01	30
toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.6.0	2018-12-01	30
toolshed.g2.bx.psu.edu/repos/eschen42/w4mcorcov/w4mcorcov/0.98.17	2018-12-01	30
Paste1	2018-12-01	29
toolshed.g2.bx.psu.edu/repos/rnateam/blockclust/blockclust/1.1.0	2018-12-01	29
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed_bedgraph/2.19.0	2018-12-01	28
toolshed.g2.bx.psu.edu/repos/iuc/kobas/kobas_annotate/0.4	2018-12-01	28
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicfindtads/hicexplorer_hicfindtads/2.1.4.0	2018-12-01	28
toolshed.g2.bx.psu.edu/repos/earlhaminst/treebest_best/treebest_best_wrapper/1.9.2	2018-12-01	28
trimmer	2018-12-01	28
toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_build_pipeline/sklearn_build_pipeline/0.9	2018-12-01	28
toolshed.g2.bx.psu.edu/repos/nml/spades/spades/3.12.0+galaxy1	2018-12-01	27
toolshed.g2.bx.psu.edu/repos/miller-lab/genome_diversity/gd_cluster_kegg/1.0.0	2018-12-01	27
toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.0	2018-12-01	27
toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.1.3	2018-12-01	27
Show tail1	2018-12-01	26
toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_searchcv/sklearn_searchcv/0.9	2018-12-01	26
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.27.0.1	2018-12-01	26
toolshed.g2.bx.psu.edu/repos/devteam/concat/gops_concat_1/1.0.1	2018-12-01	26
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.1	2018-12-01	25
toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/4.6.3	2018-12-01	25
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_multijoin_tool/1.1.1	2018-12-01	25
toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.12	2018-12-01	25
CONVERTER_bam_to_coodinate_sorted_bam	2018-12-01	24
toolshed.g2.bx.psu.edu/repos/iuc/mothur_screen_seqs/mothur_screen_seqs/1.39.5.0	2018-12-01	24
toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_mergefa/1.3.0	2018-12-01	24
toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_FPKM_count/2.6.4.1	2018-12-01	24
toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_violin/ggplot2_violin/2.2.1+galaxy0	2018-12-01	24
toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/datamash_ops/1.0.6	2018-12-01	24
toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.0.0	2018-12-01	24
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicaggregatecontacts/hicexplorer_hicaggregatecontacts/2.1.4.0	2018-12-01	24
toolshed.g2.bx.psu.edu/repos/iuc/mothur_heatmap_sim/mothur_heatmap_sim/1.39.5.0	2018-12-01	24
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_fileinfo/FileInfo/2.2.0	2018-12-01	24
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_falsediscoveryrate/FalseDiscoveryRate/2.2.0	2018-12-01	24
toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/0.7.0.3	2018-12-01	23
toolshed.g2.bx.psu.edu/repos/iuc/stacks_refmap/stacks_refmap/1.46.0	2018-12-01	23
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicplotmatrix/hicexplorer_hicplotmatrix/2.1.4.0	2018-12-01	23
CONVERTER_bam_to_bigwig_0	2018-12-01	23
toolshed.g2.bx.psu.edu/repos/iuc/mothur_summary_seqs/mothur_summary_seqs/1.36.1.0	2018-12-01	22
random_lines1	2018-12-01	22
toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_ensemble/sklearn_ensemble/0.9	2018-12-01	22
toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpSift_annotate/3.4	2018-12-01	22
toolshed.g2.bx.psu.edu/repos/iuc/mothur_screen_seqs/mothur_screen_seqs/1.36.1.0	2018-12-01	22
toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.68	2018-12-01	22
toolshed.g2.bx.psu.edu/repos/bgruening/pileometh/pileometh/0.3.0	2018-12-01	22
gtf_filter_by_attribute_values_list	2018-12-01	22
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/deeptools_compute_matrix/2.5.1.1.0	2018-12-01	22
raceid_main	2018-12-01	22
CONVERTER_bed_to_bgzip_0	2018-12-01	22
toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_svm_classifier/sklearn_svm_classifier/0.9	2018-12-01	21
toolshed.g2.bx.psu.edu/repos/iuc/raceid_inspecttrajectory/raceid_inspecttrajectory/3.0.2.1	2018-12-01	21
toolshed.g2.bx.psu.edu/repos/iuc/meme_fimo/meme_fimo/4.12.0.0	2018-12-01	21
toolshed.g2.bx.psu.edu/repos/devteam/clustalw/clustalw/2.1	2018-12-01	21
toolshed.g2.bx.psu.edu/repos/galaxyp/filter_by_fasta_ids/filter_by_fasta_ids/2.0	2018-12-01	21
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_peakpickerhires/PeakPickerHiRes/2.3.0	2018-12-01	21
toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/0.0.2	2018-12-01	21
toolshed.g2.bx.psu.edu/repos/chemteam/bio3d_rmsd/bio3d_rmsd/2.3	2018-12-01	21
toolshed.g2.bx.psu.edu/repos/iuc/trinity/trinity/2.8.4	2018-12-01	21
toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_interlacer/fastq_paired_end_interlacer/1.2.0.1	2018-12-01	21
toolshed.g2.bx.psu.edu/repos/devteam/sam_merge/sam_merge2/1.2.0	2018-12-01	21
toolshed.g2.bx.psu.edu/repos/iuc/extract_genomic_dna/Extract genomic DNA 1/3.0.3	2018-12-01	21
toolshed.g2.bx.psu.edu/repos/devteam/vcfcombine/vcfcombine/1.0.0_rc1+galaxy0	2018-12-01	21
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectRnaSeqMetrics/2.18.2.1	2018-12-01	21
toolshed.g2.bx.psu.edu/repos/iuc/newick_utils/newick_display/1.6	2018-12-01	21
toolshed.g2.bx.psu.edu/repos/rnateam/mlocarna/mlocarna/1.8.12.0	2018-12-01	20
velvetg	2018-12-01	20
toolshed.g2.bx.psu.edu/repos/iuc/samtools_sort/samtools_rmdup/1.0.1	2018-12-01	20
toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.3	2018-12-01	20
toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.0	2018-12-01	20
toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_heatmap/ggplot2_heatmap/2.2.1	2018-12-01	20
Summary_Statistics1	2018-12-01	19
toolshed.g2.bx.psu.edu/repos/iuc/mothur_unique_seqs/mothur_unique_seqs/1.39.5.0	2018-12-01	19
velveth	2018-12-01	19
CONVERTER_vcf_bgzip_to_tabix_0	2018-12-01	19
toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.0.2	2018-12-01	19
CONVERTER_vcf_to_vcf_bgzip_0	2018-12-01	19
re_he_maldi_image_registration	2018-12-01	18
toolshed.g2.bx.psu.edu/repos/iuc/mothur_tree_shared/mothur_tree_shared/1.39.5.0	2018-12-01	18
toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.13.0	2018-12-01	18
toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.0.20	2018-12-01	18
toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_bam_stat/2.6.4	2018-12-01	18
toolshed.g2.bx.psu.edu/repos/galaxyp/fasta_merge_files_and_filter_unique_sequences/fasta_merge_files_and_filter_unique_sequences/1.2.0	2018-12-01	18
CONVERTER_wig_to_bigwig	2018-12-01	18
viz_overlay_moving_and_fixed_image	2018-12-01	18
CONVERTER_interval_to_bigwig_0	2018-12-01	18
toolshed.g2.bx.psu.edu/repos/bgruening/bismark/bismark_bowtie2/0.20.0	2018-12-01	17
scale_image	2018-12-01	17
toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/2.8.1.3	2018-12-01	17
CONVERTER_gff_to_bed_0	2018-12-01	16
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_fileconverter/FileConverter/2.3.0	2018-12-01	16
CONVERTER_bed_to_fli_0	2018-12-01	16
toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy_core/3.2	2018-12-01	16
toolshed.g2.bx.psu.edu/repos/iuc/kallisto_quant/kallisto_quant/0.43.1.4	2018-12-01	16
toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/1.5.3	2018-12-01	16
toolshed.g2.bx.psu.edu/repos/iuc/trinity_filter_low_expr_transcripts/trinity_filter_low_expr_transcripts/2.8.4	2018-12-01	16
toolshed.g2.bx.psu.edu/repos/iuc/circos/circgraph/0.9-RC2	2018-12-01	16
toolshed.g2.bx.psu.edu/repos/devteam/fastq_quality_filter/cshl_fastq_quality_filter/1.0.2	2018-12-01	16
toolshed.g2.bx.psu.edu/repos/iuc/bwameth/bwameth/0.2.0.4	2018-12-01	15
toolshed.g2.bx.psu.edu/repos/eschen42/w4mcorcov/w4mcorcov/0.98.16	2018-12-01	15
toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.2.6.2	2018-12-01	15
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicbuildmatrix/hicexplorer_hicbuildmatrix/2.1.4.0	2018-12-01	15
CONVERTER_interval_to_bgzip_0	2018-12-01	15
toolshed.g2.bx.psu.edu/repos/simon-gladman/velvetoptimiser/velvetoptimiser/2.2.6	2018-12-01	15
toolshed.g2.bx.psu.edu/repos/devteam/picard/PicardASMetrics/1.56.0	2018-12-01	15
toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_heatmap2/ggplot2_heatmap2/2.2.1	2018-12-01	15
toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.39	2018-12-01	15
toolshed.g2.bx.psu.edu/repos/iuc/shovill/shovill/0.9.0	2018-12-01	15
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hiccorrelate/hicexplorer_hiccorrelate/2.1.4.0	2018-12-01	15
toolshed.g2.bx.psu.edu/repos/bebatut/cdhit/cd_hit_est/1.3	2018-12-01	14
toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_quality_report/cardinal_quality_report/1.12.1.1	2018-12-01	14
toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy1	2018-12-01	14
toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.1.4	2018-12-01	14
toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/fasta_compute_length/1.0.1	2018-12-01	14
toolshed.g2.bx.psu.edu/repos/devteam/fastq_trimmer_by_quality/fastq_quality_trimmer/1.1.1	2018-12-01	14
toolshed.g2.bx.psu.edu/repos/iuc/data_manager_gemini_database_downloader/data_manager_gemini_download/0.18.1.1	2018-12-01	14
toolshed.g2.bx.psu.edu/repos/rnateam/blockbuster/blockbuster/0.1.2	2018-12-01	14
CONVERTER_gff_to_interval_index_0	2018-12-01	14
toolshed.g2.bx.psu.edu/repos/devteam/macs/peakcalling_macs/1.0.1	2018-12-01	14
toolshed.g2.bx.psu.edu/repos/ethevenot/heatmap/Heatmap/2.2.2	2018-12-01	14
toolshed.g2.bx.psu.edu/repos/iuc/mothur_venn/mothur_venn/1.39.5.0	2018-12-01	14
toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_predictd/2.1.1.20160309.0	2018-12-01	13
toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread/2.2.1.1	2018-12-01	13
genbank_to_gff	2018-12-01	13
toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_bdgbroadcall/2.1.1.20160309.0	2018-12-01	13
CONVERTER_fasta_to_fai	2018-12-01	13
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1	2018-12-01	13
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_uniq_tool/1.1.1	2018-12-01	13
toolshed.g2.bx.psu.edu/repos/iuc/tsne/tsne/0.0.2	2018-12-01	13
toolshed.g2.bx.psu.edu/repos/wolma/mimodd_main/mimodd_varcall/0.1.8_1	2018-12-01	13
toolshed.g2.bx.psu.edu/repos/iuc/raceid_clustering/raceid_clustering/3.0.2.1	2018-12-01	13
toolshed.g2.bx.psu.edu/repos/devteam/bam_to_sam/bam_to_sam/2.0.1	2018-12-01	13
toolshed.g2.bx.psu.edu/repos/ethevenot/biosigner/biosigner/2.2.7	2018-12-01	13
toolshed.g2.bx.psu.edu/repos/earlhaminst/replace_chromosome_names/replace_chromosome_names/0.1	2018-12-01	13
gff2bed1	2018-12-01	13
toolshed.g2.bx.psu.edu/repos/peterjc/mira_assembler/mira_assembler/0.0.11	2018-12-01	13
CONVERTER_bed_to_tabix_0	2018-12-01	13
toolshed.g2.bx.psu.edu/repos/rnateam/graphclust_postprocessing/glob_report/0.5	2018-12-01	13
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idmapper/IDMapper/2.2.0	2018-12-01	12
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_highresprecursormasscorrector/HighResPrecursorMassCorrector/2.2.0	2018-12-01	12
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idconflictresolver/IDConflictResolver/2.2.0	2018-12-01	12
toolshed.g2.bx.psu.edu/repos/iuc/meme_chip/meme_chip/4.11.2+galaxy1	2018-12-01	12
toolshed.g2.bx.psu.edu/repos/ethevenot/univariate/Univariate/2.2.4	2018-12-01	12
toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_tblastx_wrapper/0.3.1	2018-12-01	12
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.27.0.1	2018-12-01	12
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_peptideindexer/PeptideIndexer/2.2.0	2018-12-01	12
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_featurefindermultiplex/FeatureFinderMultiplex/2.2.0	2018-12-01	12
toolshed.g2.bx.psu.edu/repos/iuc/trinity_abundance_estimates_to_matrix/trinity_abundance_estimates_to_matrix/2.8.4	2018-12-01	12
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_filefilter/FileFilter/2.2.0	2018-12-01	12
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idposteriorerrorprobability/IDPosteriorErrorProbability/2.2.0	2018-12-01	12
toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.1	2018-12-01	12
toolshed.g2.bx.psu.edu/repos/eschen42/w4mclassfilter/w4mclassfilter/0.98.10	2018-12-01	12
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_fidoadapter/FidoAdapter/2.2.0.1	2018-12-01	12
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_proteinquantifier/ProteinQuantifier/2.2.0	2018-12-01	12
toolshed.g2.bx.psu.edu/repos/bgruening/unique/bg_uniq/0.3	2018-12-01	12
toolshed.g2.bx.psu.edu/repos/iuc/mageck_count/mageck_count/0.5.7.4	2018-12-01	12
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicplotmatrix/hicexplorer_hicplotmatrix/2.1.0	2018-12-01	12
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idscoreswitcher/IDScoreSwitcher/2.2.0	2018-12-01	12
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/2.5.1.1.0	2018-12-01	12
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idfilter/IDFilter/2.2.0	2018-12-01	12
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_msgfplusadapter/MSGFPlusAdapter/2.2.0	2018-12-01	12
toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/1.0.1	2018-12-01	12
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hiccorrectmatrix/hicexplorer_hiccorrectmatrix/2.1.0	2018-12-01	12
toolshed.g2.bx.psu.edu/repos/iuc/mothur_classify_otu/mothur_classify_otu/1.36.1.0	2018-12-01	11
toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0	2018-12-01	11
toolshed.g2.bx.psu.edu/repos/saskia-hiltemann/krona_text/krona-text/1	2018-12-01	11
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_profile/deeptools_plot_profile/2.5.1.1.0	2018-12-01	11
toolshed.g2.bx.psu.edu/repos/iuc/mothur_align_seqs/mothur_align_seqs/1.36.1.0	2018-12-01	11
toolshed.g2.bx.psu.edu/repos/iuc/mothur_pre_cluster/mothur_pre_cluster/1.36.1.0	2018-12-01	11
toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.0.0	2018-12-01	11
toolshed.g2.bx.psu.edu/repos/bgruening/interproscan5/interproscan/5.0.0	2018-12-01	11
toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_biom/mothur_make_biom/1.36.1.0	2018-12-01	11
toolshed.g2.bx.psu.edu/repos/crs4/prokka/prokka/1.12.0	2018-12-01	11
toolshed.g2.bx.psu.edu/repos/iuc/stacks_populations/stacks_populations/1.46.0	2018-12-01	11
CONVERTER_fasta_to_2bit	2018-12-01	11
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bigwig_compare/deeptools_bigwig_compare/3.0.2.0	2018-12-01	11
toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_shared/mothur_make_shared/1.36.1.0	2018-12-01	11
toolshed.g2.bx.psu.edu/repos/iuc/mothur_filter_seqs/mothur_filter_seqs/1.36.1.0	2018-12-01	11
toolshed.g2.bx.psu.edu/repos/galaxyp/dbbuilder/dbbuilder/0.3.0	2018-12-01	11
toolshed.g2.bx.psu.edu/repos/bgruening/plotly_regression_performance_plots/plotly_regression_performance_plots/0.1	2018-12-01	11
toolshed.g2.bx.psu.edu/repos/iuc/goseq/goseq/1.26.0	2018-12-01	11
toolshed.g2.bx.psu.edu/repos/galaxyp/maldi_quant_preprocessing/maldi_quant_preprocessing/1.18.0.2	2018-12-01	11
toolshed.g2.bx.psu.edu/repos/bgruening/replace_column_by_key_value_file/replace_column_with_key_value_file/0.1	2018-12-01	11
toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_joiner/fastq_paired_end_joiner/2.0.1.1	2018-12-01	11
toolshed.g2.bx.psu.edu/repos/iuc/bwameth/bwameth/0.2.0.3	2018-12-01	11
toolshed.g2.bx.psu.edu/repos/rnateam/graphclust_aggregate_alignments/graphclust_aggregate_alignments/0.1	2018-12-01	11
toolshed.g2.bx.psu.edu/repos/iuc/mothur_merge_files/mothur_merge_files/1.36.1.0	2018-12-01	11
toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_group/mothur_make_group/1.36.1.0	2018-12-01	11
toolshed.g2.bx.psu.edu/repos/wolma/mimodd_main/mimodd_vcf_filter/0.1.8_1	2018-12-01	11
toolshed.g2.bx.psu.edu/repos/iuc/mothur_count_seqs/mothur_count_seqs/1.36.1.0	2018-12-01	11
toolshed.g2.bx.psu.edu/repos/wolma/mimodd_main/mimodd_varreport/0.1.8_1	2018-12-01	11
toolshed.g2.bx.psu.edu/repos/wolma/mimodd_main/mimodd_varextract/0.1.8_1	2018-12-01	11
toolshed.g2.bx.psu.edu/repos/iuc/mothur_unique_seqs/mothur_unique_seqs/1.36.1.0	2018-12-01	11
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.0	2018-12-01	11
toolshed.g2.bx.psu.edu/repos/iuc/mothur_cluster_split/mothur_cluster_split/1.36.1.0	2018-12-01	11
toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.2.0	2018-12-01	11
toolshed.g2.bx.psu.edu/repos/wolma/mimodd_main/mimodd_map/0.1.8_1	2018-12-01	11
toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.1.0	2018-12-01	11
toolshed.g2.bx.psu.edu/repos/iuc/raceid_filtnormconf/raceid_filtnormconf/3.0.2.1	2018-12-01	11
toolshed.g2.bx.psu.edu/repos/bgruening/diffbind/diffbind/2.6.6.4	2018-12-01	11
toolshed.g2.bx.psu.edu/repos/iuc/mothur_classify_seqs/mothur_classify_seqs/1.36.1.0	2018-12-01	11
toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.2.0	2018-12-01	11
toolshed.g2.bx.psu.edu/repos/iuc/gemini_burden/gemini_burden/0.18.1.0	2018-12-01	11
toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_download/4.1.0	2018-12-01	11
toolshed.g2.bx.psu.edu/repos/iuc/mothur_rarefaction_single/mothur_rarefaction_single/1.39.5.0	2018-12-01	10
toolshed.g2.bx.psu.edu/repos/bgruening/nanopolish_variants/nanopolish_variants/0.1.0	2018-12-01	10
toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/0.0.1	2018-12-01	10
toolshed.g2.bx.psu.edu/repos/iuc/mageck_mle/mageck_mle/0.5.7.1	2018-12-01	10
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_decoydatabase/DecoyDatabase/2.3.0	2018-12-01	10
toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.6.1.1	2018-12-01	10
toolshed.g2.bx.psu.edu/repos/devteam/sam_pileup/sam_pileup/1.1.2	2018-12-01	10
toolshed.g2.bx.psu.edu/repos/iuc/charts/charts/1.0.1	2018-12-01	10
toolshed.g2.bx.psu.edu/repos/bgruening/canu/canu/1.7	2018-12-01	10
toolshed.g2.bx.psu.edu/repos/iuc/qiime_assign_taxonomy/qiime_assign_taxonomy/1.9.1.0	2018-12-01	10
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed/2.27.0.0	2018-12-01	10
proteomics_search_tandem_1	2018-12-01	10
toolshed.g2.bx.psu.edu/repos/bgruening/plotly_ml_performance_plots/plotly_ml_performance_plots/0.1	2018-12-01	10
toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_download/4.0.0	2018-12-01	10
dexseq_annotate	2018-12-01	10
toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_shared/mothur_make_shared/1.39.5.0	2018-12-01	10
toolshed.g2.bx.psu.edu/repos/iuc/prinseq/prinseq/0.20.4	2018-12-01	9
toolshed.g2.bx.psu.edu/repos/iuc/stacks_procrad/stacks_procrad/1.46.0	2018-12-01	9
toolshed.g2.bx.psu.edu/repos/devteam/vcf2tsv/vcf2tsv/1.0.0_rc1+galaxy0	2018-12-01	9
toolshed.g2.bx.psu.edu/repos/iuc/enasearch_retrieve_data/enasearch_retrieve_data/0.1.1.0	2018-12-01	9
toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/blastxml_to_tabular/0.3.1	2018-12-01	9
toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_makeblastdb/0.3.1	2018-12-01	9
CONVERTER_sam_to_bigwig_0	2018-12-01	9
CONVERTER_vcf_to_bgzip_0	2018-12-01	9
CONVERTER_gff_to_fli_0	2018-12-01	9
toolshed.g2.bx.psu.edu/repos/peterjc/tmhmm_and_signalp/tmhmm2/0.0.16	2018-12-01	9
toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.12.5+galaxy1	2018-12-01	9
toolshed.g2.bx.psu.edu/repos/rnateam/mafft/rbc_mafft/7.221.3	2018-12-01	9
toolshed.g2.bx.psu.edu/repos/iuc/ucsc_twobittofa/ucsc-twobittofa/357	2018-12-01	9
toolshed.g2.bx.psu.edu/repos/iuc/trinity_super_transcripts/trinity_super_transcripts/2.8.4	2018-12-01	9
toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_splitter/fastq_paired_end_splitter/1.1.1	2018-12-01	9
toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.52	2018-12-01	9
toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.4.2	2018-12-01	9
toolshed.g2.bx.psu.edu/repos/devteam/fastq_stats/fastq_stats/1.0.0	2018-12-01	9
toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_filtering/cardinal_filtering/1.12.1.1	2018-12-01	8
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_DownsampleSam/2.18.2.1	2018-12-01	8
gff_filter_by_feature_count	2018-12-01	8
toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.19.3.3	2018-12-01	8
toolshed.g2.bx.psu.edu/repos/devteam/fastq_stats/fastq_stats/1.1.1	2018-12-01	8
toolshed.g2.bx.psu.edu/repos/bgruening/join_files_on_column_fuzzy/join_files_on_column_fuzzy/1.0.1	2018-12-01	8
toolshed.g2.bx.psu.edu/repos/iuc/gemini_comp_hets/gemini_comp_hets/0.18.1.0	2018-12-01	8
bed2gff1	2018-12-01	8
toolshed.g2.bx.psu.edu/repos/devteam/cluster/gops_cluster_1/1.0.0	2018-12-01	8
toolshed.g2.bx.psu.edu/repos/iuc/mothur_classify_seqs/mothur_classify_seqs/1.39.5.0	2018-12-01	8
toolshed.g2.bx.psu.edu/repos/iuc/mageck_test/mageck_test/0.5.7.1	2018-12-01	8
toolshed.g2.bx.psu.edu/repos/iuc/dexseq/dexseq_count/1.24.0.0	2018-12-01	8
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_slopbed/2.27.0.0	2018-12-01	8
toolshed.g2.bx.psu.edu/repos/iuc/mothur_count_seqs/mothur_count_seqs/1.39.5.0	2018-12-01	8
toolshed.g2.bx.psu.edu/repos/galaxyp/msconvert_nix/msconvert_nix/3.0.9992.0	2018-12-01	8
toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_bam2wig/2.6.4	2018-12-01	8
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toolshed.g2.bx.psu.edu/repos/iuc/mothur_align_seqs/mothur_align_seqs/1.39.5.0	2018-12-01	8
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toolshed.g2.bx.psu.edu/repos/bgruening/augustus/augustus/3.2.3	2018-12-01	8
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toolshed.g2.bx.psu.edu/repos/devteam/vcfvcfintersect/vcfvcfintersect/1.0.0_rc1+galaxy0	2018-12-01	8
toolshed.g2.bx.psu.edu/repos/devteam/fastq_filter/fastq_filter/1.1.1	2018-12-01	7
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toolshed.g2.bx.psu.edu/repos/devteam/samtools_bedcov/samtools_bedcov/2.0.1	2018-12-01	7
toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.1.0	2018-12-01	7
toolshed.g2.bx.psu.edu/repos/devteam/picard/rgPicardMarkDups/1.56.0	2018-12-01	7
toolshed.g2.bx.psu.edu/repos/iuc/mothur_pre_cluster/mothur_pre_cluster/1.39.5.0	2018-12-01	7
toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/2.4.0	2018-12-01	7
toolshed.g2.bx.psu.edu/repos/devteam/cummerbund/cummeRbund/2.16.0	2018-12-01	7
toolshed.g2.bx.psu.edu/repos/chemteam/mdanalysis_distance/mdanalysis_distance/0.18	2018-12-01	7
toolshed.g2.bx.psu.edu/repos/iuc/gemini_dump/gemini_dump/0.18.1.0	2018-12-01	7
toolshed.g2.bx.psu.edu/repos/iuc/pear/iuc_pear/0.9.6.1	2018-12-01	7
toolshed.g2.bx.psu.edu/repos/iuc/ncbi_eutils_esearch/ncbi_eutils_esearch/1.1	2018-12-01	7
toolshed.g2.bx.psu.edu/repos/kellrott/regex_replace/regex_replace/1.0.0	2018-12-01	7
toolshed.g2.bx.psu.edu/repos/bgruening/bismark/bismark_bowtie/0.7.12	2018-12-01	7
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_textexporter/TextExporter/2.3.0	2018-12-01	7
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicplottads/hicexplorer_hicplottads/2.1.0	2018-12-01	7
toolshed.g2.bx.psu.edu/repos/iuc/filtlong/filtlong/0.2.0	2018-12-01	7
toolshed.g2.bx.psu.edu/repos/devteam/bowtie_color_wrappers/bowtie_color_wrapper/1.1.2	2018-12-01	6
toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_histogram/ggplot2_histogram/2.2.1+galaxy0	2018-12-01	6
toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.6	2018-12-01	6
toolshed.g2.bx.psu.edu/repos/iuc/trinity_run_de_analysis/trinity_run_de_analysis/2.8.4	2018-12-01	6
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_correlation/deeptools_plot_correlation/2.0.1.0	2018-12-01	6
toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/1.6.0.2	2018-12-01	6
toolshed.g2.bx.psu.edu/repos/galaxyp/reactome_pathwaymatcher/reactome_pathwaymatcher/1.8.1.2	2018-12-01	6
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicmergematrixbins/hicexplorer_hicmergematrixbins/2.1.0	2018-12-01	6
toolshed.g2.bx.psu.edu/repos/iuc/mothur_remove_seqs/mothur_remove_seqs/1.36.1.0	2018-12-01	6
toolshed.g2.bx.psu.edu/repos/iuc/mothur_filter_seqs/mothur_filter_seqs/1.39.5.0	2018-12-01	6
toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/2.9.1.3	2018-12-01	6
toolshed.g2.bx.psu.edu/repos/iuc/seurat/seurat/2.3.4	2018-12-01	6
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicpca/hicexplorer_hicpca/2.1.0	2018-12-01	6
toolshed.g2.bx.psu.edu/repos/iuc/mothur_remove_lineage/mothur_remove_lineage/1.39.5.0	2018-12-01	6
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_correct_gc_bias/deeptools_correct_gc_bias/3.0.2.0	2018-12-01	6
toolshed.g2.bx.psu.edu/repos/ethevenot/qualitymetrics/quality_metrics/2.2.8	2018-12-01	6
toolshed.g2.bx.psu.edu/repos/iuc/poretools_hist/poretools_hist/0.6.1a1.0	2018-12-01	6
toolshed.g2.bx.psu.edu/repos/iuc/mothur_chimera_vsearch/mothur_chimera_vsearch/1.39.5.1	2018-12-01	6
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toolshed.g2.bx.psu.edu/repos/iuc/gatk2/gatk2_depth_of_coverage/2.8.0	2018-12-01	6
toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/2.9.1.4	2018-12-01	6
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_BamIndexStats/1.56.0	2018-12-01	6
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicbuildmatrix/hicexplorer_hicbuildmatrix/2.1.0	2018-12-01	6
toolshed.g2.bx.psu.edu/repos/devteam/samtools_flagstat/samtools_flagstat/2.0.1	2018-12-01	6
toolshed.g2.bx.psu.edu/repos/rnateam/graphclust_nspdk/nspdk_sparse/9.2.3	2018-12-01	6
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toolshed.g2.bx.psu.edu/repos/iuc/gemini_recessive_and_dominant/gemini_recessive_and_dominant/0.18.1.0	2018-12-01	6
toolshed.g2.bx.psu.edu/repos/rnateam/chipseeker/chipseeker/1.14.2.1	2018-12-01	6
toolshed.g2.bx.psu.edu/repos/iuc/humann2/humann2/0.11.1.0	2018-12-01	6
toolshed.g2.bx.psu.edu/repos/devteam/vcfbedintersect/vcfbedintersect/0.0.3	2018-12-01	6
toolshed.g2.bx.psu.edu/repos/iuc/mothur_count_groups/mothur_count_groups/1.39.5.0	2018-12-01	6
toolshed.g2.bx.psu.edu/repos/blankenberg/naive_variant_caller/naive_variant_caller/0.0.3	2018-12-01	6
toolshed.g2.bx.psu.edu/repos/iuc/gemini/gemini_load/0.10.1.0	2018-12-01	6
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtofastq/2.27.0.0	2018-12-01	6
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_pca/deeptools_plot_pca/2.5.1.1.0	2018-12-01	6
toolshed.g2.bx.psu.edu/repos/iuc/metaphlan2/metaphlan2/2.6.0.0	2018-12-01	6
toolshed.g2.bx.psu.edu/repos/iuc/mothur_cluster/mothur_cluster/1.39.5.0	2018-12-01	6
toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie_merge/1.3.4	2018-12-01	6
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtobam/2.27.0.0	2018-12-01	6
toolshed.g2.bx.psu.edu/repos/iuc/gemini_de_novo/gemini_de_novo/0.18.1.0	2018-12-01	6
toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy3	2018-12-01	6
toolshed.g2.bx.psu.edu/repos/peterjc/tmhmm_and_signalp/rxlr_motifs/0.0.14	2018-12-01	6
toolshed.g2.bx.psu.edu/repos/rnateam/viennarna_rnaplot/viennarna_rnaplot/2.2.10.0	2018-12-01	6
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed_histogram/2.19.0	2018-12-01	6
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicfindtads/hicexplorer_hicfindtads/2.1.0	2018-12-01	6
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CleanSam/2.18.2.1	2018-12-01	6
secure_hash_message_digest	2018-12-01	6
toolshed.g2.bx.psu.edu/repos/rnateam/graphclust_prepocessing_for_mlocarna/preMloc/0.4	2018-12-01	5
toolshed.g2.bx.psu.edu/repos/galaxyp/gffcompare_to_bed/gffcompare_to_bed/0.1.0	2018-12-01	5
toolshed.g2.bx.psu.edu/repos/iuc/mothur_fastq_info/mothur_fastq_info/1.39.5.0	2018-12-01	5
toolshed.g2.bx.psu.edu/repos/peterjc/sample_seqs/sample_seqs/0.2.5	2018-12-01	5
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toolshed.g2.bx.psu.edu/repos/devteam/merge_cols/mergeCols1/1.0.1	2018-12-01	5
toolshed.g2.bx.psu.edu/repos/iuc/gatk2/gatk2_unified_genotyper/2.8.0	2018-12-01	5
toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sra_pileup/2.9.1.2	2018-12-01	5
toolshed.g2.bx.psu.edu/repos/miller-lab/genome_diversity/gd_raxml/1.0.0	2018-12-01	5
toolshed.g2.bx.psu.edu/repos/rnateam/graphclust_preprocessing/preproc/0.5	2018-12-01	5
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_NormalizeFasta/2.18.2.1	2018-12-01	5
toolshed.g2.bx.psu.edu/repos/chemteam/mdanalysis_rdf/mdanalysis_rdf/0.18	2018-12-01	5
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hiccorrectmatrix/hicexplorer_hiccorrectmatrix/2.1.4.0	2018-12-01	5
toolshed.g2.bx.psu.edu/repos/chemteam/bio3d_rmsf/bio3d_rmsf/2.3	2018-12-01	5
toolshed.g2.bx.psu.edu/repos/iuc/mothur_cluster_split/mothur_cluster_split/1.39.5.0	2018-12-01	5
toolshed.g2.bx.psu.edu/repos/iuc/mothur_get_groups/mothur_get_groups/1.39.5.0	2018-12-01	5
toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2	2018-12-01	5
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toolshed.g2.bx.psu.edu/repos/devteam/fastq_quality_boxplot/cshl_fastq_quality_boxplot/1.0.0	2018-12-01	5
toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummer/mummer_mummer/4.0.0beta2	2018-12-01	5
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_alignmentsieve/deeptools_alignmentsieve/3.0.2.0	2018-12-01	5
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_unionbedgraph/2.27.0.0	2018-12-01	5
toolshed.g2.bx.psu.edu/repos/iuc/mothur_classify_otu/mothur_classify_otu/1.39.5.0	2018-12-01	5
toolshed.g2.bx.psu.edu/repos/peterjc/seq_filter_by_id/seq_filter_by_id/0.2.7	2018-12-01	5
toolshed.g2.bx.psu.edu/repos/iuc/meme_meme/meme_meme/4.12.0.0	2018-12-01	5
toolshed.g2.bx.psu.edu/repos/iuc/mothur_seq_error/mothur_seq_error/1.39.5.0	2018-12-01	5
toolshed.g2.bx.psu.edu/repos/rnateam/graphclust_nspdk/NSPDK_candidateClust/9.2.3	2018-12-01	5
toolshed.g2.bx.psu.edu/repos/eschen42/w4mcorcov/w4mcorcov/0.98.15	2018-12-01	5
toolshed.g2.bx.psu.edu/repos/iuc/mothur_dist_seqs/mothur_dist_seqs/1.39.5.0	2018-12-01	5
toolshed.g2.bx.psu.edu/repos/devteam/fastqtofasta/fastq_to_fasta_python/1.1.1	2018-12-01	5
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toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_profile/deeptools_plot_profile/3.0.2.0	2018-12-01	5
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toolshed.g2.bx.psu.edu/repos/iuc/qiime_pick_otus/qiime_pick_otus/1.9.1.0	2018-12-01	5
toolshed.g2.bx.psu.edu/repos/bgruening/svm_classifier/svm_classifier/0.9	2018-12-01	5
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toolshed.g2.bx.psu.edu/repos/iuc/metaphlan2krona/metaphlan2krona/2.6.0.0	2018-12-01	4
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toolshed.g2.bx.psu.edu/repos/iuc/extract_genomic_dna/Extract genomic DNA 1/3.0.2	2018-12-01	4
toolshed.g2.bx.psu.edu/repos/galaxyp/msconvert/msconvert_nix/3.0.0	2018-12-01	4
toolshed.g2.bx.psu.edu/repos/gbcs-embl-heidelberg/je_markdupes/je_markdupes/1.2.1	2018-12-01	4
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_pe_fragmentsize/deeptools_bam_pe_fragmentsize/3.0.2.0	2018-12-01	4
toolshed.g2.bx.psu.edu/repos/bgruening/sailfish/sailfish/0.10.1.1	2018-12-01	4
toolshed.g2.bx.psu.edu/repos/iuc/mothur_dist_shared/mothur_dist_shared/1.39.5.0	2018-12-01	4
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/1.1.0	2018-12-01	4
toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: getorf42/5.0.0.1	2018-12-01	4
toolshed.g2.bx.psu.edu/repos/devteam/cuffnorm/cuffnorm/2.2.1.2	2018-12-01	4
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toolshed.g2.bx.psu.edu/repos/iuc/dexseq/dexseq_count/1.26.0.0	2018-12-01	4
toolshed.g2.bx.psu.edu/repos/iuc/abricate/abricate/0.8	2018-12-01	4
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toolshed.g2.bx.psu.edu/repos/rnateam/peakachu/peakachu/0.1.0.1	2018-12-01	4
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toolshed.g2.bx.psu.edu/repos/iuc/msaboot/msaboot/0.1.2	2018-12-01	4
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toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicplotviewpoint/hicexplorer_hicplotviewpoint/2.1.4.0	2018-12-01	4
toolshed.g2.bx.psu.edu/repos/rnateam/graphclust_postprocessing_no_align/graphclust_glob_report_no_align/0.5	2018-12-01	4
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toolshed.g2.bx.psu.edu/repos/galaxyp/openms_mascotadapter/MascotAdapter/2.3.0	2018-12-01	4
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toolshed.g2.bx.psu.edu/repos/iuc/scpipe/scpipe/1.0.0	2018-12-01	4
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_mztabexporter/MzTabExporter/2.3.0	2018-12-01	4
toolshed.g2.bx.psu.edu/repos/jjohnson/rsem/extract_transcript_to_gene_map_from_trinity/1.1.17	2018-12-01	4
toolshed.g2.bx.psu.edu/repos/iuc/structure/structure/2.3.4	2018-12-01	4
toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpSift_filter/3.4	2018-12-01	4
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toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_filtering/cardinal_filtering/1.12.1.0	2018-12-01	4
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toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.1.1	2018-12-01	4
toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/column_remove_by_header/0.0.1	2018-12-01	4
toolshed.g2.bx.psu.edu/repos/iuc/poretools_qualdist/poretools_qualdist/0.6.1a1.0	2018-12-01	4
toolshed.g2.bx.psu.edu/repos/iuc/megahit/megahit/1.1.2.3	2018-12-01	4
toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.1	2018-12-01	4
toolshed.g2.bx.psu.edu/repos/devteam/vcfgenotypes/vcfgenotypes/1.0.0_rc1+galaxy0	2018-12-01	4
ucsc_table_direct_archaea1	2018-12-01	4
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bigwig_summary/deeptools_multi_bigwig_summary/3.0.1.0	2018-12-01	4
toolshed.g2.bx.psu.edu/repos/devteam/gi2taxonomy/Fetch Taxonomic Ranks/1.1.0	2018-12-01	3
toolshed.g2.bx.psu.edu/repos/iuc/bcftools_call/bcftools_call/1.4.0	2018-12-01	3
toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.1.0	2018-12-01	3
toolshed.g2.bx.psu.edu/repos/devteam/fastq_to_fasta/cshl_fastq_to_fasta/1.0.2	2018-12-01	3
toolshed.g2.bx.psu.edu/repos/iuc/qiime_split_libraries_fastq/qiime_split_libraries_fastq/1.9.1.0	2018-12-01	3
toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.5.2b-2	2018-12-01	3
toolshed.g2.bx.psu.edu/repos/iuc/idba_ud/idba_ud/1.1.3	2018-12-01	3
toolshed.g2.bx.psu.edu/repos/devteam/vcfbedintersect/vcfbedintersect/1.0.0_rc1+galaxy0	2018-12-01	3
toolshed.g2.bx.psu.edu/repos/devteam/megablast_wrapper/megablast_wrapper/1.2.0	2018-12-01	3
toolshed.g2.bx.psu.edu/repos/iuc/iwtomics_loadandplot/iwtomics_loadandplot/1.0.0.0	2018-12-01	3
toolshed.g2.bx.psu.edu/repos/iuc/graphlan/graphlan/1.0.0.0	2018-12-01	3
biomart	2018-12-01	3
toolshed.g2.bx.psu.edu/repos/iuc/qiime_extract_barcodes/qiime_extract_barcodes/1.9.1.0	2018-12-01	3
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_mascotadapteronline/MascotAdapterOnline/2.3.0	2018-12-01	3
toolshed.g2.bx.psu.edu/repos/iuc/khmer_abundance_distribution_single/khmer_abundance_distribution_single/2.0.0	2018-12-01	3
deeptools_bigwigCorrelate	2018-12-01	3
toolshed.g2.bx.psu.edu/repos/iuc/qiime_alpha_diversity/qiime_alpha_diversity/1.9.1.0	2018-12-01	3
toolshed.g2.bx.psu.edu/repos/bgruening/crispr_recognition_tool/crispr_recognition_tool/1.2.0	2018-12-01	3
toolshed.g2.bx.psu.edu/repos/lparsons/htseq_count/htseq_count/0.4.1	2018-12-01	3
toolshed.g2.bx.psu.edu/repos/nml/metaspades/metaspades/3.9.0	2018-12-01	3
toolshed.g2.bx.psu.edu/repos/iuc/bp_genbank2gff3/bp_genbank2gff3/1.0	2018-12-01	3
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_rows/1.1.0	2018-12-01	3
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.0	2018-12-01	3
toolshed.g2.bx.psu.edu/repos/pavlo-lutsik/rnbeads/rnbeads/0.91	2018-12-01	3
toolshed.g2.bx.psu.edu/repos/iuc/shovill/shovill/0.8.0	2018-12-01	3
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_coverage/deeptools_plot_coverage/3.0.2.0	2018-12-01	3
toolshed.g2.bx.psu.edu/repos/iuc/gemini_roh/gemini_roh/0.18.1.1	2018-12-01	3
toolshed.g2.bx.psu.edu/repos/iuc/pilon/pilon/1.20.1	2018-12-01	3
toolshed.g2.bx.psu.edu/repos/peterjc/mummer/mummerplot_wrapper/0.0.7	2018-12-01	3
gbk_to_orf	2018-12-01	3
toolshed.g2.bx.psu.edu/repos/galaxyp/morpheus/morpheus/2.255.0	2018-12-01	3
toolshed.g2.bx.psu.edu/repos/iuc/gemini_interactions/gemini_interactions/0.18.1.0	2018-12-01	3
toolshed.g2.bx.psu.edu/repos/devteam/fastx_quality_statistics/cshl_fastx_quality_statistics/1.0.0	2018-12-01	3
toolshed.g2.bx.psu.edu/repos/jjohnson/cdhit/cd_hit_est/1.2	2018-12-01	3
toolshed.g2.bx.psu.edu/repos/iuc/gemini/gemini_load/0.10.0.0	2018-12-01	3
toolshed.g2.bx.psu.edu/repos/iuc/vsearch/vsearch_clustering/2.8.3.0	2018-12-01	3
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_cometadapter/CometAdapter/2.3.0	2018-12-01	3
toolshed.g2.bx.psu.edu/repos/peterjc/venn_list/venn_list/0.0.11	2018-12-01	3
toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_databases/4.3r.1	2018-12-01	3
toolshed.g2.bx.psu.edu/repos/galaxyp/uniprotxml_downloader/uniprotxml_downloader/2.0.0	2018-12-01	3
toolshed.g2.bx.psu.edu/repos/iuc/varscan_somatic/varscan_somatic/2.4.3.2	2018-12-01	3
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_compnovocid/CompNovoCID/2.3.0	2018-12-01	3
CONVERTER_ref_to_seq_taxomony	2018-12-01	3
testtoolshed.g2.bx.psu.edu/repos/messersc/jamm/jamm/1.0.7	2018-12-01	3
toolshed.g2.bx.psu.edu/repos/ethevenot/checkformat/checkFormat/3.0.0	2018-12-01	3
CONVERTER_interval_to_tabix_0	2018-12-01	3
toolshed.g2.bx.psu.edu/repos/devteam/vcftools_merge/vcftools_merge/0.1.1	2018-12-01	3
toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_whitelist/umi_tools_whitelist/0.5.3.1	2018-12-01	3
toolshed.g2.bx.psu.edu/repos/iuc/gatk2/gatk2_unified_genotyper/0.0.7	2018-12-01	3
toolshed.g2.bx.psu.edu/repos/bgruening/graphmap_align/graphmap_align/0.5.2	2018-12-01	3
toolshed.g2.bx.psu.edu/repos/eschen42/w4mjoinpn/w4mjoinpn/0.98.2	2018-12-01	3
toolshed.g2.bx.psu.edu/repos/iuc/mothur_taxonomy_to_krona/mothur_taxonomy_to_krona/1.0	2018-12-01	3
CONVERTER_interval_to_bed6_0	2018-12-01	3
toolshed.g2.bx.psu.edu/repos/iuc/ucsc_fasplit/fasplit/357	2018-12-01	3
toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpsift_vartype/4.3.1	2018-12-01	3
toolshed.g2.bx.psu.edu/repos/bgruening/rnaz/rnaz/2.1.1	2018-12-01	3
toolshed.g2.bx.psu.edu/repos/iuc/dexseq/dexseq/1.24.0.0	2018-12-01	3
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicfindtads/hicexplorer_hicfindtads/2.1.2.0	2018-12-01	3
toolshed.g2.bx.psu.edu/repos/devteam/fasta_concatenate_by_species/fasta_concatenate0/0.0.0	2018-12-01	3
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicpca/hicexplorer_hicpca/2.1.4.0	2018-12-01	3
toolshed.g2.bx.psu.edu/repos/iuc/stacks_denovomap/stacks_denovomap/1.46.0	2018-12-01	3
toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_biom/mothur_make_biom/1.39.5.0	2018-12-01	3
toolshed.g2.bx.psu.edu/repos/galaxyp/hardklor/hardklor/2.30.1	2018-12-01	3
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicplottads/hicexplorer_hicplottads/2.1.2.0	2018-12-01	3
toolshed.g2.bx.psu.edu/repos/iuc/export2graphlan/export2graphlan/0.19	2018-12-01	3
proteomics_search_tandem_2	2018-12-01	3
toolshed.g2.bx.psu.edu/repos/iuc/enasearch_search_data/enasearch_search_data/0.1.1.0	2018-12-01	3
toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_group/mothur_make_group/1.39.5.0	2018-12-01	3
toolshed.g2.bx.psu.edu/repos/iuc/enasearch_retrieve_taxons/enasearch_retrieve_taxons/0.1.1.0	2018-12-01	3
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toolshed.g2.bx.psu.edu/repos/devteam/histogram/histogram_rpy/1.0.3	2018-12-01	2
toolshed.g2.bx.psu.edu/repos/iuc/masigpro/masigpro/1.49.3.1	2018-12-01	2
toolshed.g2.bx.psu.edu/repos/chemteam/mdanalysis_angle/mdanalysis_angle/0.18	2018-12-01	2
toolshed.g2.bx.psu.edu/repos/devteam/t2t_report/t2t_report/1.0.0	2018-12-01	2
toolshed.g2.bx.psu.edu/repos/iuc/varscan_somatic/varscan_somatic/2.4.3.1	2018-12-01	2
toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_dedup/umi_tools_dedup/0.5.3.0	2018-12-01	2
toolshed.g2.bx.psu.edu/repos/devteam/fastq_quality_boxplot/cshl_fastq_quality_boxplot/1.0.1	2018-12-01	2
svm_classifier	2018-12-01	2
toolshed.g2.bx.psu.edu/repos/iuc/bctools_extract_alignment_ends/bctools_extract_alignment_ends/0.2.2	2018-12-01	2
toolshed.g2.bx.psu.edu/repos/iuc/sickle/sickle/1.33.1	2018-12-01	2
toolshed.g2.bx.psu.edu/repos/galaxyp/myrimatch/myrimatch/3.0.11579.0	2018-12-01	2
intermine	2018-12-01	2
toolshed.g2.bx.psu.edu/repos/iuc/enasearch_retrieve_analysis_report/enasearch_retrieve_analysis_report/0.1.1.0	2018-12-01	2
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bam_summary/deeptools_multi_bam_summary/2.5.7.0	2018-12-01	2
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicatesWithMateCigar/2.18.2.1	2018-12-01	2
toolshed.g2.bx.psu.edu/repos/iuc/describe_samples/describe_samples/2.8.4	2018-12-01	2
toolshed.g2.bx.psu.edu/repos/iuc/extract_genomic_dna/Extract genomic DNA 1/3.0.0	2018-12-01	2
toolshed.g2.bx.psu.edu/repos/iuc/trinity_samples_qccheck/trinity_samples_qccheck/2.8.4	2018-12-01	2
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_flankbed/2.27.0.0	2018-12-01	2
toolshed.g2.bx.psu.edu/repos/galaxyp/msi_filtering/mass_spectrometry_imaging_filtering/1.10.0.6	2018-12-01	2
toolshed.g2.bx.psu.edu/repos/bgruening/uniprot_rest_interface/uniprot/0.2	2018-12-01	2
toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_fqchk/1.3.0	2018-12-01	2
toolshed.g2.bx.psu.edu/repos/chemteam/mdanalysis_dihedral/mdanalysis_dihedral/0.18	2018-12-01	2
toolshed.g2.bx.psu.edu/repos/iuc/kraken_taxonomy_report/kraken_taxonomy_report/0.0.2	2018-12-01	2
toolshed.g2.bx.psu.edu/repos/iuc/length_and_gc_content/length_and_gc_content/0.1.1	2018-12-01	2
toolshed.g2.bx.psu.edu/repos/devteam/principal_component_analysis/pca1/1.0.2	2018-12-01	2
barchart_gnuplot	2018-12-01	2
toolshed.g2.bx.psu.edu/repos/devteam/ucsc_custom_track/build_ucsc_custom_track_1/1.0.0	2018-12-01	2
toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_pca/ggplot2_pca/2.2.1	2018-12-01	2
toolshed.g2.bx.psu.edu/repos/bgruening/trna_prediction/aragorn_trna/0.6	2018-12-01	2
toolshed.g2.bx.psu.edu/repos/wolma/mimodd_main/mimodd_info/0.1.8_1	2018-12-01	2
toolshed.g2.bx.psu.edu/repos/iuc/gffcompare/gffcompare/0.9.8+galaxy1	2018-12-01	2
toolshed.g2.bx.psu.edu/repos/nml/spades/spades/3.11.1	2018-12-01	2
toolshed.g2.bx.psu.edu/repos/devteam/kraken_report/kraken-report/1.2.4	2018-12-01	2
toolshed.g2.bx.psu.edu/repos/galaxyp/msgfplus/msgfplus/0.5	2018-12-01	2
__MERGE_COLLECTION__	2018-12-01	2
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeBamAlignment/2.18.2.1	2018-12-01	2
toolshed.g2.bx.psu.edu/repos/devteam/fasta_formatter/cshl_fasta_formatter/1.0.1	2018-12-01	2
toolshed.g2.bx.psu.edu/repos/iuc/fgsea/fgsea/1.6.0	2018-12-01	2
toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_feature_selection/sklearn_feature_selection/0.9.1	2018-12-01	2
toolshed.g2.bx.psu.edu/repos/iuc/meme_fimo/meme_fimo/4.11.2.0	2018-12-01	2
toolshed.g2.bx.psu.edu/repos/devteam/tophat_fusion_post/tophat_fusion_post/0.1	2018-12-01	2
toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_subseq/1.3.0	2018-12-01	2
toolshed.g2.bx.psu.edu/repos/devteam/picard/PicardGCBiasMetrics/1.56.0	2018-12-01	2
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_coveragebed/2.27.1	2018-12-01	2
toolshed.g2.bx.psu.edu/repos/iuc/poretools_stats/poretools_stats/0.6.1a1.0	2018-12-01	2
toolshed.g2.bx.psu.edu/repos/bgruening/bismark/bismark_bowtie2/0.16.3	2018-12-01	2
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_mergebed/2.27.1	2018-12-01	2
toolshed.g2.bx.psu.edu/repos/iuc/poretools_occupancy/poretools_occupancy/0.6.1a1.0	2018-12-01	2
toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_bdgpeakcall/2.1.1.20160309.0	2018-12-01	2
toolshed.g2.bx.psu.edu/repos/rnateam/dorina/dorina_search/1.0.0	2018-12-01	2
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_correlation/deeptools_plot_correlation/2.5.7.0	2018-12-01	2
toolshed.g2.bx.psu.edu/repos/iuc/poretools_qualpos/poretools_qualpos/0.6.1a1.0	2018-12-01	2
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.7.1.1	2018-12-01	2
toolshed.g2.bx.psu.edu/repos/iuc/mummer_mummerplot/mummer_mummerplot/4.0.0beta2	2018-12-01	2
toolshed.g2.bx.psu.edu/repos/tyty/structurefold/predict_pipeline/1.0	2018-12-01	2
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toolshed.g2.bx.psu.edu/repos/bgruening/diamond/bg_diamond_makedb/0.8.24	2018-12-01	2
toolshed.g2.bx.psu.edu/repos/iuc/ebi_search_rest_results/ebi_search_rest_results/0.1.1	2018-12-01	2
CONVERTER_biom2_to_biom1	2018-12-01	2
toolshed.g2.bx.psu.edu/repos/iuc/ococo/ococo/0.1.2.6	2018-12-01	2
qual_stats_boxplot	2018-12-01	2
toolshed.g2.bx.psu.edu/repos/iuc/iqtree/iqtree/1.5.5.1	2018-12-01	2
toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0.1	2018-12-01	2
toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.36.4	2018-12-01	2
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SamToFastq/2.18.2.1	2018-12-01	2
toolshed.g2.bx.psu.edu/repos/iuc/qiime_multiple_split_libraries_fastq/qiime_multiple_split_libraries_fastq/1.9.1.0	2018-12-01	2
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idfileconverter/IDFileConverter/2.3.0	2018-12-01	2
toolshed.g2.bx.psu.edu/repos/devteam/picard/rgPicFixMate/1.56.0	2018-12-01	2
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_pca/deeptools_plot_pca/3.0.2.0	2018-12-01	2
toolshed.g2.bx.psu.edu/repos/iuc/ebi_metagenomics_run_downloader/ebi_metagenomics_run_downloader/0.1.0	2018-12-01	2
toolshed.g2.bx.psu.edu/repos/rnateam/viennarna_rnadistance/viennarna_rnadistance/2.2.10.0	2018-12-01	2
toolshed.g2.bx.psu.edu/repos/jjohnson/samtools_filter/samtools_filter/1.1.1	2018-12-01	2
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FilterSamReads/2.18.2.1	2018-12-01	2
toolshed.g2.bx.psu.edu/repos/iuc/fasttree/fasttree/2.1.10	2018-12-01	2
toolshed.g2.bx.psu.edu/repos/iuc/varscan_mpileup/varscan_mpileup/2.4.3.0	2018-12-01	2
toolshed.g2.bx.psu.edu/repos/galaxyp/flashlfq/flashlfq/0.1.99	2018-12-01	2
toolshed.g2.bx.psu.edu/repos/iuc/trinity_define_clusters_by_cutting_tree/trinity_define_clusters_by_cutting_tree/2.8.4	2018-12-01	2
toolshed.g2.bx.psu.edu/repos/iuc/mummer_nucmer/mummer_nucmer/4.0.0beta2	2018-12-01	2
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.0.0.0	2018-12-01	2
toolshed.g2.bx.psu.edu/repos/devteam/fastq_combiner/fastq_combiner/1.1.1	2018-12-01	2
toolshed.g2.bx.psu.edu/repos/devteam/vcftools_isec/vcftools_isec/0.1.1	2018-12-01	2
CONVERTER_fasta_to_bowtie_base_index	2018-12-01	2
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectInsertSizeMetrics/2.7.1.0	2018-12-01	2
toolshed.g2.bx.psu.edu/repos/devteam/fastx_quality_statistics/cshl_fastx_quality_statistics/1.0.1	2018-12-01	2
toolshed.g2.bx.psu.edu/repos/iuc/bcftools/bcfview/0.1.19	2018-12-01	2
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicmergematrixbins/hicexplorer_hicmergematrixbins/2.1.4.0	2018-12-01	2
toolshed.g2.bx.psu.edu/repos/iuc/transdecoder/transdecoder/3.0.1	2018-12-01	2
toolshed.g2.bx.psu.edu/repos/iuc/qiime_make_otu_heatmap/qiime_make_otu_heatmap/1.9.1.0	2018-12-01	2
toolshed.g2.bx.psu.edu/repos/iuc/graphlan_annotate/graphlan_annotate/1.0.0.0	2018-12-01	2
toolshed.g2.bx.psu.edu/repos/iuc/stacks_ustacks/stacks_ustacks/1.46.0	2018-12-01	1
hgv_david	2018-12-01	1
toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_spectra_plots/cardinal_spectra_plots/1.12.1.1	2018-12-01	1
toolshed.g2.bx.psu.edu/repos/rnateam/viennarna_rnapkplex/viennarna_rnapkplex/2.2.10.0	2018-12-01	1
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_precursormasscorrector/PrecursorMassCorrector/2.3.0	2018-12-01	1
toolshed.g2.bx.psu.edu/repos/rnateam/viennarna_rnapaln/viennarna_rnapaln/2.2.10.0	2018-12-01	1
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtoigv/2.27.0.0	2018-12-01	1
toolshed.g2.bx.psu.edu/repos/rnateam/viennarna_rnalalifold/viennarna_rnalalifold/2.2.10.0	2018-12-01	1
toolshed.g2.bx.psu.edu/repos/iuc/gemini_annotate/gemini_annotate/0.18.1.1	2018-12-01	1
toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_combine/cardinal_combine/1.12.1.0	2018-12-01	1
toolshed.g2.bx.psu.edu/repos/peterjc/tmhmm_and_signalp/promoter2/0.0.12	2018-12-01	1
toolshed.g2.bx.psu.edu/repos/iuc/data_manager_gemini_database_downloader/data_manager_gemini_download/0.18.1	2018-12-01	1
toolshed.g2.bx.psu.edu/repos/bebatut/format_metaphlan2_output/format_metaphlan2_output/0.1.0	2018-12-01	1
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_peakpickerwavelet/PeakPickerWavelet/2.3.0	2018-12-01	1
toolshed.g2.bx.psu.edu/repos/devteam/join/gops_join_1/0.0.1	2018-12-01	1
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_groupbybed/2.27.0.0	2018-12-01	1
toolshed.g2.bx.psu.edu/repos/iuc/gemini_actionable_mutations/gemini_actionable_mutations/0.18.1.0	2018-12-01	1
toolshed.g2.bx.psu.edu/repos/iuc/meme_meme/meme_meme/4.11.2.0	2018-12-01	1
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Count1	2018-12-01	1
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toolshed.g2.bx.psu.edu/repos/rnateam/rcas/rcas/1.1.1	2018-12-01	1
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toolshed.g2.bx.psu.edu/repos/iuc/gemini_dump/gemini_dump/0.18.1.1	2018-12-01	1
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toolshed.g2.bx.psu.edu/repos/iuc/egsea/egsea/1.6.0.1	2018-12-01	1
upload1	2018-11-01	10140
toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72	2018-11-01	3544
toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_searchcv/sklearn_searchcv/0.9	2018-11-01	2954
toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.71	2018-11-01	2921
toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.1	2018-11-01	1462
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echo_main_condor	2018-11-01	1107
toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1	2018-11-01	1088
toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/2.9.1.3	2018-11-01	1031
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toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.1.0.46-0	2018-11-01	986
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toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/0.11.2	2018-11-01	974
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toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.6.0b-1	2018-11-01	950
toolshed.g2.bx.psu.edu/repos/lparsons/htseq_count/htseq_count/0.9.1	2018-11-01	934
toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastx_wrapper/0.3.1	2018-11-01	924
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.27.0.2	2018-11-01	922
toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.4.2	2018-11-01	882
toolshed.g2.bx.psu.edu/repos/devteam/vcfallelicprimitives/vcfallelicprimitives/1.0.0_rc1+galaxy0	2018-11-01	877
toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.1.0.46-0	2018-11-01	871
toolshed.g2.bx.psu.edu/repos/bgruening/infernal/infernal_cmsearch/1.1.2.0	2018-11-01	851
toolshed.g2.bx.psu.edu/repos/bgruening/infernal/infernal_cmbuild/1.1.2.0	2018-11-01	846
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comp1	2018-11-01	728
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toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.0.2.0	2018-11-01	582
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_heatmap/deeptools_plot_heatmap/3.0.2.0	2018-11-01	562
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/deeptools_compute_matrix/3.0.2.0	2018-11-01	558
toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.6	2018-11-01	526
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0	2018-11-01	519
toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/1.3.4	2018-11-01	508
toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.1.0+galaxy3	2018-11-01	508
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toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1	2018-11-01	440
toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.3	2018-11-01	436
toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_xcmsset/abims_xcms_xcmsSet/2.1.1	2018-11-01	425
toolshed.g2.bx.psu.edu/repos/bgruening/pileometh/pileometh/0.3.0.1	2018-11-01	424
toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.4.1	2018-11-01	395
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.1	2018-11-01	377
wig_to_bigWig	2018-11-01	376
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toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.4	2018-11-01	326
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toolshed.g2.bx.psu.edu/repos/devteam/samtools_flagstat/samtools_flagstat/2.0.2	2018-11-01	312
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toolshed.g2.bx.psu.edu/repos/iuc/scpipe/scpipe/1.0.0	2018-11-01	291
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toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.2	2018-11-01	279
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toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.2.0	2018-11-01	268
toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.4.3.1	2018-11-01	267
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CONVERTER_sam_to_bigwig_0	2018-11-01	258
CONVERTER_bed_to_fli_0	2018-11-01	252
CONVERTER_bed_to_tabix_0	2018-11-01	243
toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.1.1.20160309.4	2018-11-01	241
toolshed.g2.bx.psu.edu/repos/devteam/samtools_rmdup/samtools_rmdup/2.0.1	2018-11-01	235
toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_quality_report/cardinal_quality_report/1.12.1.1	2018-11-01	224
toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.1.0	2018-11-01	222
toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.1.1.20160309.5	2018-11-01	219
toolshed.g2.bx.psu.edu/repos/peterjc/venn_list/venn_list/0.0.11	2018-11-01	219
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_profile/deeptools_plot_profile/3.1.2.0.0	2018-11-01	218
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicplotmatrix/hicexplorer_hicplotmatrix/2.1.4.0	2018-11-01	218
toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.36.0	2018-11-01	215
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.1	2018-11-01	209
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_coveragebed/2.27.0.2	2018-11-01	202
toolshed.g2.bx.psu.edu/repos/crs4/bwa_mem/bwa_mem/0.8.0	2018-11-01	199
Grouping1	2018-11-01	197
toolshed.g2.bx.psu.edu/repos/devteam/fastq_trimmer/fastq_trimmer/1.1.1	2018-11-01	192
toolshed.g2.bx.psu.edu/repos/rnateam/chipseeker/chipseeker/1.14.2.1	2018-11-01	178
toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.0	2018-11-01	176
toolshed.g2.bx.psu.edu/repos/devteam/intersect/gops_intersect_1/1.0.0	2018-11-01	159
toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_makeblastdb/0.3.1	2018-11-01	155
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toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.20.7.2	2018-11-01	153
toolshed.g2.bx.psu.edu/repos/iuc/bwameth/bwameth/0.2.0.4	2018-11-01	151
toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_build_pipeline/sklearn_build_pipeline/0.9	2018-11-01	151
toolshed.g2.bx.psu.edu/repos/galaxyp/msi_filtering/mass_spectrometry_imaging_filtering/1.10.0.6	2018-11-01	151
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hiccorrectmatrix/hicexplorer_hiccorrectmatrix/2.1.4.0	2018-11-01	148
toolshed.g2.bx.psu.edu/repos/devteam/join/gops_join_1/1.0.0	2018-11-01	147
toolshed.g2.bx.psu.edu/repos/iuc/stacks_ustacks/stacks_ustacks/1.46.0	2018-11-01	146
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectRnaSeqMetrics/2.18.2.1	2018-11-01	144
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CASM/2.18.2.1	2018-11-01	144
Grep1	2018-11-01	143
toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_deinterlacer/fastq_paired_end_deinterlacer/1.1.2	2018-11-01	142
toolshed.g2.bx.psu.edu/repos/galaxyp/maldi_quant_preprocessing/maldi_quant_preprocessing/1.18.0.2	2018-11-01	138
toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/3.2	2018-11-01	136
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_multijoin_tool/1.1.1	2018-11-01	132
toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_infer_experiment/2.6.4.1	2018-11-01	130
toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/0.5.3.2	2018-11-01	126
toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/4.6.3	2018-11-01	126
CONVERTER_interval_to_bedstrict_0	2018-11-01	125
toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_preprocessing/cardinal_preprocessing/1.12.1.1	2018-11-01	125
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.2	2018-11-01	123
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicmergematrixbins/hicexplorer_hicmergematrixbins/2.1.4.0	2018-11-01	121
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toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_mergebed/2.27.0.0	2018-11-01	118
toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.3	2018-11-01	117
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toolshed.g2.bx.psu.edu/repos/mvdbeek/add_input_name_as_column/addName/0.1.1	2018-11-01	108
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.0	2018-11-01	105
toolshed.g2.bx.psu.edu/repos/ethevenot/multivariate/Multivariate/2.3.10	2018-11-01	105
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_peakpickerhires/PeakPickerHiRes/2.3.0	2018-11-01	105
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.27.0.0	2018-11-01	104
toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: seqmatchall83/5.0.0.1	2018-11-01	102
toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2	2018-11-01	101
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/1.1.0	2018-11-01	100
toolshed.g2.bx.psu.edu/repos/devteam/get_flanks/get_flanks1/1.0.0	2018-11-01	100
toolshed.g2.bx.psu.edu/repos/devteam/samtools_slice_bam/samtools_slice_bam/2.0.1	2018-11-01	99
toolshed.g2.bx.psu.edu/repos/iuc/ngsutils_bam_filter/ngsutils_bam_filter/0.5.9	2018-11-01	97
toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/datamash_ops/1.0.6	2018-11-01	96
toolshed.g2.bx.psu.edu/repos/iuc/stacks_procrad/stacks_procrad/1.46.0	2018-11-01	95
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_falsediscoveryrate/FalseDiscoveryRate/2.3.0	2018-11-01	94
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.0	2018-11-01	94
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_fileinfo/FileInfo/2.3.0	2018-11-01	93
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/1.1.0	2018-11-01	89
toolshed.g2.bx.psu.edu/repos/bgruening/bigwig_to_bedgraph/bigwig_to_bedgraph/0.1.0	2018-11-01	88
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_peptideindexer/PeptideIndexer/2.3.0	2018-11-01	87
toolshed.g2.bx.psu.edu/repos/devteam/bam_to_sam/bam_to_sam/2.0.1	2018-11-01	87
toolshed.g2.bx.psu.edu/repos/eschen42/w4mclassfilter/w4mclassfilter/0.98.11	2018-11-01	86
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toolshed.g2.bx.psu.edu/repos/iuc/mothur_summary_seqs/mothur_summary_seqs/1.36.1.0	2018-11-01	82
toolshed.g2.bx.psu.edu/repos/devteam/concat/gops_concat_1/1.0.1	2018-11-01	81
toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.1	2018-11-01	80
toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.1	2018-11-01	80
toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/1.6.2	2018-11-01	80
toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_data_exporter/cardinal_data_exporter/1.12.1.0	2018-11-01	79
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.1	2018-11-01	79
toolshed.g2.bx.psu.edu/repos/rnateam/blockclust/blockclust/1.1.0	2018-11-01	79
toolshed.g2.bx.psu.edu/repos/bgruening/join_files_on_column_fuzzy/join_files_on_column_fuzzy/1.0.0	2018-11-01	79
toolshed.g2.bx.psu.edu/repos/iuc/mothur_screen_seqs/mothur_screen_seqs/1.36.1.0	2018-11-01	78
toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.34.9.9	2018-11-01	77
toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_heatmap2/ggplot2_heatmap2/2.2.1+galaxy1	2018-11-01	77
toolshed.g2.bx.psu.edu/repos/iuc/samtools_sort/samtools_sort/1.0.2	2018-11-01	76
toolshed.g2.bx.psu.edu/repos/iuc/gtftobed12/gtftobed12/357	2018-11-01	75
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_subtractbed/2.27.0.0	2018-11-01	75
toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/0.7.0.3	2018-11-01	75
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bam_summary/deeptools_multi_bam_summary/3.0.2.0	2018-11-01	75
toolshed.g2.bx.psu.edu/repos/galaxyp/msconvert_nix/msconvert_nix/3.0.9992.0	2018-11-01	74
toolshed.g2.bx.psu.edu/repos/galaxyp/maldi_quant_peak_detection/maldi_quant_peak_detection/1.18.0.2	2018-11-01	74
toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/2.0.0	2018-11-01	72
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_textexporter/TextExporter/2.3.0	2018-11-01	72
toolshed.g2.bx.psu.edu/repos/crs4/prokka/prokka/1.13	2018-11-01	72
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_correlation/deeptools_plot_correlation/3.0.2.0	2018-11-01	70
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toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.3.1	2018-11-01	66
toolshed.g2.bx.psu.edu/repos/devteam/varscan_version_2/varscan/2.4.2	2018-11-01	65
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idfilter/IDFilter/2.3.0	2018-11-01	65
toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_interlacer/fastq_paired_end_interlacer/1.2.0.1	2018-11-01	65
toolshed.g2.bx.psu.edu/repos/iuc/gatk2/gatk2_depth_of_coverage/2.8.0	2018-11-01	64
toolshed.g2.bx.psu.edu/repos/devteam/fastq_trimmer_by_quality/fastq_quality_trimmer/1.1.1	2018-11-01	64
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_mztabexporter/MzTabExporter/2.3.0	2018-11-01	64
toolshed.g2.bx.psu.edu/repos/rnateam/graphclust_nspdk/nspdk_sparse/9.2.2	2018-11-01	64
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.1	2018-11-01	63
toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0.2	2018-11-01	63
toolshed.g2.bx.psu.edu/repos/devteam/fastq_filter/fastq_filter/1.1.1	2018-11-01	62
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_xtandemadapter/XTandemAdapter/2.3.0	2018-11-01	62
toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/2.2.1.2	2018-11-01	62
CONVERTER_len_to_linecount	2018-11-01	62
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toolshed.g2.bx.psu.edu/repos/devteam/sam_merge/sam_merge2/1.2.0	2018-11-01	60
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.27.0.0	2018-11-01	60
CONVERTER_fasta_to_len	2018-11-01	60
toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.2	2018-11-01	60
toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1.1	2018-11-01	59
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_msgfplusadapter/MSGFPlusAdapter/2.3.0	2018-11-01	59
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_fileinfo/FileInfo/2.2.0	2018-11-01	58
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_falsediscoveryrate/FalseDiscoveryRate/2.2.0	2018-11-01	58
toolshed.g2.bx.psu.edu/repos/rnateam/piranha/piranha/0.1.0	2018-11-01	58
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_fingerprint/deeptools_plot_fingerprint/3.0.2.0	2018-11-01	57
toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.4.2	2018-11-01	56
toolshed.g2.bx.psu.edu/repos/rnateam/graphclust_postprocessing/glob_report/0.4	2018-11-01	55
toolshed.g2.bx.psu.edu/repos/devteam/fastqtofasta/fastq_to_fasta_python/1.0.0	2018-11-01	55
toolshed.g2.bx.psu.edu/repos/bgruening/uniprot_rest_interface/uniprot/0.2	2018-11-01	55
toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.4.0d-2	2018-11-01	54
__EXPORT_HISTORY__	2018-11-01	54
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/2.4.1.0	2018-11-01	54
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeSamFiles/2.18.2.1	2018-11-01	54
toolshed.g2.bx.psu.edu/repos/devteam/samtools_rmdup/samtools_rmdup/2.0	2018-11-01	54
toolshed.g2.bx.psu.edu/repos/rnateam/structure_to_gspan/structure_to_gspan/0.3	2018-11-01	53
toolshed.g2.bx.psu.edu/repos/rnateam/graphclust_preprocessing/preproc/0.4	2018-11-01	53
toolshed.g2.bx.psu.edu/repos/iuc/ngsutils_bam_filter/ngsutils_bam_filter/0.5.8.1	2018-11-01	53
toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.6.1.1	2018-11-01	52
toolshed.g2.bx.psu.edu/repos/iuc/metaphlan2/metaphlan2/2.6.0.0	2018-11-01	52
Summary_Statistics1	2018-11-01	52
toolshed.g2.bx.psu.edu/repos/iuc/kallisto_quant/kallisto_quant/0.43.1.3	2018-11-01	52
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toolshed.g2.bx.psu.edu/repos/devteam/fastq_to_fasta/cshl_fastq_to_fasta/1.0.2	2018-11-01	52
toolshed.g2.bx.psu.edu/repos/rnateam/viennarna_rnafold/viennarna_rnafold/2.2.10.4	2018-11-01	52
toolshed.g2.bx.psu.edu/repos/rnateam/graphclust_nspdk/NSPDK_candidateClust/9.2.2	2018-11-01	51
toolshed.g2.bx.psu.edu/repos/rnateam/graphclust_prepocessing_for_mlocarna/preMloc/0.3	2018-11-01	51
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.1	2018-11-01	51
toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_bam_stat/2.6.4	2018-11-01	51
toolshed.g2.bx.psu.edu/repos/devteam/fasta_filter_by_length/fasta_filter_by_length/1.1	2018-11-01	50
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicbuildmatrix/hicexplorer_hicbuildmatrix/2.1.4.0	2018-11-01	49
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_profile/deeptools_plot_profile/3.0.2.0	2018-11-01	49
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.27.0.1	2018-11-01	49
toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/bwa_wrapper/1.2.3	2018-11-01	48
toolshed.g2.bx.psu.edu/repos/galaxyp/thermo_raw_file_converter/thermo_raw_file_converter/0.0.1	2018-11-01	48
toolshed.g2.bx.psu.edu/repos/devteam/vcfbedintersect/vcfbedintersect/0.0.3	2018-11-01	48
toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_splitter/fastq_paired_end_splitter/1.1.1	2018-11-01	48
toolshed.g2.bx.psu.edu/repos/iuc/humann2/humann2/0.11.1.0	2018-11-01	47
toolshed.g2.bx.psu.edu/repos/bgruening/graphicsmagick_image_convert/graphicsmagick_image_convert/1.3.26	2018-11-01	47
toolshed.g2.bx.psu.edu/repos/devteam/dna_filtering/histogram_rpy/1.0.3	2018-11-01	47
velveth	2018-11-01	47
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hiccorrectmatrix/hicexplorer_hiccorrectmatrix/2.1.0	2018-11-01	46
toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.6.0	2018-11-01	46
toolshed.g2.bx.psu.edu/repos/rnateam/metilene/metilene/0.2.6.1	2018-11-01	46
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicplotmatrix/hicexplorer_hicplotmatrix/2.1.0	2018-11-01	46
toolshed.g2.bx.psu.edu/repos/iuc/mothur_summary_seqs/mothur_summary_seqs/1.39.5.0	2018-11-01	44
toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_shared/mothur_make_shared/1.36.1.0	2018-11-01	44
toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.39	2018-11-01	44
toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.1.3	2018-11-01	44
toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.5.0.1	2018-11-01	44
toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie_merge/1.3.4	2018-11-01	43
toolshed.g2.bx.psu.edu/repos/devteam/samtool_filter2/samtool_filter2/1.8	2018-11-01	43
toolshed.g2.bx.psu.edu/repos/devteam/add_value/addValue/1.0.0	2018-11-01	43
toolshed.g2.bx.psu.edu/repos/wolma/mimodd_main/mimodd_vcf_filter/0.1.8_1	2018-11-01	43
CONVERTER_fasta_to_2bit	2018-11-01	43
toolshed.g2.bx.psu.edu/repos/iuc/mothur_unique_seqs/mothur_unique_seqs/1.36.1.0	2018-11-01	43
toolshed.g2.bx.psu.edu/repos/iuc/raceid_inspectclusters/raceid_inspectclusters/3.0.2.1	2018-11-01	42
velvetg	2018-11-01	42
CONVERTER_fastq_to_fqtoc0	2018-11-01	42
toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/peptide_shaker/1.16.26	2018-11-01	41
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicplottads/hicexplorer_hicplottads/2.1.4.0	2018-11-01	41
toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/search_gui/3.3.3.0	2018-11-01	41
toolshed.g2.bx.psu.edu/repos/iuc/goseq/goseq/1.26.0	2018-11-01	40
toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_heatmap2/ggplot2_heatmap2/2.2.1	2018-11-01	40
toolshed.g2.bx.psu.edu/repos/wolma/mimodd_main/mimodd_varcall/0.1.8_1	2018-11-01	40
toolshed.g2.bx.psu.edu/repos/nml/spades/spades/3.12.0	2018-11-01	40
toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.1	2018-11-01	40
toolshed.g2.bx.psu.edu/repos/wolma/mimodd_main/mimodd_varextract/0.1.8_1	2018-11-01	40
toolshed.g2.bx.psu.edu/repos/iuc/mothur_pre_cluster/mothur_pre_cluster/1.36.1.0	2018-11-01	39
toolshed.g2.bx.psu.edu/repos/iuc/mothur_count_seqs/mothur_count_seqs/1.36.1.0	2018-11-01	39
toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_filtering/cardinal_filtering/1.12.1.1	2018-11-01	39
toolshed.g2.bx.psu.edu/repos/rnateam/blockclust/blockclust/1.0.0	2018-11-01	39
toolshed.g2.bx.psu.edu/repos/iuc/mothur_classify_seqs/mothur_classify_seqs/1.36.1.0	2018-11-01	39
toolshed.g2.bx.psu.edu/repos/iuc/mothur_filter_seqs/mothur_filter_seqs/1.36.1.0	2018-11-01	39
toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.2.2	2018-11-01	39
toolshed.g2.bx.psu.edu/repos/iuc/mothur_align_seqs/mothur_align_seqs/1.36.1.0	2018-11-01	39
toolshed.g2.bx.psu.edu/repos/wolma/mimodd_main/mimodd_map/0.1.8_1	2018-11-01	39
toolshed.g2.bx.psu.edu/repos/iuc/mothur_classify_otu/mothur_classify_otu/1.36.1.0	2018-11-01	39
toolshed.g2.bx.psu.edu/repos/saskia-hiltemann/krona_text/krona-text/1	2018-11-01	39
CONVERTER_vcf_bgzip_to_tabix_0	2018-11-01	39
toolshed.g2.bx.psu.edu/repos/iuc/metaphlan2krona/metaphlan2krona/2.6.0.0	2018-11-01	39
toolshed.g2.bx.psu.edu/repos/iuc/trinity/trinity/2.8.4	2018-11-01	39
CONVERTER_vcf_to_vcf_bgzip_0	2018-11-01	39
toolshed.g2.bx.psu.edu/repos/wolma/mimodd_main/mimodd_varreport/0.1.8_1	2018-11-01	39
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed/2.27.0.0	2018-11-01	39
toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.1.0	2018-11-01	39
toolshed.g2.bx.psu.edu/repos/iuc/mothur_cluster_split/mothur_cluster_split/1.36.1.0	2018-11-01	39
toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_download/4.1.0	2018-11-01	39
toolshed.g2.bx.psu.edu/repos/iuc/extract_genomic_dna/Extract genomic DNA 1/3.0.3	2018-11-01	38
toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_feature_selection/sklearn_feature_selection/0.9.1	2018-11-01	38
toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastp_wrapper/0.3.1	2018-11-01	38
toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.69	2018-11-01	37
toolshed.g2.bx.psu.edu/repos/iuc/mothur_corr_axes/mothur_corr_axes/1.36.1.0	2018-11-01	37
toolshed.g2.bx.psu.edu/repos/eschen42/w4mcorcov/w4mcorcov/0.98.15	2018-11-01	37
toolshed.g2.bx.psu.edu/repos/devteam/merge/gops_merge_1/1.0.0	2018-11-01	36
toolshed.g2.bx.psu.edu/repos/iuc/meme_meme/meme_meme/4.12.0.0	2018-11-01	36
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idposteriorerrorprobability/IDPosteriorErrorProbability/2.3.0	2018-11-01	36
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed_bedgraph/2.19.0	2018-11-01	36
toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_group/mothur_make_group/1.36.1.0	2018-11-01	36
toolshed.g2.bx.psu.edu/repos/iuc/mothur_nmds/mothur_nmds/1.36.1.0	2018-11-01	36
toolshed.g2.bx.psu.edu/repos/rnateam/mirdeep2_mapper/rbc_mirdeep2_mapper/2.0.0	2018-11-01	36
toolshed.g2.bx.psu.edu/repos/iuc/mothur_merge_files/mothur_merge_files/1.36.1.0	2018-11-01	35
toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_bam2wig/2.6.4	2018-11-01	35
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.27.0.1	2018-11-01	35
toolshed.g2.bx.psu.edu/repos/devteam/cuffdiff/cuffdiff/2.2.1.5	2018-11-01	35
toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_biom/mothur_make_biom/1.36.1.0	2018-11-01	34
toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_fqchk/1.3.0	2018-11-01	34
toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.3	2018-11-01	34
toolshed.g2.bx.psu.edu/repos/iuc/newick_utils/newick_display/1.6	2018-11-01	33
toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.1.1.20160309.3	2018-11-01	32
toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_combine/cardinal_combine/1.12.1.0	2018-11-01	32
toolshed.g2.bx.psu.edu/repos/devteam/fastq_quality_filter/cshl_fastq_quality_filter/1.0.2	2018-11-01	32
toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_svm_classifier/sklearn_svm_classifier/0.9	2018-11-01	32
CONVERTER_bedgraph_to_bigwig	2018-11-01	32
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idscoreswitcher/IDScoreSwitcher/2.3.0	2018-11-01	32
toolshed.g2.bx.psu.edu/repos/galaxyp/filter_by_fasta_ids/filter_by_fasta_ids/2.0	2018-11-01	32
toolshed.g2.bx.psu.edu/repos/iuc/mothur_screen_seqs/mothur_screen_seqs/1.39.5.0	2018-11-01	32
toolshed.g2.bx.psu.edu/repos/devteam/subtract/gops_subtract_1/1.0.0	2018-11-01	32
toolshed.g2.bx.psu.edu/repos/rnateam/blockbuster/blockbuster/0.1.2	2018-11-01	32
toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.0.6	2018-11-01	32
toolshed.g2.bx.psu.edu/repos/lparsons/fastq_join/fastq_join/1.1.2-806	2018-11-01	31
toolshed.g2.bx.psu.edu/repos/iuc/gemini_query/gemini_query/0.18.1.0	2018-11-01	31
toolshed.g2.bx.psu.edu/repos/iuc/humann2_renorm_table/humann2_renorm_table/0.11.1.0	2018-11-01	31
toolshed.g2.bx.psu.edu/repos/iuc/samtools_sort/samtools_rmdup/1.0.1	2018-11-01	30
toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.2.0	2018-11-01	30
CONVERTER_fasta_to_tabular	2018-11-01	30
toolshed.g2.bx.psu.edu/repos/crs4/prokka/prokka/1.12.0	2018-11-01	30
toolshed.g2.bx.psu.edu/repos/devteam/fastq_to_fasta/cshl_fastq_to_fasta/1.0.0	2018-11-01	30
toolshed.g2.bx.psu.edu/repos/galaxyp/gffcompare_to_bed/gffcompare_to_bed/0.1.0	2018-11-01	30
toolshed.g2.bx.psu.edu/repos/simon-gladman/velvetoptimiser/velvetoptimiser/2.2.6	2018-11-01	30
toolshed.g2.bx.psu.edu/repos/iuc/prinseq/prinseq/0.20.4	2018-11-01	30
toolshed.g2.bx.psu.edu/repos/lparsons/htseq_count/htseq_count/0.6.1galaxy1	2018-11-01	30
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_pe_fragmentsize/deeptools_bam_pe_fragmentsize/3.0.2.0	2018-11-01	30
toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/0.0.1	2018-11-01	29
toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_heatmap/ggplot2_heatmap/2.2.1	2018-11-01	29
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idfilter/IDFilter/2.2.0	2018-11-01	29
toolshed.g2.bx.psu.edu/repos/iuc/gemini_load/gemini_load/0.18.1.0	2018-11-01	29
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_fidoadapter/FidoAdapter/2.2.0.1	2018-11-01	29
toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_contigs/mothur_make_contigs/1.39.5.0	2018-11-01	29
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_alignmentsieve/deeptools_alignmentsieve/3.0.2.0	2018-11-01	29
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idscoreswitcher/IDScoreSwitcher/2.2.0	2018-11-01	29
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_peptideindexer/PeptideIndexer/2.2.0	2018-11-01	29
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idposteriorerrorprobability/IDPosteriorErrorProbability/2.2.0	2018-11-01	29
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idmapper/IDMapper/2.2.0	2018-11-01	28
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_proteinquantifier/ProteinQuantifier/2.2.0	2018-11-01	28
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_filefilter/FileFilter/2.2.0	2018-11-01	28
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_highresprecursormasscorrector/HighResPrecursorMassCorrector/2.2.0	2018-11-01	28
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idconflictresolver/IDConflictResolver/2.2.0	2018-11-01	28
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_msgfplusadapter/MSGFPlusAdapter/2.2.0	2018-11-01	28
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_featurefindermultiplex/FeatureFinderMultiplex/2.2.0	2018-11-01	28
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_fileconverter/FileConverter/2.3.0	2018-11-01	28
toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3r.1	2018-11-01	28
toolshed.g2.bx.psu.edu/repos/devteam/picard/rgPicardMarkDups/1.56.0	2018-11-01	28
ia_coordinates_of_roi	2018-11-01	28
toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.0	2018-11-01	28
toolshed.g2.bx.psu.edu/repos/devteam/coverage/gops_coverage_1/1.0.0	2018-11-01	27
toolshed.g2.bx.psu.edu/repos/jjohnson/rsem/rsem_prepare_reference/1.1.17	2018-11-01	27
mergeCols1	2018-11-01	27
toolshed.g2.bx.psu.edu/repos/devteam/merge_cols/mergeCols1/1.0.1	2018-11-01	27
toolshed.g2.bx.psu.edu/repos/galaxyp/msi_qualitycontrol/mass_spectrometry_imaging_qc/1.10.0.7	2018-11-01	26
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toolshed.g2.bx.psu.edu/repos/rnateam/blockbuster/blockbuster/0.1.1.1	2018-11-01	26
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toolshed.g2.bx.psu.edu/repos/iuc/mothur_heatmap_sim/mothur_heatmap_sim/1.39.5.0	2018-11-01	26
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bigwig_summary/deeptools_multi_bigwig_summary/3.0.2.0	2018-11-01	25
toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/2.9.1.3	2018-11-01	25
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_fidoadapter/FidoAdapter/2.3.0	2018-11-01	25
toolshed.g2.bx.psu.edu/repos/iuc/meme_fimo/meme_fimo/4.12.0.0	2018-11-01	25
toolshed.g2.bx.psu.edu/repos/iuc/raceid_inspecttrajectory/raceid_inspecttrajectory/3.0.2.1	2018-11-01	24
toolshed.g2.bx.psu.edu/repos/iuc/goseq/goseq/1.30.1	2018-11-01	24
toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_annotate/4.3+t.galaxy0	2018-11-01	24
toolshed.g2.bx.psu.edu/repos/galaxyp/dbbuilder/dbbuilder/0.3.0	2018-11-01	24
toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/0.8.2	2018-11-01	24
toolshed.g2.bx.psu.edu/repos/iuc/mothur_unique_seqs/mothur_unique_seqs/1.39.5.0	2018-11-01	23
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicplottads/hicexplorer_hicplottads/2.1.0	2018-11-01	23
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicpca/hicexplorer_hicpca/2.1.0	2018-11-01	23
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicmergematrixbins/hicexplorer_hicmergematrixbins/2.1.0	2018-11-01	23
toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/1.6.0.2	2018-11-01	23
toolshed.g2.bx.psu.edu/repos/devteam/bowtie_wrappers/bowtie_wrapper/1.2.0	2018-11-01	23
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicfindtads/hicexplorer_hicfindtads/2.1.0	2018-11-01	23
toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_sample/1.3.0	2018-11-01	23
toolshed.g2.bx.psu.edu/repos/iuc/sickle/sickle/1.33.1	2018-11-01	23
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicbuildmatrix/hicexplorer_hicbuildmatrix/2.1.0	2018-11-01	23
toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_spectra_plots/cardinal_spectra_plots/1.12.1.1	2018-11-01	23
toolshed.g2.bx.psu.edu/repos/iuc/mothur_taxonomy_to_krona/mothur_taxonomy_to_krona/1.0	2018-11-01	23
toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.1	2018-11-01	23
toolshed.g2.bx.psu.edu/repos/iuc/sqlite_to_tabular/sqlite_to_tabular/2.0.0	2018-11-01	22
dorina_search	2018-11-01	22
CONVERTER_fasta_to_fai	2018-11-01	22
toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.1.4	2018-11-01	22
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bigwig_compare/deeptools_bigwig_compare/3.0.2.0	2018-11-01	22
toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/0.5.3.2	2018-11-01	22
toolshed.g2.bx.psu.edu/repos/gbcs-embl-heidelberg/je_clip/je_clip/1.2.1	2018-11-01	21
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SortSam/2.18.2.1	2018-11-01	21
raceid_main	2018-11-01	21
toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.3	2018-11-01	21
toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_mz_images/cardinal_mz_images/1.12.1.1	2018-11-01	21
toolshed.g2.bx.psu.edu/repos/devteam/pileup_parser/pileup_parser/1.0.2	2018-11-01	21
toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_bdgpeakcall/2.1.1.20160309.0	2018-11-01	20
toolshed.g2.bx.psu.edu/repos/bgruening/diffbind/diffbind/2.6.6.4	2018-11-01	20
toolshed.g2.bx.psu.edu/repos/iuc/filtlong/filtlong/0.2.0	2018-11-01	20
toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_segmentations/cardinal_segmentations/1.12.1.1	2018-11-01	20
toolshed.g2.bx.psu.edu/repos/iuc/mothur_chimera_vsearch/mothur_chimera_vsearch/1.39.5.1	2018-11-01	20
toolshed.g2.bx.psu.edu/repos/iuc/transdecoder/transdecoder/3.0.1	2018-11-01	20
toolshed.g2.bx.psu.edu/repos/iuc/mothur_tree_shared/mothur_tree_shared/1.39.5.0	2018-11-01	20
toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_nn_classifier/sklearn_nn_classifier/0.9	2018-11-01	19
toolshed.g2.bx.psu.edu/repos/bgruening/nn_classifier/nn_classifier/0.9	2018-11-01	19
toolshed.g2.bx.psu.edu/repos/devteam/histogram/histogram_rpy/1.0.3	2018-11-01	19
toolshed.g2.bx.psu.edu/repos/galaxyp/unipept/unipept/2.0.1	2018-11-01	18
toolshed.g2.bx.psu.edu/repos/devteam/kraken/kraken/1.2.4	2018-11-01	18
toolshed.g2.bx.psu.edu/repos/iuc/mothur_pcoa/mothur_pcoa/1.36.1.0	2018-11-01	18
toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_ensemble/sklearn_ensemble/0.9	2018-11-01	18
toolshed.g2.bx.psu.edu/repos/iuc/mothur_homova/mothur_homova/1.36.1.0	2018-11-01	18
toolshed.g2.bx.psu.edu/repos/iuc/mothur_tree_shared/mothur_tree_shared/1.36.1.0	2018-11-01	18
toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.0	2018-11-01	18
toolshed.g2.bx.psu.edu/repos/bebatut/combine_metaphlan2_humann2/combine_metaphlan2_humann2/0.1.0	2018-11-01	18
toolshed.g2.bx.psu.edu/repos/iuc/mothur_heatmap_sim/mothur_heatmap_sim/1.36.1.0	2018-11-01	18
toolshed.g2.bx.psu.edu/repos/iuc/mothur_amova/mothur_amova/1.36.1.0	2018-11-01	18
toolshed.g2.bx.psu.edu/repos/devteam/fastx_trimmer/cshl_fastx_trimmer/1.0.2	2018-11-01	18
toolshed.g2.bx.psu.edu/repos/iuc/mothur_parsimony/mothur_parsimony/1.36.1.0	2018-11-01	18
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1	2018-11-01	17
toolshed.g2.bx.psu.edu/repos/iuc/shovill/shovill/1.0.4	2018-11-01	17
CONVERTER_bam_to_bigwig_0	2018-11-01	17
toolshed.g2.bx.psu.edu/repos/iuc/meme_chip/meme_chip/4.11.2+galaxy1	2018-11-01	17
toolshed.g2.bx.psu.edu/repos/iuc/pygenometracks/pygenomeTracks/2.0.1	2018-11-01	17
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.7.1.1	2018-11-01	17
toolshed.g2.bx.psu.edu/repos/devteam/samtools_flagstat/samtools_flagstat/2.0.1	2018-11-01	17
toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.0.20	2018-11-01	17
toolshed.g2.bx.psu.edu/repos/bgruening/canu/canu/1.7	2018-11-01	17
toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpsift_vartype/4.3.1	2018-11-01	17
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/1.1.0	2018-11-01	17
toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_joiner/fastq_paired_end_joiner/2.0.1.1	2018-11-01	16
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.0	2018-11-01	16
toolshed.g2.bx.psu.edu/repos/devteam/vcfgenotypes/vcfgenotypes/1.0.0_rc1+galaxy0	2018-11-01	16
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_coveragebed/2.27.0.3	2018-11-01	16
toolshed.g2.bx.psu.edu/repos/devteam/sam_pileup/sam_pileup/1.1.2	2018-11-01	16
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toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_dedup/umi_tools_dedup/0.5.3.0	2018-11-01	16
toolshed.g2.bx.psu.edu/repos/bebatut/format_metaphlan2_output/format_metaphlan2_output/0.1.0	2018-11-01	16
toolshed.g2.bx.psu.edu/repos/peterjc/blast2go/blast2go/0.0.9	2018-11-01	16
toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.1.0	2018-11-01	16
toolshed.g2.bx.psu.edu/repos/iuc/gemini_recessive_and_dominant/gemini_recessive_and_dominant/0.18.1.0	2018-11-01	16
toolshed.g2.bx.psu.edu/repos/galaxyp/msi_spectra_plot/mass_spectrometry_imaging_mzplots/1.10.0.6	2018-11-01	16
toolshed.g2.bx.psu.edu/repos/iuc/vsearch/vsearch_dereplication/1.9.7.0	2018-11-01	16
toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_mergepe/1.3.0	2018-11-01	16
toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.36.4	2018-11-01	16
scale_image	2018-11-01	15
toolshed.g2.bx.psu.edu/repos/iuc/gatk2/gatk2_unified_genotyper/2.8.0	2018-11-01	15
toolshed.g2.bx.psu.edu/repos/peterjc/mira_assembler/mira_assembler/0.0.11	2018-11-01	15
toolshed.g2.bx.psu.edu/repos/iuc/pureclip/pureclip/1.0.4	2018-11-01	15
toolshed.g2.bx.psu.edu/repos/iuc/raceid_filtnormconf/raceid_filtnormconf/3.0.2.1	2018-11-01	15
toolshed.g2.bx.psu.edu/repos/rnateam/sortmerna/bg_sortmerna/2.1b.4	2018-11-01	15
toolshed.g2.bx.psu.edu/repos/iuc/mothur_align_seqs/mothur_align_seqs/1.39.5.0	2018-11-01	15
toolshed.g2.bx.psu.edu/repos/iuc/stacks_refmap/stacks_refmap/1.46.0	2018-11-01	15
toolshed.g2.bx.psu.edu/repos/iuc/circos/circgraph/0.9-RC2	2018-11-01	15
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multiintersectbed/2.27.0.0	2018-11-01	15
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicpca/hicexplorer_hicpca/2.1.4.0	2018-11-01	15
toolshed.g2.bx.psu.edu/repos/bgruening/pileometh/pileometh/0.3.0	2018-11-01	15
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hiccomparematrices/hicexplorer_hiccomparematrices/2.1.4.0	2018-11-01	15
toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.68	2018-11-01	14
CONVERTER_gff_to_bed_0	2018-11-01	14
toolshed.g2.bx.psu.edu/repos/devteam/cuffmerge/cuffmerge/2.2.1.1	2018-11-01	14
toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.19.3.3	2018-11-01	14
toolshed.g2.bx.psu.edu/repos/iuc/ebi_search_rest_results/ebi_search_rest_results/0.1.1	2018-11-01	14
toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/2.8.1.3	2018-11-01	14
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_annotatebed/2.27.0.0	2018-11-01	14
toolshed.g2.bx.psu.edu/repos/iuc/roary/roary/3.10.2	2018-11-01	14
toolshed.g2.bx.psu.edu/repos/devteam/megablast_wrapper/megablast_wrapper/1.2.0	2018-11-01	14
toolshed.g2.bx.psu.edu/repos/bgruening/bismark/bismark_bowtie2/0.20.0	2018-11-01	14
toolshed.g2.bx.psu.edu/repos/devteam/fastx_artifacts_filter/cshl_fastx_artifacts_filter/1.0.0	2018-11-01	14
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idmerger/IDMerger/2.3.0	2018-11-01	14
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/deeptools_compute_matrix/2.5.1.1.0	2018-11-01	14
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicsummatrices/hicexplorer_hicsummatrices/2.1.4.0	2018-11-01	14
toolshed.g2.bx.psu.edu/repos/bgruening/augustus/augustus/3.2.3	2018-11-01	14
toolshed.g2.bx.psu.edu/repos/iuc/gemini_comp_hets/gemini_comp_hets/0.18.1.0	2018-11-01	14
toolshed.g2.bx.psu.edu/repos/iuc/gemini_de_novo/gemini_de_novo/0.18.1.0	2018-11-01	14
toolshed.g2.bx.psu.edu/repos/peterjc/tmhmm_and_signalp/tmhmm2/0.0.16	2018-11-01	14
toolshed.g2.bx.psu.edu/repos/iuc/mothur_remove_seqs/mothur_remove_seqs/1.36.1.0	2018-11-01	14
toolshed.g2.bx.psu.edu/repos/iuc/raceid_clustering/raceid_clustering/3.0.2.1	2018-11-01	13
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1	2018-11-01	13
toolshed.g2.bx.psu.edu/repos/devteam/fastx_nucleotides_distribution/cshl_fastx_nucleotides_distribution/1.0.0	2018-11-01	13
toolshed.g2.bx.psu.edu/repos/crs4/sopra/sopra_wpc/0.1	2018-11-01	13
toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.16.5	2018-11-01	13
toolshed.g2.bx.psu.edu/repos/iuc/rnaspades/rnaspades/3.9.0.1	2018-11-01	13
CONVERTER_bed_to_gff_0	2018-11-01	13
toolshed.g2.bx.psu.edu/repos/ethevenot/univariate/Univariate/2.2.4	2018-11-01	12
toolshed.g2.bx.psu.edu/repos/bjoern-gruening/sed_wrapper/sed_stream_editor/0.0.1	2018-11-01	12
CONVERTER_interval_to_bigwig_0	2018-11-01	12
genomespace_exporter	2018-11-01	12
toolshed.g2.bx.psu.edu/repos/devteam/clustalw/clustalw/2.1	2018-11-01	12
toolshed.g2.bx.psu.edu/repos/ethevenot/biosigner/biosigner/2.2.7	2018-11-01	12
toolshed.g2.bx.psu.edu/repos/iuc/mothur_cluster_split/mothur_cluster_split/1.39.5.0	2018-11-01	12
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicfindtads/hicexplorer_hicfindtads/2.1.4.0	2018-11-01	12
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_decoydatabase/DecoyDatabase/2.3.0	2018-11-01	12
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.0.0	2018-11-01	12
toolshed.g2.bx.psu.edu/repos/iuc/raceid_trajectory/raceid_trajectory/3.0.2.1	2018-11-01	12
toolshed.g2.bx.psu.edu/repos/rnateam/graphclust_aggregate_alignments/graphclust_aggregate_alignments/0.1	2018-11-01	12
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FastqToSam/2.18.2.1	2018-11-01	12
toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/column_remove_by_header/0.0.1	2018-11-01	12
toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.5.2b-2	2018-11-01	12
toolshed.g2.bx.psu.edu/repos/iuc/mothur_count_seqs/mothur_count_seqs/1.39.5.0	2018-11-01	12
toolshed.g2.bx.psu.edu/repos/bgruening/split_file_on_column/tp_split_on_column/0.2	2018-11-01	12
toolshed.g2.bx.psu.edu/repos/devteam/correlation/cor2/1.0.0	2018-11-01	12
toolshed.g2.bx.psu.edu/repos/bgruening/plotly_ml_performance_plots/plotly_ml_performance_plots/0.1	2018-11-01	12
toolshed.g2.bx.psu.edu/repos/iuc/mothur_classify_otu/mothur_classify_otu/1.39.5.0	2018-11-01	11
toolshed.g2.bx.psu.edu/repos/iuc/megahit/megahit/1.1.2.3	2018-11-01	11
toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.2	2018-11-01	11
toolshed.g2.bx.psu.edu/repos/iuc/qiime_assign_taxonomy/qiime_assign_taxonomy/1.9.1.0	2018-11-01	11
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_pca/deeptools_plot_pca/3.1.2.0.0	2018-11-01	11
toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.13.0	2018-11-01	11
toolshed.g2.bx.psu.edu/repos/iuc/trinity_run_de_analysis/trinity_run_de_analysis/2.8.4	2018-11-01	11
toolshed.g2.bx.psu.edu/repos/iuc/gatk2/gatk2_realigner_target_creator/2.8.0	2018-11-01	11
toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_FPKM_count/2.6.4.1	2018-11-01	11
toolshed.g2.bx.psu.edu/repos/iuc/column_order_header_sort/column_order_header_sort/0.0.1	2018-11-01	11
toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.12.5+galaxy1	2018-11-01	11
bwtool-lift	2018-11-01	11
toolshed.g2.bx.psu.edu/repos/iuc/trinity_abundance_estimates_to_matrix/trinity_abundance_estimates_to_matrix/2.8.4	2018-11-01	10
toolshed.g2.bx.psu.edu/repos/peterjc/blast_rbh/blast_reciprocal_best_hits/0.1.11	2018-11-01	10
toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.12	2018-11-01	10
toolshed.g2.bx.psu.edu/repos/iuc/stacks_populations/stacks_populations/1.46.0	2018-11-01	10
viz_overlay_moving_and_fixed_image	2018-11-01	10
CONVERTER_gff_to_interval_index_0	2018-11-01	10
toolshed.g2.bx.psu.edu/repos/devteam/fastqtofasta/fastq_to_fasta_python/1.1.1	2018-11-01	10
toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/1.0.1	2018-11-01	10
toolshed.g2.bx.psu.edu/repos/bgruening/unique/bg_uniq/0.3	2018-11-01	10
toolshed.g2.bx.psu.edu/repos/iuc/star_fusion/star_fusion/0.5.4-3	2018-11-01	10
toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_shared/mothur_make_shared/1.39.5.0	2018-11-01	10
toolshed.g2.bx.psu.edu/repos/rnateam/mirdeep2_quantifier/rbc_mirdeep2_quantifier/2.0.0	2018-11-01	10
toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_duplication/2.6.4	2018-11-01	10
toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread/2.2.1.1	2018-11-01	10
toolshed.g2.bx.psu.edu/repos/iuc/kallisto_quant/kallisto_quant/0.43.1.4	2018-11-01	10
toolshed.g2.bx.psu.edu/repos/iuc/mothur_venn/mothur_venn/1.39.5.0	2018-11-01	10
ip_projective_transformation_points	2018-11-01	10
re_he_maldi_image_registration	2018-11-01	10
toolshed.g2.bx.psu.edu/repos/rnateam/mirdeep2/rbc_mirdeep2/2.0.0	2018-11-01	10
toolshed.g2.bx.psu.edu/repos/bgruening/plotly_regression_performance_plots/plotly_regression_performance_plots/0.1	2018-11-01	10
toolshed.g2.bx.psu.edu/repos/bebatut/cdhit/cd_hit_est/1.3	2018-11-01	10
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicatesWithMateCigar/2.18.2.1	2018-11-01	10
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.0	2018-11-01	10
toolshed.g2.bx.psu.edu/repos/peterjc/seq_filter_by_id/seq_filter_by_id/0.2.7	2018-11-01	10
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_uniq_tool/1.1.1	2018-11-01	10
CONVERTER_interval_to_bgzip_0	2018-11-01	9
toolshed.g2.bx.psu.edu/repos/iuc/extract_genomic_dna/Extract genomic DNA 1/3.0.2	2018-11-01	9
toolshed.g2.bx.psu.edu/repos/bebatut/group_humann2_uniref_abundances_to_go/group_humann2_uniref_abundances_to_go/1.2.0	2018-11-01	9
toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_mergefa/1.3.0	2018-11-01	9
toolshed.g2.bx.psu.edu/repos/iuc/picrust_categorize/picrust_categorize/1.1.1.0	2018-11-01	9
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_DownsampleSam/2.18.2.1	2018-11-01	9
toolshed.g2.bx.psu.edu/repos/iuc/mothur_classify_seqs/mothur_classify_seqs/1.39.5.0	2018-11-01	9
toolshed.g2.bx.psu.edu/repos/jjohnson/rsem/rsem_calculate_expression/1.1.17	2018-11-01	9
toolshed.g2.bx.psu.edu/repos/iuc/shovill/shovill/0.9.0	2018-11-01	9
random_lines1	2018-11-01	9
toolshed.g2.bx.psu.edu/repos/bgruening/replace_column_by_key_value_file/replace_column_with_key_value_file/0.1	2018-11-01	9
toolshed.g2.bx.psu.edu/repos/iuc/graphlan_annotate/graphlan_annotate/1.0.0.0	2018-11-01	9
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_jaccard/2.27.0.0	2018-11-01	9
toolshed.g2.bx.psu.edu/repos/iuc/graphlan/graphlan/1.0.0.0	2018-11-01	9
toolshed.g2.bx.psu.edu/repos/eschen42/w4mcorcov/w4mcorcov/0.98.16	2018-11-01	9
toolshed.g2.bx.psu.edu/repos/bgruening/interproscan5/interproscan/5.0.0	2018-11-01	9
toolshed.g2.bx.psu.edu/repos/iuc/export2graphlan/export2graphlan/0.19	2018-11-01	9
toolshed.g2.bx.psu.edu/repos/kellrott/regex_replace/regex_replace/1.0.0	2018-11-01	9
toolshed.g2.bx.psu.edu/repos/iuc/gffcompare/gffcompare/0.9.8	2018-11-01	9
toolshed.g2.bx.psu.edu/repos/iuc/mothur_pre_cluster/mothur_pre_cluster/1.39.5.0	2018-11-01	9
toolshed.g2.bx.psu.edu/repos/iuc/mothur_rarefaction_single/mothur_rarefaction_single/1.36.1.0	2018-11-01	9
toolshed.g2.bx.psu.edu/repos/iuc/mothur_rarefaction_single/mothur_rarefaction_single/1.39.5.0	2018-11-01	9
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddOrReplaceReadGroups/2.18.2.1	2018-11-01	9
toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.6.1	2018-11-01	9
toolshed.g2.bx.psu.edu/repos/tgac/miranda/miranda/3.3a	2018-11-01	9
toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy_core/3.2	2018-11-01	9
toolshed.g2.bx.psu.edu/repos/iuc/humann2_genefamilies_genus_level/humann2_genefamilies_genus_level/0.11.1.0	2018-11-01	9
toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: primersearch81/5.0.0.1	2018-11-01	8
__MERGE_COLLECTION__	2018-11-01	8
toolshed.g2.bx.psu.edu/repos/jjohnson/rsem/extract_transcript_to_gene_map_from_trinity/1.1.17	2018-11-01	8
toolshed.g2.bx.psu.edu/repos/bgruening/protein_properties/bg_protein_properties/0.1.0	2018-11-01	8
CONVERTER_ref_to_seq_taxomony	2018-11-01	8
toolshed.g2.bx.psu.edu/repos/devteam/gi2taxonomy/Fetch Taxonomic Ranks/1.1.0	2018-11-01	8
toolshed.g2.bx.psu.edu/repos/iuc/egsea/egsea/1.6.0.1	2018-11-01	8
toolshed.g2.bx.psu.edu/repos/peterjc/sample_seqs/sample_seqs/0.2.5	2018-11-01	8
toolshed.g2.bx.psu.edu/repos/devteam/sicer/peakcalling_sicer/0.0.2	2018-11-01	8
toolshed.g2.bx.psu.edu/repos/devteam/picard/PicardASMetrics/1.56.0	2018-11-01	8
toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: cpgplot15/5.0.0	2018-11-01	8
toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_bdgbroadcall/2.1.1.20160309.0	2018-11-01	8
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toolshed.g2.bx.psu.edu/repos/lparsons/htseq_count/htseq_count/0.6.1galaxy2	2018-11-01	8
toolshed.g2.bx.psu.edu/repos/iuc/enasearch_retrieve_taxons/enasearch_retrieve_taxons/0.1.1.0	2018-11-01	8
toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/1.3.3.1	2018-11-01	8
toolshed.g2.bx.psu.edu/repos/devteam/macs/peakcalling_macs/1.0.1	2018-11-01	8
toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_biom/mothur_make_biom/1.39.5.0	2018-11-01	8
toolshed.g2.bx.psu.edu/repos/devteam/fasta_concatenate_by_species/fasta_concatenate0/0.0.0	2018-11-01	8
toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_tblastn_wrapper/0.2.01	2018-11-01	8
toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_group/umi_tools_group/0.5.3.0	2018-11-01	8
CONVERTER_gff_to_fli_0	2018-11-01	8
toolshed.g2.bx.psu.edu/repos/iuc/gubbins/gubbins/0.1.0	2018-11-01	8
CONVERTER_vcf_to_bgzip_0	2018-11-01	8
toolshed.g2.bx.psu.edu/repos/galaxyp/fasta_merge_files_and_filter_unique_sequences/fasta_merge_files_and_filter_unique_sequences/1.2.0	2018-11-01	8
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toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy3	2018-11-01	8
toolshed.g2.bx.psu.edu/repos/iuc/mothur_filter_seqs/mothur_filter_seqs/1.39.5.0	2018-11-01	8
toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/search_gui/3.2.13	2018-11-01	8
toolshed.g2.bx.psu.edu/repos/bgruening/antismash/antismash/4.1	2018-11-01	7
toolshed.g2.bx.psu.edu/repos/peterjc/tmhmm_and_signalp/signalp3/0.0.19	2018-11-01	7
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_profile/deeptools_plot_profile/2.5.1.1.0	2018-11-01	7
toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_group/mothur_make_group/1.39.5.0	2018-11-01	7
wc_gnu	2018-11-01	7
toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sra_pileup/2.9.1.2	2018-11-01	7
toolshed.g2.bx.psu.edu/repos/iuc/bwameth/bwameth/0.2.0.3	2018-11-01	7
toolshed.g2.bx.psu.edu/repos/devteam/xy_plot/XY_Plot_1/1.0.2	2018-11-01	7
toolshed.g2.bx.psu.edu/repos/iuc/mothur_sub_sample/mothur_sub_sample/1.39.5.0	2018-11-01	7
trimmer	2018-11-01	7
toolshed.g2.bx.psu.edu/repos/iuc/charts/charts/1.0.1	2018-11-01	7
toolshed.g2.bx.psu.edu/repos/iuc/fraggenescan/fraggenescan/1.30.0	2018-11-01	7
toolshed.g2.bx.psu.edu/repos/devteam/fastq_manipulation/fastq_manipulation/1.1.1	2018-11-01	7
toolshed.g2.bx.psu.edu/repos/devteam/vcfvcfintersect/vcfvcfintersect/1.0.0_rc1+galaxy0	2018-11-01	7
toolshed.g2.bx.psu.edu/repos/bgruening/graphmap_align/graphmap_align/0.5.2	2018-11-01	7
toolshed.g2.bx.psu.edu/repos/iuc/mothur_count_groups/mothur_count_groups/1.36.1.0	2018-11-01	7
CONVERTER_vcf_to_tabix_0	2018-11-01	7
toolshed.g2.bx.psu.edu/repos/iuc/ncbi_eutils_esearch/ncbi_eutils_esearch/1.1	2018-11-01	7
toolshed.g2.bx.psu.edu/repos/iuc/gatk2/gatk2_variant_select/2.8.0	2018-11-01	7
toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0	2018-11-01	7
toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_download/4.3r.1	2018-11-01	7
toolshed.g2.bx.psu.edu/repos/iuc/migmap/migmap/1.0.2.2	2018-11-01	7
extract_bcs.py	2018-11-01	6
toolshed.g2.bx.psu.edu/repos/iuc/mageck_count/mageck_count/0.5.7.4	2018-11-01	6
toolshed.g2.bx.psu.edu/repos/lparsons/htseq_count/htseq_count/0.6.1galaxy3	2018-11-01	6
toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/1.0	2018-11-01	6
toolshed.g2.bx.psu.edu/repos/iuc/mothur_remove_lineage/mothur_remove_lineage/1.39.5.0	2018-11-01	6
toolshed.g2.bx.psu.edu/repos/iuc/trinity_analyze_diff_expr/trinity_analyze_diff_expr/2.8.4	2018-11-01	6
qual_stats_boxplot	2018-11-01	6
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicplotdistvscounts/hicexplorer_hicplotdistvscounts/2.1.4.0	2018-11-01	6
toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_distribution/2.6.4.1	2018-11-01	6
toolshed.g2.bx.psu.edu/repos/iuc/trinity_super_transcripts/trinity_super_transcripts/2.8.4	2018-11-01	6
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_consensusid/ConsensusID/2.3.0	2018-11-01	6
toolshed.g2.bx.psu.edu/repos/devteam/cummerbund_to_tabular/cummerbund_to_cuffdiff/1.0.1	2018-11-01	6
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_closestbed/2.27.0.0	2018-11-01	6
CONVERTER_interval_to_bed6_0	2018-11-01	6
toolshed.g2.bx.psu.edu/repos/devteam/data_manager_build_kraken_database/kraken_database_builder/1.1	2018-11-01	6
toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_tblastx_wrapper/0.3.1	2018-11-01	6
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_NormalizeFasta/2.18.2.1	2018-11-01	6
toolshed.g2.bx.psu.edu/repos/devteam/vcfselectsamples/vcfselectsamples/1.0.0_rc1+galaxy0	2018-11-01	6
toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3+t.galaxy0	2018-11-01	6
toolshed.g2.bx.psu.edu/repos/peterjc/tmhmm_and_signalp/rxlr_motifs/0.0.14	2018-11-01	6
toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: palindrome65/5.0.0.1	2018-11-01	6
toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.5.2b-0	2018-11-01	6
CONVERTER_interval_to_tabix_0	2018-11-01	6
toolshed.g2.bx.psu.edu/repos/rnateam/mafft/rbc_mafft/7.221.3	2018-11-01	6
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hictransform/hicexplorer_hictransform/2.1.4.0	2018-11-01	6
toolshed.g2.bx.psu.edu/repos/jjohnson/samtools_filter/samtools_filter/1.1.1	2018-11-01	6
toolshed.g2.bx.psu.edu/repos/devteam/fastx_nucleotides_distribution/cshl_fastx_nucleotides_distribution/1.0.1	2018-11-01	6
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_heatmap/deeptools_plot_heatmap/2.5.7.0	2018-11-01	6
toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/peptide_shaker/1.16.4	2018-11-01	6
genomespace_importer	2018-11-01	6
toolshed.g2.bx.psu.edu/repos/iuc/trinity_gene_to_trans_map/trinity_gene_to_trans_map/2.8.4	2018-11-01	6
toolshed.g2.bx.psu.edu/repos/iuc/meme_dreme/meme_dreme/4.11.2.0	2018-11-01	6
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toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.0.0	2018-11-01	5
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_proteinquantifier/ProteinQuantifier/2.3.0	2018-11-01	5
CONVERTER_wig_to_bigwig	2018-11-01	5
toolshed.g2.bx.psu.edu/repos/iuc/describe_samples/describe_samples/2.8.4	2018-11-01	5
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtofastq/2.27.0.0	2018-11-01	5
toolshed.g2.bx.psu.edu/repos/devteam/fastq_combiner/fastq_combiner/1.1.1	2018-11-01	5
Count1	2018-11-01	5
toolshed.g2.bx.psu.edu/repos/blankenberg/naive_variant_caller/naive_variant_caller/0.0.3	2018-11-01	5
toolshed.g2.bx.psu.edu/repos/iuc/mothur_dist_shared/mothur_dist_shared/1.39.5.0	2018-11-01	5
toolshed.g2.bx.psu.edu/repos/eschen42/w4mclassfilter/w4mclassfilter/0.98.10	2018-11-01	5
toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_pca/ggplot2_pca/2.2.1	2018-11-01	5
toolshed.g2.bx.psu.edu/repos/iuc/bp_genbank2gff3/bp_genbank2gff3/1.0	2018-11-01	5
toolshed.g2.bx.psu.edu/repos/iuc/trinity_samples_qccheck/trinity_samples_qccheck/2.8.4	2018-11-01	5
toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_wrapper_2/1.3.2	2018-11-01	5
toolshed.g2.bx.psu.edu/repos/nml/metaspades/metaspades/3.9.0	2018-11-01	5
toolshed.g2.bx.psu.edu/repos/devteam/vcfcombine/vcfcombine/1.0.0_rc1+galaxy0	2018-11-01	5
toolshed.g2.bx.psu.edu/repos/devteam/cuffnorm/cuffnorm/2.2.1.2	2018-11-01	5
toolshed.g2.bx.psu.edu/repos/devteam/fastq_quality_boxplot/cshl_fastq_quality_boxplot/1.0.0	2018-11-01	5
toolshed.g2.bx.psu.edu/repos/iuc/ruvseq/ruvseq/1.12.0	2018-11-01	5
toolshed.g2.bx.psu.edu/repos/bgruening/nucleosome_prediction/Nucleosome/3.0	2018-11-01	5
toolshed.g2.bx.psu.edu/repos/devteam/samtools_bedcov/samtools_bedcov/2.0.1	2018-11-01	5
toolshed.g2.bx.psu.edu/repos/iuc/stacks_denovomap/stacks_denovomap/1.46.0	2018-11-01	5
toolshed.g2.bx.psu.edu/repos/iuc/qiime_pick_open_reference_otus/qiime_pick_open_reference_otus/1.9.1.0	2018-11-01	5
toolshed.g2.bx.psu.edu/repos/galaxyp/uniprotxml_downloader/uniprotxml_downloader/2.0.0	2018-11-01	5
toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/blastxml_to_tabular/0.3.1	2018-11-01	5
toolshed.g2.bx.psu.edu/repos/iuc/qiime_pick_otus/qiime_pick_otus/1.9.1.0	2018-11-01	5
echo_main_env	2018-11-01	5
toolshed.g2.bx.psu.edu/repos/crs4/muscle/muscle/0.0.11	2018-11-01	5
toolshed.g2.bx.psu.edu/repos/gbcs-embl-heidelberg/je_markdupes/je_markdupes/1.2.1	2018-11-01	5
toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.0.0	2018-11-01	5
bed2gff1	2018-11-01	4
toolshed.g2.bx.psu.edu/repos/iuc/mothur_metastats/mothur_metastats/1.36.1.0	2018-11-01	4
toolshed.g2.bx.psu.edu/repos/iuc/enasearch_search_data/enasearch_search_data/0.1.1.0	2018-11-01	4
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/1.136.0	2018-11-01	4
toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_contigs/mothur_make_contigs/1.36.1.0	2018-11-01	4
toolshed.g2.bx.psu.edu/repos/bgruening/minced/minced/0.1.5	2018-11-01	4
toolshed.g2.bx.psu.edu/repos/iuc/mothur_remove_groups/mothur_remove_groups/1.36.1.0	2018-11-01	4
CONVERTER_bz2_to_uncompressed	2018-11-01	4
toolshed.g2.bx.psu.edu/repos/iuc/mothur_remove_lineage/mothur_remove_lineage/1.36.1.0	2018-11-01	4
toolshed.g2.bx.psu.edu/repos/iuc/mothur_get_groups/mothur_get_groups/1.39.5.0	2018-11-01	4
toolshed.g2.bx.psu.edu/repos/iuc/mothur_get_groups/mothur_get_groups/1.36.1.0	2018-11-01	4
toolshed.g2.bx.psu.edu/repos/iuc/mothur_seq_error/mothur_seq_error/1.36.1.0	2018-11-01	4
toolshed.g2.bx.psu.edu/repos/iuc/mothur_seq_error/mothur_seq_error/1.39.5.0	2018-11-01	4
toolshed.g2.bx.psu.edu/repos/iuc/mothur_sub_sample/mothur_sub_sample/1.36.1.0	2018-11-01	4
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_filefilter/FileFilter/2.3.0	2018-11-01	4
toolshed.g2.bx.psu.edu/repos/iuc/mothur_dist_shared/mothur_dist_shared/1.36.1.0	2018-11-01	4
toolshed.g2.bx.psu.edu/repos/iuc/mothur_dist_seqs/mothur_dist_seqs/1.36.1.0	2018-11-01	4
toolshed.g2.bx.psu.edu/repos/iuc/mothur_summary_single/mothur_summary_single/1.36.1.0	2018-11-01	4
toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_generalized_linear/sklearn_generalized_linear/0.9	2018-11-01	4
toolshed.g2.bx.psu.edu/repos/iuc/mothur_summary_single/mothur_summary_single/1.39.5.0	2018-11-01	4
toolshed.g2.bx.psu.edu/repos/iuc/mothur_count_groups/mothur_count_groups/1.39.5.0	2018-11-01	4
toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_whitelist/umi_tools_whitelist/0.5.3.1	2018-11-01	4
toolshed.g2.bx.psu.edu/repos/iuc/mothur_cluster/mothur_cluster/1.39.5.0	2018-11-01	4
toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.67	2018-11-01	4
toolshed.g2.bx.psu.edu/repos/iuc/mothur_cluster/mothur_cluster/1.36.1.0	2018-11-01	4
toolshed.g2.bx.psu.edu/repos/devteam/cluster/gops_cluster_1/1.0.0	2018-11-01	4
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SamToFastq/2.18.2.1	2018-11-01	4
toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_tblastn_wrapper/0.3.1	2018-11-01	4
toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.1.0	2018-11-01	4
toolshed.g2.bx.psu.edu/repos/devteam/fastx_quality_statistics/cshl_fastx_quality_statistics/1.0.1	2018-11-01	4
toolshed.g2.bx.psu.edu/repos/iuc/gemini_db_info/gemini_db_info/0.18.1.0	2018-11-01	4
toolshed.g2.bx.psu.edu/repos/iuc/mothur_chimera_uchime/mothur_chimera_uchime/1.36.1.0	2018-11-01	4
toolshed.g2.bx.psu.edu/repos/ethevenot/checkformat/checkFormat/3.0.0	2018-11-01	4
toolshed.g2.bx.psu.edu/repos/peterjc/tmhmm_and_signalp/wolf_psort/0.0.11	2018-11-01	4
toolshed.g2.bx.psu.edu/repos/anton/vcfvcfintersect/vcfvcfintersect/0.0.1	2018-11-01	4
toolshed.g2.bx.psu.edu/repos/iuc/ncbi_eutils_efetch/ncbi_eutils_efetch/1.1	2018-11-01	4
gff2bed1	2018-11-01	4
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idconflictresolver/IDConflictResolver/2.3.0	2018-11-01	4
toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.4.1	2018-11-01	4
toolshed.g2.bx.psu.edu/repos/iuc/pear/iuc_pear/0.9.6.1	2018-11-01	4
toolshed.g2.bx.psu.edu/repos/iuc/pilon/pilon/1.20.1	2018-11-01	4
toolshed.g2.bx.psu.edu/repos/devteam/tophat2/tophat2/2.1.0	2018-11-01	4
toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_group/abims_xcms_group/2.1.1	2018-11-01	4
toolshed.g2.bx.psu.edu/repos/bgruening/bismark/bismark_bowtie/0.7.12	2018-11-01	4
deeptools_bigwigCorrelate	2018-11-01	4
toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.3.0	2018-11-01	4
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_unionbedgraph/2.27.0.0	2018-11-01	4
biomart	2018-11-01	4
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idmapper/IDMapper/2.3.0	2018-11-01	4
toolshed.g2.bx.psu.edu/repos/devteam/fastq_stats/fastq_stats/1.0.0	2018-11-01	4
toolshed.g2.bx.psu.edu/repos/iuc/qiime_summarize_taxa/qiime_summarize_taxa/1.9.1.0	2018-11-01	4
toolshed.g2.bx.psu.edu/repos/iuc/mothur_remove_groups/mothur_remove_groups/1.39.5.0	2018-11-01	3
toolshed.g2.bx.psu.edu/repos/iuc/mothur_venn/mothur_venn/1.36.1.0	2018-11-01	3
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_enrichment/deeptools_plot_enrichment/3.0.2.0	2018-11-01	3
toolshed.g2.bx.psu.edu/repos/galaxyp/msi_ion_images/mass_spectrometry_imaging_ion_images/1.10.0.5	2018-11-01	3
toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_quality_report/cardinal_quality_report/1.12.1.0	2018-11-01	3
toolshed.g2.bx.psu.edu/repos/iuc/mothur_lefse/mothur_lefse/1.36.1.0	2018-11-01	3
toolshed.g2.bx.psu.edu/repos/iuc/gatk2/gatk2_haplotype_caller/2.8.0	2018-11-01	3
toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_predictd/2.1.1.20160309.0	2018-11-01	3
toolshed.g2.bx.psu.edu/repos/devteam/vcfannotate/vcfannotate/1.0.0_rc1+galaxy0	2018-11-01	3
toolshed.g2.bx.psu.edu/repos/iuc/ncbi_eutils_elink/ncbi_eutils_elink/1.1	2018-11-01	3
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_coverage/deeptools_plot_coverage/3.0.2.0	2018-11-01	3
flexbar_no_split	2018-11-01	3
toolshed.g2.bx.psu.edu/repos/devteam/fastx_collapser/cshl_fastx_collapser/1.0.1	2018-11-01	3
toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_junction_saturation/2.6.4.1	2018-11-01	3
rm_spurious_events.py	2018-11-01	3
toolshed.g2.bx.psu.edu/repos/galaxyp/msconvert/msconvert_nix/3.0.0	2018-11-01	3
toolshed.g2.bx.psu.edu/repos/iuc/mothur_dist_seqs/mothur_dist_seqs/1.39.5.0	2018-11-01	3
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReorderSam/2.18.2.1	2018-11-01	3
extract_aln_ends.py	2018-11-01	3
toolshed.g2.bx.psu.edu/repos/jjohnson/sqlite_to_tabular/sqlite_to_tabular/0.0.1	2018-11-01	3
toolshed.g2.bx.psu.edu/repos/iuc/mothur_merge_files/mothur_merge_files/1.39.5.0	2018-11-01	3
toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastx_wrapper/0.1.00	2018-11-01	3
toolshed.g2.bx.psu.edu/repos/iuc/abricate/abricate/0.8	2018-11-01	3
toolshed.g2.bx.psu.edu/repos/bgruening/wtdbg/wtdbg/1.2.8.1	2018-11-01	3
toolshed.g2.bx.psu.edu/repos/jjohnson/query_tabular/query_tabular/3.0.0	2018-11-01	3
toolshed.g2.bx.psu.edu/repos/peterjc/blastxml_to_top_descr/blastxml_to_top_descr/0.1.1	2018-11-01	3
toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.2.6	2018-11-01	3
toolshed.g2.bx.psu.edu/repos/devteam/samtools_flagstat/samtools_flagstat/2.0	2018-11-01	3
toolshed.g2.bx.psu.edu/repos/peterjc/tmhmm_and_signalp/promoter2/0.0.12	2018-11-01	3
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toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_shufflebed/2.27.0.0	2018-11-01	3
toolshed.g2.bx.psu.edu/repos/iuc/qiime_alpha_diversity/qiime_alpha_diversity/1.9.1.0	2018-11-01	3
remove_tail.py	2018-11-01	3
toolshed.g2.bx.psu.edu/repos/iuc/mothur_classify_rf/mothur_classify_rf/1.36.1.0	2018-11-01	3
toolshed.g2.bx.psu.edu/repos/devteam/fastx_quality_statistics/cshl_fastx_quality_statistics/1.0.0	2018-11-01	3
bed_to_bigBed	2018-11-01	3
mosaik_wrapper	2018-11-01	3
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coords2clnt.py	2018-11-01	3
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_slopbed/2.27.0.0	2018-11-01	3
CONVERTER_sam_to_unsorted_bam	2018-11-01	3
merge_pcr_duplicates.py	2018-11-01	3
toolshed.g2.bx.psu.edu/repos/galaxyp/msi_combine/mass_spectrometry_imaging_combine/1.10.0.5	2018-11-01	3
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_clusterbed/2.27.0.0	2018-11-01	3
gene2exon1	2018-11-01	3
toolshed.g2.bx.psu.edu/repos/lparsons/fastq_join/fastq_join/1.1.2-806.1	2018-11-01	3
toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.2.0	2018-11-01	3
toolshed.g2.bx.psu.edu/repos/bgruening/nanopolish_variants/nanopolish_variants/0.1.0	2018-11-01	3
toolshed.g2.bx.psu.edu/repos/bgruening/diamond/bg_diamond/0.8.24.1	2018-11-01	3
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/deeptools_compute_matrix/2.5.7.0	2018-11-01	3
toolshed.g2.bx.psu.edu/repos/bgruening/column_arrange_by_header/bg_column_arrange_by_header/0.1	2018-11-01	3
toolshed.g2.bx.psu.edu/repos/nml/spades/spades/3.11.1	2018-11-01	3
toolshed.g2.bx.psu.edu/repos/peterjc/tmhmm_and_signalp/Psortb/0.0.9	2018-11-01	3
toolshed.g2.bx.psu.edu/repos/jjohnson/cdhit/cd_hit_est/1.2	2018-11-01	3
modENCODEworm	2018-11-01	3
toolshed.g2.bx.psu.edu/repos/devteam/bam_to_sam/bam_to_sam/2.0	2018-11-01	3
toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_d_wrapper/1.3.2	2018-11-01	3
Interval2Maf1	2018-11-01	3
toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/0.8.1+galaxy0	2018-11-01	2
toolshed.g2.bx.psu.edu/repos/earlhaminst/ensembl_get_sequences/get_sequences/0.1.2	2018-11-01	2
toolshed.g2.bx.psu.edu/repos/bgruening/svm_classifier/svm_classifier/0.9	2018-11-01	2
toolshed.g2.bx.psu.edu/repos/iuc/kraken_taxonomy_report/kraken_taxonomy_report/0.0.2	2018-11-01	2
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/2.5.7.0	2018-11-01	2
toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/2.2.1+galaxy0	2018-11-01	2
toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastx_wrapper/0.3.0	2018-11-01	2
toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastp_wrapper/0.0.20	2018-11-01	2
toolshed.g2.bx.psu.edu/repos/devteam/count_covariates/gatk_count_covariates/0.0.5	2018-11-01	2
genbank_to_gff	2018-11-01	2
toolshed.g2.bx.psu.edu/repos/rnateam/rnashapes/RNAshapes/3.3.0	2018-11-01	2
gbk_to_orf	2018-11-01	2
toolshed.g2.bx.psu.edu/repos/devteam/fastx_reverse_complement/cshl_fastx_reverse_complement/1.0.2	2018-11-01	2
toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: backtranseq2/5.0.0	2018-11-01	2
toolshed.g2.bx.psu.edu/repos/devteam/kraken_translate/kraken-translate/1.2.3	2018-11-01	2
toolshed.g2.bx.psu.edu/repos/ethevenot/qualitymetrics/quality_metrics/2.2.8	2018-11-01	2
toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_retcor/abims_xcms_retcor/2.1.1	2018-11-01	2
toolshed.g2.bx.psu.edu/repos/devteam/scatterplot/scatterplot_rpy/1.0.3	2018-11-01	2
toolshed.g2.bx.psu.edu/repos/iuc/meme_chip/meme_chip/4.11.2	2018-11-01	2
toolshed.g2.bx.psu.edu/repos/galaxyp/reactome_pathwaymatcher/reactome_pathwaymatcher/1.8.1.2	2018-11-01	2
toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_merge/xcms_merge/1.1.0	2018-11-01	2
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_featurefindermultiplex/FeatureFinderMultiplex/2.3.0	2018-11-01	2
toolshed.g2.bx.psu.edu/repos/devteam/principal_component_analysis/pca1/1.0.2	2018-11-01	2
toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_fillpeaks/abims_xcms_fillPeaks/2.1.1	2018-11-01	2
toolshed.g2.bx.psu.edu/repos/iuc/varscan_mpileup/varscan_mpileup/2.4.3.0	2018-11-01	2
toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/4.3+t.galaxy0	2018-11-01	2
toolshed.g2.bx.psu.edu/repos/bgruening/bamhash/bamhash/1.1	2018-11-01	2
toolshed.g2.bx.psu.edu/repos/lecorguille/camera_annotate/abims_CAMERA_annotateDiffreport/2.2.2	2018-11-01	2
foldchange_heatmap	2018-11-01	2
toolshed.g2.bx.psu.edu/repos/rnateam/intarna/intarna/2.2.0	2018-11-01	2
toolshed.g2.bx.psu.edu/repos/galaxyp/msi_preprocessing/mass_spectrometry_imaging_preprocessing/1.10.0.7	2018-11-01	2
toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastx_wrapper/0.1.08	2018-11-01	2
toolshed.g2.bx.psu.edu/repos/bgruening/diffbind/diffbind/2.6.6.1	2018-11-01	2
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_textexporter/TextExporter/2.2.0	2018-11-01	2
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtoigv/2.27.0.0	2018-11-01	2
gtf2bedgraph	2018-11-01	2
toolshed.g2.bx.psu.edu/repos/iuc/deg_annotate/deg_annotate/1.0	2018-11-01	2
toolshed.g2.bx.psu.edu/repos/iuc/ncbi_eutils_einfo/ncbi_eutils_einfo/1.1	2018-11-01	2
toolshed.g2.bx.psu.edu/repos/devteam/fastq_stats/fastq_stats/1.1.1	2018-11-01	2
toolshed.g2.bx.psu.edu/repos/crs4/ssake/ssake/0.0.10	2018-11-01	2
toolshed.g2.bx.psu.edu/repos/devteam/t2t_report/t2t_report/1.0.0	2018-11-01	2
toolshed.g2.bx.psu.edu/repos/iuc/idba_ud/idba_ud/1.1.3	2018-11-01	2
CONVERTER_bam_to_qname_sorted_bam	2018-11-01	2
toolshed.g2.bx.psu.edu/repos/iuc/intervene/intervene_pairwise/0.6.4	2018-11-01	2
gff_filter_by_attribute	2018-11-01	2
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multicovtbed/2.27.0.0	2018-11-01	2
Paste1	2018-11-01	2
toolshed.g2.bx.psu.edu/repos/miller-lab/genome_diversity/gd_raxml/1.0.0	2018-11-01	2
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_fuzzydiff/FuzzyDiff/2.3.0	2018-11-01	2
hgv_david	2018-11-01	2
toolshed.g2.bx.psu.edu/repos/bebatut/format_cd_hit_output/format_cd_hit_output/1.0.0	2018-11-01	2
toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: etandem33/5.0.0.1	2018-11-01	2
toolshed.g2.bx.psu.edu/repos/devteam/vcfleftalign/vcfleftalign/1.0.0_rc1+galaxy0	2018-11-01	2
toolshed.g2.bx.psu.edu/repos/devteam/vcfbedintersect/vcfbedintersect/1.0.0_rc1+galaxy0	2018-11-01	2
toolshed.g2.bx.psu.edu/repos/bgruening/natural_product_likeness/ctb_np-likeness-calculator/2.1	2018-11-01	2
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_fisher/2.27.0.0	2018-11-01	2
toolshed.g2.bx.psu.edu/repos/devteam/cummerbund/cummeRbund/2.16.0	2018-11-01	2
toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: equicktandem31/5.0.0.1	2018-11-01	2
toolshed.g2.bx.psu.edu/repos/iuc/ebi_metagenomics_run_downloader/ebi_metagenomics_run_downloader/0.1.0	2018-11-01	2
toolshed.g2.bx.psu.edu/repos/devteam/vcfgeno2haplo/vcfgeno2haplo/1.0.0_rc1+galaxy0	2018-11-01	2
toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_geneBody_coverage2/2.6.4.1	2018-11-01	2
toolshed.g2.bx.psu.edu/repos/gga/apollo_list_organism/list_organism/3.1	2018-11-01	2
toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3k.0	2018-11-01	2
toolshed.g2.bx.psu.edu/repos/iuc/trinity_contig_exn50_statistic/trinity_contig_exn50_statistic/2.8.4	2018-11-01	2
toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_infer_experiment/2.6.4	2018-11-01	2
toolshed.g2.bx.psu.edu/repos/anton/vcfbedintersect/vcfbedintersect/0.0.1	2018-11-01	2
toolshed.g2.bx.psu.edu/repos/anton/vcfannotate/vcfannotate/0.0.1	2018-11-01	2
toolshed.g2.bx.psu.edu/repos/devteam/express/express/1.1.1	2018-11-01	2
toolshed.g2.bx.psu.edu/repos/iuc/kallisto_pseudo/kallisto_pseudo/0.43.1.1	2018-11-01	2
toolshed.g2.bx.psu.edu/repos/devteam/vcftools_annotate/vcftools_annotate/0.1	2018-11-01	2
toolshed.g2.bx.psu.edu/repos/devteam/freebayes_wrapper/freebayes_wrapper/0.5.0	2018-11-01	2
toolshed.g2.bx.psu.edu/repos/rnateam/viennarna_rnaduplex/viennarna_rnaduplex/2.2.10.0	2018-11-01	2
toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fastq/tabular_to_fastq/1.0.0	2018-11-01	1
gtf_filter_by_attribute_values_list	2018-11-01	1
toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_rpsblast_wrapper/0.3.1	2018-11-01	1
toolshed.g2.bx.psu.edu/repos/galaxyp/mass_spectrometry_imaging_segmentations/mass_spectrometry_imaging_segmentations/1.7.0.2	2018-11-01	1
toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy1	2018-11-01	1
toolshed.g2.bx.psu.edu/repos/iuc/enasearch_retrieve_data/enasearch_retrieve_data/0.1.1.0	2018-11-01	1
toolshed.g2.bx.psu.edu/repos/peterjc/venn_list/venn_list/0.0.3	2018-11-01	1
toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.5.0	2018-11-01	1
toolshed.g2.bx.psu.edu/repos/iuc/migmap/migmap/1.0.2.1	2018-11-01	1
toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.3.1	2018-11-01	1
toolshed.g2.bx.psu.edu/repos/devteam/t2ps/Draw_phylogram/1.0.0	2018-11-01	1
toolshed.g2.bx.psu.edu/repos/bgruening/hicup_mapper/hicup_mapper/0.5.10.0	2018-11-01	1
toolshed.g2.bx.psu.edu/repos/ethevenot/heatmap/Heatmap/2.2.2	2018-11-01	1
toolshed.g2.bx.psu.edu/repos/iuc/gemini/gemini_load/0.10.1.0	2018-11-01	1
toolshed.g2.bx.psu.edu/repos/devteam/vcftools_isec/vcftools_isec/0.1.1	2018-11-01	1
toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3r.0	2018-11-01	1
toolshed.g2.bx.psu.edu/repos/iuc/gatk2/gatk2_variant_annotator/2.8.0	2018-11-01	1
toolshed.g2.bx.psu.edu/repos/iuc/meme_psp_gen/meme_psp_gen/4.12.0.0	2018-11-01	1
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FixMateInformation/2.18.2.1	2018-11-01	1
toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.3.5	2018-11-01	1
toolshed.g2.bx.psu.edu/repos/devteam/vcftools_merge/vcftools_merge/0.1.1	2018-11-01	1
toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_download/4.3+T.galaxy2	2018-11-01	1
toolshed.g2.bx.psu.edu/repos/gga/apollo_feat_from_gff3/feat_from_gff3/1.0	2018-11-01	1
toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_get_chr_names/4.3+T.galaxy1	2018-11-01	1
toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.38	2018-11-01	1
toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpSift_annotate/3.4	2018-11-01	1
toolshed.g2.bx.psu.edu/repos/devteam/vcffixup/vcffixup/1.0.0_rc1+galaxy0	2018-11-01	1
toolshed.g2.bx.psu.edu/repos/iuc/gatk2/gatk2_realigner_target_creator/0.0.7	2018-11-01	1
toolshed.g2.bx.psu.edu/repos/devteam/samtools_phase/samtools_phase/2.0.1	2018-11-01	1
toolshed.g2.bx.psu.edu/repos/iuc/ococo/ococo/0.1.2.6	2018-11-01	1
toolshed.g2.bx.psu.edu/repos/devteam/samtools_reheader/samtools_reheader/2.0.1	2018-11-01	1
toolshed.g2.bx.psu.edu/repos/devteam/count_gff_features/count_gff_features/0.2	2018-11-01	1
toolshed.g2.bx.psu.edu/repos/iuc/gatk2/gatk2_indel_realigner/2.8.0	2018-11-01	1
toolshed.g2.bx.psu.edu/repos/eschen42/w4mjoinpn/w4mjoinpn/0.98.2	2018-11-01	1
toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastx_wrapper/0.2.01	2018-11-01	1
toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.2.6.2	2018-11-01	1
toolshed.g2.bx.psu.edu/repos/iuc/ucsc_twobittofa/ucsc-twobittofa/357	2018-11-01	1
toolshed.g2.bx.psu.edu/repos/rnateam/dorina/dorina_search/1.0.0	2018-11-01	1
toolshed.g2.bx.psu.edu/repos/iuc/picrust_predict_metagenomes/picrust_predict_metagenomes/1.1.1.0	2018-11-01	1
toolshed.g2.bx.psu.edu/repos/rnateam/sortmerna/bg_sortmerna/2.1b.5	2018-11-01	1
toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fastq/tabular_to_fastq/1.1.1	2018-11-01	1
toolshed.g2.bx.psu.edu/repos/iuc/mothur_deunique_seqs/mothur_deunique_seqs/1.39.5.0	2018-11-01	1
toolshed.g2.bx.psu.edu/repos/devteam/weblogo3/rgweblogo3/3.5.0	2018-11-01	1
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeSamFiles/2.7.1.0	2018-11-01	1
createInterval	2018-11-01	1
cshl_awk_tool	2018-11-01	1
toolshed.g2.bx.psu.edu/repos/devteam/kraken_report/kraken-report/1.2.4	2018-11-01	1
toolshed.g2.bx.psu.edu/repos/galaxyp/decoyfasta/decoyfasta/0.2.0	2018-11-01	1
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toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastp_wrapper/0.2.01	2018-11-01	1
toolshed.g2.bx.psu.edu/repos/pavlo-lutsik/rnbeads/rnbeads/0.91	2018-11-01	1
toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.1.8.0	2018-11-01	1
toolshed.g2.bx.psu.edu/repos/bgruening/sailfish/sailfish/0.10.1.1	2018-11-01	1
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toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastp_wrapper/0.2.00	2018-11-01	1
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toolshed.g2.bx.psu.edu/repos/galaxyp/msi_ion_images/mass_spectrometry_imaging_ion_images/1.10.0.4	2018-11-01	1
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MeanQualityByCycle/2.18.2.1	2018-11-01	1
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toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed_histogram/2.19.0	2018-11-01	1
Extract genomic DNA 1	2018-11-01	1
toolshed.g2.bx.psu.edu/repos/galaxyp/msconvert/msconvert_win/3.0.0	2018-11-01	1
Extract_features1	2018-11-01	1
toolshed.g2.bx.psu.edu/repos/bgruening/plotly_parallel_coordinates_plot/plotly_parallel_coordinates_plot/0.1	2018-11-01	1
toolshed.g2.bx.psu.edu/repos/devteam/ucsc_custom_track/build_ucsc_custom_track_1/1.0.0	2018-11-01	1
toolshed.g2.bx.psu.edu/repos/bgruening/crispr_recognition_tool/crispr_recognition_tool/1.2.0	2018-11-01	1
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_xmlvalidator/XMLValidator/2.3.0	2018-11-01	1
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_xtandemadapter/XTandemAdapter/2.2.0.1	2018-11-01	1
toolshed.g2.bx.psu.edu/repos/iuc/kobas/kobas_annotate/0.4	2018-11-01	1
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectInsertSizeMetrics/2.18.2.1	2018-11-01	1
toolshed.g2.bx.psu.edu/repos/iuc/trinity_gene_to_trans_map/trinity_gene_to_trans_map/2.6.6	2018-11-01	1
toolshed.g2.bx.psu.edu/repos/iuc/disco/disco/1.2.0	2018-11-01	1
toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_dropse/1.3.0	2018-11-01	1
toolshed.g2.bx.psu.edu/repos/iuc/qiime_count_seqs/qiime_count_seqs/1.9.1.0	2018-11-01	1
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_mascotadapter/MascotAdapter/2.3.0	2018-11-01	1
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toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_RPKM_saturation/2.6.4.1	2018-11-01	1
toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.12.5+galaxy1	2018-11-01	1
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_featurefindermetabo/FeatureFinderMetabo/2.3.0	2018-11-01	1
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toolshed.g2.bx.psu.edu/repos/iuc/qiime_make_phylogeny/qiime_make_phylogeny/1.9.1.0	2018-11-01	1
toolshed.g2.bx.psu.edu/repos/fcaramia/varscan/varscan_somatic/2.3.5	2018-11-01	1
toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastdbcmd_wrapper/0.3.1	2018-11-01	1
toolshed.g2.bx.psu.edu/repos/iuc/bam_to_scidx/bam_to_scidx/1.0.1	2018-11-01	1
toolshed.g2.bx.psu.edu/repos/iuc/iqtree/iqtree/1.5.5.1	2018-11-01	1
toolshed.g2.bx.psu.edu/repos/devteam/vcf2pgsnp/vcf2pgSnp/1.0.0	2018-11-01	1
toolshed.g2.bx.psu.edu/repos/iuc/intervene/intervene_upset/0.6.4	2018-11-01	1
toolshed.g2.bx.psu.edu/repos/devteam/vcf2tsv/vcf2tsv/0.0.3	2018-11-01	1
toolshed.g2.bx.psu.edu/repos/iuc/stacks_genotypes/stacks_genotypes/1.46.0	2018-11-01	1
toolshed.g2.bx.psu.edu/repos/iuc/mothur_list_seqs/mothur_list_seqs/1.39.5.0	2018-11-01	1
toolshed.g2.bx.psu.edu/repos/devteam/dgidb_annotator/dgidb_annotator/0.1	2018-11-01	1
toolshed.g2.bx.psu.edu/repos/iuc/qiime_pick_rep_set/qiime_pick_rep_set/1.9.1.0	2018-11-01	1
toolshed.g2.bx.psu.edu/repos/nick/allele_counts/allele_counts_1/1.2	2018-11-01	1
toolshed.g2.bx.psu.edu/repos/iuc/resize_coordinate_window/resize_coordinate_window/1.0.1	2018-11-01	1
toolshed.g2.bx.psu.edu/repos/iuc/mothur_phylotype/mothur_phylotype/1.39.5.0	2018-11-01	1
toolshed.g2.bx.psu.edu/repos/iuc/exonerate/exonerate/2.4.0	2018-11-01	1
toolshed.g2.bx.psu.edu/repos/iuc/hmmer3/hmmer_phmmer/0.1.0	2018-11-01	1
toolshed.g2.bx.psu.edu/repos/iuc/hmmer3/hmmer_jackhmmer/0.1.0	2018-11-01	1
toolshed.g2.bx.psu.edu/repos/iuc/mothur_pcr_seqs/mothur_pcr_seqs/1.39.5.0	2018-11-01	1
CONVERTER_fasta_to_bowtie_base_index	2018-11-01	1
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicplotviewpoint/hicexplorer_hicplotviewpoint/2.1.4.0	2018-11-01	1
toolshed.g2.bx.psu.edu/repos/devteam/vcf2tsv/vcf2tsv/1.0.0_rc1+galaxy0	2018-11-01	1
toolshed.g2.bx.psu.edu/repos/earlhaminst/replace_chromosome_names/replace_chromosome_names/0.1	2018-11-01	1
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toolshed.g2.bx.psu.edu/repos/crs4/edena/edena_ovl_wrapper/0.3	2018-11-01	1
toolshed.g2.bx.psu.edu/repos/iuc/hmmer3/hmmer_hmmscan/0.1.0	2018-11-01	1
toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: einverted28/5.0.0.1	2018-11-01	1
toolshed.g2.bx.psu.edu/repos/bgruening/infernal/infernal_cmalign/1.1.2.0	2018-11-01	1
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toolshed.g2.bx.psu.edu/repos/anton/vcfallelicprimitives/vcfallelicprimitives/0.0.1	2018-11-01	1
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_cometadapter/CometAdapter/2.3.0	2018-11-01	1
toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_databases/4.3r.1	2018-11-01	1
toolshed.g2.bx.psu.edu/repos/anton/vcfcheck/vcfcheck/0.0.1	2018-11-01	1
upload1	2018-10-01	16154
toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastx_wrapper/0.3.0	2018-10-01	14675
toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_searchcv/sklearn_searchcv/0.9	2018-10-01	6439
toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.71	2018-10-01	3033
echo_main_handler0	2018-10-01	2977
echo_main_handler5	2018-10-01	2975
echo_main_handler2	2018-10-01	2975
echo_main_handler3	2018-10-01	2975
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echo_main_handler4	2018-10-01	2975
echo_main_handler10	2018-10-01	2974
echo_main_drmaa	2018-10-01	2974
echo_main_handler8	2018-10-01	2974
echo_main_handler11	2018-10-01	2974
echo_main_handler6	2018-10-01	2974
echo_main_handler9	2018-10-01	2974
echo_main_handler7	2018-10-01	2974
echo_main_condor	2018-10-01	2972
toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72	2018-10-01	2542
toolshed.g2.bx.psu.edu/repos/earlhaminst/ensembl_get_sequences/get_sequences/0.1.2	2018-10-01	2336
toolshed.g2.bx.psu.edu/repos/bgruening/infernal/infernal_cmsearch/1.1.2.0	2018-10-01	2069
toolshed.g2.bx.psu.edu/repos/bgruening/infernal/infernal_cmbuild/1.1.2.0	2018-10-01	2038
toolshed.g2.bx.psu.edu/repos/rnateam/graphclust_cmfinder/cmFinder/0.4	2018-10-01	2028
toolshed.g2.bx.psu.edu/repos/rnateam/graphclust_mlocarna/locarna_best_subtree/0.4	2018-10-01	1984
Cut1	2018-10-01	1685
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toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_heatmap/deeptools_plot_heatmap/3.0.2.0	2018-10-01	1452
toolshed.g2.bx.psu.edu/repos/rnateam/graphclust_align_cluster/graphclust_align_cluster/0.1	2018-10-01	1441
toolshed.g2.bx.psu.edu/repos/devteam/vcffilter/vcffilter2/1.0.0_rc1+galaxy1	2018-10-01	1355
toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.36.5	2018-10-01	1350
toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1	2018-10-01	1291
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/deeptools_compute_matrix/3.0.2.0	2018-10-01	1283
toolshed.g2.bx.psu.edu/repos/devteam/vcfallelicprimitives/vcfallelicprimitives/1.0.0_rc1+galaxy0	2018-10-01	1276
toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.1.0.46-0	2018-10-01	1238
toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.1.0.46-0	2018-10-01	1142
toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.1.0	2018-10-01	1051
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toolshed.g2.bx.psu.edu/repos/rnateam/viennarna_rnafold/viennarna_rnafold/2.2.10.4	2018-10-01	958
toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.4.2	2018-10-01	881
toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/1.6.3	2018-10-01	666
toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.1.0+galaxy3	2018-10-01	630
cat1	2018-10-01	620
toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/1.3.4	2018-10-01	610
Grep1	2018-10-01	606
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_fileinfo/FileInfo/2.3.0	2018-10-01	580
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toolshed.g2.bx.psu.edu/repos/lparsons/htseq_count/htseq_count/0.9.1	2018-10-01	550
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.0.2.0	2018-10-01	542
toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.6.0b-1	2018-10-01	535
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.2	2018-10-01	534
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.1	2018-10-01	502
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1	2018-10-01	470
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CONVERTER_interval_to_bed_0	2018-10-01	441
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_falsediscoveryrate/FalseDiscoveryRate/2.3.0	2018-10-01	431
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_profile/deeptools_plot_profile/3.0.2.0	2018-10-01	425
toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_xcmsset/abims_xcms_xcmsSet/2.1.1	2018-10-01	422
toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.4.1	2018-10-01	421
toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.4.3.1	2018-10-01	416
toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.1	2018-10-01	415
ebi_sra_main	2018-10-01	414
toolshed.g2.bx.psu.edu/repos/rnateam/viennarna_rnaplot/viennarna_rnaplot/2.2.10.0	2018-10-01	410
addValue	2018-10-01	394
CONVERTER_gz_to_uncompressed	2018-10-01	392
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed_bedgraph/2.19.0	2018-10-01	392
toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.3	2018-10-01	363
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_profile/deeptools_plot_profile/3.1.2.0.0	2018-10-01	362
toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.2	2018-10-01	359
toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/0.11.2	2018-10-01	323
toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.12	2018-10-01	323
toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_filtering/cardinal_filtering/1.12.1.0	2018-10-01	309
wig_to_bigWig	2018-10-01	304
ucsc_table_direct1	2018-10-01	303
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toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.36.0	2018-10-01	287
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idmapper/IDMapper/2.3.0	2018-10-01	279
toolshed.g2.bx.psu.edu/repos/devteam/samtools_flagstat/samtools_flagstat/2.0.2	2018-10-01	276
toolshed.g2.bx.psu.edu/repos/devteam/intersect/gops_intersect_1/1.0.0	2018-10-01	269
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idscoreswitcher/IDScoreSwitcher/2.3.0	2018-10-01	268
Grouping1	2018-10-01	266
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idposteriorerrorprobability/IDPosteriorErrorProbability/2.3.0	2018-10-01	261
toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/2.9.1.3	2018-10-01	259
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_peptideindexer/PeptideIndexer/2.3.0	2018-10-01	246
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicbuildmatrix/hicexplorer_hicbuildmatrix/2.1.4.0	2018-10-01	245
toolshed.g2.bx.psu.edu/repos/devteam/samtools_rmdup/samtools_rmdup/2.0.1	2018-10-01	243
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.0	2018-10-01	237
toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.6	2018-10-01	234
toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_build_pipeline/sklearn_build_pipeline/0.9	2018-10-01	233
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0	2018-10-01	233
CONVERTER_bedgraph_to_bigwig	2018-10-01	228
toolshed.g2.bx.psu.edu/repos/bgruening/pileometh/pileometh/0.3.0.1	2018-10-01	221
trimmer	2018-10-01	220
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/1.1.0	2018-10-01	217
toolshed.g2.bx.psu.edu/repos/devteam/tophat2/tophat2/2.1.1	2018-10-01	211
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_fidoadapter/FidoAdapter/2.3.0	2018-10-01	211
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idfilter/IDFilter/2.3.0	2018-10-01	210
toolshed.g2.bx.psu.edu/repos/devteam/join/gops_join_1/1.0.0	2018-10-01	203
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicplotmatrix/hicexplorer_hicplotmatrix/2.1.4.0	2018-10-01	194
toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.2.6	2018-10-01	192
toolshed.g2.bx.psu.edu/repos/ethevenot/multivariate/Multivariate/2.3.10	2018-10-01	191
toolshed.g2.bx.psu.edu/repos/devteam/samtools_slice_bam/samtools_slice_bam/2.0.1	2018-10-01	190
toolshed.g2.bx.psu.edu/repos/iuc/meme_fimo/meme_fimo/4.12.0.0	2018-10-01	186
toolshed.g2.bx.psu.edu/repos/bjoern-gruening/sed_wrapper/sed_stream_editor/0.0.1	2018-10-01	186
toolshed.g2.bx.psu.edu/repos/devteam/fastq_to_fasta/cshl_fastq_to_fasta/1.0.0	2018-10-01	180
toolshed.g2.bx.psu.edu/repos/galaxyp/thermo_raw_file_converter/thermo_raw_file_converter/0.0.1	2018-10-01	178
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_isobaricanalyzer/IsobaricAnalyzer/2.3.0	2018-10-01	177
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_xtandemadapter/XTandemAdapter/2.3.0	2018-10-01	176
toolshed.g2.bx.psu.edu/repos/bgruening/nanopolish_variants/nanopolish_variants/0.1.0	2018-10-01	175
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_coveragebed/2.27.0.2	2018-10-01	171
toolshed.g2.bx.psu.edu/repos/iuc/circos/circgraph/0.9-RC2	2018-10-01	164
toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_contigs/mothur_make_contigs/1.39.5.0	2018-10-01	164
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hiccorrectmatrix/hicexplorer_hiccorrectmatrix/2.1.4.0	2018-10-01	160
toolshed.g2.bx.psu.edu/repos/iuc/ngsutils_bam_filter/ngsutils_bam_filter/0.5.9	2018-10-01	152
toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.34.9.9	2018-10-01	150
sort1	2018-10-01	146
toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.68	2018-10-01	144
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toolshed.g2.bx.psu.edu/repos/devteam/fastq_trimmer/fastq_trimmer/1.1.1	2018-10-01	134
comp1	2018-10-01	134
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.27.0.2	2018-10-01	133
toolshed.g2.bx.psu.edu/repos/iuc/extract_genomic_dna/Extract genomic DNA 1/3.0.3	2018-10-01	133
toolshed.g2.bx.psu.edu/repos/crs4/prokka/prokka/1.13	2018-10-01	131
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_msgfplusadapter/MSGFPlusAdapter/2.3.0	2018-10-01	130
toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/2.2.1.2	2018-10-01	129
toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.3.0	2018-10-01	129
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_proteinquantifier/ProteinQuantifier/2.3.0	2018-10-01	128
toolshed.g2.bx.psu.edu/repos/crs4/bwa_mem/bwa_mem/0.8.0	2018-10-01	126
toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_fastq/mothur_make_fastq/1.36.1.0	2018-10-01	125
toolshed.g2.bx.psu.edu/repos/bgruening/unique/bg_uniq/0.3	2018-10-01	124
toolshed.g2.bx.psu.edu/repos/galaxyp/dbbuilder/dbbuilder/0.3.0	2018-10-01	124
toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_quality_report/cardinal_quality_report/1.12.1.0	2018-10-01	124
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idconflictresolver/IDConflictResolver/2.3.0	2018-10-01	124
toolshed.g2.bx.psu.edu/repos/devteam/vcfbedintersect/vcfbedintersect/0.0.3	2018-10-01	123
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.0.0	2018-10-01	123
toolshed.g2.bx.psu.edu/repos/devteam/clustalw/clustalw/2.1	2018-10-01	123
toolshed.g2.bx.psu.edu/repos/iuc/filtlong/filtlong/0.2.0	2018-10-01	121
toolshed.g2.bx.psu.edu/repos/devteam/get_flanks/get_flanks1/1.0.0	2018-10-01	120
toolshed.g2.bx.psu.edu/repos/devteam/fasta_filter_by_length/fasta_filter_by_length/1.1	2018-10-01	113
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicplottads/hicexplorer_hicplottads/2.1.4.0	2018-10-01	111
toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/search_gui/3.3.3.0	2018-10-01	109
toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_data_exporter/cardinal_data_exporter/1.12.1.0	2018-10-01	107
Paste1	2018-10-01	103
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicmergematrixbins/hicexplorer_hicmergematrixbins/2.1.4.0	2018-10-01	102
toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_preprocessing/cardinal_preprocessing/1.12.1.0	2018-10-01	101
toolshed.g2.bx.psu.edu/repos/iuc/trinity_align_and_estimate_abundance/trinity_align_and_estimate_abundance/2.8.4	2018-10-01	101
toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_infer_experiment/2.6.4.1	2018-10-01	100
toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.0	2018-10-01	99
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toolshed.g2.bx.psu.edu/repos/anton/vcfallelicprimitives/vcfallelicprimitives/0.0.1	2018-10-01	98
toolshed.g2.bx.psu.edu/repos/devteam/vcfallelicprimitives/vcfallelicprimitives/0.0.3	2018-10-01	96
toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.3	2018-10-01	93
dorina_search	2018-10-01	92
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.1	2018-10-01	92
toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.0.6	2018-10-01	92
toolshed.g2.bx.psu.edu/repos/bgruening/bismark/bismark_bowtie/0.7.12	2018-10-01	91
toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.13.0	2018-10-01	91
toolshed.g2.bx.psu.edu/repos/devteam/fastq_trimmer_by_quality/fastq_quality_trimmer/1.1.1	2018-10-01	89
toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.2	2018-10-01	88
toolshed.g2.bx.psu.edu/repos/bgruening/nucleosome_prediction/Nucleosome/3.0	2018-10-01	87
toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.3.1	2018-10-01	87
toolshed.g2.bx.psu.edu/repos/devteam/fastq_filter/fastq_filter/1.1.1	2018-10-01	86
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.1	2018-10-01	85
velveth	2018-10-01	85
toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0.2	2018-10-01	85
toolshed.g2.bx.psu.edu/repos/devteam/merge_cols/mergeCols1/1.0.1	2018-10-01	84
toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/datamash_ops/1.0.6	2018-10-01	82
toolshed.g2.bx.psu.edu/repos/iuc/bwameth/bwameth/0.2.0.4	2018-10-01	81
toolshed.g2.bx.psu.edu/repos/galaxyp/proteomics_moff/proteomics_moff/1.2.1.1	2018-10-01	81
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_filefilter/FileFilter/2.3.0	2018-10-01	81
toolshed.g2.bx.psu.edu/repos/devteam/sam_merge/sam_merge2/1.2.0	2018-10-01	81
toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.1.1.20160309.5	2018-10-01	81
CONVERTER_bam_to_coodinate_sorted_bam	2018-10-01	80
toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.4	2018-10-01	80
toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.0	2018-10-01	80
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_textexporter/TextExporter/2.3.0	2018-10-01	79
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.1	2018-10-01	79
toolshed.g2.bx.psu.edu/repos/bgruening/bismark/bismark_bowtie2/0.20.0	2018-10-01	78
toolshed.g2.bx.psu.edu/repos/ethevenot/biosigner/biosigner/2.2.7	2018-10-01	78
ia_coordinates_of_roi	2018-10-01	77
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed/2.27.0.0	2018-10-01	76
toolshed.g2.bx.psu.edu/repos/rnateam/structure_to_gspan/structure_to_gspan/0.3	2018-10-01	76
toolshed.g2.bx.psu.edu/repos/galaxyp/maldi_quant_preprocessing/maldi_quant_preprocessing/1.18.0.0	2018-10-01	74
toolshed.g2.bx.psu.edu/repos/iuc/metaphlan2/metaphlan2/2.6.0.0	2018-10-01	74
toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/peptide_shaker/1.16.26	2018-10-01	73
CONVERTER_interval_to_bedstrict_0	2018-10-01	73
toolshed.g2.bx.psu.edu/repos/rnateam/metilene/metilene/0.2.6.1	2018-10-01	69
toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.4.1	2018-10-01	69
toolshed.g2.bx.psu.edu/repos/jjohnson/samtools_filter/samtools_filter/1.1.1	2018-10-01	69
toolshed.g2.bx.psu.edu/repos/devteam/add_value/addValue/1.0.0	2018-10-01	67
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toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_histogram/ggplot2_histogram/2.2.1+galaxy0	2018-10-01	67
toolshed.g2.bx.psu.edu/repos/rnateam/graphclust_cmfinder/cmFinder/0.3	2018-10-01	66
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/1.1.0	2018-10-01	66
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bam_summary/deeptools_multi_bam_summary/3.0.2.0	2018-10-01	66
toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/4.6.3	2018-10-01	66
toolshed.g2.bx.psu.edu/repos/galaxyp/maldi_quant_peak_detection/maldi_quant_peak_detection/1.18.0.0	2018-10-01	66
toolshed.g2.bx.psu.edu/repos/rnateam/graphclust_mlocarna/locarna_best_subtree/0.3	2018-10-01	66
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_correlation/deeptools_plot_correlation/3.0.2.0	2018-10-01	65
toolshed.g2.bx.psu.edu/repos/mvdbeek/add_input_name_as_column/addName/0.1.1	2018-10-01	65
toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.39	2018-10-01	64
toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.1.4	2018-10-01	63
toolshed.g2.bx.psu.edu/repos/devteam/dna_filtering/histogram_rpy/1.0.3	2018-10-01	63
toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_spectra_plots/cardinal_spectra_plots/1.12.1.0	2018-10-01	63
toolshed.g2.bx.psu.edu/repos/ethevenot/univariate/Univariate/2.2.4	2018-10-01	62
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_compare/deeptools_bam_compare/3.0.2.0	2018-10-01	62
toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.2.2	2018-10-01	62
toolshed.g2.bx.psu.edu/repos/iuc/megahit/megahit/1.1.2.3	2018-10-01	61
wc_gnu	2018-10-01	61
toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.1.1.20160309.4	2018-10-01	61
toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_heatmap2/ggplot2_heatmap2/2.2.1+galaxy1	2018-10-01	60
toolshed.g2.bx.psu.edu/repos/galaxyp/msi_filtering/mass_spectrometry_imaging_filtering/1.10.0.6	2018-10-01	60
extract_bcs.py	2018-10-01	60
CONVERTER_fastq_to_fqtoc0	2018-10-01	59
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_qccalculator/QCCalculator/2.3.0	2018-10-01	59
toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_mz_images/cardinal_mz_images/1.12.1.0	2018-10-01	59
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1	2018-10-01	58
velvetg	2018-10-01	57
toolshed.g2.bx.psu.edu/repos/iuc/metaphlan2krona/metaphlan2krona/2.6.0.0	2018-10-01	57
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idmerger/IDMerger/2.3.0	2018-10-01	57
Summary_Statistics1	2018-10-01	57
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/1.1.0	2018-10-01	56
toolshed.g2.bx.psu.edu/repos/devteam/merge/gops_merge_1/1.0.0	2018-10-01	56
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.0	2018-10-01	55
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_featurefindermultiplex/FeatureFinderMultiplex/2.3.0	2018-10-01	54
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_decoydatabase/DecoyDatabase/2.3.0	2018-10-01	54
mergeCols1	2018-10-01	54
toolshed.g2.bx.psu.edu/repos/eschen42/w4mclassfilter/w4mclassfilter/0.98.11	2018-10-01	54
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectRnaSeqMetrics/2.18.2.1	2018-10-01	54
toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.0	2018-10-01	53
toolshed.g2.bx.psu.edu/repos/devteam/samtools_flagstat/samtools_flagstat/2.0.1	2018-10-01	51
toolshed.g2.bx.psu.edu/repos/nml/metaspades/metaspades/3.9.0	2018-10-01	51
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeSamFiles/2.18.2.1	2018-10-01	50
toolshed.g2.bx.psu.edu/repos/galaxyp/fasta_merge_files_and_filter_unique_sequences/fasta_merge_files_and_filter_unique_sequences/1.2.0	2018-10-01	50
toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.0.2.29-1	2018-10-01	50
toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_segmentations/cardinal_segmentations/1.12.1.0	2018-10-01	48
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_windowbed/2.27.0.0	2018-10-01	48
toolshed.g2.bx.psu.edu/repos/iuc/mothur_unique_seqs/mothur_unique_seqs/1.39.5.0	2018-10-01	48
__SORTLIST__	2018-10-01	48
CONVERTER_bed_gff_or_vcf_to_bigwig_0	2018-10-01	48
toolshed.g2.bx.psu.edu/repos/ethevenot/heatmap/Heatmap/2.2.2	2018-10-01	48
toolshed.g2.bx.psu.edu/repos/galaxyp/msi_combine/mass_spectrometry_imaging_combine/1.10.0.4	2018-10-01	47
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CASM/2.18.2.1	2018-10-01	47
toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.20.7.2	2018-10-01	47
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bigwig_compare/deeptools_bigwig_compare/3.0.2.0	2018-10-01	47
toolshed.g2.bx.psu.edu/repos/iuc/meme_meme/meme_meme/4.12.0.0	2018-10-01	46
viz_overlay_moving_and_fixed_image	2018-10-01	46
toolshed.g2.bx.psu.edu/repos/rnateam/chipseeker/chipseeker/1.14.2.1	2018-10-01	46
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bigwig_summary/deeptools_multi_bigwig_summary/3.0.2.0	2018-10-01	46
toolshed.g2.bx.psu.edu/repos/iuc/gemini_load/gemini_load/0.18.1.0	2018-10-01	45
toolshed.g2.bx.psu.edu/repos/iuc/mothur_summary_seqs/mothur_summary_seqs/1.39.5.0	2018-10-01	45
toolshed.g2.bx.psu.edu/repos/iuc/pygenometracks/pygenomeTracks/2.0.1	2018-10-01	45
toolshed.g2.bx.psu.edu/repos/iuc/fraggenescan/fraggenescan/1.30.0	2018-10-01	44
toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0	2018-10-01	44
toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_deinterlacer/fastq_paired_end_deinterlacer/1.1.2	2018-10-01	44
toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_bdgpeakcall/2.1.1.20160309.0	2018-10-01	44
toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/2.0.0	2018-10-01	43
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_fingerprint/deeptools_plot_fingerprint/3.0.2.0	2018-10-01	43
toolshed.g2.bx.psu.edu/repos/devteam/samtool_filter2/samtool_filter2/1.8	2018-10-01	42
toolshed.g2.bx.psu.edu/repos/iuc/goseq/goseq/1.30.1	2018-10-01	42
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_falsediscoveryrate/FalseDiscoveryRate/2.2.0	2018-10-01	42
toolshed.g2.bx.psu.edu/repos/devteam/correlation/cor2/1.0.0	2018-10-01	42
ip_projective_transformation	2018-10-01	41
toolshed.g2.bx.psu.edu/repos/rnateam/graphclust_preprocessing/preproc/0.5	2018-10-01	41
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.0	2018-10-01	41
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_featurefindercentroided/FeatureFinderCentroided/2.3.0	2018-10-01	41
toolshed.g2.bx.psu.edu/repos/iuc/prinseq/prinseq/0.20.4	2018-10-01	41
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.7.1.1	2018-10-01	41
toolshed.g2.bx.psu.edu/repos/iuc/mothur_screen_seqs/mothur_screen_seqs/1.39.5.0	2018-10-01	40
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicfindtads/hicexplorer_hicfindtads/2.1.4.0	2018-10-01	40
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1	2018-10-01	39
toolshed.g2.bx.psu.edu/repos/bgruening/bigwig_to_bedgraph/bigwig_to_bedgraph/0.1.0	2018-10-01	39
CONVERTER_fasta_to_tabular	2018-10-01	39
toolshed.g2.bx.psu.edu/repos/devteam/fastq_quality_filter/cshl_fastq_quality_filter/1.0.0	2018-10-01	39
toolshed.g2.bx.psu.edu/repos/iuc/humann2/humann2/0.11.1.0	2018-10-01	39
toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_predictd/2.1.1.20160309.0	2018-10-01	38
toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_geneBody_coverage/2.6.4.3	2018-10-01	38
toolshed.g2.bx.psu.edu/repos/devteam/fastqtofasta/fastq_to_fasta_python/1.0.0	2018-10-01	38
toolshed.g2.bx.psu.edu/repos/rnateam/graphclust_aggregate_alignments/graphclust_aggregate_alignments/0.1	2018-10-01	38
toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.5.0.1	2018-10-01	38
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_filemerger/FileMerger/2.3.0	2018-10-01	38
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_mapstatistics/MapStatistics/2.3.0	2018-10-01	38
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.27.0.0	2018-10-01	38
toolshed.g2.bx.psu.edu/repos/iuc/charts/charts/1.0.1	2018-10-01	38
toolshed.g2.bx.psu.edu/repos/devteam/freebayes_wrapper/freebayes_wrapper/0.5.0	2018-10-01	37
toolshed.g2.bx.psu.edu/repos/galaxyp/msi_ion_images/mass_spectrometry_imaging_ion_images/1.10.0.5	2018-10-01	37
toolshed.g2.bx.psu.edu/repos/devteam/fastx_reverse_complement/cshl_fastx_reverse_complement/1.0.2	2018-10-01	36
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idmassaccuracy/IDMassAccuracy/2.3.0	2018-10-01	36
toolshed.g2.bx.psu.edu/repos/bgruening/graphicsmagick_image_convert/graphicsmagick_image_convert/1.3.26	2018-10-01	36
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_proteinresolver/ProteinResolver/2.3.0	2018-10-01	36
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_fileinfo/FileInfo/2.2.0	2018-10-01	36
toolshed.g2.bx.psu.edu/repos/iuc/varscan_somatic/varscan_somatic/2.4.3.1	2018-10-01	36
toolshed.g2.bx.psu.edu/repos/devteam/cuffdiff/cuffdiff/2.2.1.5	2018-10-01	36
toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/1.6.2	2018-10-01	36
toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: geecee41/5.0.0	2018-10-01	36
toolshed.g2.bx.psu.edu/repos/devteam/fastx_reverse_complement/cshl_fastx_reverse_complement/1.0.0	2018-10-01	36
toolshed.g2.bx.psu.edu/repos/rnateam/graphclust_postprocessing/glob_report/0.4	2018-10-01	35
toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.6.1.1	2018-10-01	35
toolshed.g2.bx.psu.edu/repos/rnateam/graphclust_prepocessing_for_mlocarna/preMloc/0.3	2018-10-01	35
toolshed.g2.bx.psu.edu/repos/eschen42/w4mclassfilter/w4mclassfilter/0.98.10	2018-10-01	35
toolshed.g2.bx.psu.edu/repos/rnateam/graphclust_nspdk/NSPDK_candidateClust/9.2.2	2018-10-01	35
toolshed.g2.bx.psu.edu/repos/rnateam/graphclust_nspdk/nspdk_sparse/9.2.2	2018-10-01	35
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SortSam/2.18.2.1	2018-10-01	35
toolshed.g2.bx.psu.edu/repos/rnateam/graphclust_preprocessing/preproc/0.4	2018-10-01	35
toolshed.g2.bx.psu.edu/repos/iuc/heinz/heinz_scoring/1.0	2018-10-01	34
toolshed.g2.bx.psu.edu/repos/iuc/dexseq/dexseq_count/1.24.0.0	2018-10-01	34
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_mergebed/2.27.0.0	2018-10-01	34
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicpca/hicexplorer_hicpca/2.1.4.0	2018-10-01	34
toolshed.g2.bx.psu.edu/repos/iuc/varscan_copynumber/varscan_copynumber/2.4.3.1	2018-10-01	34
ip_projective_transformation_points	2018-10-01	34
toolshed.g2.bx.psu.edu/repos/iuc/egsea/egsea/1.6.0.1	2018-10-01	32
toolshed.g2.bx.psu.edu/repos/iuc/poretools_extract/poretools_extract/0.6.1a1.0	2018-10-01	32
toolshed.g2.bx.psu.edu/repos/iuc/mothur_heatmap_sim/mothur_heatmap_sim/1.39.5.0	2018-10-01	32
toolshed.g2.bx.psu.edu/repos/galaxyp/maldi_quant_peak_detection/maldi_quant_peak_detection/1.18.0.1	2018-10-01	32
CONVERTER_bam_to_qname_sorted_bam	2018-10-01	32
toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/2.8.1.3	2018-10-01	32
toolshed.g2.bx.psu.edu/repos/iuc/humann2_renorm_table/humann2_renorm_table/0.11.1.0	2018-10-01	31
toolshed.g2.bx.psu.edu/repos/iuc/stacks_procrad/stacks_procrad/1.46.0	2018-10-01	31
extract_aln_ends.py	2018-10-01	30
merge_pcr_duplicates.py	2018-10-01	30
scale_image	2018-10-01	30
remove_tail.py	2018-10-01	30
toolshed.g2.bx.psu.edu/repos/devteam/samtools_flagstat/samtools_flagstat/2.0	2018-10-01	30
flexbar_no_split	2018-10-01	30
toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_bam2wig/2.6.4	2018-10-01	30
rm_spurious_events.py	2018-10-01	30
__UNZIP_COLLECTION__	2018-10-01	30
coords2clnt.py	2018-10-01	30
toolshed.g2.bx.psu.edu/repos/devteam/bam_to_sam/bam_to_sam/2.0	2018-10-01	30
toolshed.g2.bx.psu.edu/repos/ethevenot/checkformat/checkFormat/3.0.0	2018-10-01	29
toolshed.g2.bx.psu.edu/repos/iuc/pear/iuc_pear/0.9.6.1	2018-10-01	29
toolshed.g2.bx.psu.edu/repos/devteam/bowtie_wrappers/bowtie_wrapper/1.2.0	2018-10-01	29
toolshed.g2.bx.psu.edu/repos/galaxyp/lfq_protein_quant/lfq_protein_quant/1.0	2018-10-01	29
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_multijoin_tool/1.1.1	2018-10-01	29
toolshed.g2.bx.psu.edu/repos/nml/spades/spades/3.11.1+galaxy1	2018-10-01	29
toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: getorf42/5.0.0.1	2018-10-01	29
toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: revseq82/5.0.0	2018-10-01	29
toolshed.g2.bx.psu.edu/repos/iuc/column_order_header_sort/column_order_header_sort/0.0.1	2018-10-01	29
toolshed.g2.bx.psu.edu/repos/bgruening/canu/canu/1.7	2018-10-01	29
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_pca/deeptools_plot_pca/3.1.2.0.0	2018-10-01	29
toolshed.g2.bx.psu.edu/repos/rnateam/graphclust_postprocessing_no_align/graphclust_glob_report_no_align/0.5	2018-10-01	29
toolshed.g2.bx.psu.edu/repos/iuc/heinz/heinz_bum/1.0	2018-10-01	29
toolshed.g2.bx.psu.edu/repos/iuc/mothur_pre_cluster/mothur_pre_cluster/1.39.5.0	2018-10-01	28
toolshed.g2.bx.psu.edu/repos/iuc/heinz/heinz/1.0	2018-10-01	28
toolshed.g2.bx.psu.edu/repos/devteam/macs/peakcalling_macs/1.0.1	2018-10-01	28
__EXPORT_HISTORY__	2018-10-01	27
toolshed.g2.bx.psu.edu/repos/iuc/heinz/heinz_visualization/0.1.0	2018-10-01	27
toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/1.6.1.0	2018-10-01	27
toolshed.g2.bx.psu.edu/repos/iuc/gemini_query/gemini_query/0.18.1.0	2018-10-01	27
toolshed.g2.bx.psu.edu/repos/iuc/fgsea/fgsea/1.6.0	2018-10-01	27
toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.5.2b-2	2018-10-01	27
toolshed.g2.bx.psu.edu/repos/devteam/cummerbund/cummeRbund/2.16.0	2018-10-01	26
toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_infer_experiment/2.6.4	2018-10-01	26
toolshed.g2.bx.psu.edu/repos/iuc/samtools_sort/samtools_sort/1.0.2	2018-10-01	26
toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/3.2	2018-10-01	26
toolshed.g2.bx.psu.edu/repos/devteam/vcf2tsv/vcf2tsv/1.0.0_rc1+galaxy0	2018-10-01	26
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.27.0.0	2018-10-01	26
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/2.5.7.0	2018-10-01	26
toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/2.9.1.3	2018-10-01	26
toolshed.g2.bx.psu.edu/repos/iuc/trinity_align_and_estimate_abundance/trinity_align_and_estimate_abundance/2.8.3	2018-10-01	25
toolshed.g2.bx.psu.edu/repos/iuc/gtftobed12/gtftobed12/357	2018-10-01	25
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idmapper/IDMapper/2.2.0	2018-10-01	25
toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.4.3.0	2018-10-01	25
toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_joiner/fastq_paired_end_joiner/2.0.1.1	2018-10-01	25
toolshed.g2.bx.psu.edu/repos/iuc/mothur_count_seqs/mothur_count_seqs/1.39.5.0	2018-10-01	25
toolshed.g2.bx.psu.edu/repos/iuc/trinity/trinity/2.8.4	2018-10-01	25
re_he_maldi_image_registration	2018-10-01	25
random_lines1	2018-10-01	25
toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotateMyIDs/3.5.0.0	2018-10-01	24
toolshed.g2.bx.psu.edu/repos/iuc/extract_genomic_dna/Extract genomic DNA 1/3.0.2	2018-10-01	24
toolshed.g2.bx.psu.edu/repos/iuc/vsearch/vsearch_dereplication/1.9.7.0	2018-10-01	23
toolshed.g2.bx.psu.edu/repos/bgruening/split_file_on_column/tp_split_on_column/0.2	2018-10-01	23
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_mztabexporter/MzTabExporter/2.3.0	2018-10-01	23
toolshed.g2.bx.psu.edu/repos/devteam/fastq_to_tabular/fastq_to_tabular/1.1.0	2018-10-01	23
toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.6.0	2018-10-01	23
toolshed.g2.bx.psu.edu/repos/rnateam/graphclust_nspdk/nspdk_sparse/9.2.3	2018-10-01	23
bg_statistical_hypothesis_testing	2018-10-01	23
toolshed.g2.bx.psu.edu/repos/galaxyp/msi_qualitycontrol/mass_spectrometry_imaging_qc/1.10.0.7	2018-10-01	23
toolshed.g2.bx.psu.edu/repos/rnateam/sortmerna/bg_sortmerna/2.1b.4	2018-10-01	23
toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.69	2018-10-01	23
toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/2.4.0	2018-10-01	22
toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_distribution/2.6.4.1	2018-10-01	22
toolshed.g2.bx.psu.edu/repos/bebatut/combine_metaphlan2_humann2/combine_metaphlan2_humann2/0.1.0	2018-10-01	22
toolshed.g2.bx.psu.edu/repos/devteam/fastx_trimmer/cshl_fastx_trimmer/1.0.0	2018-10-01	22
__DATA_FETCH__	2018-10-01	21
toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2	2018-10-01	21
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_consensusid/ConsensusID/2.3.0	2018-10-01	21
bwtool-lift	2018-10-01	21
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idfilter/IDFilter/2.2.0	2018-10-01	21
toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.3	2018-10-01	21
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_peptideindexer/PeptideIndexer/2.2.0	2018-10-01	21
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idscoreswitcher/IDScoreSwitcher/2.2.0	2018-10-01	21
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_xtandemadapter/XTandemAdapter/2.2.0.1	2018-10-01	21
toolshed.g2.bx.psu.edu/repos/peterjc/sample_seqs/sample_seqs/0.2.5	2018-10-01	21
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_fidoadapter/FidoAdapter/2.2.0.1	2018-10-01	21
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idposteriorerrorprobability/IDPosteriorErrorProbability/2.2.0	2018-10-01	21
toolshed.g2.bx.psu.edu/repos/rnateam/graphclust_prepocessing_for_mlocarna/preMloc/0.4	2018-10-01	21
toolshed.g2.bx.psu.edu/repos/iuc/mothur_chimera_vsearch/mothur_chimera_vsearch/1.39.5.1	2018-10-01	21
toolshed.g2.bx.psu.edu/repos/rnateam/graphclust_nspdk/NSPDK_candidateClust/9.2.3	2018-10-01	21
toolshed.g2.bx.psu.edu/repos/devteam/cuffmerge/cuffmerge/2.2.1.1	2018-10-01	21
CONVERTER_fasta_to_fai	2018-10-01	20
toolshed.g2.bx.psu.edu/repos/eschen42/w4mcorcov/w4mcorcov/0.98.15	2018-10-01	20
toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/fasta_compute_length/1.0.1	2018-10-01	20
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_compare/deeptools_bam_compare/2.5.1.1.0	2018-10-01	20
raceid3	2018-10-01	20
toolshed.g2.bx.psu.edu/repos/devteam/picard/rgPicardMarkDups/1.56.0	2018-10-01	20
toolshed.g2.bx.psu.edu/repos/devteam/fastx_quality_statistics/cshl_fastx_quality_statistics/1.0.0	2018-10-01	19
toolshed.g2.bx.psu.edu/repos/iuc/mothur_align_seqs/mothur_align_seqs/1.39.5.0	2018-10-01	19
toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_RPKM_saturation/2.6.4.1	2018-10-01	19
toolshed.g2.bx.psu.edu/repos/bgruening/uniprot_rest_interface/uniprot/0.2	2018-10-01	19
proteomics_search_tandem_1	2018-10-01	19
toolshed.g2.bx.psu.edu/repos/devteam/sam_pileup/sam_pileup/1.1.2	2018-10-01	19
MAF_To_Fasta1	2018-10-01	19
toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_makeblastdb/0.3.0	2018-10-01	19
toolshed.g2.bx.psu.edu/repos/iuc/stacks_denovomap/stacks_denovomap/1.46.0	2018-10-01	19
toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_shared/mothur_make_shared/1.39.5.0	2018-10-01	19
toolshed.g2.bx.psu.edu/repos/rnateam/peakachu/peakachu/0.1.0.1	2018-10-01	19
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_proteinquantifier/ProteinQuantifier/2.2.0	2018-10-01	18
toolshed.g2.bx.psu.edu/repos/bgruening/replace_column_by_key_value_file/replace_column_with_key_value_file/0.1	2018-10-01	18
toolshed.g2.bx.psu.edu/repos/galaxyp/maldi_quant_preprocessing/maldi_quant_preprocessing/1.18.0.1	2018-10-01	18
toolshed.g2.bx.psu.edu/repos/iuc/mothur_filter_seqs/mothur_filter_seqs/1.39.5.0	2018-10-01	18
toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread/2.2.1.1	2018-10-01	18
toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fastq/tabular_to_fastq/1.0.0	2018-10-01	18
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.0	2018-10-01	18
toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_RPKM_count/2.4	2018-10-01	18
dexseq_annotate	2018-10-01	17
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/deeptools_compute_matrix/2.5.1.1.0	2018-10-01	17
toolshed.g2.bx.psu.edu/repos/iuc/poretools_tabular/poretools_tabular/0.6.1a1.0	2018-10-01	17
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_BedToIntervalList/2.18.2.1	2018-10-01	17
toolshed.g2.bx.psu.edu/repos/bgruening/join_files_on_column_fuzzy/join_files_on_column_fuzzy/1.0.0	2018-10-01	17
toolshed.g2.bx.psu.edu/repos/lparsons/fastq_join/fastq_join/1.1.2-806	2018-10-01	17
toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.1.0	2018-10-01	17
toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_dedup/umi_tools_dedup/0.5.3.0	2018-10-01	17
toolshed.g2.bx.psu.edu/repos/iuc/dexseq/dexseq/1.24.0.0	2018-10-01	17
toolshed.g2.bx.psu.edu/repos/iuc/meme_chip/meme_chip/4.11.2	2018-10-01	16
toolshed.g2.bx.psu.edu/repos/peterjc/seq_filter_by_id/seq_filter_by_id/0.2.7	2018-10-01	16
toolshed.g2.bx.psu.edu/repos/iuc/metaphlan_hclust_heatmap/metaphlan_hclust_heatmap/2.6.0.0	2018-10-01	16
CONVERTER_bed_to_bgzip_0	2018-10-01	16
CONVERTER_gff_to_bed_0	2018-10-01	16
toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.1.1.20160309.0	2018-10-01	16
toolshed.g2.bx.psu.edu/repos/iuc/describe_samples/describe_samples/2.8.4	2018-10-01	16
toolshed.g2.bx.psu.edu/repos/nml/spades/spades/3.11.1	2018-10-01	16
toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_distribution/2.6.4	2018-10-01	16
toolshed.g2.bx.psu.edu/repos/devteam/vcfbedintersect/vcfbedintersect/1.0.0_rc1+galaxy0	2018-10-01	15
toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.12.5+galaxy1	2018-10-01	15
toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3r.1	2018-10-01	15
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_pca/deeptools_plot_pca/2.5.7.0	2018-10-01	15
toolshed.g2.bx.psu.edu/repos/bgruening/diffbind/diffbind/2.6.6.4	2018-10-01	15
toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.1.1.20160309.3	2018-10-01	15
toolshed.g2.bx.psu.edu/repos/devteam/bam_to_sam/bam_to_sam/2.0.1	2018-10-01	15
toolshed.g2.bx.psu.edu/repos/devteam/fastq_stats/fastq_stats/1.1.1	2018-10-01	15
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_textexporter/TextExporter/2.2.0	2018-10-01	15
toolshed.g2.bx.psu.edu/repos/iuc/mothur_remove_seqs/mothur_remove_seqs/1.36.1.0	2018-10-01	15
toolshed.g2.bx.psu.edu/repos/iuc/mothur_remove_lineage/mothur_remove_lineage/1.39.5.0	2018-10-01	15
toolshed.g2.bx.psu.edu/repos/iuc/gemini/gemini_load/0.10.1.0	2018-10-01	15
modENCODEworm	2018-10-01	15
toolshed.g2.bx.psu.edu/repos/devteam/subtract/gops_subtract_1/1.0.0	2018-10-01	15
toolshed.g2.bx.psu.edu/repos/iuc/trinity_run_de_analysis/trinity_run_de_analysis/2.8.4	2018-10-01	14
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_sequencecoveragecalculator/SequenceCoverageCalculator/2.3.0	2018-10-01	14
toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/1.4.6.p5	2018-10-01	14
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bigwig_summary/deeptools_multi_bigwig_summary/2.5.7.0	2018-10-01	14
toolshed.g2.bx.psu.edu/repos/devteam/fastq_quality_filter/cshl_fastq_quality_filter/1.0.2	2018-10-01	14
toolshed.g2.bx.psu.edu/repos/devteam/fastq_manipulation/fastq_manipulation/1.1.1	2018-10-01	14
toolshed.g2.bx.psu.edu/repos/devteam/fastqtofasta/fastq_to_fasta_python/1.1.1	2018-10-01	13
toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1.1	2018-10-01	13
CONVERTER_ref_to_seq_taxomony	2018-10-01	13
toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.1	2018-10-01	13
toolshed.g2.bx.psu.edu/repos/iuc/mothur_classify_seqs/mothur_classify_seqs/1.39.5.0	2018-10-01	13
toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sra_pileup/2.9.1.2	2018-10-01	13
toolshed.g2.bx.psu.edu/repos/iuc/mothur_rarefaction_single/mothur_rarefaction_single/1.39.5.0	2018-10-01	13
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idconflictresolver/IDConflictResolver/2.2.0	2018-10-01	13
toolshed.g2.bx.psu.edu/repos/iuc/export2graphlan/export2graphlan/0.19	2018-10-01	12
toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_download/4.3r.1	2018-10-01	12
toolshed.g2.bx.psu.edu/repos/galaxyp/msi_combine/mass_spectrometry_imaging_combine/1.10.0.5	2018-10-01	12
toolshed.g2.bx.psu.edu/repos/iuc/nonpareil/nonpareil/3.1.1.0	2018-10-01	12
toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/0.5.3.2	2018-10-01	12
toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_inner_distance/2.6.4.1	2018-10-01	12
toolshed.g2.bx.psu.edu/repos/iuc/mothur_corr_axes/mothur_corr_axes/1.36.1.0	2018-10-01	12
toolshed.g2.bx.psu.edu/repos/iuc/hmmer3/hmmer_hmmbuild/0.1.0	2018-10-01	12
toolshed.g2.bx.psu.edu/repos/galaxyp/msconvert/idconvert/3.0.0	2018-10-01	12
toolshed.g2.bx.psu.edu/repos/bebatut/format_metaphlan2_output/format_metaphlan2_output/0.1.0	2018-10-01	12
toolshed.g2.bx.psu.edu/repos/devteam/fastq_combiner/fastq_combiner/1.1.1	2018-10-01	12
toolshed.g2.bx.psu.edu/repos/iuc/hmmer3/hmmer_hmmsearch/0.1.0	2018-10-01	12
toolshed.g2.bx.psu.edu/repos/lparsons/htseq_count/htseq_count/0.6.1galaxy1	2018-10-01	12
toolshed.g2.bx.psu.edu/repos/bgruening/bismark/bismark_methylation_extractor/0.20.0	2018-10-01	12
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.0	2018-10-01	12
toolshed.g2.bx.psu.edu/repos/iuc/newick_utils/newick_display/1.6	2018-10-01	12
__IMPORT_HISTORY__	2018-10-01	12
toolshed.g2.bx.psu.edu/repos/iuc/mothur_nmds/mothur_nmds/1.36.1.0	2018-10-01	12
toolshed.g2.bx.psu.edu/repos/iuc/humann2_genefamilies_genus_level/humann2_genefamilies_genus_level/0.11.1.0	2018-10-01	11
toolshed.g2.bx.psu.edu/repos/iuc/mothur_get_groups/mothur_get_groups/1.39.5.0	2018-10-01	11
toolshed.g2.bx.psu.edu/repos/iuc/graphlan/graphlan/1.0.0.0	2018-10-01	11
toolshed.g2.bx.psu.edu/repos/devteam/principal_component_analysis/pca1/1.0.2	2018-10-01	11
CONVERTER_sam_to_bigwig_0	2018-10-01	11
toolshed.g2.bx.psu.edu/repos/galaxyp/msi_spectra_plot/mass_spectrometry_imaging_mzplots/1.10.0.6	2018-10-01	11
toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.6.1	2018-10-01	11
toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_interlacer/fastq_paired_end_interlacer/1.2.0.1	2018-10-01	11
toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.1	2018-10-01	11
toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3+t.galaxy0	2018-10-01	11
toolshed.g2.bx.psu.edu/repos/iuc/gatk2/gatk2_realigner_target_creator/2.8.0	2018-10-01	11
toolshed.g2.bx.psu.edu/repos/bgruening/svm_classifier/svm_classifier/0.9	2018-10-01	11
CONVERTER_bz2_to_uncompressed	2018-10-01	11
toolshed.g2.bx.psu.edu/repos/iuc/graphlan_annotate/graphlan_annotate/1.0.0.0	2018-10-01	11
toolshed.g2.bx.psu.edu/repos/rnateam/piranha/piranha/0.1.0	2018-10-01	11
toolshed.g2.bx.psu.edu/repos/iuc/samtools_sort/samtools_rmdup/1.0.1	2018-10-01	11
toolshed.g2.bx.psu.edu/repos/bgruening/interproscan5/interproscan/5.0.0	2018-10-01	10
toolshed.g2.bx.psu.edu/repos/devteam/fastq_to_fasta/cshl_fastq_to_fasta/1.0.2	2018-10-01	10
toolshed.g2.bx.psu.edu/repos/devteam/vcftools_isec/vcftools_isec/0.1.1	2018-10-01	10
toolshed.g2.bx.psu.edu/repos/rnateam/mafft/rbc_mafft/7.221.3	2018-10-01	10
toolshed.g2.bx.psu.edu/repos/iuc/mothur_sub_sample/mothur_sub_sample/1.39.5.0	2018-10-01	10
toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_infer_experiment/2.4	2018-10-01	10
toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastp_wrapper/0.3.0	2018-10-01	10
toolshed.g2.bx.psu.edu/repos/rnateam/blockclust/blockclust/1.0.0	2018-10-01	10
toolshed.g2.bx.psu.edu/repos/devteam/flanking_features/flanking_features_1/4.0.1	2018-10-01	10
toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_group/mothur_make_group/1.39.5.0	2018-10-01	10
CONVERTER_bed_to_fli_0	2018-10-01	10
CONVERTER_interval_to_bed12_0	2018-10-01	10
toolshed.g2.bx.psu.edu/repos/devteam/fastx_trimmer/cshl_fastx_trimmer/1.0.2	2018-10-01	10
CONVERTER_bed_to_gff_0	2018-10-01	10
toolshed.g2.bx.psu.edu/repos/iuc/mothur_seq_error/mothur_seq_error/1.39.5.0	2018-10-01	9
CONVERTER_vcf_bgzip_to_tabix_0	2018-10-01	9
toolshed.g2.bx.psu.edu/repos/iuc/mothur_taxonomy_to_krona/mothur_taxonomy_to_krona/1.0	2018-10-01	9
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtofastq/2.27.0.0	2018-10-01	9
toolshed.g2.bx.psu.edu/repos/iuc/data_manager_bwameth_index_builder/bwameth_index_builder_data_manager/1.0.0	2018-10-01	9
CONVERTER_bam_to_bigwig_0	2018-10-01	9
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hiccomparematrices/hicexplorer_hiccomparematrices/2.1.4.0	2018-10-01	9
toolshed.g2.bx.psu.edu/repos/galaxyp/msconvert_nix/msconvert_nix/3.0.9992.0	2018-10-01	9
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_peakpickerhires/PeakPickerHiRes/2.3.0	2018-10-01	9
CONVERTER_vcf_to_vcf_bgzip_0	2018-10-01	9
toolshed.g2.bx.psu.edu/repos/iuc/trinity/trinity/2.8.3	2018-10-01	9
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idfileconverter/IDFileConverter/2.3.0	2018-10-01	9
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_heatmap/deeptools_plot_heatmap/2.5.1.1.0	2018-10-01	9
toolshed.g2.bx.psu.edu/repos/blankenberg/naive_variant_caller/naive_variant_caller/0.0.3	2018-10-01	9
toolshed.g2.bx.psu.edu/repos/devteam/vcfvcfintersect/vcfvcfintersect/1.0.0_rc1+galaxy0	2018-10-01	9
toolshed.g2.bx.psu.edu/repos/galaxyp/filter_by_fasta_ids/filter_by_fasta_ids/2.0	2018-10-01	9
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtobam/2.27.0.0	2018-10-01	9
toolshed.g2.bx.psu.edu/repos/iuc/gemini_comp_hets/gemini_comp_hets/0.18.1.0	2018-10-01	9
toolshed.g2.bx.psu.edu/repos/iuc/bctools_extract_alignment_ends/bctools_extract_alignment_ends/0.2.2	2018-10-01	8
toolshed.g2.bx.psu.edu/repos/iuc/mothur_summary_single/mothur_summary_single/1.39.5.0	2018-10-01	8
toolshed.g2.bx.psu.edu/repos/devteam/megablast_wrapper/megablast_wrapper/1.2.0	2018-10-01	8
toolshed.g2.bx.psu.edu/repos/peterjc/blastxml_to_top_descr/blastxml_to_top_descr/0.1.1	2018-10-01	8
toolshed.g2.bx.psu.edu/repos/iuc/mothur_dist_seqs/mothur_dist_seqs/1.39.5.0	2018-10-01	8
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddOrReplaceReadGroups/2.18.2.1	2018-10-01	8
toolshed.g2.bx.psu.edu/repos/bgruening/pileometh/pileometh/0.3.0	2018-10-01	8
toolshed.g2.bx.psu.edu/repos/peterjc/blast_rbh/blast_reciprocal_best_hits/0.1.11	2018-10-01	8
toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy3	2018-10-01	8
toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_makeblastdb/0.3.1	2018-10-01	8
toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_rpsblast_wrapper/0.3.0	2018-10-01	8
toolshed.g2.bx.psu.edu/repos/iuc/pilon/pilon/1.20.1	2018-10-01	8
toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_quality_report/cardinal_quality_report/1.12.1.1	2018-10-01	8
toolshed.g2.bx.psu.edu/repos/devteam/xy_plot/XY_Plot_1/1.0.2	2018-10-01	8
toolshed.g2.bx.psu.edu/repos/iuc/mothur_classify_otu/mothur_classify_otu/1.39.5.0	2018-10-01	8
toolshed.g2.bx.psu.edu/repos/iuc/transdecoder/transdecoder/3.0.1	2018-10-01	8
toolshed.g2.bx.psu.edu/repos/galaxyp/msi_preprocessing/mass_spectrometry_imaging_preprocessing/1.10.0.4	2018-10-01	8
toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_combine/cardinal_combine/1.12.1.0	2018-10-01	7
toolshed.g2.bx.psu.edu/repos/bgruening/uniprot_rest_interface/uniprot/0.1	2018-10-01	7
toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.6	2018-10-01	7
toolshed.g2.bx.psu.edu/repos/bgruening/graphmap_align/graphmap_align/0.5.2	2018-10-01	7
toolshed.g2.bx.psu.edu/repos/iuc/mothur_tree_shared/mothur_tree_shared/1.39.5.0	2018-10-01	7
flexbardsc	2018-10-01	7
toolshed.g2.bx.psu.edu/repos/iuc/shovill/shovill/0.9.0	2018-10-01	7
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_subtractbed/2.27.0.0	2018-10-01	7
CONVERTER_bed_to_tabix_0	2018-10-01	7
toolshed.g2.bx.psu.edu/repos/iuc/mothur_remove_groups/mothur_remove_groups/1.39.5.0	2018-10-01	7
toolshed.g2.bx.psu.edu/repos/iuc/stacks_populations/stacks_populations/1.46.0	2018-10-01	7
toolshed.g2.bx.psu.edu/repos/rnateam/blockbuster/blockbuster/0.1.2	2018-10-01	7
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_featurefindermultiplex/FeatureFinderMultiplex/2.2.0	2018-10-01	7
toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_ensemble/sklearn_ensemble/0.9	2018-10-01	7
toolshed.g2.bx.psu.edu/repos/devteam/cummerbund_to_tabular/cummerbund_to_cuffdiff/1.0.1	2018-10-01	7
toolshed.g2.bx.psu.edu/repos/iuc/gemini_db_info/gemini_db_info/0.18.1.0	2018-10-01	7
toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.12.4.0	2018-10-01	7
toolshed.g2.bx.psu.edu/repos/iuc/mothur_cluster/mothur_cluster/1.39.5.0	2018-10-01	7
toolshed.g2.bx.psu.edu/repos/iuc/sickle/sickle/1.33.1	2018-10-01	7
toolshed.g2.bx.psu.edu/repos/galaxyp/decoyfasta/decoyfasta/0.2.0	2018-10-01	7
__MERGE_COLLECTION__	2018-10-01	7
toolshed.g2.bx.psu.edu/repos/devteam/fastx_clipper/cshl_fastx_clipper/1.0.1	2018-10-01	7
toolshed.g2.bx.psu.edu/repos/iuc/intervene/intervene_upset/0.6.4	2018-10-01	7
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_correlation/deeptools_plot_correlation/2.5.7.0	2018-10-01	6
toolshed.g2.bx.psu.edu/repos/galaxyp/msi_preprocessing/mass_spectrometry_imaging_preprocessing/1.10.0.7	2018-10-01	6
toolshed.g2.bx.psu.edu/repos/iuc/mothur_tree_shared/mothur_tree_shared/1.36.1.0	2018-10-01	6
qual_stats_boxplot	2018-10-01	6
toolshed.g2.bx.psu.edu/repos/iuc/mothur_cluster_split/mothur_cluster_split/1.39.5.0	2018-10-01	6
toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie_merge/1.3.4	2018-10-01	6
gene2exon1	2018-10-01	6
toolshed.g2.bx.psu.edu/repos/iuc/mothur_venn/mothur_venn/1.39.5.0	2018-10-01	6
toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.0.5.2	2018-10-01	6
toolshed.g2.bx.psu.edu/repos/iuc/trinity_abundance_estimates_to_matrix/trinity_abundance_estimates_to_matrix/2.8.4	2018-10-01	6
CONVERTER_len_to_linecount	2018-10-01	6
toolshed.g2.bx.psu.edu/repos/iuc/mothur_count_groups/mothur_count_groups/1.39.5.0	2018-10-01	6
toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_splitter/fastq_paired_end_splitter/1.1.1	2018-10-01	6
ChangeCase	2018-10-01	6
toolshed.g2.bx.psu.edu/repos/iuc/mothur_pcoa/mothur_pcoa/1.36.1.0	2018-10-01	6
toolshed.g2.bx.psu.edu/repos/iuc/mothur_heatmap_sim/mothur_heatmap_sim/1.36.1.0	2018-10-01	6
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_clusterbed/2.27.0.0	2018-10-01	6
toolshed.g2.bx.psu.edu/repos/iuc/pureclip/pureclip/1.0.4	2018-10-01	6
toolshed.g2.bx.psu.edu/repos/iuc/mothur_parsimony/mothur_parsimony/1.36.1.0	2018-10-01	6
toolshed.g2.bx.psu.edu/repos/rnateam/blockbuster/blockbuster/0.1.1.1	2018-10-01	6
toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_RNA_fragment_size/2.6.4.1	2018-10-01	6
toolshed.g2.bx.psu.edu/repos/iuc/mothur_amova/mothur_amova/1.36.1.0	2018-10-01	6
CONVERTER_gff_to_interval_index_0	2018-10-01	6
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.0.0	2018-10-01	6
toolshed.g2.bx.psu.edu/repos/devteam/pileup_parser/pileup_parser/1.0.2	2018-10-01	6
toolshed.g2.bx.psu.edu/repos/gbcs-embl-heidelberg/je_demultiplex/je_demultiplex/1.2.1	2018-10-01	6
toolshed.g2.bx.psu.edu/repos/iuc/mothur_homova/mothur_homova/1.36.1.0	2018-10-01	6
gff2bed1	2018-10-01	6
toolshed.g2.bx.psu.edu/repos/iuc/gemini_de_novo/gemini_de_novo/0.18.1.0	2018-10-01	6
toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/2.2.1+galaxy0	2018-10-01	6
CONVERTER_fasta_to_len	2018-10-01	6
toolshed.g2.bx.psu.edu/repos/iuc/jcvi_gff_stats/jcvi_gff_stats/0.8.4	2018-10-01	5
toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.1.0	2018-10-01	5
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_EstimateLibraryComplexity/2.18.2.1	2018-10-01	5
toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.4.0	2018-10-01	5
toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_pca/ggplot2_pca/2.2.1	2018-10-01	5
toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.1	2018-10-01	5
toolshed.g2.bx.psu.edu/repos/galaxyp/reactome_pathwaymatcher/reactome_pathwaymatcher/1.8.1.2	2018-10-01	5
toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_count/umi_tools_count/0.5.3.2	2018-10-01	5
toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/blastxml_to_tabular/0.3.0	2018-10-01	5
toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/1.0.0	2018-10-01	5
toolshed.g2.bx.psu.edu/repos/bebatut/cdhit/cd_hit_est/1.3	2018-10-01	5
toolshed.g2.bx.psu.edu/repos/devteam/fastq_quality_boxplot/cshl_fastq_quality_boxplot/1.0.0	2018-10-01	5
toolshed.g2.bx.psu.edu/repos/iuc/stacks_refmap/stacks_refmap/1.46.0	2018-10-01	5
toolshed.g2.bx.psu.edu/repos/iuc/enasearch_search_data/enasearch_search_data/0.1.1.0	2018-10-01	5
toolshed.g2.bx.psu.edu/repos/iuc/mothur_dist_shared/mothur_dist_shared/1.39.5.0	2018-10-01	5
toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.1.3	2018-10-01	5
toolshed.g2.bx.psu.edu/repos/devteam/data_manager_bwa_mem_index_builder/bwa_mem_index_builder_data_manager/0.0.3	2018-10-01	5
toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_heatmap/ggplot2_heatmap/2.2.1	2018-10-01	5
toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_annotate/4.3.0	2018-10-01	5
toolshed.g2.bx.psu.edu/repos/galaxyp/uniprotxml_downloader/uniprotxml_downloader/2.0.0	2018-10-01	5
toolshed.g2.bx.psu.edu/repos/kellrott/regex_replace/regex_replace/1.0.0	2018-10-01	5
toolshed.g2.bx.psu.edu/repos/iuc/gemini_region/gemini_region/0.18.1.0	2018-10-01	5
toolshed.g2.bx.psu.edu/repos/bgruening/natural_product_likeness/ctb_np-likeness-calculator/2.1	2018-10-01	5
toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_bdgbroadcall/2.1.1.20160309.0	2018-10-01	5
toolshed.g2.bx.psu.edu/repos/devteam/xy_plot/XY_Plot_1/1.0.1	2018-10-01	5
toolshed.g2.bx.psu.edu/repos/galaxyp/mass_spectrometry_imaging_segmentations/mass_spectrometry_imaging_segmentations/1.10.0.4	2018-10-01	5
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_proteininference/ProteinInference/2.3.0	2018-10-01	5
toolshed.g2.bx.psu.edu/repos/lparsons/htseq_count/htseq_count/0.6.1galaxy3	2018-10-01	4
toolshed.g2.bx.psu.edu/repos/iuc/bwameth/bwameth/0.2.0.3	2018-10-01	4
toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.2.6.2	2018-10-01	4
toolshed.g2.bx.psu.edu/repos/bgruening/sailfish/sailfish/0.10.1.1	2018-10-01	4
toolshed.g2.bx.psu.edu/repos/iuc/ebi_search_rest_results/ebi_search_rest_results/0.1.1	2018-10-01	4
toolshed.g2.bx.psu.edu/repos/peterjc/mummer/mummerplot_wrapper/0.0.7	2018-10-01	4
toolshed.g2.bx.psu.edu/repos/devteam/fastq_quality_converter/cshl_fastq_quality_converter/1.0.0	2018-10-01	4
CONVERTER_wig_to_bigwig	2018-10-01	4
toolshed.g2.bx.psu.edu/repos/devteam/picard/rgPicFixMate/1.56.0	2018-10-01	4
toolshed.g2.bx.psu.edu/repos/peterjc/blast2go/blast2go/0.0.9	2018-10-01	4
toolshed.g2.bx.psu.edu/repos/devteam/picard/PicardASMetrics/1.56.0	2018-10-01	4
toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_group/abims_xcms_group/2.1.1	2018-10-01	4
toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_heatmap2/ggplot2_heatmap2/2.2.1	2018-10-01	4
CONVERTER_fasta_to_bowtie_base_index	2018-10-01	4
CONVERTER_interval_to_bigwig_0	2018-10-01	4
toolshed.g2.bx.psu.edu/repos/iuc/iqtree/iqtree/1.5.5.1	2018-10-01	4
toolshed.g2.bx.psu.edu/repos/iuc/qiime_assign_taxonomy/qiime_assign_taxonomy/1.9.1.0	2018-10-01	4
toolshed.g2.bx.psu.edu/repos/jjohnson/cdhit/cd_hit_protein/1.2	2018-10-01	4
CONVERTER_vcf_to_bgzip_0	2018-10-01	4
toolshed.g2.bx.psu.edu/repos/iuc/mothur_merge_files/mothur_merge_files/1.39.5.0	2018-10-01	4
toolshed.g2.bx.psu.edu/repos/iuc/gemini_gene_wise/gemini_gene_wise/0.18.1.0	2018-10-01	4
toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_feature_selection/sklearn_feature_selection/0.9.1	2018-10-01	4
toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.5.2b-1	2018-10-01	4
toolshed.g2.bx.psu.edu/repos/devteam/cuffdiff/cuffdiff/2.2.1.1	2018-10-01	4
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.27.0.1	2018-10-01	4
toolshed.g2.bx.psu.edu/repos/devteam/varscan_version_2/varscan/2.4.2	2018-10-01	4
toolshed.g2.bx.psu.edu/repos/devteam/fastq_stats/fastq_stats/1.0.0	2018-10-01	4
toolshed.g2.bx.psu.edu/repos/ethevenot/qualitymetrics/quality_metrics/2.2.8	2018-10-01	4
toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.67	2018-10-01	4
toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_rpstblastn_wrapper/0.3.0	2018-10-01	4
toolshed.g2.bx.psu.edu/repos/devteam/data_manager_bowtie2_index_builder/bowtie2_index_builder_data_manager/2.3.0	2018-10-01	4
toolshed.g2.bx.psu.edu/repos/peterjc/venn_list/venn_list/0.0.11	2018-10-01	4
toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_tblastn_wrapper/0.3.0	2018-10-01	4
toolshed.g2.bx.psu.edu/repos/galaxyp/msgfplus/msgfplus/0.5	2018-10-01	4
toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0.1	2018-10-01	4
hgv_david	2018-10-01	4
toolshed.g2.bx.psu.edu/repos/iuc/ucsc_fasplit/fasplit/357	2018-10-01	4
methtools_calling	2018-10-01	4
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/2.5.1.1.0	2018-10-01	4
toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/0.7.0.3	2018-10-01	4
toolshed.g2.bx.psu.edu/repos/devteam/ucsc_custom_track/build_ucsc_custom_track_1/1.0.0	2018-10-01	4
toolshed.g2.bx.psu.edu/repos/iuc/varscan_mpileup/varscan_mpileup/2.4.3.0	2018-10-01	4
toolshed.g2.bx.psu.edu/repos/devteam/gi2taxonomy/Fetch Taxonomic Ranks/1.1.0	2018-10-01	4
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multiintersectbed/2.27.0.0	2018-10-01	4
toolshed.g2.bx.psu.edu/repos/bebatut/cdhit/cd_hit_protein/1.3	2018-10-01	4
toolshed.g2.bx.psu.edu/repos/iuc/trinity_super_transcripts/trinity_super_transcripts/2.8.4	2018-10-01	4
toolshed.g2.bx.psu.edu/repos/bgruening/rnaz/rnaz/2.1.1	2018-10-01	4
toolshed.g2.bx.psu.edu/repos/devteam/fastx_barcode_splitter/cshl_fastx_barcode_splitter/1.0.0	2018-10-01	4
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_profile/deeptools_plot_profile/2.5.1.1.0	2018-10-01	4
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.27.0.1	2018-10-01	4
toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3.0	2018-10-01	3
toolshed.g2.bx.psu.edu/repos/bebatut/group_humann2_uniref_abundances_to_go/group_humann2_uniref_abundances_to_go/1.2.0	2018-10-01	3
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_uniq_tool/1.1.1	2018-10-01	3
bed2gff1	2018-10-01	3
toolshed.g2.bx.psu.edu/repos/iuc/ncbi_eutils_egquery/ncbi_eutils_egquery/1.1	2018-10-01	3
toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.0.0	2018-10-01	3
toolshed.g2.bx.psu.edu/repos/earlhaminst/replace_chromosome_names/replace_chromosome_names/0.1	2018-10-01	3
toolshed.g2.bx.psu.edu/repos/saskia-hiltemann/krona_text/krona-text/1	2018-10-01	3
toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastx_wrapper/0.3.1	2018-10-01	3
CONVERTER_vcf_to_tabix_0	2018-10-01	3
toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/0.8.1+galaxy0	2018-10-01	3
toolshed.g2.bx.psu.edu/repos/pavlo-lutsik/rnbeads/rnbeads/0.91	2018-10-01	3
toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_nn_classifier/sklearn_nn_classifier/0.9	2018-10-01	3
toolshed.g2.bx.psu.edu/repos/iuc/mothur_summary_seqs/mothur_summary_seqs/1.36.1.0	2018-10-01	3
toolshed.g2.bx.psu.edu/repos/nml/spades/spades/1.2	2018-10-01	3
toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/column_remove_by_header/0.0.1	2018-10-01	3
toolshed.g2.bx.psu.edu/repos/bgruening/trna_prediction/trnascan/0.4	2018-10-01	3
toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.2.0	2018-10-01	3
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicatesWithMateCigar/2.18.2.1	2018-10-01	3
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_featurefindermetabo/FeatureFinderMetabo/2.3.0	2018-10-01	3
toolshed.g2.bx.psu.edu/repos/bgruening/diamond/bg_diamond/0.8.24.1	2018-10-01	3
toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_bam_stat/2.6.4	2018-10-01	3
toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_generalized_linear/sklearn_generalized_linear/0.9	2018-10-01	3
toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_databases/4.3r.1	2018-10-01	3
echo_main_env	2018-10-01	3
toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_geneBody_coverage/2.6.4.1	2018-10-01	3
toolshed.g2.bx.psu.edu/repos/devteam/cuffcompare/cuffcompare/2.2.1.1	2018-10-01	3
toolshed.g2.bx.psu.edu/repos/rnateam/rcas/rcas/1.1.1	2018-10-01	3
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.7.1.2	2018-10-01	3
Count1	2018-10-01	3
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_multiplexresolver/MultiplexResolver/2.3.0	2018-10-01	3
toolshed.g2.bx.psu.edu/repos/iuc/varscan_somatic/varscan_somatic/2.4.3.0	2018-10-01	3
biomart	2018-10-01	3
toolshed.g2.bx.psu.edu/repos/iuc/qiime_pick_open_reference_otus/qiime_pick_open_reference_otus/1.9.1.0	2018-10-01	3
toolshed.g2.bx.psu.edu/repos/devteam/vcfallelicprimitives/vcfallelicprimitives/1.0.0_rc1.0	2018-10-01	3
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicplotdistvscounts/hicexplorer_hicplotdistvscounts/2.1.4.0	2018-10-01	3
MAF_Reverse_Complement_1	2018-10-01	3
toolshed.g2.bx.psu.edu/repos/bgruening/plotly_ml_performance_plots/plotly_ml_performance_plots/0.1	2018-10-01	3
toolshed.g2.bx.psu.edu/repos/bgruening/plotly_parallel_coordinates_plot/plotly_parallel_coordinates_plot/0.1	2018-10-01	3
toolshed.g2.bx.psu.edu/repos/iuc/qiime_pick_closed_reference_otus/qiime_pick_closed_reference_otus/1.9.1.0	2018-10-01	3
toolshed.g2.bx.psu.edu/repos/iuc/gemini_stats/gemini_stats/0.18.1.0	2018-10-01	3
CONVERTER_fasta_to_2bit	2018-10-01	3
toolshed.g2.bx.psu.edu/repos/devteam/samtools_split/samtools_split/1.3.1	2018-10-01	3
toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.3.1	2018-10-01	3
toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_tblastx_wrapper/0.3.0	2018-10-01	3
secure_hash_message_digest	2018-10-01	3
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_closestbed/2.27.0.0	2018-10-01	3
toolshed.g2.bx.psu.edu/repos/rnateam/segemehl/segemehl/0.2.0.3	2018-10-01	3
toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/0.8.1+galaxy0	2018-10-01	3
toolshed.g2.bx.psu.edu/repos/iuc/qiime_multiple_join_paired_ends/qiime_multiple_join_paired_ends/1.9.1.0	2018-10-01	3
toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.3.5	2018-10-01	3
toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_mergefa/1.2.0	2018-10-01	3
toolshed.g2.bx.psu.edu/repos/peterjc/mira_assembler/mira_assembler/0.0.11	2018-10-01	3
toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.1.0-1	2018-10-01	3
toolshed.g2.bx.psu.edu/repos/iuc/trinity_abundance_estimates_to_matrix/trinity_abundance_estimates_to_matrix/2.8.3	2018-10-01	3
toolshed.g2.bx.psu.edu/repos/galaxyp/msconvert/msconvert_win/3.0.0	2018-10-01	3
toolshed.g2.bx.psu.edu/repos/wolma/mimodd_main/mimodd_header/0.1.8_1	2018-10-01	3
toolshed.g2.bx.psu.edu/repos/eschen42/w4mjoinpn/w4mjoinpn/0.98.2	2018-10-01	3
toolshed.g2.bx.psu.edu/repos/iuc/bctools_remove_tail/bctools_remove_tail/0.2.2	2018-10-01	3
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.1	2018-10-01	3
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_flankbed/2.27.0.0	2018-10-01	3
toolshed.g2.bx.psu.edu/repos/earlhaminst/ete/species_tree_generator/3.0.0b35	2018-10-01	3
p_clip_peaks	2018-10-01	3
toolshed.g2.bx.psu.edu/repos/galaxyp/myrimatch/myrimatch/3.0.11579.0	2018-10-01	3
toolshed.g2.bx.psu.edu/repos/rnateam/viennarna_rnaalifold/viennarna_rnaalifold/2.2.10.1	2018-10-01	3
toolshed.g2.bx.psu.edu/repos/iuc/roary/roary/3.10.2	2018-10-01	3
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_BamIndexStats/1.56.0	2018-10-01	3
toolshed.g2.bx.psu.edu/repos/iuc/plasflow/PlasFlow/1.0	2018-10-01	3
toolshed.g2.bx.psu.edu/repos/bgruening/augustus/augustus/3.2.3	2018-10-01	3
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_slopbed/2.27.0.0	2018-10-01	3
toolshed.g2.bx.psu.edu/repos/iuc/enasearch_retrieve_data/enasearch_retrieve_data/0.1.1.0	2018-10-01	3
toolshed.g2.bx.psu.edu/repos/galaxyp/maldi_quant_peak_detection/maldi_quant_peak_detection/1.18.0.2	2018-10-01	3
toolshed.g2.bx.psu.edu/repos/iuc/kobas/kobas_annotate/0.4	2018-10-01	2
toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_FPKM_count/2.6.4.1	2018-10-01	2
toolshed.g2.bx.psu.edu/repos/bonsai/sortmerna/sortmerna_wrapper/1.0	2018-10-01	2
toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.4.0.0	2018-10-01	2
toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.0.3	2018-10-01	2
toolshed.g2.bx.psu.edu/repos/crs4/muscle/muscle/0.0.11	2018-10-01	2
toolshed.g2.bx.psu.edu/repos/bgruening/trna_prediction/aragorn_trna/0.6	2018-10-01	2
toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastdbcmd_wrapper/0.3.0	2018-10-01	2
toolshed.g2.bx.psu.edu/repos/miller-lab/genome_diversity/gd_make_gd_file/1.0.0	2018-10-01	2
toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_quality/2.6.4	2018-10-01	2
toolshed.g2.bx.psu.edu/repos/iuc/goseq/goseq/1.30.0	2018-10-01	2
toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/1.0	2018-10-01	2
toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_violin/ggplot2_violin/2.2.1+galaxy0	2018-10-01	2
toolshed.g2.bx.psu.edu/repos/devteam/vcfcombine/vcfcombine/1.0.0_rc1+galaxy0	2018-10-01	2
toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_wrapper_2/1.3.2	2018-10-01	2
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_unfold_column_tool/1.1.1	2018-10-01	2
toolshed.g2.bx.psu.edu/repos/devteam/t_test_two_samples/t_test_two_samples/1.0.1	2018-10-01	2
toolshed.g2.bx.psu.edu/repos/devteam/bamtools_split/bamSplit/2.4.0	2018-10-01	2
toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.1.0.20151222.0	2018-10-01	2
toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_retcor/abims_xcms_retcor/2.1.1	2018-10-01	2
toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_merge/xcms_merge/1.1.0	2018-10-01	2
toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_group/abims_xcms_group/2.1.0	2018-10-01	2
toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_fillpeaks/abims_xcms_fillPeaks/2.1.1	2018-10-01	2
toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/0.3	2018-10-01	2
toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/0.6	2018-10-01	2
toolshed.g2.bx.psu.edu/repos/lecorguille/camera_annotate/abims_CAMERA_annotateDiffreport/2.2.2	2018-10-01	2
toolshed.g2.bx.psu.edu/repos/lecorguille/camera_annotate/abims_CAMERA_annotateDiffreport/2.2.0	2018-10-01	2
foldchange_heatmap	2018-10-01	2
toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastx_wrapper/0.2.01	2018-10-01	2
toolshed.g2.bx.psu.edu/repos/iuc/meme_dreme/meme_dreme/4.11.2.0	2018-10-01	2
genomespace_importer	2018-10-01	2
toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.4.1	2018-10-01	2
CONVERTER_sam_to_unsorted_bam	2018-10-01	2
CONVERTER_interval_to_tabix_0	2018-10-01	2
hgv_linkToGProfile	2018-10-01	2
toolshed.g2.bx.psu.edu/repos/iuc/gemini_actionable_mutations/gemini_actionable_mutations/0.18.1.0	2018-10-01	2
CONVERTER_interval_to_bgzip_0	2018-10-01	2
toolshed.g2.bx.psu.edu/repos/devteam/concat/gops_concat_1/1.0.1	2018-10-01	2
toolshed.g2.bx.psu.edu/repos/iuc/mothur_count_groups/mothur_count_groups/1.36.1.0	2018-10-01	2
toolshed.g2.bx.psu.edu/repos/iuc/gatk2/gatk2_realigner_target_creator/0.0.7	2018-10-01	2
toolshed.g2.bx.psu.edu/repos/devteam/sicer/peakcalling_sicer/0.0.1	2018-10-01	2
toolshed.g2.bx.psu.edu/repos/iuc/gatk2/gatk2_depth_of_coverage/2.8.0	2018-10-01	2
toolshed.g2.bx.psu.edu/repos/iuc/gatk2/gatk2_base_recalibrator/2.8.0	2018-10-01	2
toolshed.g2.bx.psu.edu/repos/iuc/trinity/trinity/2.6.6	2018-10-01	2
toolshed.g2.bx.psu.edu/repos/galaxyp/maldi_quant_preprocessing/maldi_quant_preprocessing/1.18.0.2	2018-10-01	2
CONVERTER_gff_to_fli_0	2018-10-01	2
toolshed.g2.bx.psu.edu/repos/iuc/mothur_fastq_info/mothur_fastq_info/1.39.5.0	2018-10-01	2
toolshed.g2.bx.psu.edu/repos/devteam/cuffmerge/cuffmerge/0.0.6	2018-10-01	2
toolshed.g2.bx.psu.edu/repos/bgruening/protease_prediction/eden_protease_prediction/0.9	2018-10-01	2
toolshed.g2.bx.psu.edu/repos/iuc/trinity_run_de_analysis/trinity_run_de_analysis/2.8.3	2018-10-01	2
methtools_dmr	2018-10-01	2
toolshed.g2.bx.psu.edu/repos/bgruening/nn_classifier/nn_classifier/0.9	2018-10-01	2
wiggle2simple1	2018-10-01	2
toolshed.g2.bx.psu.edu/repos/iuc/exonerate/exonerate/2.4.0	2018-10-01	2
toolshed.g2.bx.psu.edu/repos/devteam/draw_stacked_barplots/draw_stacked_barplots/1.0.0	2018-10-01	2
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_featurelinkerunlabeledqt/FeatureLinkerUnlabeledQT/2.3.0	2018-10-01	2
toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_shared/mothur_make_shared/1.36.1.0	2018-10-01	2
toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: etandem33/5.0.0.1	2018-10-01	2
toolshed.g2.bx.psu.edu/repos/galaxyp/idconvert/idconvert/3.0.0	2018-10-01	2
toolshed.g2.bx.psu.edu/repos/bgruening/hicup_mapper/hicup_mapper/0.5.10.0	2018-10-01	2
toolshed.g2.bx.psu.edu/repos/iuc/star_fusion/star_fusion/0.5.4-3	2018-10-01	2
r_correlation_matrix	2018-10-01	2
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicsummatrices/hicexplorer_hicsummatrices/2.1.4.0	2018-10-01	2
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicplotviewpoint/hicexplorer_hicplotviewpoint/2.1.4.0	2018-10-01	2
toolshed.g2.bx.psu.edu/repos/earlhaminst/t_coffee/t_coffee/11.0.8	2018-10-01	2
toolshed.g2.bx.psu.edu/repos/rnateam/mlocarna/mlocarna/1.8.12.0	2018-10-01	2
toolshed.g2.bx.psu.edu/repos/iuc/mothur_rarefaction_single/mothur_rarefaction_single/1.36.1.0	2018-10-01	2
toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: supermatcher95/5.0.0.1	2018-10-01	2
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_fileconverter/FileConverter/2.1.0	2018-10-01	2
CONVERTER_biom2_to_biom1	2018-10-01	2
toolshed.g2.bx.psu.edu/repos/fcaramia/varscan/varscan_somatic/2.3.5	2018-10-01	2
toolshed.g2.bx.psu.edu/repos/rnateam/rcas/rcas/1.5.4	2018-10-01	2
toolshed.g2.bx.psu.edu/repos/iuc/mothur_screen_seqs/mothur_screen_seqs/1.36.1.0	2018-10-01	2
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_fileconverter/FileConverter/2.3.0	2018-10-01	2
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_ticcalculator/TICCalculator/2.3.0	2018-10-01	2
toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/2.8.0	2018-10-01	2
toolshed.g2.bx.psu.edu/repos/devteam/fasta_formatter/cshl_fasta_formatter/1.0.1	2018-10-01	2
toolshed.g2.bx.psu.edu/repos/rnateam/sortmerna/bg_sortmerna/2.1b.5	2018-10-01	2
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_NormalizeFasta/2.18.2.1	2018-10-01	2
toolshed.g2.bx.psu.edu/repos/iuc/mothur_unique_seqs/mothur_unique_seqs/1.36.1.0	2018-10-01	2
toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpSift_annotate/3.4	2018-10-01	2
toolshed.g2.bx.psu.edu/repos/bgruening/glimmer3/glimmer_knowlegde-based/0.2	2018-10-01	2
toolshed.g2.bx.psu.edu/repos/iuc/describe_samples/describe_samples/2.8.3	2018-10-01	2
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SamToFastq/2.18.2.1	2018-10-01	2
toolshed.g2.bx.psu.edu/repos/iuc/ncbi_eutils_efetch/ncbi_eutils_efetch/1.1	2018-10-01	2
toolshed.g2.bx.psu.edu/repos/iuc/ncbi_eutils_esearch/ncbi_eutils_esearch/1.1	2018-10-01	2
toolshed.g2.bx.psu.edu/repos/bgruening/antismash/antismash/4.1	2018-10-01	2
toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy_core/3.2	2018-10-01	2
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_correlation/deeptools_plot_correlation/2.5.1.1.0	2018-10-01	2
toolshed.g2.bx.psu.edu/repos/iuc/bp_genbank2gff3/bp_genbank2gff3/1.0	2018-10-01	2
toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_mergefa/1.3.0	2018-10-01	2
blockbuster	2018-10-01	2
toolshed.g2.bx.psu.edu/repos/iuc/qiime_beta_diversity_through_plots/qiime_beta_diversity_through_plots/1.9.1.0	2018-10-01	2
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_map/2.27.0.0	2018-10-01	2
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bam_summary/deeptools_multi_bam_summary/2.5.1.1.0	2018-10-01	2
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/deeptools_compute_matrix/3.0.1.0	2018-10-01	2
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_overlapbed/2.27.0.0	2018-10-01	2
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multicovtbed/2.27.0.0	2018-10-01	2
toolshed.g2.bx.psu.edu/repos/chemteam/gmx_setup/gmx_setup/2018.2	2018-10-01	2
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bam_summary/deeptools_multi_bam_summary/2.5.7.0	2018-10-01	1
toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastdbcmd_info/0.3.0	2018-10-01	1
toolshed.g2.bx.psu.edu/repos/iuc/data_manager_star_index_builder/rna_star_index_builder_data_manager/0.0.5	2018-10-01	1
toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_duplication/2.6.4	2018-10-01	1
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_featurelinkerunlabeled/FeatureLinkerUnlabeled/2.3.0	2018-10-01	1
toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_svm_classifier/sklearn_svm_classifier/0.9	2018-10-01	1
toolshed.g2.bx.psu.edu/repos/devteam/short_reads_trim_seq/trim_reads/1.0.0	2018-10-01	1
toolshed.g2.bx.psu.edu/repos/devteam/t2ps/Draw_phylogram/1.0.0	2018-10-01	1
toolshed.g2.bx.psu.edu/repos/devteam/count_gff_features/count_gff_features/0.2	2018-10-01	1
toolshed.g2.bx.psu.edu/repos/iuc/vt_variant_tools/vt_normalize/0.1.0	2018-10-01	1
toolshed.g2.bx.psu.edu/repos/chemteam/packmol/packmol/18.169	2018-10-01	1
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_masscalculator/MassCalculator/2.3.0	2018-10-01	1
toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_preprocessing/cardinal_preprocessing/1.12.1.1	2018-10-01	1
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hiccorrelate/hicexplorer_hiccorrelate/2.1.4.0	2018-10-01	1
toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: cirdna11/5.0.0	2018-10-01	1
toolshed.g2.bx.psu.edu/repos/iuc/mothur_pre_cluster/mothur_pre_cluster/1.36.1.0	2018-10-01	1
toolshed.g2.bx.psu.edu/repos/galaxyp/idpquery/idpquery/3.0.11392.0	2018-10-01	1
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_coverage/deeptools_plot_coverage/3.0.2.0	2018-10-01	1
toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_fillpeaks/abims_xcms_fillPeaks/2.1.0	2018-10-01	1
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed_histogram/2.19.0	2018-10-01	1
toolshed.g2.bx.psu.edu/repos/iuc/mothur_seq_error/mothur_seq_error/1.36.1.0	2018-10-01	1
toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: dotpath25/5.0.0.1	2018-10-01	1
toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_bam2wig/2.4galaxy1	2018-10-01	1
toolshed.g2.bx.psu.edu/repos/iuc/qiime_summarize_taxa/qiime_summarize_taxa/1.9.1.0	2018-10-01	1
toolshed.g2.bx.psu.edu/repos/devteam/fastq_to_tabular/fastq_to_tabular/1.1.1	2018-10-01	1
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_xmlvalidator/XMLValidator/2.3.0	2018-10-01	1
toolshed.g2.bx.psu.edu/repos/devteam/samtools_flagstat/samtools_flagstat/1.0.0	2018-10-01	1
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_gc_bias/deeptools_compute_gc_bias/2.5.1.1.0	2018-10-01	1
toolshed.g2.bx.psu.edu/repos/iuc/qiime_plot_taxa_summary/qiime_plot_taxa_summary/1.9.1.0	2018-10-01	1
flexbar_split_RR_bcs	2018-10-01	1
toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastp_wrapper/0.3.1	2018-10-01	1
toolshed.g2.bx.psu.edu/repos/iuc/mothur_metastats/mothur_metastats/1.36.1.0	2018-10-01	1
toolshed.g2.bx.psu.edu/repos/jjohnson/find_in_reference/find_in_reference/0.0.3	2018-10-01	1
toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastx_wrapper/0.1.08	2018-10-01	1
toolshed.g2.bx.psu.edu/repos/iuc/disco/disco/1.2.0	2018-10-01	1
toolshed.g2.bx.psu.edu/repos/devteam/find_diag_hits/find_diag_hits/1.0.0	2018-10-01	1
toolshed.g2.bx.psu.edu/repos/iuc/mothur_pairwise_seqs/mothur_pairwise_seqs/1.39.5.0	2018-10-01	1
toolshed.g2.bx.psu.edu/repos/gga/apollo_fetch_jbrowse/fetch_jbrowse/3.3	2018-10-01	1
toolshed.g2.bx.psu.edu/repos/iuc/rnaspades/rnaspades/3.9.0.1	2018-10-01	1
toolshed.g2.bx.psu.edu/repos/iuc/gatk2/gatk2_variant_eval/2.8.0	2018-10-01	1
toolshed.g2.bx.psu.edu/repos/wolma/mimodd_main/mimodd_varcall/0.1.8_1	2018-10-01	1
toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: wordcount109/5.0.0.1	2018-10-01	1
toolshed.g2.bx.psu.edu/repos/iuc/ebi_metagenomics_run_downloader/ebi_metagenomics_run_downloader/0.1.0	2018-10-01	1
toolshed.g2.bx.psu.edu/repos/devteam/vcfannotate/vcfannotate/1.0.0_rc1+galaxy0	2018-10-01	1
toolshed.g2.bx.psu.edu/repos/iuc/mothur_remove_lineage/mothur_remove_lineage/1.36.1.0	2018-10-01	1
toolshed.g2.bx.psu.edu/repos/hammock/hammock/hammock_1.0/1.1.1	2018-10-01	1
toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: transeq101/5.0.0	2018-10-01	1
genomespace_exporter	2018-10-01	1
toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/0.7.0	2018-10-01	1
toolshed.g2.bx.psu.edu/repos/iuc/mothur_remove_groups/mothur_remove_groups/1.36.1.0	2018-10-01	1
toolshed.g2.bx.psu.edu/repos/fcaramia/varscan/varscan_mpileup/2.3.5	2018-10-01	1
toolshed.g2.bx.psu.edu/repos/iuc/gemini_lof_sieve/gemini_lof_sieve/0.18.1.0	2018-10-01	1
toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: seqret84/5.0.0	2018-10-01	1
toolshed.g2.bx.psu.edu/repos/iuc/poretools_qualpos/poretools_qualpos/0.6.1a1.0	2018-10-01	1
toolshed.g2.bx.psu.edu/repos/melpetera/generic_filter/generic_filter/2017.06	2018-10-01	1
toolshed.g2.bx.psu.edu/repos/iuc/ococo/ococo/0.1.2.6	2018-10-01	1
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools/deeptools_bamCoverage/1.1.0	2018-10-01	1
toolshed.g2.bx.psu.edu/repos/iuc/qiime_make_phylogeny/qiime_make_phylogeny/1.9.1.0	2018-10-01	1
toolshed.g2.bx.psu.edu/repos/iuc/data_manager_hisat2_index_builder/hisat2_index_builder_data_manager/2.0.5	2018-10-01	1
toolshed.g2.bx.psu.edu/repos/iuc/khmer_partition/khmer_partition/2.0.0	2018-10-01	1
toolshed.g2.bx.psu.edu/repos/bgruening/bismark/bismark_pretty_report/0.20.0	2018-10-01	1
toolshed.g2.bx.psu.edu/repos/tgac/miranda/miranda/3.3a	2018-10-01	1
toolshed.g2.bx.psu.edu/repos/iuc/humann2_renorm_table/humann2_renorm_table/0.9.9.0	2018-10-01	1
toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_junction_saturation/2.6.4.1	2018-10-01	1
toolshed.g2.bx.psu.edu/repos/ethevenot/qualitymetrics/quality_metrics/2.2.6	2018-10-01	1
translate_nucleotides	2018-10-01	1
toolshed.g2.bx.psu.edu/repos/iuc/poretools_qualdist/poretools_qualdist/0.6.1a1.0	2018-10-01	1
toolshed.g2.bx.psu.edu/repos/iuc/khmer_extract_partitions/khmer_extract_partitions/2.0.0	2018-10-01	1
barchart_gnuplot	2018-10-01	1
toolshed.g2.bx.psu.edu/repos/iuc/seurat/seurat/2.3.4	2018-10-01	1
toolshed.g2.bx.psu.edu/repos/devteam/fastx_clipper/cshl_fastx_clipper/1.0.3	2018-10-01	1
toolshed.g2.bx.psu.edu/repos/iuc/intervene/intervene_pairwise/0.6.4	2018-10-01	1
toolshed.g2.bx.psu.edu/repos/bgruening/bamhash/bamhash/1.1	2018-10-01	1
toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_tblastx_wrapper/0.3.1	2018-10-01	1
toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.2.0	2018-10-01	1
toolshed.g2.bx.psu.edu/repos/iuc/khmer_abundance_distribution_single/khmer_abundance_distribution_single/2.0.0	2018-10-01	1
toolshed.g2.bx.psu.edu/repos/iuc/mothur_dist_seqs/mothur_dist_seqs/1.36.1.0	2018-10-01	1
MAF_Thread_For_Species1	2018-10-01	1
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtoigv/2.27.0.0	2018-10-01	1
toolshed.g2.bx.psu.edu/repos/iuc/mothur_cluster_split/mothur_cluster_split/1.36.1.0	2018-10-01	1
toolshed.g2.bx.psu.edu/repos/chemteam/gmx_solvate/gmx_solvate/2018.2	2018-10-01	1
toolshed.g2.bx.psu.edu/repos/anton/vcfannotate/vcfannotate/0.0.1	2018-10-01	1
toolshed.g2.bx.psu.edu/repos/iuc/mothur_classify_seqs/mothur_classify_seqs/1.36.1.0	2018-10-01	1
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_highresprecursormasscorrector/HighResPrecursorMassCorrector/2.3.0	2018-10-01	1
toolshed.g2.bx.psu.edu/repos/iuc/length_and_gc_content/length_and_gc_content/0.1.1	2018-10-01	1
toolshed.g2.bx.psu.edu/repos/bgruening/protein_properties/bg_protein_properties/0.1.0	2018-10-01	1
toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_databases/4.0.0	2018-10-01	1
toolshed.g2.bx.psu.edu/repos/iuc/trinity_samples_qccheck/trinity_samples_qccheck/2.8.4	2018-10-01	1
toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_group/umi_tools_group/0.5.3.0	2018-10-01	1
toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.34.9.7	2018-10-01	1
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.0.0	2018-10-01	1
toolshed.g2.bx.psu.edu/repos/devteam/vcftools_compare/vcftools_compare/0.1	2018-10-01	1
toolshed.g2.bx.psu.edu/repos/iuc/mothur_classify_rf/mothur_classify_rf/1.36.1.0	2018-10-01	1
toolshed.g2.bx.psu.edu/repos/devteam/complement/gops_complement_1/1.0.0	2018-10-01	1
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_pe_fragmentsize/deeptools_bam_pe_fragmentsize/3.0.2.0	2018-10-01	1
Extract_features1	2018-10-01	1
toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_download/4.0.0	2018-10-01	1
toolshed.g2.bx.psu.edu/repos/galaxyp/msi_filtering/mass_spectrometry_imaging_filtering/1.10.0.4	2018-10-01	1
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectBaseDistributionByCycle/2.18.2.1	2018-10-01	1
toolshed.g2.bx.psu.edu/repos/iuc/tsne/tsne/0.0.2	2018-10-01	1
toolshed.g2.bx.psu.edu/repos/devteam/fastx_renamer/cshl_fastx_renamer/0.0.11	2018-10-01	1
toolshed.g2.bx.psu.edu/repos/iuc/mothur_filter_seqs/mothur_filter_seqs/1.36.1.0	2018-10-01	1
toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_download/4.1.0	2018-10-01	1
toolshed.g2.bx.psu.edu/repos/devteam/vcftools_merge/vcftools_merge/0.1.1	2018-10-01	1
toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_download/4.3r.0	2018-10-01	1
toolshed.g2.bx.psu.edu/repos/earlhaminst/ensembl_get_feature_info/get_feature_info/0.1.2	2018-10-01	1
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_precursormasscorrector/PrecursorMassCorrector/2.3.0	2018-10-01	1
toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_clf_metrics/sklearn_clf_metrics/0.9	2018-10-01	1
toolshed.g2.bx.psu.edu/repos/iuc/mothur_cluster/mothur_cluster/1.36.1.0	2018-10-01	1
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_compnovo/CompNovo/2.3.0	2018-10-01	1
toolshed.g2.bx.psu.edu/repos/iuc/msaboot/msaboot/0.1.2	2018-10-01	1
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toolshed.g2.bx.psu.edu/repos/ethevenot/multivariate/Multivariate/2.3.10	2018-09-01	101
toolshed.g2.bx.psu.edu/repos/iuc/graphlan_annotate/graphlan_annotate/1.0.0.0	2018-09-01	97
extract_bcs.py	2018-09-01	96
toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.4.1	2018-09-01	93
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.27.0.0	2018-09-01	92
Convert characters1	2018-09-01	92
toolshed.g2.bx.psu.edu/repos/devteam/samtools_rmdup/samtools_rmdup/2.0.1	2018-09-01	91
toolshed.g2.bx.psu.edu/repos/devteam/samtools_slice_bam/samtools_slice_bam/2.0.1	2018-09-01	90
toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/peptide_shaker/1.16.26	2018-09-01	88
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bam_summary/deeptools_multi_bam_summary/3.0.2.0	2018-09-01	86
toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.69	2018-09-01	86
toolshed.g2.bx.psu.edu/repos/iuc/metaphlan2/metaphlan2/2.6.0.0	2018-09-01	86
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_mergebed/2.27.0.0	2018-09-01	83
toolshed.g2.bx.psu.edu/repos/galaxyp/mass_spectrometry_imaging_segmentations/mass_spectrometry_imaging_segmentations/1.10.0.4	2018-09-01	81
sort1	2018-09-01	80
toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastx_wrapper/0.3.0	2018-09-01	78
CONVERTER_fastq_to_fqtoc0	2018-09-01	76
CONVERTER_bedgraph_to_bigwig	2018-09-01	76
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idposteriorerrorprobability/IDPosteriorErrorProbability/2.3.0	2018-09-01	76
toolshed.g2.bx.psu.edu/repos/devteam/get_flanks/get_flanks1/1.0.0	2018-09-01	74
toolshed.g2.bx.psu.edu/repos/ethevenot/univariate/Univariate/2.2.4	2018-09-01	74
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.0	2018-09-01	74
toolshed.g2.bx.psu.edu/repos/bgruening/nanopolish_variants/nanopolish_variants/0.1.0	2018-09-01	73
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicplottads/hicexplorer_hicplottads/2.1.2.0	2018-09-01	71
toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.3.0	2018-09-01	71
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/1.1.0	2018-09-01	70
toolshed.g2.bx.psu.edu/repos/devteam/add_value/addValue/1.0.0	2018-09-01	70
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_fileinfo/FileInfo/2.2.0	2018-09-01	69
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_falsediscoveryrate/FalseDiscoveryRate/2.2.0	2018-09-01	69
toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0	2018-09-01	68
toolshed.g2.bx.psu.edu/repos/bebatut/combine_metaphlan2_humann2/combine_metaphlan2_humann2/0.1.0	2018-09-01	67
CONVERTER_bam_to_qname_sorted_bam	2018-09-01	66
toolshed.g2.bx.psu.edu/repos/devteam/samtool_filter2/samtool_filter2/1.8	2018-09-01	66
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_fingerprint/deeptools_plot_fingerprint/3.0.2.0	2018-09-01	66
Paste1	2018-09-01	66
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_profile/deeptools_plot_profile/3.0.2.0	2018-09-01	64
toolshed.g2.bx.psu.edu/repos/devteam/tophat2/tophat2/2.1.1	2018-09-01	63
toolshed.g2.bx.psu.edu/repos/iuc/sickle/sickle/1.33.1	2018-09-01	63
dorina_search	2018-09-01	62
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.1	2018-09-01	61
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.1	2018-09-01	61
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.7.1.2	2018-09-01	60
toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_infer_experiment/2.6.4	2018-09-01	60
toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_geneBody_coverage/2.6.4.1	2018-09-01	60
toolshed.g2.bx.psu.edu/repos/devteam/samtools_flagstat/samtools_flagstat/2.0.1	2018-09-01	60
toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_distribution/2.6.4	2018-09-01	60
toolshed.g2.bx.psu.edu/repos/iuc/gtftobed12/gtftobed12/357	2018-09-01	59
velveth	2018-09-01	59
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicplottads/hicexplorer_hicplottads/2.1.4.0	2018-09-01	59
toolshed.g2.bx.psu.edu/repos/peterjc/blastxml_to_top_descr/blastxml_to_top_descr/0.1.1	2018-09-01	58
toolshed.g2.bx.psu.edu/repos/iuc/goseq/goseq/1.26.0	2018-09-01	58
toolshed.g2.bx.psu.edu/repos/eschen42/w4mclassfilter/w4mclassfilter/0.98.10	2018-09-01	57
toolshed.g2.bx.psu.edu/repos/iuc/metagenomeseq_normalization/metagenomeseq_normalizaton/1.16.0-0.0.1	2018-09-01	56
toolshed.g2.bx.psu.edu/repos/iuc/vsearch/vsearch_dereplication/2.8.3.0	2018-09-01	55
toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_makeblastdb/0.3.0	2018-09-01	55
toolshed.g2.bx.psu.edu/repos/galaxyp/msi_ion_images/mass_spectrometry_imaging_ion_images/1.10.0.5	2018-09-01	54
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_fileinfo/FileInfo/2.3.0	2018-09-01	54
toolshed.g2.bx.psu.edu/repos/devteam/cummerbund/cummeRbund/2.16.0	2018-09-01	54
trimmer	2018-09-01	53
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicbuildmatrix/hicexplorer_hicbuildmatrix/2.1.2.0	2018-09-01	52
toolshed.g2.bx.psu.edu/repos/bgruening/bigwig_to_bedgraph/bigwig_to_bedgraph/0.1.0	2018-09-01	51
toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.1	2018-09-01	51
toolshed.g2.bx.psu.edu/repos/bgruening/infernal/infernal_cmsearch/1.1.2.0	2018-09-01	51
toolshed.g2.bx.psu.edu/repos/rnateam/graphclust_mlocarna/locarna_best_subtree/0.3	2018-09-01	50
toolshed.g2.bx.psu.edu/repos/bgruening/canu/canu/1.7	2018-09-01	50
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SamToFastq/2.18.2.1	2018-09-01	50
toolshed.g2.bx.psu.edu/repos/rnateam/graphclust_cmfinder/cmFinder/0.3	2018-09-01	50
__UNZIP_COLLECTION__	2018-09-01	50
toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_dedup/umi_tools_dedup/0.5.3.0	2018-09-01	50
toolshed.g2.bx.psu.edu/repos/bgruening/infernal/infernal_cmbuild/1.1.2.0	2018-09-01	50
toolshed.g2.bx.psu.edu/repos/iuc/metaphlan2krona/metaphlan2krona/2.6.0.0	2018-09-01	49
extract_aln_ends.py	2018-09-01	49
toolshed.g2.bx.psu.edu/repos/devteam/bam_to_sam/bam_to_sam/2.0	2018-09-01	49
toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/1.6.1.0	2018-09-01	49
toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.2.6	2018-09-01	48
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_fidoadapter/FidoAdapter/2.3.0	2018-09-01	48
remove_tail.py	2018-09-01	48
coords2clnt.py	2018-09-01	48
rm_spurious_events.py	2018-09-01	48
flexbar_no_split	2018-09-01	48
toolshed.g2.bx.psu.edu/repos/iuc/dexseq/dexseq_count/1.24.0.0	2018-09-01	48
toolshed.g2.bx.psu.edu/repos/devteam/samtools_flagstat/samtools_flagstat/2.0	2018-09-01	48
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idfilter/IDFilter/2.3.0	2018-09-01	48
toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/1.5.3	2018-09-01	48
merge_pcr_duplicates.py	2018-09-01	48
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idscoreswitcher/IDScoreSwitcher/2.3.0	2018-09-01	47
toolshed.g2.bx.psu.edu/repos/bebatut/format_metaphlan2_output/format_metaphlan2_output/0.1.0	2018-09-01	46
thermo_raw_file_converter	2018-09-01	46
mergeCols1	2018-09-01	46
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bigwig_compare/deeptools_bigwig_compare/3.0.2.0	2018-09-01	46
toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/datamash_ops/1.0.6	2018-09-01	46
toolshed.g2.bx.psu.edu/repos/devteam/subtract/gops_subtract_1/1.0.0	2018-09-01	44
toolshed.g2.bx.psu.edu/repos/galaxyp/maldi_quant_preprocessing/maldi_quant_preprocessing/1.18.0.0	2018-09-01	44
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_fileconverter/FileConverter/2.1.0	2018-09-01	44
toolshed.g2.bx.psu.edu/repos/iuc/vsearch/vsearch_dereplication/1.9.7.0	2018-09-01	43
toolshed.g2.bx.psu.edu/repos/devteam/macs/peakcalling_macs/1.0.1	2018-09-01	43
toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/3.2	2018-09-01	42
toolshed.g2.bx.psu.edu/repos/iuc/humann2/humann2/0.11.1.0	2018-09-01	42
toolshed.g2.bx.psu.edu/repos/ethevenot/biosigner/biosigner/2.2.7	2018-09-01	42
Show tail1	2018-09-01	41
toolshed.g2.bx.psu.edu/repos/iuc/samtools_sort/samtools_rmdup/1.0.1	2018-09-01	41
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicmergematrixbins/hicexplorer_hicmergematrixbins/2.1.4.0	2018-09-01	41
toolshed.g2.bx.psu.edu/repos/devteam/correlation/cor2/1.0.0	2018-09-01	40
toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.1.0.46-0	2018-09-01	40
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_xtandemadapter/XTandemAdapter/2.2.0.1	2018-09-01	40
toolshed.g2.bx.psu.edu/repos/ethevenot/heatmap/Heatmap/2.2.2	2018-09-01	40
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicfindtads/hicexplorer_hicfindtads/2.1.4.0	2018-09-01	40
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idposteriorerrorprobability/IDPosteriorErrorProbability/2.2.0	2018-09-01	40
toolshed.g2.bx.psu.edu/repos/jjohnson/samtools_filter/samtools_filter/1.1.1	2018-09-01	38
toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.6.1	2018-09-01	38
Summary_Statistics1	2018-09-01	38
toolshed.g2.bx.psu.edu/repos/iuc/goseq/goseq/1.30.0	2018-09-01	38
toolshed.g2.bx.psu.edu/repos/bgruening/unique/bg_uniq/0.3	2018-09-01	37
toolshed.g2.bx.psu.edu/repos/galaxyp/msi_combine/mass_spectrometry_imaging_combine/1.10.0.5	2018-09-01	36
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_peptideindexer/PeptideIndexer/2.2.0	2018-09-01	36
toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_feature_selection/sklearn_feature_selection/0.9.1	2018-09-01	36
toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/4.6.3	2018-09-01	36
toolshed.g2.bx.psu.edu/repos/ethevenot/checkformat/checkFormat/3.0.0	2018-09-01	36
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idfilter/IDFilter/2.2.0	2018-09-01	36
toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotateMyIDs/3.5.0.0	2018-09-01	35
toolshed.g2.bx.psu.edu/repos/devteam/concat/gops_concat_1/1.0.1	2018-09-01	35
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idscoreswitcher/IDScoreSwitcher/2.2.0	2018-09-01	35
toolshed.g2.bx.psu.edu/repos/iuc/meme_fimo/meme_fimo/4.12.0.0	2018-09-01	35
toolshed.g2.bx.psu.edu/repos/devteam/subtract_query/subtract_query1/0.1	2018-09-01	35
toolshed.g2.bx.psu.edu/repos/iuc/extract_genomic_dna/Extract genomic DNA 1/3.0.3	2018-09-01	34
toolshed.g2.bx.psu.edu/repos/rnateam/metilene/metilene/0.2.6.1	2018-09-01	34
toolshed.g2.bx.psu.edu/repos/devteam/cluster/gops_cluster_1/1.0.0	2018-09-01	34
toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_bam2wig/2.6.4	2018-09-01	34
toolshed.g2.bx.psu.edu/repos/devteam/histogram/histogram_rpy/1.0.3	2018-09-01	34
velvetg	2018-09-01	34
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bigwig_summary/deeptools_multi_bigwig_summary/3.0.2.0	2018-09-01	33
toolshed.g2.bx.psu.edu/repos/iuc/humann2_genefamilies_genus_level/humann2_genefamilies_genus_level/0.11.1.0	2018-09-01	33
toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.1.0	2018-09-01	32
toolshed.g2.bx.psu.edu/repos/nml/spades/spades/3.11.1	2018-09-01	32
toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/2.4.0	2018-09-01	32
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicfindtads/hicexplorer_hicfindtads/2.1.2.0	2018-09-01	32
CONVERTER_interval_to_bed12_0	2018-09-01	31
toolshed.g2.bx.psu.edu/repos/devteam/fastq_quality_filter/cshl_fastq_quality_filter/1.0.0	2018-09-01	31
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1	2018-09-01	31
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_fidoadapter/FidoAdapter/2.2.0.1	2018-09-01	31
toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_heatmap/ggplot2_heatmap/2.2.1	2018-09-01	31
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_textexporter/TextExporter/2.2.0	2018-09-01	31
toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastp_wrapper/0.3.0	2018-09-01	30
toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.4.0	2018-09-01	30
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicpca/hicexplorer_hicpca/2.1.4.0	2018-09-01	30
toolshed.g2.bx.psu.edu/repos/iuc/meme_meme/meme_meme/4.12.0.0	2018-09-01	30
toolshed.g2.bx.psu.edu/repos/iuc/idr/idr/2.0.3	2018-09-01	29
toolshed.g2.bx.psu.edu/repos/galaxyp/filter_by_fasta_ids/filter_by_fasta_ids/2.0	2018-09-01	29
toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.2.6.2	2018-09-01	29
toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.0.6	2018-09-01	29
toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_splitter/fastq_paired_end_splitter/1.1.1	2018-09-01	28
toolshed.g2.bx.psu.edu/repos/galaxyp/maldi_quant_peak_detection/maldi_quant_peak_detection/1.18.0.0	2018-09-01	28
toolshed.g2.bx.psu.edu/repos/devteam/fastq_to_tabular/fastq_to_tabular/1.1.1	2018-09-01	28
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.0	2018-09-01	28
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.27.0.1	2018-09-01	28
toolshed.g2.bx.psu.edu/repos/rnateam/chipseeker/chipseeker/1.14.2.1	2018-09-01	28
toolshed.g2.bx.psu.edu/repos/iuc/column_order_header_sort/column_order_header_sort/0.0.1	2018-09-01	28
CONVERTER_bed_gff_or_vcf_to_bigwig_0	2018-09-01	27
toolshed.g2.bx.psu.edu/repos/kellrott/regex_replace/regex_replace/1.0.0	2018-09-01	27
toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_geneBody_coverage2/2.6.4.1	2018-09-01	27
toolshed.g2.bx.psu.edu/repos/iuc/megahit/megahit/1.1.2.3	2018-09-01	27
toolshed.g2.bx.psu.edu/repos/iuc/circos/circgraph/0.9-RC2	2018-09-01	27
toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1.1	2018-09-01	27
toolshed.g2.bx.psu.edu/repos/devteam/picard/rgPicardMarkDups/1.56.0	2018-09-01	27
toolshed.g2.bx.psu.edu/repos/devteam/sam_merge/sam_merge2/1.2.0	2018-09-01	26
toolshed.g2.bx.psu.edu/repos/nml/metaspades/metaspades/3.9.0	2018-09-01	26
toolshed.g2.bx.psu.edu/repos/galaxyp/quantp/quantp/1.0.0	2018-09-01	26
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_subtractbed/2.27.0.0	2018-09-01	25
toolshed.g2.bx.psu.edu/repos/bebatut/group_humann2_uniref_abundances_to_go/group_humann2_uniref_abundances_to_go/1.2.0	2018-09-01	25
toolshed.g2.bx.psu.edu/repos/iuc/mothur_summary_seqs/mothur_summary_seqs/1.39.5.0	2018-09-01	25
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_clusterbed/2.27.0.0	2018-09-01	25
toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.0	2018-09-01	24
dexseq_annotate	2018-09-01	24
toolshed.g2.bx.psu.edu/repos/devteam/fastq_trimmer/fastq_trimmer/1.1.1	2018-09-01	24
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_coveragebed/2.27.0.3	2018-09-01	24
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.27.0.0	2018-09-01	24
toolshed.g2.bx.psu.edu/repos/iuc/trinity_align_and_estimate_abundance/trinity_align_and_estimate_abundance/2.8.3	2018-09-01	24
toolshed.g2.bx.psu.edu/repos/devteam/fasta_filter_by_length/fasta_filter_by_length/1.1	2018-09-01	24
toolshed.g2.bx.psu.edu/repos/devteam/fastq_filter/fastq_filter/1.1.1	2018-09-01	24
__EXPORT_HISTORY__	2018-09-01	24
toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.52	2018-09-01	24
toolshed.g2.bx.psu.edu/repos/peterjc/seq_filter_by_id/seq_filter_by_id/0.2.7	2018-09-01	23
toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/2.2.1.2	2018-09-01	23
toolshed.g2.bx.psu.edu/repos/iuc/vegan_rarefaction/vegan_rarefaction/2.4-3	2018-09-01	23
toolshed.g2.bx.psu.edu/repos/devteam/merge/gops_merge_1/1.0.0	2018-09-01	23
toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/2.0.0	2018-09-01	23
toolshed.g2.bx.psu.edu/repos/iuc/samtools_sort/samtools_sort/1.0.2	2018-09-01	22
toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.34.9.8	2018-09-01	22
toolshed.g2.bx.psu.edu/repos/bgruening/split_file_on_column/tp_split_on_column/0.2	2018-09-01	22
toolshed.g2.bx.psu.edu/repos/rnateam/mafft/rbc_mafft/7.221.3	2018-09-01	22
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_xtandemadapter/XTandemAdapter/2.3.0	2018-09-01	22
toolshed.g2.bx.psu.edu/repos/devteam/fastq_trimmer_by_quality/fastq_quality_trimmer/1.1.1	2018-09-01	22
toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/blastxml_to_tabular/0.3.0	2018-09-01	22
__IMPORT_HISTORY__	2018-09-01	21
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idconflictresolver/IDConflictResolver/2.2.0	2018-09-01	21
toolshed.g2.bx.psu.edu/repos/crs4/prokka/prokka/1.13	2018-09-01	21
toolshed.g2.bx.psu.edu/repos/devteam/bam_to_sam/bam_to_sam/2.0.1	2018-09-01	21
modENCODEworm	2018-09-01	21
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_featurefindermultiplex/FeatureFinderMultiplex/2.2.0	2018-09-01	21
toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.6.0	2018-09-01	21
toolshed.g2.bx.psu.edu/repos/iuc/extract_genomic_dna/Extract genomic DNA 1/3.0.2	2018-09-01	21
toolshed.g2.bx.psu.edu/repos/devteam/merge_cols/mergeCols1/1.0.1	2018-09-01	21
CONVERTER_bam_to_coodinate_sorted_bam	2018-09-01	21
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_proteinquantifier/ProteinQuantifier/2.2.0	2018-09-01	21
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idmapper/IDMapper/2.2.0	2018-09-01	21
CONVERTER_wiggle_to_interval_0	2018-09-01	21
CONVERTER_gff_to_bed_0	2018-09-01	21
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_filefilter/FileFilter/2.3.0	2018-09-01	20
toolshed.g2.bx.psu.edu/repos/rnateam/sortmerna/bg_sortmerna/2.1b.4	2018-09-01	20
CONVERTER_fasta_to_fai	2018-09-01	20
toolshed.g2.bx.psu.edu/repos/bgruening/diamond/bg_diamond/0.8.24.1	2018-09-01	20
toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.39	2018-09-01	20
toolshed.g2.bx.psu.edu/repos/iuc/pygenometracks/pygenomeTracks/2.0.1	2018-09-01	19
toolshed.g2.bx.psu.edu/repos/iuc/qiime_split_libraries_fastq/qiime_split_libraries_fastq/1.9.1.0	2018-09-01	19
toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.20.7.2	2018-09-01	19
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_qccalculator/QCCalculator/2.3.0	2018-09-01	18
toolshed.g2.bx.psu.edu/repos/bebatut/cdhit/cd_hit_protein/1.3	2018-09-01	18
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_decoydatabase/DecoyDatabase/2.3.0	2018-09-01	18
toolshed.g2.bx.psu.edu/repos/devteam/cummerbund_to_tabular/cummerbund_to_cuffdiff/1.0.1	2018-09-01	18
toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.3.1	2018-09-01	18
toolshed.g2.bx.psu.edu/repos/devteam/fastx_barcode_splitter/cshl_fastx_barcode_splitter/1.0.0	2018-09-01	18
toolshed.g2.bx.psu.edu/repos/devteam/bowtie_wrappers/bowtie_wrapper/1.2.0	2018-09-01	18
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicplotviewpoint/hicexplorer_hicplotviewpoint/2.1.4.0	2018-09-01	17
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeSamFiles/2.18.2.1	2018-09-01	17
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SortSam/2.18.2.1	2018-09-01	17
toolshed.g2.bx.psu.edu/repos/eschen42/w4mcorcov/w4mcorcov/0.98.13	2018-09-01	17
toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.12	2018-09-01	17
toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/1.1.2	2018-09-01	17
toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_nn_classifier/sklearn_nn_classifier/0.9	2018-09-01	17
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_mztabexporter/MzTabExporter/2.3.0	2018-09-01	17
toolshed.g2.bx.psu.edu/repos/devteam/samtools_flagstat/samtools_flagstat/1.0.0	2018-09-01	17
toolshed.g2.bx.psu.edu/repos/bgruening/uniprot_rest_interface/uniprot/0.1	2018-09-01	17
toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.3.5	2018-09-01	16
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_windowbed/2.27.0.0	2018-09-01	16
toolshed.g2.bx.psu.edu/repos/iuc/mothur_screen_seqs/mothur_screen_seqs/1.39.5.0	2018-09-01	16
toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.0	2018-09-01	16
toolshed.g2.bx.psu.edu/repos/gbcs-embl-heidelberg/je_demultiplex/je_demultiplex/1.2	2018-09-01	16
toolshed.g2.bx.psu.edu/repos/iuc/metaphlan_hclust_heatmap/metaphlan_hclust_heatmap/2.6.0.0	2018-09-01	16
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_filemerger/FileMerger/2.3.0	2018-09-01	16
toolshed.g2.bx.psu.edu/repos/bgruening/nn_classifier/nn_classifier/0.9	2018-09-01	16
toolshed.g2.bx.psu.edu/repos/iuc/mothur_heatmap_bin/mothur_heatmap_bin/1.39.5.0	2018-09-01	16
toolshed.g2.bx.psu.edu/repos/iuc/fraggenescan/fraggenescan/1.30.0	2018-09-01	16
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_featurefindercentroided/FeatureFinderCentroided/2.3.0	2018-09-01	15
gtf_filter_by_attribute_values_list	2018-09-01	15
toolshed.g2.bx.psu.edu/repos/iuc/trinity/trinity/2.8.3	2018-09-01	15
toolshed.g2.bx.psu.edu/repos/devteam/fastq_to_fasta/cshl_fastq_to_fasta/1.0.0	2018-09-01	15
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_pca/deeptools_plot_pca/3.0.2.0	2018-09-01	15
toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_build_pipeline/sklearn_build_pipeline/0.9	2018-09-01	15
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed/2.27.0.0	2018-09-01	15
__SORTLIST__	2018-09-01	15
toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_bam_stat/2.6.4	2018-09-01	15
toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_interlacer/fastq_paired_end_interlacer/1.2.0.1	2018-09-01	14
toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_tblastn_wrapper/0.1.01	2018-09-01	14
toolshed.g2.bx.psu.edu/repos/devteam/vcftools_annotate/vcftools_annotate/0.1	2018-09-01	14
flexbardsc	2018-09-01	14
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_alignmentsieve/deeptools_alignmentsieve/3.0.2.0	2018-09-01	14
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_textexporter/TextExporter/2.3.0	2018-09-01	14
toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.4	2018-09-01	14
toolshed.g2.bx.psu.edu/repos/earlhaminst/ensembl_get_sequences/get_sequences/0.1.2	2018-09-01	13
toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_tblastx_wrapper/0.3.0	2018-09-01	13
toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/bwa_wrapper/1.2.3	2018-09-01	13
CONVERTER_fasta_to_tabular	2018-09-01	13
toolshed.g2.bx.psu.edu/repos/iuc/transdecoder/transdecoder/3.0.1	2018-09-01	13
raceid3	2018-09-01	13
toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.1.0+galaxy2	2018-09-01	13
genomespace_importer	2018-09-01	13
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.1	2018-09-01	13
CONVERTER_wig_to_bigwig	2018-09-01	13
toolshed.g2.bx.psu.edu/repos/peterjc/mira_assembler/mira_assembler/0.0.11	2018-09-01	13
Count1	2018-09-01	13
toolshed.g2.bx.psu.edu/repos/lecorguille/camera_annotate/abims_CAMERA_annotateDiffreport/2.2.2	2018-09-01	13
toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_fillpeaks/abims_xcms_fillPeaks/2.1.1	2018-09-01	13
toolshed.g2.bx.psu.edu/repos/eschen42/w4mclassfilter/w4mclassfilter/0.98.11	2018-09-01	13
toolshed.g2.bx.psu.edu/repos/rnateam/sortmerna/bg_sortmerna/2.1b.5	2018-09-01	13
toolshed.g2.bx.psu.edu/repos/galaxyp/msconvert/msconvert_nix/3.0.0	2018-09-01	13
toolshed.g2.bx.psu.edu/repos/iuc/mothur_unique_seqs/mothur_unique_seqs/1.39.5.0	2018-09-01	13
toolshed.g2.bx.psu.edu/repos/lparsons/fastq_join/fastq_join/1.1.2-806	2018-09-01	13
toolshed.g2.bx.psu.edu/repos/iuc/datamash_reverse/datamash_reverse/1.1.0	2018-09-01	13
toolshed.g2.bx.psu.edu/repos/iuc/prinseq/prinseq/0.20.4	2018-09-01	13
toolshed.g2.bx.psu.edu/repos/lparsons/fastq_join/fastq_join/1.1.2-806.1	2018-09-01	12
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CASM/2.18.2.1	2018-09-01	12
toolshed.g2.bx.psu.edu/repos/devteam/dna_filtering/histogram_rpy/1.0.3	2018-09-01	12
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1	2018-09-01	12
toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/0.4.4.0	2018-09-01	12
toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_geneBody_coverage/2.6.4.2	2018-09-01	12
toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/0.8.2	2018-09-01	12
toolshed.g2.bx.psu.edu/repos/iuc/gemini_load/gemini_load/0.18.1.0	2018-09-01	12
toolshed.g2.bx.psu.edu/repos/iuc/mothur_corr_axes/mothur_corr_axes/1.36.1.0	2018-09-01	12
toolshed.g2.bx.psu.edu/repos/iuc/mothur_heatmap_sim/mothur_heatmap_sim/1.39.5.0	2018-09-01	12
toolshed.g2.bx.psu.edu/repos/iuc/mothur_nmds/mothur_nmds/1.36.1.0	2018-09-01	12
toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_tblastn_wrapper/0.3.0	2018-09-01	12
toolshed.g2.bx.psu.edu/repos/devteam/fastx_collapser/cshl_fastx_collapser/1.0.0	2018-09-01	12
toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.1	2018-09-01	12
CONVERTER_bed_to_gff_0	2018-09-01	11
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idfileconverter/IDFileConverter/2.3.0	2018-09-01	11
toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_joiner/fastq_paired_end_joiner/2.0.1.1	2018-09-01	11
toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.1.3	2018-09-01	11
toolshed.g2.bx.psu.edu/repos/peterjc/blast_rbh/blast_reciprocal_best_hits/0.1.11	2018-09-01	11
toolshed.g2.bx.psu.edu/repos/iuc/egsea/egsea/1.6.0.1	2018-09-01	11
proteomics_search_interprophet_1	2018-09-01	11
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_pe_fragmentsize/deeptools_bam_pe_fragmentsize/3.0.2.0	2018-09-01	11
toolshed.g2.bx.psu.edu/repos/devteam/ucsc_custom_track/build_ucsc_custom_track_1/1.0.0	2018-09-01	11
toolshed.g2.bx.psu.edu/repos/lparsons/htseq_count/htseq_count/0.6.1galaxy1	2018-09-01	11
toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.1.1.20160309.3	2018-09-01	11
toolshed.g2.bx.psu.edu/repos/iuc/qiime_validate_mapping_file/qiime_validate_mapping_file/1.9.1.0	2018-09-01	11
toolshed.g2.bx.psu.edu/repos/devteam/cuffdiff/cuffdiff/2.2.1.5	2018-09-01	11
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_peakpickerhires/PeakPickerHiRes/2.3.0	2018-09-01	11
toolshed.g2.bx.psu.edu/repos/iuc/qiime_pick_otus/qiime_pick_otus/1.9.1.0	2018-09-01	10
toolshed.g2.bx.psu.edu/repos/iuc/disco/disco/1.2.0	2018-09-01	10
toolshed.g2.bx.psu.edu/repos/bjoern-gruening/sed_wrapper/sed_stream_editor/0.0.1	2018-09-01	10
toolshed.g2.bx.psu.edu/repos/iuc/mothur_rarefaction_single/mothur_rarefaction_single/1.39.5.0	2018-09-01	10
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/1.136.0	2018-09-01	10
genomespace_exporter	2018-09-01	10
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_uniq_tool/1.1.1	2018-09-01	10
toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.6.1.1	2018-09-01	10
toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.19.3.3	2018-09-01	10
toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpSift_filter/3.4	2018-09-01	10
CONVERTER_interval_to_bed6_0	2018-09-01	10
toolshed.g2.bx.psu.edu/repos/devteam/principal_component_analysis/pca1/1.0.2	2018-09-01	10
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.0.0	2018-09-01	10
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_nucbed/2.27.0.1	2018-09-01	10
toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_contigs/mothur_make_contigs/1.39.5.0	2018-09-01	10
toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpsift_vartype/4.3+t.galaxy0	2018-09-01	9
toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/2.8.1.3	2018-09-01	9
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_unionbedgraph/2.27.0.0	2018-09-01	9
toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_shared/mothur_make_shared/1.39.5.0	2018-09-01	9
toolshed.g2.bx.psu.edu/repos/iuc/mothur_count_seqs/mothur_count_seqs/1.39.5.0	2018-09-01	9
toolshed.g2.bx.psu.edu/repos/bgruening/chemical_data_sources/ctb_online_data_fetch/0.2	2018-09-01	9
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_qcexporter/QCExporter/2.3.0	2018-09-01	9
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/2.5.7.0	2018-09-01	9
toolshed.g2.bx.psu.edu/repos/iuc/qiime_pick_closed_reference_otus/qiime_pick_closed_reference_otus/1.9.1.0	2018-09-01	9
toolshed.g2.bx.psu.edu/repos/devteam/clustalw/clustalw/2.1	2018-09-01	9
toolshed.g2.bx.psu.edu/repos/bgruening/racon/racon/1.3.1	2018-09-01	9
toolshed.g2.bx.psu.edu/repos/iuc/enasearch_search_data/enasearch_search_data/0.1.1.0	2018-09-01	8
toolshed.g2.bx.psu.edu/repos/galaxyp/msconvert/msconvert_win/3.0.0	2018-09-01	8
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_heatmap/deeptools_plot_heatmap/3.0.1.0	2018-09-01	8
toolshed.g2.bx.psu.edu/repos/rnateam/viennarna_rnafold/viennarna_rnafold/2.2.10.4	2018-09-01	8
toolshed.g2.bx.psu.edu/repos/bgruening/openbabel/ctb_compound_convert/0.1	2018-09-01	8
toolshed.g2.bx.psu.edu/repos/iuc/hmmer3/hmmer_hmmbuild/0.1.0	2018-09-01	8
toolshed.g2.bx.psu.edu/repos/bgruening/diffbind/diffbind/2.6.6.4	2018-09-01	8
toolshed.g2.bx.psu.edu/repos/iuc/pureclip/pureclip/1.0.4	2018-09-01	8
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.7.1.1	2018-09-01	8
toolshed.g2.bx.psu.edu/repos/iuc/mothur_classify_otu/mothur_classify_otu/1.39.5.0	2018-09-01	8
toolshed.g2.bx.psu.edu/repos/bgruening/uniprot_rest_interface/uniprot/0.2	2018-09-01	8
toolshed.g2.bx.psu.edu/repos/iuc/hmmer3/hmmer_hmmsearch/0.1.0	2018-09-01	8
toolshed.g2.bx.psu.edu/repos/iuc/charts/charts/1.0.1	2018-09-01	8
toolshed.g2.bx.psu.edu/repos/iuc/nonpareil/nonpareil/3.1.1.0	2018-09-01	8
toolshed.g2.bx.psu.edu/repos/iuc/bctools_extract_crosslinked_nucleotides/bctools_extract_crosslinked_nucleotides/0.2.1	2018-09-01	8
toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3r.1	2018-09-01	8
toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0	2018-09-01	8
toolshed.g2.bx.psu.edu/repos/ethevenot/qualitymetrics/quality_metrics/2.2.8	2018-09-01	8
proteomics_search_protein_prophet_1	2018-09-01	8
wiggle2simple1	2018-09-01	7
toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.3	2018-09-01	7
toolshed.g2.bx.psu.edu/repos/galaxyp/reactome_pathwaymatcher/reactome_pathwaymatcher/1.8.1.2	2018-09-01	7
toolshed.g2.bx.psu.edu/repos/saskia-hiltemann/krona_text/krona-text/1	2018-09-01	7
toolshed.g2.bx.psu.edu/repos/galaxyp/dbbuilder/dbbuilder/0.3.0	2018-09-01	7
toolshed.g2.bx.psu.edu/repos/iuc/qiime_align_seqs/qiime_align_seqs/1.9.1.0	2018-09-01	7
toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.1	2018-09-01	7
toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_merge/xcms_merge/1.1.0	2018-09-01	7
toolshed.g2.bx.psu.edu/repos/iuc/dexseq/dexseq/1.24.0.0	2018-09-01	7
toolshed.g2.bx.psu.edu/repos/iuc/gemini_recessive_and_dominant/gemini_recessive_and_dominant/0.18.1.0	2018-09-01	7
CONVERTER_vcf_to_vcf_bgzip_0	2018-09-01	7
toolshed.g2.bx.psu.edu/repos/iuc/mothur_pre_cluster/mothur_pre_cluster/1.39.5.0	2018-09-01	7
gene2exon1	2018-09-01	7
toolshed.g2.bx.psu.edu/repos/galaxyp/msi_combine/mass_spectrometry_imaging_combine/1.10.0.4	2018-09-01	7
toolshed.g2.bx.psu.edu/repos/iuc/mothur_pcoa/mothur_pcoa/1.39.5.0	2018-09-01	7
toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/peptide_shaker/1.11.0	2018-09-01	7
CONVERTER_vcf_bgzip_to_tabix_0	2018-09-01	7
toolshed.g2.bx.psu.edu/repos/iuc/gemini_de_novo/gemini_de_novo/0.18.1.0	2018-09-01	7
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectRnaSeqMetrics/2.18.2.1	2018-09-01	7
toolshed.g2.bx.psu.edu/repos/iuc/mothur_chimera_vsearch/mothur_chimera_vsearch/1.39.5.1	2018-09-01	7
toolshed.g2.bx.psu.edu/repos/devteam/cuffnorm/cuffnorm/2.2.1.2	2018-09-01	7
toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_data_preprocess/sklearn_data_preprocess/0.9	2018-09-01	7
toolshed.g2.bx.psu.edu/repos/iuc/seurat/seurat/2.3.4	2018-09-01	7
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hiccorrectmatrix/hicexplorer_hiccorrectmatrix/2.1.2.0	2018-09-01	6
toolshed.g2.bx.psu.edu/repos/iuc/mothur_homova/mothur_homova/1.36.1.0	2018-09-01	6
toolshed.g2.bx.psu.edu/repos/rnateam/viennarna_rnaplot/viennarna_rnaplot/2.2.10.0	2018-09-01	6
toolshed.g2.bx.psu.edu/repos/iuc/qiime_pick_open_reference_otus/qiime_pick_open_reference_otus/1.9.1.0	2018-09-01	6
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddOrReplaceReadGroups/2.18.2.1	2018-09-01	6
toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/search_gui/3.2.13.3	2018-09-01	6
toolshed.g2.bx.psu.edu/repos/iuc/mothur_remove_seqs/mothur_remove_seqs/1.36.1.0	2018-09-01	6
toolshed.g2.bx.psu.edu/repos/iuc/mothur_filter_seqs/mothur_filter_seqs/1.39.5.0	2018-09-01	6
CONVERTER_bam_to_bigwig_0	2018-09-01	6
toolshed.g2.bx.psu.edu/repos/iuc/pilon/pilon/1.20.1	2018-09-01	6
toolshed.g2.bx.psu.edu/repos/earlhaminst/ensembl_get_feature_info/get_feature_info/0.1.2	2018-09-01	6
toolshed.g2.bx.psu.edu/repos/melpetera/batchcorrection/Determine_BC/2.1.2	2018-09-01	6
toolshed.g2.bx.psu.edu/repos/iuc/mothur_cluster_split/mothur_cluster_split/1.39.5.0	2018-09-01	6
toolshed.g2.bx.psu.edu/repos/iuc/mothur_taxonomy_to_krona/mothur_taxonomy_to_krona/1.0	2018-09-01	6
toolshed.g2.bx.psu.edu/repos/iuc/mothur_amova/mothur_amova/1.36.1.0	2018-09-01	6
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_consensusid/ConsensusID/2.2.0	2018-09-01	6
bed2gff1	2018-09-01	6
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_featurefindermultiplex/FeatureFinderMultiplex/2.3.0	2018-09-01	6
toolshed.g2.bx.psu.edu/repos/iuc/mothur_heatmap_sim/mothur_heatmap_sim/1.36.1.0	2018-09-01	6
toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread/2.2.1.1	2018-09-01	6
toolshed.g2.bx.psu.edu/repos/devteam/samtools_split/samtools_split/1.3.1	2018-09-01	6
toolshed.g2.bx.psu.edu/repos/devteam/fastx_trimmer/cshl_fastx_trimmer/1.0.0	2018-09-01	6
toolshed.g2.bx.psu.edu/repos/iuc/mothur_pcoa/mothur_pcoa/1.36.1.0	2018-09-01	6
toolshed.g2.bx.psu.edu/repos/iuc/mothur_tree_shared/mothur_tree_shared/1.36.1.0	2018-09-01	6
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicplotdistvscounts/hicexplorer_hicplotdistvscounts/2.1.4.0	2018-09-01	6
toolshed.g2.bx.psu.edu/repos/iuc/mothur_parsimony/mothur_parsimony/1.36.1.0	2018-09-01	6
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_featurefindermetabo/FeatureFinderMetabo/2.3.0	2018-09-01	6
toolshed.g2.bx.psu.edu/repos/iuc/qiime_make_otu_heatmap/qiime_make_otu_heatmap/1.9.1.0	2018-09-01	6
toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/fasta_compute_length/1.0.1	2018-09-01	6
toolshed.g2.bx.psu.edu/repos/iuc/goseq/goseq/0.2.2	2018-09-01	6
toolshed.g2.bx.psu.edu/repos/peterjc/venn_list/venn_list/0.0.11	2018-09-01	6
toolshed.g2.bx.psu.edu/repos/devteam/fastx_nucleotides_distribution/cshl_fastx_nucleotides_distribution/1.0.1	2018-09-01	6
toolshed.g2.bx.psu.edu/repos/bgruening/join_files_on_column_fuzzy/join_files_on_column_fuzzy/1.0.0	2018-09-01	6
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SortSam/2.7.1.1	2018-09-01	5
gff2bed1	2018-09-01	5
toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/search_gui/2.9.0	2018-09-01	5
toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fastq/tabular_to_fastq/1.1.1	2018-09-01	5
toolshed.g2.bx.psu.edu/repos/galaxyp/msi_preprocessing/mass_spectrometry_imaging_preprocessing/1.10.0.4	2018-09-01	5
toolshed.g2.bx.psu.edu/repos/peterjc/blast2go/blast2go/0.0.9	2018-09-01	5
toolshed.g2.bx.psu.edu/repos/devteam/vcffilter/vcffilter2/0.0.3	2018-09-01	5
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_randombed/2.27.0.0	2018-09-01	5
toolshed.g2.bx.psu.edu/repos/iuc/trinity_abundance_estimates_to_matrix/trinity_abundance_estimates_to_matrix/2.8.3	2018-09-01	5
toolshed.g2.bx.psu.edu/repos/iuc/mothur_sub_sample/mothur_sub_sample/1.39.5.0	2018-09-01	5
toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_heatmap2/ggplot2_heatmap2/2.2.1+galaxy1	2018-09-01	5
CONVERTER_ref_to_seq_taxomony	2018-09-01	5
toolshed.g2.bx.psu.edu/repos/devteam/xy_plot/XY_Plot_1/1.0.2	2018-09-01	5
toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_mergefa/1.2.0	2018-09-01	5
toolshed.g2.bx.psu.edu/repos/devteam/cuffquant/cuffquant/2.2.1.1	2018-09-01	5
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idmerger/IDMerger/2.2.0	2018-09-01	5
toolshed.g2.bx.psu.edu/repos/bgruening/openbabel/ctb_change_title/0.0.1	2018-09-01	5
toolshed.g2.bx.psu.edu/repos/devteam/bamtools_split/bamSplit/2.4.0	2018-09-01	5
toolshed.g2.bx.psu.edu/repos/iuc/mothur_classify_seqs/mothur_classify_seqs/1.39.5.0	2018-09-01	5
toolshed.g2.bx.psu.edu/repos/bgruening/column_arrange_by_header/bg_column_arrange_by_header/0.1	2018-09-01	5
toolshed.g2.bx.psu.edu/repos/iuc/bp_genbank2gff3/bp_genbank2gff3/1.0	2018-09-01	5
methtools_calling	2018-09-01	5
toolshed.g2.bx.psu.edu/repos/blankenberg/naive_variant_caller/naive_variant_caller/0.0.3	2018-09-01	5
toolshed.g2.bx.psu.edu/repos/devteam/fastx_quality_statistics/cshl_fastx_quality_statistics/1.0.0	2018-09-01	5
toolshed.g2.bx.psu.edu/repos/devteam/cuffmerge/cuffmerge/2.2.1.1	2018-09-01	5
toolshed.g2.bx.psu.edu/repos/iuc/ncbi_eutils_efetch/ncbi_eutils_efetch/1.1	2018-09-01	5
toolshed.g2.bx.psu.edu/repos/iuc/qiime_extract_barcodes/qiime_extract_barcodes/1.9.1.0	2018-09-01	5
foldchange_heatmap	2018-09-01	5
toolshed.g2.bx.psu.edu/repos/iuc/qiime_multiple_split_libraries_fastq/qiime_multiple_split_libraries_fastq/1.9.1.0	2018-09-01	5
toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/2.9.1.3	2018-09-01	4
convert_bc_to_binary_RY.py	2018-09-01	4
toolshed.g2.bx.psu.edu/repos/tgac/miranda/miranda/3.3a	2018-09-01	4
toolshed.g2.bx.psu.edu/repos/rnateam/splitfasta/rbc_splitfasta/0.2.0	2018-09-01	4
toolshed.g2.bx.psu.edu/repos/rnateam/peakachu/peakachu/0.1.0.1	2018-09-01	4
toolshed.g2.bx.psu.edu/repos/rnateam/mirdeep2/rbc_mirdeep2/2.0.0	2018-09-01	4
toolshed.g2.bx.psu.edu/repos/rnateam/mirdeep2_mapper/rbc_mirdeep2_mapper/2.0.0	2018-09-01	4
CONVERTER_gff_to_fli_0	2018-09-01	4
CONVERTER_gff_to_interval_index_0	2018-09-01	4
toolshed.g2.bx.psu.edu/repos/rnateam/blockclust/blockclust/1.0.0	2018-09-01	4
toolshed.g2.bx.psu.edu/repos/rnateam/blockbuster/blockbuster/0.1.1.1	2018-09-01	4
CONVERTER_interval_to_bigwig_0	2018-09-01	4
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flexbar_split_RR_bcs	2018-09-01	4
toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie_merge/1.3.4	2018-09-01	4
toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/1.3.3.1	2018-09-01	4
r_correlation_matrix	2018-09-01	4
toolshed.g2.bx.psu.edu/repos/iuc/stacks_procrad/stacks_procrad/1.46.0	2018-09-01	4
toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpSift_annotate/3.4	2018-09-01	4
toolshed.g2.bx.psu.edu/repos/anton/vcfallelicprimitives/vcfallelicprimitives/0.0.1	2018-09-01	4
toolshed.g2.bx.psu.edu/repos/iuc/shovill/shovill/0.9.0	2018-09-01	4
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/2.4.1.0	2018-09-01	4
toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.4.0d-2	2018-09-01	4
toolshed.g2.bx.psu.edu/repos/iuc/raceid_main/raceid_main/1.0.0	2018-09-01	4
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/deeptools_compute_matrix/3.0.1.0	2018-09-01	4
toolshed.g2.bx.psu.edu/repos/iuc/qiime_make_phylogeny/qiime_make_phylogeny/1.9.1.0	2018-09-01	4
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_heatmap/deeptools_plot_heatmap/2.5.1.1.0	2018-09-01	4
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_pca/deeptools_plot_pca/3.1.2.0.0	2018-09-01	4
toolshed.g2.bx.psu.edu/repos/iuc/mothur_remove_rare/mothur_remove_rare/1.39.5.0	2018-09-01	4
toolshed.g2.bx.psu.edu/repos/iuc/mothur_remove_lineage/mothur_remove_lineage/1.39.5.0	2018-09-01	4
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicsummatrices/hicexplorer_hicsummatrices/2.1.2.0	2018-09-01	4
toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_biom/mothur_make_biom/1.39.5.0	2018-09-01	4
toolshed.g2.bx.psu.edu/repos/iuc/mothur_list_otulabels/mothur_list_otulabels/1.39.5.0	2018-09-01	4
toolshed.g2.bx.psu.edu/repos/bgruening/nucleosome_prediction/Nucleosome/3.0	2018-09-01	4
toolshed.g2.bx.psu.edu/repos/iuc/mothur_count_groups/mothur_count_groups/1.39.5.0	2018-09-01	4
toolshed.g2.bx.psu.edu/repos/iuc/mothur_align_seqs/mothur_align_seqs/1.39.5.0	2018-09-01	4
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_multijoin_tool/1.1.1	2018-09-01	4
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.0	2018-09-01	4
toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_predictd/2.1.1.20160309.0	2018-09-01	4
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_unfold_column_tool/1.1.1	2018-09-01	4
toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.4.2	2018-09-01	4
toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/0.7.0.3	2018-09-01	4
toolshed.g2.bx.psu.edu/repos/iuc/gatk2/gatk2_depth_of_coverage/2.8.0	2018-09-01	4
toolshed.g2.bx.psu.edu/repos/devteam/fastq_stats/fastq_stats/1.1.1	2018-09-01	4
toolshed.g2.bx.psu.edu/repos/devteam/fastx_nucleotides_distribution/cshl_fastx_nucleotides_distribution/1.0.0	2018-09-01	4
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.27.0.1	2018-09-01	4
toolshed.g2.bx.psu.edu/repos/devteam/freebayes_wrapper/freebayes_wrapper/0.5.0	2018-09-01	4
toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/0.8.1+galaxy0	2018-09-01	4
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicatesWithMateCigar/2.18.2.1	2018-09-01	4
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_msgfplusadapter/MSGFPlusAdapter/2.2.0	2018-09-01	4
toolshed.g2.bx.psu.edu/repos/devteam/samtools_bedcov/samtools_bedcov/2.0.1	2018-09-01	4
toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/0.0.1	2018-09-01	4
toolshed.g2.bx.psu.edu/repos/devteam/samtools_rmdup/samtools_rmdup/2.0	2018-09-01	4
toolshed.g2.bx.psu.edu/repos/devteam/varscan_version_2/varscan/0.1	2018-09-01	4
toolshed.g2.bx.psu.edu/repos/bgruening/bismark/bismark_bowtie2/0.16.3	2018-09-01	3
toolshed.g2.bx.psu.edu/repos/iuc/filtlong/filtlong/0.2.0	2018-09-01	3
toolshed.g2.bx.psu.edu/repos/iuc/enasearch_retrieve_run_report/enasearch_retrieve_run_report/0.1.1.0	2018-09-01	3
toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/1.2.5	2018-09-01	3
toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0.2	2018-09-01	3
toolshed.g2.bx.psu.edu/repos/iuc/gemini/gemini_load/0.10.1.0	2018-09-01	3
toolshed.g2.bx.psu.edu/repos/iuc/mothur_rarefaction_shared/mothur_rarefaction_shared/1.39.5.0	2018-09-01	3
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicsummatrices/hicexplorer_hicsummatrices/2.1.4.0	2018-09-01	3
biomart	2018-09-01	3
toolshed.g2.bx.psu.edu/repos/nml/spades/spades/1.2	2018-09-01	3
toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sra_pileup/2.8.1.2	2018-09-01	3
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FastqToSam/2.18.2.1	2018-09-01	3
toolshed.g2.bx.psu.edu/repos/iuc/fasttree/fasttree/2.1.10	2018-09-01	3
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtoigv/2.27.0.0	2018-09-01	3
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.1	2018-09-01	3
toolshed.g2.bx.psu.edu/repos/iuc/qiime_summarize_taxa_through_plots/qiime_summarize_taxa_through_plots/1.9.1.0	2018-09-01	3
toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy1	2018-09-01	3
toolshed.g2.bx.psu.edu/repos/devteam/complement/gops_complement_1/1.0.0	2018-09-01	3
proteomics_search_peptide_prophet_1	2018-09-01	3
toolshed.g2.bx.psu.edu/repos/devteam/fasta_formatter/cshl_fasta_formatter/1.0.0	2018-09-01	3
bg_statistical_hypothesis_testing	2018-09-01	3
toolshed.g2.bx.psu.edu/repos/iuc/qiime_multiple_join_paired_ends/qiime_multiple_join_paired_ends/1.9.1.0	2018-09-01	3
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_flankbed/2.27.0.0	2018-09-01	3
toolshed.g2.bx.psu.edu/repos/iuc/xpath/xpath/1.0.0	2018-09-01	3
toolshed.g2.bx.psu.edu/repos/iuc/roary/roary/3.10.2	2018-09-01	3
toolshed.g2.bx.psu.edu/repos/iuc/pick_open_reference_otus/pick_open_reference_otus/1.9.1.0	2018-09-01	3
toolshed.g2.bx.psu.edu/repos/eschen42/w4mjoinpn/w4mjoinpn/0.98.2	2018-09-01	3
toolshed.g2.bx.psu.edu/repos/iuc/mothur_get_oturep/mothur_get_oturep/1.39.5.0	2018-09-01	3
toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_compound_convert/openbabel_compound_convert/2.4.1.0	2018-09-01	3
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_closestbed/2.27.0.0	2018-09-01	3
toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.34.9.7	2018-09-01	3
toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_tin/2.6.4.1	2018-09-01	3
toolshed.g2.bx.psu.edu/repos/iuc/khmer_abundance_distribution_single/khmer_abundance_distribution_single/2.0.0	2018-09-01	3
toolshed.g2.bx.psu.edu/repos/devteam/vcfallelicprimitives/vcfallelicprimitives/1.0.0_rc1.0	2018-09-01	3
toolshed.g2.bx.psu.edu/repos/galaxyp/fasta_merge_files_and_filter_unique_sequences/fasta_merge_files_and_filter_unique_sequences/1.2.0	2018-09-01	3
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toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multiintersectbed/2.27.0.0	2018-09-01	3
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_seedlistgenerator/SeedListGenerator/2.3.0	2018-09-01	3
toolshed.g2.bx.psu.edu/repos/galaxyp/msconvert_nix/msconvert_nix/3.0.9992.0	2018-09-01	3
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CleanSam/2.18.2.1	2018-09-01	3
toolshed.g2.bx.psu.edu/repos/iuc/pick_closed_reference_otus/pick_closed_reference_otus/1.9.1.0	2018-09-01	3
toolshed.g2.bx.psu.edu/repos/devteam/fastq_to_fasta/cshl_fastq_to_fasta/1.0.2	2018-09-01	3
toolshed.g2.bx.psu.edu/repos/bgruening/find_subsequences/bg_find_subsequences/0.2	2018-09-01	3
toolshed.g2.bx.psu.edu/repos/iuc/mothur_summary_seqs/mothur_summary_seqs/1.36.1.0	2018-09-01	3
CONVERTER_sam_to_bigwig_0	2018-09-01	3
Extract_features1	2018-09-01	3
toolshed.g2.bx.psu.edu/repos/iuc/qiime_count_seqs/qiime_count_seqs/1.9.1.0	2018-09-01	3
toolshed.g2.bx.psu.edu/repos/iuc/ncbi_eutils_ecitmatch/ncbi_eutils_ecitmatch/1.1	2018-09-01	3
toolshed.g2.bx.psu.edu/repos/wolma/mimodd_main/mimodd_convert/0.1.8_1	2018-09-01	3
toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: shuffleseq87/5.0.0.1	2018-09-01	3
toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.1.4	2018-09-01	3
toolshed.g2.bx.psu.edu/repos/iuc/snpsift_dbnsfp/snpSift_dbnsfp/4.3.0	2018-09-01	3
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/deeptools_compute_matrix/2.5.7.0	2018-09-01	3
smooth_running_window	2018-09-01	3
toolshed.g2.bx.psu.edu/repos/bgruening/antismash/antismash/4.1	2018-09-01	3
toolshed.g2.bx.psu.edu/repos/nick/allele_counts/allele_counts_1/1.2	2018-09-01	3
toolshed.g2.bx.psu.edu/repos/iuc/mothur_dist_shared/mothur_dist_shared/1.39.5.0	2018-09-01	2
toolshed.g2.bx.psu.edu/repos/bgruening/bismark/bismark_methylation_extractor/0.16.3	2018-09-01	2
toolshed.g2.bx.psu.edu/repos/bgruening/sailfish/sailfish/0.10.1.1	2018-09-01	2
toolshed.g2.bx.psu.edu/repos/iuc/mothur_dist_seqs/mothur_dist_seqs/1.39.5.0	2018-09-01	2
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_BamIndexStats/1.56.0	2018-09-01	2
toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_model_validation/sklearn_model_validation/0.9	2018-09-01	2
toolshed.g2.bx.psu.edu/repos/devteam/picard/PicardASMetrics/1.56.0	2018-09-01	2
methtools_dmr	2018-09-01	2
toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_numeric_clustering/sklearn_numeric_clustering/0.9	2018-09-01	2
toolshed.g2.bx.psu.edu/repos/iuc/mothur_count_groups/mothur_count_groups/1.36.1.0	2018-09-01	2
toolshed.g2.bx.psu.edu/repos/devteam/fastx_reverse_complement/cshl_fastx_reverse_complement/1.0.0	2018-09-01	2
toolshed.g2.bx.psu.edu/repos/iuc/mothur_biom_info/mothur_biom_info/1.39.5.0	2018-09-01	2
toolshed.g2.bx.psu.edu/repos/iuc/ucsc_fasplit/fasplit/357	2018-09-01	2
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.1	2018-09-01	2
toolshed.g2.bx.psu.edu/repos/galaxyp/uniprotxml_downloader/uniprotxml_downloader/2.0.0	2018-09-01	2
toolshed.g2.bx.psu.edu/repos/devteam/scatterplot/scatterplot_rpy/1.0.0	2018-09-01	2
toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/0.5.3.2	2018-09-01	2
toolshed.g2.bx.psu.edu/repos/iuc/valet/valet/1.0.0	2018-09-01	2
toolshed.g2.bx.psu.edu/repos/iuc/varscan_mpileup/varscan_mpileup/2.4.3.0	2018-09-01	2
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ValidateSamFile/2.18.2.1	2018-09-01	2
toolshed.g2.bx.psu.edu/repos/iuc/qiime_summarize_taxa/qiime_summarize_taxa/1.9.1.0	2018-09-01	2
toolshed.g2.bx.psu.edu/repos/iuc/vegan_diversity/vegan_diversity/2.4-3	2018-09-01	2
toolshed.g2.bx.psu.edu/repos/iuc/megahit/megahit/1.1.2.2	2018-09-01	2
toolshed.g2.bx.psu.edu/repos/iuc/vsearch/vsearch_clustering/2.8.3.0	2018-09-01	2
gff_filter_by_feature_count	2018-09-01	2
toolshed.g2.bx.psu.edu/repos/iuc/qiime_split_libraries/qiime_split_libraries/1.9.1.0	2018-09-01	2
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.0	2018-09-01	2
toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_bdgpeakcall/2.1.1.20160309.0	2018-09-01	2
CONVERTER_fasta_to_len	2018-09-01	2
genbank_to_gff	2018-09-01	2
toolshed.g2.bx.psu.edu/repos/iuc/length_and_gc_content/length_and_gc_content/0.1.1	2018-09-01	2
toolshed.g2.bx.psu.edu/repos/devteam/fastq_stats/fastq_stats/1.0.0	2018-09-01	2
toolshed.g2.bx.psu.edu/repos/iuc/intervene/intervene_upset/0.6.4	2018-09-01	2
toolshed.g2.bx.psu.edu/repos/bgruening/wtdbg/wtdbg/1.2.8.1	2018-09-01	2
toolshed.g2.bx.psu.edu/repos/iuc/ncbi_eutils_esearch/ncbi_eutils_esearch/1.1	2018-09-01	2
toolshed.g2.bx.psu.edu/repos/bonsai/sortmerna/merged_paired_reads_wrapper/1.0	2018-09-01	2
toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy_core/3.2	2018-09-01	2
toolshed.g2.bx.psu.edu/repos/iuc/ebi_search_rest_results/ebi_search_rest_results/0.1.1	2018-09-01	2
toolshed.g2.bx.psu.edu/repos/iuc/ruvseq/ruvseq/1.12.0	2018-09-01	2
toolshed.g2.bx.psu.edu/repos/bonsai/sortmerna/sortmerna_wrapper/1.0	2018-09-01	2
toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: tranalign100/5.0.0	2018-09-01	2
toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.0.5.2	2018-09-01	2
toolshed.g2.bx.psu.edu/repos/crs4/edena/edena_ovl_wrapper/0.3	2018-09-01	2
toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/1.0.1	2018-09-01	2
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_profile/deeptools_plot_profile/2.5.1.1.0	2018-09-01	2
toolshed.g2.bx.psu.edu/repos/devteam/varscan_version_2/varscan/2.4.2	2018-09-01	2
barchart_gnuplot	2018-09-01	2
bg_protein_properties	2018-09-01	2
toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_violin/ggplot2_violin/2.2.1	2018-09-01	2
toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: getorf42/5.0.0.1	2018-09-01	2
toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_pca/ggplot2_pca/2.2.1	2018-09-01	2
toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.5.0	2018-09-01	2
toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.1.0.46-0	2018-09-01	2
toolshed.g2.bx.psu.edu/repos/iuc/qiime_collapse_samples/qiime_collapse_samples/1.9.1.0	2018-09-01	2
echo_main_env	2018-09-01	2
toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.2.2	2018-09-01	2
toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.2.0	2018-09-01	2
toolshed.g2.bx.psu.edu/repos/iuc/qiime_alpha_diversity/qiime_alpha_diversity/1.9.1.0	2018-09-01	2
toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_quality/2.6.4	2018-09-01	2
toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: etandem33/5.0.0.1	2018-09-01	2
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_coverage/deeptools_plot_coverage/3.0.2.0	2018-09-01	2
toolshed.g2.bx.psu.edu/repos/iuc/mothur_venn/mothur_venn/1.39.5.0	2018-09-01	2
toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/1.0	2018-09-01	2
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed/2.24.0	2018-09-01	2
toolshed.g2.bx.psu.edu/repos/iuc/gemini_comp_hets/gemini_comp_hets/0.18.1.0	2018-09-01	2
toolshed.g2.bx.psu.edu/repos/devteam/fastx_clipper/cshl_fastx_clipper/1.0.1	2018-09-01	2
toolshed.g2.bx.psu.edu/repos/devteam/cuffcompare/cuffcompare/2.2.1.1	2018-09-01	2
toolshed.g2.bx.psu.edu/repos/devteam/data_manager_build_kraken_database/kraken_database_builder/1.1	2018-09-01	2
toolshed.g2.bx.psu.edu/repos/bgruening/crispr_recognition_tool/crispr_recognition_tool/1.2.0	2018-09-01	2
toolshed.g2.bx.psu.edu/repos/iuc/mothur_unique_seqs/mothur_unique_seqs/1.36.1.0	2018-09-01	2
toolshed.g2.bx.psu.edu/repos/iuc/flash/flash/1.2.11.3	2018-09-01	2
toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/1.6.3	2018-09-01	2
CONVERTER_len_to_linecount	2018-09-01	2
toolshed.g2.bx.psu.edu/repos/devteam/vcftools_isec/vcftools_isec/0.1.1	2018-09-01	2
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_expandbed/2.27.0.0	2018-09-01	2
toolshed.g2.bx.psu.edu/repos/iuc/mothur_tree_shared/mothur_tree_shared/1.39.5.0	2018-09-01	2
toolshed.g2.bx.psu.edu/repos/wolma/mimodd_main/mimodd_varcall/0.1.8_1	2018-09-01	2
toolshed.g2.bx.psu.edu/repos/wolma/mimodd_main/mimodd_map/0.1.8_1	2018-09-01	2
toolshed.g2.bx.psu.edu/repos/devteam/sam_bitwise_flag_filter/sam_bw_filter/1.0.0	2018-09-01	2
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_qcextractor/QCExtractor/2.3.0	2018-09-01	2
toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_download/4.3r.1	2018-09-01	2
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hiccorrectmatrix/hicexplorer_hiccorrectmatrix/1.7.1.0	2018-09-01	2
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hiccorrectmatrix/hicexplorer_hiccorrectmatrix/2.0.0	2018-09-01	2
toolshed.g2.bx.psu.edu/repos/iuc/qiime_make_otu_table/qiime_make_otu_table/1.9.1.0	2018-09-01	2
toolshed.g2.bx.psu.edu/repos/iuc/mothur_screen_seqs/mothur_screen_seqs/1.36.1.0	2018-09-01	2
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicpca/hicexplorer_hicpca/2.1.2.0	2018-09-01	2
toolshed.g2.bx.psu.edu/repos/iuc/mothur_rarefaction_single/mothur_rarefaction_single/1.36.1.0	2018-09-01	2
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FixMateInformation/2.18.2.1	2018-09-01	2
toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_shared/mothur_make_shared/1.36.1.0	2018-09-01	2
toolshed.g2.bx.psu.edu/repos/iuc/stacks_denovomap/stacks_denovomap/1.46.0	2018-09-01	2
toolshed.g2.bx.psu.edu/repos/bgruening/interproscan5/interproscan/5.0.0	2018-09-01	2
toolshed.g2.bx.psu.edu/repos/bgruening/lighter/lighter/1.0	2018-09-01	2
toolshed.g2.bx.psu.edu/repos/iuc/data_manager_star_index_builder/rna_star_index_builder_data_manager/0.0.4	2018-09-01	2
toolshed.g2.bx.psu.edu/repos/bgruening/minced/minced/0.1.5	2018-09-01	2
toolshed.g2.bx.psu.edu/repos/bgruening/nanopolish_eventalign/nanopolish_eventalign/0.1.0	2018-09-01	2
toolshed.g2.bx.psu.edu/repos/bgruening/openbabel/ctb_remIons/1.0	2018-09-01	2
toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/4.5	2018-09-01	2
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectInsertSizeMetrics/2.18.2.1	2018-09-01	2
toolshed.g2.bx.psu.edu/repos/bgruening/protein_properties/bg_protein_properties/0.1.0	2018-09-01	2
mosaik_wrapper	2018-09-01	2
CONVERTER_bed_to_bgzip_0	2018-09-01	2
toolshed.g2.bx.psu.edu/repos/bgruening/replace_column_by_key_value_file/replace_column_with_key_value_file/0.1	2018-09-01	2
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_qccalculator/QCCalculator/2.2.0	2018-09-01	1
toolshed.g2.bx.psu.edu/repos/iuc/qiime_beta_diversity_through_plots/qiime_beta_diversity_through_plots/1.9.1.0	2018-09-01	1
toolshed.g2.bx.psu.edu/repos/iuc/qiime_core_diversity/qiime_core_diversity/1.9.1.0	2018-09-01	1
toolshed.g2.bx.psu.edu/repos/iuc/qiime_filter_otus_from_otu_table/qiime_filter_otus_from_otu_table/1.9.1.0	2018-09-01	1
toolshed.g2.bx.psu.edu/repos/galaxyp/openms_mapstatistics/MapStatistics/2.3.0	2018-09-01	1
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_estimatereadfiltering/deeptools_estimatereadfiltering/3.0.2.0	2018-09-01	1
toolshed.g2.bx.psu.edu/repos/iuc/qiime_upgma_cluster/qiime_upgma_cluster/1.9.1.0	2018-09-01	1
toolshed.g2.bx.psu.edu/repos/wolma/mimodd_main/mimodd_varreport/0.1.8_1	2018-09-01	1
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/deeptools_compute_matrix/2.5.1.1.0	2018-09-01	1
toolshed.g2.bx.psu.edu/repos/iuc/qiime_plot_taxa_summary/qiime_plot_taxa_summary/1.9.1.0	2018-09-01	1
toolshed.g2.bx.psu.edu/repos/iuc/qiime_pick_rep_set/qiime_pick_rep_set/1.9.1.0	2018-09-01	1
chromatra_l	2018-09-01	1
toolshed.g2.bx.psu.edu/repos/wolma/mimodd_main/mimodd_varextract/0.1.8_1	2018-09-01	1
toolshed.g2.bx.psu.edu/repos/wolma/mimodd_main/mimodd_sort/0.1.8_1	2018-09-01	1
toolshed.g2.bx.psu.edu/repos/devteam/fastx_clipper/cshl_fastx_clipper/1.0.3	2018-09-01	1
toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_deinterlacer/fastq_paired_end_deinterlacer/1.1.2	2018-09-01	1
toolshed.g2.bx.psu.edu/repos/devteam/fastq_manipulation/fastq_manipulation/1.1.1	2018-09-01	1
toolshed.g2.bx.psu.edu/repos/rnateam/structure_to_gspan/structure_to_gspan/0.3	2018-09-01	1
CONVERTER_bed_to_fli_0	2018-09-01	1
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_groupbybed/2.27.0.0	2018-09-01	1
toolshed.g2.bx.psu.edu/repos/devteam/fastq_to_tabular/fastq_to_tabular/1.1.0	2018-09-01	1
toolshed.g2.bx.psu.edu/repos/earlhaminst/t_coffee/t_coffee/11.0.8	2018-09-01	1
toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.1.8.0	2018-09-01	1
CONVERTER_fasta_to_bowtie_base_index	2018-09-01	1
toolshed.g2.bx.psu.edu/repos/earlhaminst/replace_chromosome_names/replace_chromosome_names/0.1	2018-09-01	1
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed_histogram/2.19.0	2018-09-01	1
toolshed.g2.bx.psu.edu/repos/rnateam/mirdeep2_quantifier/rbc_mirdeep2_quantifier/2.0.0	2018-09-01	1
toolshed.g2.bx.psu.edu/repos/rnateam/graphclust_preprocessing/preproc/0.4	2018-09-01	1
toolshed.g2.bx.psu.edu/repos/iuc/ebi_metagenomics_run_downloader/ebi_metagenomics_run_downloader/0.1.0	2018-09-01	1
toolshed.g2.bx.psu.edu/repos/devteam/flanking_features/flanking_features_1/4.0.1	2018-09-01	1
toolshed.g2.bx.psu.edu/repos/earlhaminst/ete/species_tree_generator/3.0.0b35	2018-09-01	1
toolshed.g2.bx.psu.edu/repos/rnateam/graphclust_prepocessing_for_mlocarna/preMloc/0.3	2018-09-01	1
toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: merger54/5.0.0.1	2018-09-01	1
toolshed.g2.bx.psu.edu/repos/rnateam/graphclust_postprocessing/glob_report/0.4	2018-09-01	1
toolshed.g2.bx.psu.edu/repos/iuc/enasearch_retrieve_data/enasearch_retrieve_data/0.1.1.0	2018-09-01	1
toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/0.0.3	2018-09-01	1
toolshed.g2.bx.psu.edu/repos/rnateam/graphclust_nspdk/nspdk_sparse/9.2.2	2018-09-01	1
toolshed.g2.bx.psu.edu/repos/earlhaminst/ensembl_get_genetree/get_genetree/0.1.2	2018-09-01	1
toolshed.g2.bx.psu.edu/repos/devteam/draw_stacked_barplots/draw_stacked_barplots/1.0.0	2018-09-01	1
toolshed.g2.bx.psu.edu/repos/iuc/exonerate/exonerate/2.4.0	2018-09-01	1
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_overlapbed/2.27.0.0	2018-09-01	1
toolshed.g2.bx.psu.edu/repos/rnateam/graphclust_nspdk/NSPDK_candidateClust/9.2.2	2018-09-01	1
toolshed.g2.bx.psu.edu/repos/devteam/data_manager_build_kraken_database/kraken_database_builder/1.0.2	2018-09-01	1
toolshed.g2.bx.psu.edu/repos/devteam/data_manager_bowtie2_index_builder/bowtie2_index_builder_data_manager/2.3.0	2018-09-01	1
toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.36.4	2018-09-01	1
CONVERTER_sam_to_unsorted_bam	2018-09-01	1
toolshed.g2.bx.psu.edu/repos/peterjc/sample_seqs/sample_seqs/0.2.5	2018-09-01	1
toolshed.g2.bx.psu.edu/repos/iuc/gatk2/gatk2_haplotype_caller/2.8.0	2018-09-01	1
toolshed.g2.bx.psu.edu/repos/devteam/vcffilter/vcffilter2/1.0.0_rc1+galaxy1	2018-09-01	1
toolshed.g2.bx.psu.edu/repos/devteam/count_gff_features/count_gff_features/0.2	2018-09-01	1
toolshed.g2.bx.psu.edu/repos/peterjc/mummer/mummerplot_wrapper/0.0.7	2018-09-01	1
toolshed.g2.bx.psu.edu/repos/iuc/gatk2/gatk2_unified_genotyper/2.8.0	2018-09-01	1
toolshed.g2.bx.psu.edu/repos/iuc/gatk2/gatk2_variant_annotator/2.8.0	2018-09-01	1
toolshed.g2.bx.psu.edu/repos/iuc/gatk2/gatk2_variant_filtration/2.8.0	2018-09-01	1
toolshed.g2.bx.psu.edu/repos/pavlo-lutsik/rnbeads/rnbeads/0.91	2018-09-01	1
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtobam/2.27.0.0	2018-09-01	1
toolshed.g2.bx.psu.edu/repos/devteam/vcfcombine/vcfcombine/1.0.0_rc1.0	2018-09-01	1
toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_duplication/2.6.4	2018-09-01	1
toolshed.g2.bx.psu.edu/repos/galaxyp/msgfplus/msgfplus/0.5	2018-09-01	1
toolshed.g2.bx.psu.edu/repos/devteam/kernel_principal_component_analysis/kpca1/1.0.0	2018-09-01	1
toolshed.g2.bx.psu.edu/repos/devteam/basecoverage/gops_basecoverage_1/1.0.0	2018-09-01	1
toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_FPKM_count/2.6.4.1	2018-09-01	1
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_annotatebed/2.27.0.0	2018-09-01	1
toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_histogram/ggplot2_histogram/2.2.1	2018-09-01	1
toolshed.g2.bx.psu.edu/repos/devteam/vcfallelicprimitives/vcfallelicprimitives/0.0.3	2018-09-01	1
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_spacingbed/2.27.0.0	2018-09-01	1
toolshed.g2.bx.psu.edu/repos/devteam/vcf2tsv/vcf2tsv/0.0.3	2018-09-01	1
toolshed.g2.bx.psu.edu/repos/devteam/megablast_wrapper/megablast_wrapper/1.2.0	2018-09-01	1
toolshed.g2.bx.psu.edu/repos/miller-lab/genome_diversity/gd_new_oscar/1.0.0	2018-09-01	1
toolshed.g2.bx.psu.edu/repos/iuc/heinz/heinz/1.0	2018-09-01	1
toolshed.g2.bx.psu.edu/repos/devteam/megablast_xml_parser/megablast_xml_parser/1.0.0	2018-09-01	1
toolshed.g2.bx.psu.edu/repos/iuc/bctools_extract_alignment_ends/bctools_extract_alignment_ends/0.2.2	2018-09-01	1
toolshed.g2.bx.psu.edu/repos/iuc/heinz/heinz_bum/1.0	2018-09-01	1
toolshed.g2.bx.psu.edu/repos/iuc/heinz/heinz_scoring/1.0	2018-09-01	1
toolshed.g2.bx.psu.edu/repos/iuc/heinz/heinz_visualization/0.1.0	2018-09-01	1
toolshed.g2.bx.psu.edu/repos/crs4/muscle/muscle/0.0.11	2018-09-01	1
toolshed.g2.bx.psu.edu/repos/lparsons/htseq_count/htseq_count/0.6.1galaxy3	2018-09-01	1
toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/0.8.1+galaxy0	2018-09-01	1
bigwig_to_bedgraph	2018-09-01	1
__FLATTEN__	2018-09-01	1
toolshed.g2.bx.psu.edu/repos/bgruening/trna_prediction/aragorn_trna/0.6	2018-09-01	1
toolshed.g2.bx.psu.edu/repos/iuc/iqtree/iqtree/1.5.5.1	2018-09-01	1
toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/0.1	2018-09-01	1
toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastdbcmd_wrapper/0.3.0	2018-09-01	1
toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.12.5+galaxy0	2018-09-01	1
toolshed.g2.bx.psu.edu/repos/lecorguille/anova/abims_anova/1.2.1	2018-09-01	1
toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/0.7.0	2018-09-01	1
toolshed.g2.bx.psu.edu/repos/iuc/abricate/abricate_list/0.8	2018-09-01	1
toolshed.g2.bx.psu.edu/repos/iuc/abricate/abricate/0.8	2018-09-01	1
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