Mercurial > repos > bgruening > create_tool_recommendation_model
view test-data/test_tool_usage @ 1:12764915e1c5 draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit edeb85d311990eabd65f3c4576fbeabc6d9165c9"
author | bgruening |
---|---|
date | Wed, 25 Sep 2019 06:42:40 -0400 |
parents | 9bf25dbe00ad |
children | 76251d1ccdcc |
line wrap: on
line source
upload1 2019-03-01 176 toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72 2019-03-01 97 toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.0.2.0 2019-03-01 67 toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/1.6.3+galaxy2 2019-03-01 53 toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/2.9.1.3 2019-03-01 51 toolshed.g2.bx.psu.edu/repos/devteam/samtools_flagstat/samtools_flagstat/2.0.2 2019-03-01 38 toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/1.1.0 2019-03-01 38 toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.7 2019-03-01 31 toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.52 2019-03-01 30 toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.6.0b-1 2019-03-01 28 CONVERTER_gz_to_uncompressed 2019-03-01 26 toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_compare/deeptools_bam_compare/3.0.2.0 2019-03-01 25 toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.36.5 2019-03-01 25 toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.1.1.20160309.5 2019-03-01 22 toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.2 2019-03-01 21 toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.5 2019-03-01 19 toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.3.1 2019-03-01 18 toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/deeptools_compute_matrix/3.0.2.0 2019-03-01 17 toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_infer_experiment/2.6.4.1 2019-03-01 17 toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_gc_bias/deeptools_compute_gc_bias/3.0.2.0 2019-03-01 16 toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_fingerprint/deeptools_plot_fingerprint/3.0.2.0 2019-03-01 16 toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_classification/cardinal_classification/1.12.1.2 2019-03-01 16 toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.1.0+galaxy4 2019-03-01 13 toolshed.g2.bx.psu.edu/repos/iuc/flash/flash/1.2.11.3 2019-03-01 13 toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0 2019-03-01 13 toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/1.4.6.p5 2019-03-01 12 toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bam_summary/deeptools_multi_bam_summary/3.0.2.0 2019-03-01 12 toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_preprocessing/cardinal_preprocessing/1.12.1.2 2019-03-01 12 cat1 2019-03-01 11 toolshed.g2.bx.psu.edu/repos/iuc/ngsutils_bam_filter/ngsutils_bam_filter/0.5.9 2019-03-01 11 toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.1.0 2019-03-01 10 wig_to_bigWig 2019-03-01 10 CONVERTER_interval_to_bed_0 2019-03-01 10 toolshed.g2.bx.psu.edu/repos/iuc/goseq/goseq/1.34.0 2019-03-01 9 toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.27.1 2019-03-01 9 toolshed.g2.bx.psu.edu/repos/bgruening/pileometh/pileometh/0.3.0.1 2019-03-01 9 toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.6 2019-03-01 9 toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicplottads/hicexplorer_hicplottads/2.1.4.0 2019-03-01 9 toolshed.g2.bx.psu.edu/repos/peterjc/blast_rbh/blast_reciprocal_best_hits/0.1.11 2019-03-01 7 toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_correlation/deeptools_plot_correlation/3.0.2.0 2019-03-01 7 toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.1 2019-03-01 6 toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.0.1.0 2019-03-01 6 secure_hash_message_digest 2019-03-01 6 CONVERTER_interval_to_bedstrict_0 2019-03-01 6 toolshed.g2.bx.psu.edu/repos/iuc/gtftobed12/gtftobed12/357 2019-03-01 6 CONVERTER_bedgraph_to_bigwig 2019-03-01 5 toolshed.g2.bx.psu.edu/repos/devteam/concat/gops_concat_1/1.0.1 2019-03-01 5 toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_heatmap/deeptools_plot_heatmap/3.0.2.0 2019-03-01 5 toolshed.g2.bx.psu.edu/repos/devteam/fastqtofasta/fastq_to_fasta_python/1.1.1 2019-03-01 5 toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_group/mothur_make_group/1.39.5.0 2019-03-01 5 toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastp_wrapper/0.3.1 2019-03-01 5 toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_makeblastdb/0.3.1 2019-03-01 4 wc_gnu 2019-03-01 4 __SET_METADATA__ 2019-03-01 4 toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.7.0 2019-03-01 4 toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_filtering/cardinal_filtering/1.12.1.2 2019-03-01 4 toolshed.g2.bx.psu.edu/repos/iuc/bwameth/bwameth/0.2.0.4 2019-03-01 4 toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.27.0.1 2019-03-01 4 toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.1 2019-03-01 4 Filter1 2019-03-01 4 toolshed.g2.bx.psu.edu/repos/lparsons/fastq_join/fastq_join/1.1.2-806 2019-03-01 4 toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_profile/deeptools_plot_profile/3.1.2.0.0 2019-03-01 3 toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.2.0 2019-03-01 3 toolshed.g2.bx.psu.edu/repos/bgruening/graphicsmagick_image_convert/graphicsmagick_image_convert/1.3.31 2019-03-01 3 toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/2.9.1.4 2019-03-01 3 toolshed.g2.bx.psu.edu/repos/devteam/fastq_filter/fastq_filter/1.1.1 2019-03-01 3 toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/0.0.2 2019-03-01 3 toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.1.4 2019-03-01 3 toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3 2019-03-01 3 toolshed.g2.bx.psu.edu/repos/imgteam/coordinates_of_roi/ip_coordinates_of_roi/0.0.3 2019-03-01 3 Grouping1 2019-03-01 3 toolshed.g2.bx.psu.edu/repos/devteam/fastq_to_fasta/cshl_fastq_to_fasta/1.0.2 2019-03-01 3 toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.1.0 2019-03-01 2 toolshed.g2.bx.psu.edu/repos/bgruening/graphicsmagick_image_convert/graphicsmagick_image_convert/1.3.26 2019-03-01 2 toolshed.g2.bx.psu.edu/repos/galaxyp/filter_by_fasta_ids/filter_by_fasta_ids/2.1 2019-03-01 2 toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_closestbed/2.27.1 2019-03-01 2 toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_combine/cardinal_combine/1.12.1.2 2019-03-01 2 toolshed.g2.bx.psu.edu/repos/tgac/miranda/miranda/3.3a 2019-03-01 2 toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_mergebed/2.27.0.0 2019-03-01 2 toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1 2019-03-01 2 toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicplotmatrix/hicexplorer_hicplotmatrix/2.1.4.0 2019-03-01 2 toolshed.g2.bx.psu.edu/repos/iuc/mothur_merge_files/mothur_merge_files/1.39.5.0 2019-03-01 2 toolshed.g2.bx.psu.edu/repos/peterjc/seq_filter_by_id/seq_filter_by_id/0.2.7 2019-03-01 2 toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1 2019-03-01 2 sklearn_ensemble 2019-03-01 2 toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.4.2 2019-03-01 2 toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_quality_report/cardinal_quality_report/1.12.1.2 2019-03-01 2 toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_segmentations/cardinal_segmentations/1.12.1.2 2019-03-01 2 ebi_sra_main 2019-03-01 2 toolshed.g2.bx.psu.edu/repos/devteam/intersect/gops_intersect_1/1.0.0 2019-03-01 2 join1 2019-03-01 2 toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_tblastn_wrapper/0.3.1 2019-03-01 2 toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.0 2019-03-01 2 sort1 2019-03-01 2 toolshed.g2.bx.psu.edu/repos/galaxyp/maldi_quant_peak_detection/maldi_quant_peak_detection/1.18.0.3 2019-03-01 2 toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.2+galaxy2 2019-03-01 1 toolshed.g2.bx.psu.edu/repos/iuc/goseq/goseq/1.32.0 2019-03-01 1 toolshed.g2.bx.psu.edu/repos/iuc/goseq/goseq/1.30.1 2019-03-01 1 toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/3.2+galaxy1 2019-03-01 1 toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.38 2019-03-01 1 toolshed.g2.bx.psu.edu/repos/miller-lab/genome_diversity/gd_raxml/1.0.0 2019-03-01 1 toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_slopbed/2.27.0.0 2019-03-01 1 toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_pca/deeptools_plot_pca/3.1.2.0.0 2019-03-01 1 re_he_maldi_image_registration 2019-03-01 1 toolshed.g2.bx.psu.edu/repos/imgteam/overlay_moving_and_fixed_image/ip_viz_overlay_moving_and_fixed_image/0.0.1 2019-03-01 1 toolshed.g2.bx.psu.edu/repos/devteam/samtool_filter2/samtool_filter2/1.8 2019-03-01 1 toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_ensemble/sklearn_ensemble/1.0 2019-03-01 1 CONVERTER_fastq_to_fqtoc0 2019-03-01 1 toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicpca/hicexplorer_hicpca/2.1.4.0 2019-03-01 1 toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_heatmap2/ggplot2_heatmap2/2.2.1+galaxy1 2019-03-01 1 toolshed.g2.bx.psu.edu/repos/iuc/metaphlan2/metaphlan2/2.6.0.0 2019-03-01 1 toolshed.g2.bx.psu.edu/repos/imgteam/scale_image/ip_scale_image/0.2 2019-03-01 1 toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.1 2019-03-01 1 toolshed.g2.bx.psu.edu/repos/iuc/mothur_unique_seqs/mothur_unique_seqs/1.39.5.0 2019-03-01 1 toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastdbcmd_info/0.3.1 2019-03-01 1 toolshed.g2.bx.psu.edu/repos/imgteam/landmark_registration/ip_landmark_registration/0.0.2 2019-03-01 1 toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_classification/cardinal_classification/1.12.1.0 2019-03-01 1 toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.0 2019-03-01 1 toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.6.1.1 2019-03-01 1 Grep1 2019-03-01 1 toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_joiner/fastq_paired_end_joiner/2.0.1.1 2019-03-01 1 toolshed.g2.bx.psu.edu/repos/bgruening/join_files_on_column_fuzzy/join_files_on_column_fuzzy/1.0.1 2019-03-01 1 toolshed.g2.bx.psu.edu/repos/iuc/migmap/migmap/1.0.2.2 2019-03-01 1 toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/0.5.3.2 2019-03-01 1 toolshed.g2.bx.psu.edu/repos/devteam/get_flanks/get_flanks1/1.0.0 2019-03-01 1 __TAG_FROM_FILE__ 2019-03-01 1 toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_AddOrReplaceReadGroups/2.18.2.1 2019-03-01 1 toolshed.g2.bx.psu.edu/repos/iuc/metaphlan2krona/metaphlan2krona/2.6.0.0 2019-03-01 1 toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.27.0.0 2019-03-01 1 toolshed.g2.bx.psu.edu/repos/iuc/varscan_mpileup/varscan_mpileup/2.4.3.1 2019-03-01 1 toolshed.g2.bx.psu.edu/repos/iuc/ncbi_eutils_esearch/ncbi_eutils_esearch/1.2 2019-03-01 1 upload1 2019-02-01 17338 toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72 2019-02-01 5617 toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.1.0 2019-02-01 5086 toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1 2019-02-01 4696 toolshed.g2.bx.psu.edu/repos/rnateam/intarna/intarna/2.2.0 2019-02-01 4562 Paste1 2019-02-01 4331 Show beginning1 2019-02-01 4201 Cut1 2019-02-01 3502 Filter1 2019-02-01 2510 toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.36.5 2019-02-01 2334 toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.1.0.46-0 2019-02-01 2174 toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/1.1.0 2019-02-01 1965 toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1 2019-02-01 1871 CONVERTER_gz_to_uncompressed 2019-02-01 1815 toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/2.9.1.3 2019-02-01 1776 toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.1.0.46-0 2019-02-01 1775 toolshed.g2.bx.psu.edu/repos/devteam/vcffilter/vcffilter2/1.0.0_rc1+galaxy1 2019-02-01 1664 toolshed.g2.bx.psu.edu/repos/devteam/vcfallelicprimitives/vcfallelicprimitives/0.0.3 2019-02-01 1495 toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.6.0b-1 2019-02-01 1296 toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3 2019-02-01 1282 __SET_METADATA__ 2019-02-01 1025 toolshed.g2.bx.psu.edu/repos/crs4/prokka/prokka/1.13 2019-02-01 969 toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.0.2.0 2019-02-01 931 toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/1.6.3+galaxy2 2019-02-01 899 toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/deeptools_compute_matrix/3.0.2.0 2019-02-01 897 toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_wrapper_2/1.3.2 2019-02-01 885 toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.4.2 2019-02-01 848 toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_heatmap/deeptools_plot_heatmap/3.0.2.0 2019-02-01 818 toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_contigs/mothur_make_contigs/1.39.5.0 2019-02-01 800 toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/1.1.0 2019-02-01 794 toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.1 2019-02-01 782 toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.5 2019-02-01 723 toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.1 2019-02-01 692 toolshed.g2.bx.psu.edu/repos/lparsons/htseq_count/htseq_count/0.9.1 2019-02-01 669 toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.52 2019-02-01 619 toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.27.1 2019-02-01 591 toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.71 2019-02-01 560 cat1 2019-02-01 550 toolshed.g2.bx.psu.edu/repos/devteam/vcfallelicprimitives/vcfallelicprimitives/1.0.0_rc1+galaxy0 2019-02-01 505 wig_to_bigWig 2019-02-01 499 toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_dedup/umi_tools_dedup/0.5.3.0 2019-02-01 495 addValue 2019-02-01 492 toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.27.0.1 2019-02-01 449 toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.1 2019-02-01 449 toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.4.3.1 2019-02-01 403 toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_joiner/fastq_paired_end_joiner/2.0.1.1 2019-02-01 400 toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.1.1.20160309.5 2019-02-01 396 toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.1.0+galaxy4 2019-02-01 394 join1 2019-02-01 373 toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.0 2019-02-01 360 toolshed.g2.bx.psu.edu/repos/peterjc/seq_filter_by_id/seq_filter_by_id/0.2.7 2019-02-01 359 comp1 2019-02-01 354 toolshed.g2.bx.psu.edu/repos/bgruening/infernal/infernal_cmsearch/1.1.2.0 2019-02-01 350 toolshed.g2.bx.psu.edu/repos/rnateam/graphclust_cmfinder/cmFinder/0.4 2019-02-01 350 toolshed.g2.bx.psu.edu/repos/rnateam/graphclust_mlocarna/locarna_best_subtree/0.4 2019-02-01 350 toolshed.g2.bx.psu.edu/repos/bgruening/infernal/infernal_cmbuild/1.1.2.0 2019-02-01 350 toolshed.g2.bx.psu.edu/repos/iuc/hmmer3/hmmer_hmmbuild/0.1.0 2019-02-01 341 toolshed.g2.bx.psu.edu/repos/iuc/hmmer3/hmmer_hmmsearch/0.1.0 2019-02-01 340 toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_profile/deeptools_plot_profile/3.1.2.0.0 2019-02-01 328 toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.7 2019-02-01 327 toolshed.g2.bx.psu.edu/repos/devteam/samtools_rmdup/samtools_rmdup/2.0.1 2019-02-01 321 toolshed.g2.bx.psu.edu/repos/devteam/vcffilter/vcffilter2/1.0.0_rc1+galaxy2 2019-02-01 313 toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed_bedgraph/2.19.0 2019-02-01 307 ebi_sra_main 2019-02-01 306 toolshed.g2.bx.psu.edu/repos/rnateam/chipseeker/chipseeker/1.16.2 2019-02-01 302 toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.6 2019-02-01 298 Remove beginning1 2019-02-01 286 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 CONVERTER_interval_to_bedstrict_0 2019-02-01 227 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 Convert characters1 2019-02-01 185 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 __ZIP_COLLECTION__ 2019-02-01 162 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 __UNZIP_COLLECTION__ 2019-02-01 132 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 __EXPORT_HISTORY__ 2019-02-01 37 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 __SORTLIST__ 2019-02-01 21 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 toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idfilter/IDFilter/2.3.0 2019-02-01 17 toolshed.g2.bx.psu.edu/repos/iuc/egsea/egsea/1.10.0 2019-02-01 17 toolshed.g2.bx.psu.edu/repos/rnateam/graphclust_postprocessing/glob_report/0.5 2019-02-01 17 toolshed.g2.bx.psu.edu/repos/iuc/meme_chip/meme_chip/4.11.2+galaxy1 2019-02-01 17 toolshed.g2.bx.psu.edu/repos/galaxyp/maldi_quant_preprocessing/maldi_quant_preprocessing/1.18.0.3 2019-02-01 17 toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_feature_selection/sklearn_feature_selection/1.0.1 2019-02-01 17 toolshed.g2.bx.psu.edu/repos/bgruening/nucleosome_prediction/Nucleosome/3.0 2019-02-01 17 toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_classification/cardinal_classification/1.12.1.0 2019-02-01 17 toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpSift_filter/3.4 2019-02-01 17 toolshed.g2.bx.psu.edu/repos/bgruening/split_file_on_column/tp_split_on_column/0.2 2019-02-01 17 toolshed.g2.bx.psu.edu/repos/iuc/rnaspades/rnaspades/3.9.0.1 2019-02-01 17 toolshed.g2.bx.psu.edu/repos/galaxyp/openms_featurefindermultiplex/FeatureFinderMultiplex/2.3.0 2019-02-01 17 toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_interlacer/fastq_paired_end_interlacer/1.2.0.1 2019-02-01 17 toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_whitelist/umi_tools_whitelist/0.5.3.1 2019-02-01 17 toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_group/umi_tools_group/0.5.3.0 2019-02-01 17 toolshed.g2.bx.psu.edu/repos/galaxyp/openms_filefilter/FileFilter/2.3.0 2019-02-01 17 toolshed.g2.bx.psu.edu/repos/devteam/bamtools_split/bamSplit/2.4.0 2019-02-01 17 scale_image 2019-02-01 17 toolshed.g2.bx.psu.edu/repos/bgruening/graphicsmagick_image_convert/graphicsmagick_image_convert/1.3.31 2019-02-01 16 toolshed.g2.bx.psu.edu/repos/rnateam/graphclust_nspdk/NSPDK_candidateClust/9.2.3 2019-02-01 16 toolshed.g2.bx.psu.edu/repos/iuc/meme_fimo/meme_fimo/4.12.0.0 2019-02-01 16 toolshed.g2.bx.psu.edu/repos/iuc/gemini_inheritance/gemini_inheritance/0.20.1 2019-02-01 16 toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/0.0.3 2019-02-01 16 toolshed.g2.bx.psu.edu/repos/rnateam/graphclust_prepocessing_for_mlocarna/preMloc/0.4 2019-02-01 16 toolshed.g2.bx.psu.edu/repos/jjohnson/samtools_filter/samtools_filter/1.1.1 2019-02-01 16 toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_multicovtbed/2.27.1 2019-02-01 16 toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedpetobam/2.27.0.0 2019-02-01 16 toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idmapper/IDMapper/2.3.0 2019-02-01 16 toolshed.g2.bx.psu.edu/repos/rnateam/sortmerna/bg_sortmerna/2.1b.5 2019-02-01 16 toolshed.g2.bx.psu.edu/repos/galaxyp/msconvert/msconvert/3.0.19052.0 2019-02-01 16 toolshed.g2.bx.psu.edu/repos/iuc/gatk2/gatk2_base_recalibrator/2.8.0 2019-02-01 16 toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedpetobam/2.27.1 2019-02-01 16 toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.1.0 2019-02-01 16 toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_coveragebed/2.27.0.2 2019-02-01 16 toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fastq/tabular_to_fastq/1.0.0 2019-02-01 16 CONVERTER_interval_to_bed12_0 2019-02-01 15 toolshed.g2.bx.psu.edu/repos/galaxyp/msi_qualitycontrol/mass_spectrometry_imaging_qc/1.10.0.7 2019-02-01 15 toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_splitter/fastq_paired_end_splitter/1.1.1 2019-02-01 15 toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/1.1.1 2019-02-01 15 toolshed.g2.bx.psu.edu/repos/gbcs-embl-heidelberg/je_demultiplex_illu/je_demultiplex_illu/1.2.1 2019-02-01 15 toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.39 2019-02-01 15 toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.1.1 2019-02-01 15 toolshed.g2.bx.psu.edu/repos/devteam/cluster/gops_cluster_1/1.0.0 2019-02-01 15 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 toolshed.g2.bx.psu.edu/repos/iuc/mothur_sub_sample/mothur_sub_sample/1.39.5.0 2019-02-01 14 toolshed.g2.bx.psu.edu/repos/iuc/meme_fimo/meme_fimo/4.11.2.0 2019-02-01 14 toolshed.g2.bx.psu.edu/repos/iuc/pureclip/pureclip/1.0.4 2019-02-01 14 toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_clusterbed/2.27.0.0 2019-02-01 14 toolshed.g2.bx.psu.edu/repos/bebatut/combine_metaphlan2_humann2/combine_metaphlan2_humann2/0.1.0 2019-02-01 14 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 toolshed.g2.bx.psu.edu/repos/peterjc/venn_list/venn_list/0.0.11 2019-02-01 14 toolshed.g2.bx.psu.edu/repos/iuc/hmmer3/hmmer_hmmscan/0.1.0 2019-02-01 14 toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: cpgplot15/5.0.0 2019-02-01 14 toolshed.g2.bx.psu.edu/repos/iuc/mothur_count_groups/mothur_count_groups/1.39.5.0 2019-02-01 14 toolshed.g2.bx.psu.edu/repos/iuc/qiime_validate_mapping_file/qiime_validate_mapping_file/1.9.1.0 2019-02-01 14 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 toolshed.g2.bx.psu.edu/repos/iuc/mothur_classify_seqs/mothur_classify_seqs/1.39.5.0 2019-02-01 13 toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.4.0d-2 2019-02-01 13 toolshed.g2.bx.psu.edu/repos/iuc/mothur_classify_otu/mothur_classify_otu/1.39.5.0 2019-02-01 13 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 toolshed.g2.bx.psu.edu/repos/rnateam/viennarna_rnaalifold/viennarna_rnaalifold/2.2.10.0 2019-02-01 12 CONVERTER_bz2_to_uncompressed 2019-02-01 12 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 toolshed.g2.bx.psu.edu/repos/devteam/vcftools_merge/vcftools_merge/0.1.1 2019-02-01 12 toolshed.g2.bx.psu.edu/repos/iuc/newick_utils/newick_display/1.6 2019-02-01 12 toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_filtering/cardinal_filtering/1.12.1.0 2019-02-01 12 toolshed.g2.bx.psu.edu/repos/devteam/vcftools_isec/vcftools_isec/0.1.1 2019-02-01 12 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 toolshed.g2.bx.psu.edu/repos/galaxyp/msconvert_nix/msconvert_nix/3.0.9992.0 2019-02-01 11 toolshed.g2.bx.psu.edu/repos/saskia-hiltemann/krona_text/krona-text/1 2019-02-01 11 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 toolshed.g2.bx.psu.edu/repos/iuc/meme_meme/meme_meme/4.12.0.0 2019-02-01 11 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 toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy_core/3.2 2019-02-01 10 toolshed.g2.bx.psu.edu/repos/iuc/ruvseq/ruvseq/1.12.0 2019-02-01 10 toolshed.g2.bx.psu.edu/repos/galaxyp/openms_decoydatabase/DecoyDatabase/2.3.0 2019-02-01 10 Sff_extractor 2019-02-01 10 toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_unionbedgraph/2.27.1 2019-02-01 10 toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hictransform/hicexplorer_hictransform/2.1.4.0 2019-02-01 10 toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.20.7.2 2019-02-01 10 CONVERTER_fasta_to_2bit 2019-02-01 10 toolshed.g2.bx.psu.edu/repos/galaxyp/filter_by_fasta_ids/filter_by_fasta_ids/1.0 2019-02-01 10 toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hiccomparematrices/hicexplorer_hiccomparematrices/2.1.4.0 2019-02-01 10 toolshed.g2.bx.psu.edu/repos/bebatut/group_humann2_uniref_abundances_to_go/group_humann2_uniref_abundances_to_go/1.2.0 2019-02-01 10 toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.38.3+galaxy1 2019-02-01 10 toolshed.g2.bx.psu.edu/repos/devteam/fastq_stats/fastq_stats/1.0.0 2019-02-01 10 toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.6.1.1 2019-02-01 10 toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_point/ggplot2_point/2.2.1+galaxy0 2019-02-01 10 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 toolshed.g2.bx.psu.edu/repos/devteam/dna_filtering/histogram_rpy/1.0.3 2019-02-01 9 toolshed.g2.bx.psu.edu/repos/devteam/megablast_xml_parser/megablast_xml_parser/1.0.0 2019-02-01 9 toolshed.g2.bx.psu.edu/repos/iuc/gatk2/gatk2_print_reads/2.8.0 2019-02-01 9 CONVERTER_gff_to_fli_0 2019-02-01 9 toolshed.g2.bx.psu.edu/repos/devteam/cuffnorm/cuffnorm/2.2.1.2 2019-02-01 9 toolshed.g2.bx.psu.edu/repos/iuc/trinity_abundance_estimates_to_matrix/trinity_abundance_estimates_to_matrix/2.8.4 2019-02-01 9 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 toolshed.g2.bx.psu.edu/repos/imgteam/scale_image/ip_scale_image/0.2 2019-02-01 8 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 toolshed.g2.bx.psu.edu/repos/galaxyp/filter_by_fasta_ids/filter_by_fasta_ids/2.0 2019-02-01 8 toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_gc_bias/deeptools_compute_gc_bias/2.5.7.0 2019-02-01 8 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 toolshed.g2.bx.psu.edu/repos/iuc/circos/circgraph/0.9-RC2 2019-02-01 8 toolshed.g2.bx.psu.edu/repos/iuc/meme_dreme/meme_dreme/4.11.2.0 2019-02-01 8 toolshed.g2.bx.psu.edu/repos/iuc/varscan_mpileup/varscan_mpileup/2.4.3.1 2019-02-01 8 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 CONVERTER_bed_to_tabix_0 2019-02-01 6 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 __FILTER_FROM_FILE__ 2019-02-01 6 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 __FLATTEN__ 2019-02-01 5 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 CONVERTER_ref_to_seq_taxomony 2019-02-01 3 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 CONVERTER_wig_to_bigwig 2019-02-01 3 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 toolshed.g2.bx.psu.edu/repos/galaxyp/msi_filtering/mass_spectrometry_imaging_filtering/1.7.0.1 2019-02-01 2 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 toolshed.g2.bx.psu.edu/repos/imgteam/2d_auto_threshold/ip_threshold/0.0.3 2019-02-01 2 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 MAF_To_Fasta1 2019-02-01 2 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 toolshed.g2.bx.psu.edu/repos/jjohnson/rsem/extract_transcript_to_gene_map_from_trinity/1.1.17 2019-02-01 2 genomespace_importer 2019-02-01 2 toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.0 2019-02-01 2 toolshed.g2.bx.psu.edu/repos/iuc/merge_metaphlan_tables/merge_metaphlan_tables/2.6.0.0 2019-02-01 2 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 toolshed.g2.bx.psu.edu/repos/devteam/subtract_query/subtract_query1/0.1 2019-02-01 2 toolshed.g2.bx.psu.edu/repos/iuc/mothur_chimera_vsearch/mothur_chimera_vsearch/1.39.5.0 2019-02-01 2 toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/1.5.3 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/iuc/disco/disco/1.2.0 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicatesWithMateCigar/2.18.2.1 2019-02-01 1 secure_hash_message_digest 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/iuc/heinz/heinz_scoring/1.0 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/crs4/prokka/prokka/1.12.0 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/iuc/heinz/heinz_visualization/0.1.0 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_nucbed/2.27.1 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/iuc/heinz/heinz_bum/1.0 2019-02-01 1 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 toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.24.0 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_fqchk/1.3.1 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/galaxyp/openms_msgfplusadapter/MSGFPlusAdapter/2.2.0 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/devteam/generate_pc_lda_matrix/generate_matrix_for_pca_and_lda1/1.0.0 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/iuc/varscan_copynumber/varscan_copynumber/2.4.3.2 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/jjohnson/query_tabular/query_tabular/5.0.0 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/devteam/ucsc_custom_track/build_ucsc_custom_track_1/1.0.0 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/iuc/mothur_cluster/mothur_cluster/1.39.5.0 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/iuc/qiime_alpha_diversity/qiime_alpha_diversity/1.9.1.0 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/0.2 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/imgteam/concat_channels/ip_concat_channels/0.1 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/galaxyp/openms_filefilter/FileFilter/2.2.0 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/iuc/ebi_metagenomics_run_downloader/ebi_metagenomics_run_downloader/0.1.0 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/devteam/basecoverage/gops_basecoverage_1/1.0.0 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/iuc/mothur_seq_error/mothur_seq_error/1.39.5.0 2019-02-01 1 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 toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: vectorstrip106/5.0.0.1 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_annotatebed/2.27.1 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_overlapbed/2.27.1 2019-02-01 1 CONVERTER_biom2_to_biom1 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/galaxyp/openms_fidoadapter/FidoAdapter/2.2.0.1 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/bgruening/hicup_deduplicator/hicup_deduplicator/0.1.0 2019-02-01 1 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 toolshed.g2.bx.psu.edu/repos/iuc/raceid_filtnormconf/raceid_filtnormconf/3.0.2.1 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/search_gui/3.2.11 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_enrichment/deeptools_plot_enrichment/3.0.2.0 2019-02-01 1 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 toolshed.g2.bx.psu.edu/repos/chemteam/packmol/packmol/18.169 2019-02-01 1 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 toolshed.g2.bx.psu.edu/repos/galaxyp/openms_featurefindersuperhirn/FeatureFinderSuperHirn/2.3.0 2019-02-01 1 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 toolshed.g2.bx.psu.edu/repos/galaxyp/gffcompare_to_bed/gffcompare_to_bed/0.1.0 2019-02-01 1 PerM 2019-02-01 1 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 toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_contigs/mothur_make_contigs/1.36.1.0 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fastq/tabular_to_fastq/1.1.1 2019-02-01 1 CONVERTER_sdf_to_smiles 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/iuc/gemini_fusions/gemini_fusions/0.20.1 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/devteam/vcfhethom/vcfhethom/1.0.0_rc1+galaxy0 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/iuc/poretools_occupancy/poretools_occupancy/0.6.1a1.0 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/imgteam/detection_viz/ip_detection_viz/0.1 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idscoreswitcher/IDScoreSwitcher/2.2.0 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: plotorf76/5.0.0 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/rnateam/peakachu/peakachu/0.1.0.0 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/devteam/bamleftalign/bamleftalign/0.0.2 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/devteam/pileup_interval/pileup_interval/1.0.2 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/bgruening/rnaz_select_seqs/rnaz_select_seqs/2.1 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/iuc/hmmer3/hmmer_hmmalign/0.1.0 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.2.0 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/search_gui/3.2.13.2 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/search_gui/3.2.13.3 2019-02-01 1 dexseq_map 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/peterjc/tmhmm_and_signalp/tmhmm2/0.0.13 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_windowbed/2.27.0.0 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/galaxyp/openms_mztabexporter/MzTabExporter/2.3.0 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/galaxyp/morpheus/morpheus/2.255.0 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_map/2.27.0.0 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/galaxyp/openms_qccalculator/QCCalculator/2.3.0 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.26.0.0 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/iuc/megahit_contig2fastg/megahit_contig2fastg/1.1.3+galaxy1 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/iuc/qiime_split_libraries_fastq/qiime_split_libraries_fastq/1.9.1.0 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/iuc/bcftools/bcftools_view/0.1.19.0 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idmassaccuracy/IDMassAccuracy/2.3.0 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/iuc/hmmer3/hmmer_nhmmscan/0.1.0 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idfilter/IDFilter/2.2.0 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/galaxyp/openms_mssimulator/MSSimulator/2.3.0 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_biom/mothur_make_biom/1.39.5.0 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicaggregatecontacts/hicexplorer_hicaggregatecontacts/2.1.4.0 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_makewindowsbed/2.27.0.0 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectWgsMetrics/2.18.2.1 2019-02-01 1 CONVERTER_maf_to_interval_0 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/galaxyp/msconvert/msconvert_nix/3.0.0 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/iuc/qiime_summarize_taxa_through_plots/qiime_summarize_taxa_through_plots/1.9.1.0 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/deeptools_compute_matrix/2.2.3.0 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_joiner/fastq_paired_end_joiner/2.0.0 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/devteam/vcfsort/vcfsort/1.0.0_rc1+galaxy0 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/iuc/poretools_qualpos/poretools_qualpos/0.6.1a1.0 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/devteam/vcftools_annotate/vcftools_annotate/0.1 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/galaxyp/uniprotxml_downloader/uniprotxml_downloader/2.0.0 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectRnaSeqMetrics/2.7.1.1 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/rnateam/sortmerna/bg_sortmerna/2.1b.4 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/bgruening/trna_prediction/trnascan/0.4 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_joiner/fastq_paired_end_joiner/1.0.0 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectRnaSeqMetrics/2.7.1.0 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_randsample/2.1.1.20160309.0 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/iuc/vsearch/vsearch_clustering/2.8.3.0 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idmapper/IDMapper/2.2.0 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/iuc/intervene/intervene_pairwise/0.6.4 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.1.8.3 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/imgteam/permutate_axis/ip_permutate_axis/0.1 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.0 2019-02-01 1 CONVERTER_interval_to_tabix_0 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/iuc/iqtree/iqtree/1.5.5.1 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/yhoogstrate/segmentation_fold/smf_utils_fix-fasta-headers/smf-v1.7-0_utils-v2.1.1-1 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/rnateam/metilene/metilene/0.2-4.0 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/galaxyp/openms_featurefindermultiplex/FeatureFinderMultiplex/2.2.0 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.1 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/devteam/fasta_formatter/cshl_fasta_formatter/1.0.1 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/bgruening/glimmer3/glimmer_build-icm/0.2 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/iuc/poretools_tabular/poretools_tabular/0.6.1a1.0 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/iuc/mothur_venn/mothur_venn/1.39.5.0 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/galaxyp/openms_highresprecursormasscorrector/HighResPrecursorMassCorrector/2.2.0 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_bdgdiff/2.1.1.20160309.1 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.0.0 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/galaxyp/openms_proteinquantifier/ProteinQuantifier/2.2.0 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/iuc/roary/roary/0.1.0 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/devteam/fastq_manipulation/fastq_manipulation/1.1.1 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_slopbed/2.27.1 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/miller-lab/genome_diversity/gd_multiple_to_gd_genotype/1.0.0 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/2.2.2.0 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/bgruening/plotly_ml_performance_plots/plotly_ml_performance_plots/0.1 2019-02-01 1 gff_filter_by_feature_count 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/devteam/ctd_batch/ctdBatch_1/1.0.0 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/iuc/qiime_make_phylogeny/qiime_make_phylogeny/1.9.1.0 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/earlhaminst/hcluster_sg/hcluster_sg/0.5.1.1 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/devteam/dgidb_annotator/dgidb_annotate/0.1 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/devteam/weblogo3/rgweblogo3/3.5.0 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/iuc/ngsutils_bam_filter/ngsutils_bam_filter/0.5.7.0 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_searchcv/sklearn_searchcv/0.9 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/rnateam/cofold/cofold/2.0.4.0 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.2+galaxy2 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/rnateam/dorina/dorina_search/1.0.0 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/wolma/mimodd_main/mimodd_varcall/0.1.8_1 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_numeric_clustering/sklearn_numeric_clustering/1.0 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/iuc/zerone/zerone/1.0 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_sample/1.3.1 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/galaxyp/openms_mapnormalizer/MapNormalizer/2.3.0 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/iuc/jcvi_gff_stats/jcvi_gff_stats/0.8.4 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/iuc/qiime_make_otu_table/qiime_make_otu_table/1.9.1.0 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/jjohnson/rsem/rsem_prepare_reference/1.1.17 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/iuc/fasta_nucleotide_color_plot/four_color_plot/1.0.0 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_mergepe/1.3.1 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idposteriorerrorprobability/IDPosteriorErrorProbability/2.2.0 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/galaxyp/openms_peptideindexer/PeptideIndexer/2.2.0 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/iuc/abricate/abricate_list/0.8 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/bgruening/simsearch/ctb_simsearch/0.2 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/galaxyp/openms_mascotadapter/MascotAdapter/2.3.0 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/iuc/qiime_filter_alignment/qiime_filter_alignment/1.9.1.0 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/iuc/scpipe/scpipe/1.0.0 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_build_pipeline/sklearn_build_pipeline/0.9 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/lparsons/htseq_count/htseq_count/0.6.1galaxy3 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.1 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/gga/apollo_list_organism/list_organism/3.1 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/galaxyp/openms_featurefindercentroided/FeatureFinderCentroided/2.3.0 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idconflictresolver/IDConflictResolver/2.2.0 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/rnateam/viennarna_rnafold/viennarna_rnafold/2.2.10.0 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/iuc/ncbi_eutils_efetch/ncbi_eutils_efetch/1.2 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/1.6.1.0 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/1.6.0.7 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/galaxyp/openms_mascotadapteronline/MascotAdapterOnline/2.3.0 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/galaxyp/msi_qualitycontrol/mass_spectrometry_imaging_qc/1.7.0.5 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/lparsons/htseq_count/htseq_count/0.6.1galaxy1 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/jjohnson/filter_bed_on_splice_junctions/filter_bed_on_splice_junctions/0.0.1 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/iuc/qiime_collapse_samples/qiime_collapse_samples/1.9.1.0 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/iuc/ucsc_twobittofa/ucsc-twobittofa/357 2019-02-01 1 toolshed.g2.bx.psu.edu/repos/iuc/trinity_gene_to_trans_map/trinity_gene_to_trans_map/2.8.4 2019-02-01 1 upload1 2019-01-01 15621 toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_searchcv/sklearn_searchcv/1.0 2019-01-01 9452 toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72 2019-01-01 3708 toolshed.g2.bx.psu.edu/repos/iuc/stacks_procrad/stacks_procrad/1.46.0 2019-01-01 3002 Cut1 2019-01-01 2540 toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.71 2019-01-01 2381 toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.36.5 2019-01-01 2309 toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.1.0.46-0 2019-01-01 1879 toolshed.g2.bx.psu.edu/repos/devteam/vcffilter/vcffilter2/1.0.0_rc1+galaxy1 2019-01-01 1533 toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_tblastn_wrapper/0.3.1 2019-01-01 1475 toolshed.g2.bx.psu.edu/repos/mvdbeek/add_input_name_as_column/addName/0.1.1 2019-01-01 1449 toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.4.2 2019-01-01 1392 toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_NormalizeFasta/2.18.2.1 2019-01-01 1277 toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1 2019-01-01 1193 toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0 2019-01-01 1171 Filter1 2019-01-01 1157 CONVERTER_gz_to_uncompressed 2019-01-01 1155 __SET_METADATA__ 2019-01-01 1057 toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/2.9.1.3 2019-01-01 1009 toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.0.2.0 2019-01-01 975 toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_coveragebed/2.27.0.2 2019-01-01 926 toolshed.g2.bx.psu.edu/repos/devteam/vcfallelicprimitives/vcfallelicprimitives/0.0.3 2019-01-01 918 toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.1.0.46-0 2019-01-01 859 toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/1.6.3+galaxy2 2019-01-01 852 addValue 2019-01-01 849 toolshed.g2.bx.psu.edu/repos/devteam/samtools_rmdup/samtools_rmdup/2.0.1 2019-01-01 762 toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/deeptools_compute_matrix/3.0.2.0 2019-01-01 716 toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.4 2019-01-01 681 toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed/2.27.0.0 2019-01-01 625 toolshed.g2.bx.psu.edu/repos/devteam/vcfallelicprimitives/vcfallelicprimitives/1.0.0_rc1.0 2019-01-01 621 toolshed.g2.bx.psu.edu/repos/devteam/samtools_flagstat/samtools_flagstat/2.0.2 2019-01-01 621 toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.1.1.20160309.5 2019-01-01 614 toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.6.0b-1 2019-01-01 600 toolshed.g2.bx.psu.edu/repos/crs4/prokka/prokka/1.13 2019-01-01 575 toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_heatmap/deeptools_plot_heatmap/3.0.2.0 2019-01-01 563 toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.27.0.2 2019-01-01 563 toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.6 2019-01-01 520 toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/1.6.3 2019-01-01 492 toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/3.2 2019-01-01 458 toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.1 2019-01-01 433 toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3 2019-01-01 433 ebi_sra_main 2019-01-01 431 toolshed.g2.bx.psu.edu/repos/lparsons/htseq_count/htseq_count/0.9.1 2019-01-01 423 toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1 2019-01-01 402 toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.1.0+galaxy3 2019-01-01 396 toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_profile/deeptools_plot_profile/3.1.2.0.0 2019-01-01 393 join1 2019-01-01 388 toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_quality_report/cardinal_quality_report/1.12.1.1 2019-01-01 384 toolshed.g2.bx.psu.edu/repos/galaxyp/maldi_quant_preprocessing/maldi_quant_preprocessing/1.18.0.2 2019-01-01 383 toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.4 2019-01-01 370 toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.1 2019-01-01 366 toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.3 2019-01-01 354 toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.4.1 2019-01-01 345 toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.27.1 2019-01-01 334 toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.4.3.1 2019-01-01 334 toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.1 2019-01-01 326 toolshed.g2.bx.psu.edu/repos/devteam/samtool_filter2/samtool_filter2/1.8 2019-01-01 320 Remove beginning1 2019-01-01 317 CONVERTER_interval_to_bed_0 2019-01-01 316 toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.0 2019-01-01 303 ucsc_table_direct1 2019-01-01 298 Summary_Statistics1 2019-01-01 294 toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.12 2019-01-01 286 toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/1.3.4 2019-01-01 270 toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.2.0 2019-01-01 249 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 Show tail1 2019-01-01 75 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 sort1 2019-01-01 50 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 Show beginning1 2019-01-01 42 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 __ZIP_COLLECTION__ 2019-01-01 37 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 CONVERTER_bam_to_bigwig_0 2019-01-01 35 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 toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_contigs/mothur_make_contigs/1.39.5.0 2019-01-01 33 secure_hash_message_digest 2019-01-01 33 __EXPORT_HISTORY__ 2019-01-01 33 toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.19.5 2019-01-01 33 CONVERTER_gff_to_bed_0 2019-01-01 32 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 __IMPORT_HISTORY__ 2019-01-01 12 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 CONVERTER_vcf_to_tabix_0 2019-01-01 5 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 CONVERTER_interval_to_bed6_0 2019-01-01 3 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 __SORTLIST__ 2019-01-01 3 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 __RELABEL_FROM_FILE__ 2019-01-01 3 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 __DATA_FETCH__ 2019-01-01 1 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 toolshed.g2.bx.psu.edu/repos/iuc/gemini_de_novo/gemini_de_novo/0.18.1.0 2019-01-01 1 toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_QualityScoreDistribution/2.18.2.1 2019-01-01 1 toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_annotate/4.1.1 2019-01-01 1 toolshed.g2.bx.psu.edu/repos/iuc/gemini_comp_hets/gemini_comp_hets/0.18.1.0 2019-01-01 1 toolshed.g2.bx.psu.edu/repos/iuc/gemini_burden/gemini_burden/0.20.1 2019-01-01 1 toolshed.g2.bx.psu.edu/repos/devteam/vcftools_annotate/vcftools_annotate/0.1 2019-01-01 1 toolshed.g2.bx.psu.edu/repos/galaxyp/openms_filemerger/FileMerger/2.3.0 2019-01-01 1 CONVERTER_interval_to_tabix_0 2019-01-01 1 toolshed.g2.bx.psu.edu/repos/iuc/gatk2/gatk2_variant_select/2.8.0 2019-01-01 1 toolshed.g2.bx.psu.edu/repos/iuc/gatk2/gatk2_variant_combine/2.8.0 2019-01-01 1 toolshed.g2.bx.psu.edu/repos/rnateam/aresite2/AREsite2_REST/0.1.2 2019-01-01 1 toolshed.g2.bx.psu.edu/repos/iuc/gatk2/gatk2_variant_annotator/2.8.0 2019-01-01 1 toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bedtoigv/2.27.1 2019-01-01 1 toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_RevertSam/2.18.2.1 2019-01-01 1 CONVERTER_interval_to_bgzip_0 2019-01-01 1 toolshed.g2.bx.psu.edu/repos/bgruening/find_subsequences/bg_find_subsequences/0.2 2019-01-01 1 toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_download/4.3+T.galaxy1 2019-01-01 1 toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_download/4.3k.0 2019-01-01 1 toolshed.g2.bx.psu.edu/repos/devteam/cuffdiff/cuffdiff/2.2.1.5 2019-01-01 1 toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_databases/4.0.0 2019-01-01 1 toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_complementbed/2.27.0.0 2019-01-01 1 toolshed.g2.bx.psu.edu/repos/galaxyp/bed_to_protein_map/bed_to_protein_map/0.1.0 2019-01-01 1 toolshed.g2.bx.psu.edu/repos/iuc/mummer_delta_filter/mummer_delta_filter/4.0.0beta2 2019-01-01 1 toolshed.g2.bx.psu.edu/repos/anton/vcfbedintersect/vcfbedintersect/0.0.2 2019-01-01 1 toolshed.g2.bx.psu.edu/repos/earlhaminst/blast_parser/blast_parser/0.1.2 2019-01-01 1 toolshed.g2.bx.psu.edu/repos/earlhaminst/ensembl_get_feature_info/get_feature_info/0.1.2 2019-01-01 1 toolshed.g2.bx.psu.edu/repos/earlhaminst/ensembl_get_genetree/get_genetree/0.1.2 2019-01-01 1 toolshed.g2.bx.psu.edu/repos/earlhaminst/ensembl_get_sequences/get_sequences/0.1.2 2019-01-01 1 toolshed.g2.bx.psu.edu/repos/iuc/ncbi_eutils_ecitmatch/ncbi_eutils_ecitmatch/1.2 2019-01-01 1 toolshed.g2.bx.psu.edu/repos/iuc/ncbi_eutils_efetch/ncbi_eutils_efetch/1.1 2019-01-01 1 toolshed.g2.bx.psu.edu/repos/bebatut/cdhit/cd_hit_protein/1.3 2019-01-01 1 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 toolshed.g2.bx.psu.edu/repos/iuc/ncbi_eutils_einfo/ncbi_eutils_einfo/1.1 2019-01-01 1 toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_coveragebed/2.27.1 2019-01-01 1 toolshed.g2.bx.psu.edu/repos/earlhaminst/ete/ete_init_taxdb/3.0.0b35 2019-01-01 1 toolshed.g2.bx.psu.edu/repos/iuc/ncbi_eutils_esearch/ncbi_eutils_esearch/1.1 2019-01-01 1 toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ValidateSamFile/2.18.2.1 2019-01-01 1 toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: backtranseq2/5.0.0 2019-01-01 1 toolshed.g2.bx.psu.edu/repos/earlhaminst/hcluster_sg_parser/hcluster_sg_parser/0.2.0 2019-01-01 1 toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idfileconverter/IDFileConverter/2.3.0 2019-01-01 1 bed2gff1 2019-01-01 1 CONVERTER_fasta_to_bowtie_color_index 2019-01-01 1 toolshed.g2.bx.psu.edu/repos/iuc/pick_closed_reference_otus/pick_closed_reference_otus/1.9.1.0 2019-01-01 1 toolshed.g2.bx.psu.edu/repos/earlhaminst/t_coffee/t_coffee/11.0.8 2019-01-01 1 toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: newcpgreport57/5.0.0.1 2019-01-01 1 toolshed.g2.bx.psu.edu/repos/iuc/pick_open_reference_otus/pick_open_reference_otus/1.9.1.0 2019-01-01 1 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 toolshed.g2.bx.psu.edu/repos/iuc/picrust_metagenome_contributions/picrust_metagenome_contributions/1.1.1.0 2019-01-01 1 toolshed.g2.bx.psu.edu/repos/bgruening/autodock_vina/docking/0.1.0 2019-01-01 1 toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: seqmatchall83/5.0.0.1 2019-01-01 1 toolshed.g2.bx.psu.edu/repos/devteam/plot_from_lda/plot_for_lda_output1/1.0.1 2019-01-01 1 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 CONVERTER_biom2_to_biom1 2019-01-01 1 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 toolshed.g2.bx.psu.edu/repos/rnateam/pipmir/pipmir/0.1.0 2019-01-01 1 toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: wordcount109/5.0.0.1 2019-01-01 1 toolshed.g2.bx.psu.edu/repos/devteam/express/express/1.1.1 2019-01-01 1 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 CONVERTER_Bam_Bai_0 2019-01-01 1 toolshed.g2.bx.psu.edu/repos/iuc/data_manager_gemini_database_downloader/data_manager_gemini_download/0.20.1 2019-01-01 1 toolshed.g2.bx.psu.edu/repos/galaxyp/openms_mapstatistics/MapStatistics/2.3.0 2019-01-01 1 toolshed.g2.bx.psu.edu/repos/iuc/column_order_header_sort/column_order_header_sort/0.0.1 2019-01-01 1 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 toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_windowbed/2.27.1 2019-01-01 1 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 toolshed.g2.bx.psu.edu/repos/devteam/fastq_quality_converter/cshl_fastq_quality_converter/1.0.1 2019-01-01 1 toolshed.g2.bx.psu.edu/repos/devteam/fastq_quality_filter/cshl_fastq_quality_filter/1.0.0 2019-01-01 1 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 Filter1 2018-12-01 2654 toolshed.g2.bx.psu.edu/repos/bgruening/infernal/infernal_cmsearch/1.1.2.0 2018-12-01 2061 toolshed.g2.bx.psu.edu/repos/bgruening/infernal/infernal_cmbuild/1.1.2.0 2018-12-01 2060 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 ucsc_table_direct1 2018-12-01 1628 toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.6 2018-12-01 1578 toolshed.g2.bx.psu.edu/repos/rnateam/graphclust_mlocarna/locarna_best_subtree/0.3 2018-12-01 1575 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 __SET_METADATA__ 2018-12-01 1455 Cut1 2018-12-01 1313 toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/1.3.4 2018-12-01 1143 ChangeCase 2018-12-01 1029 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 toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.1.0.46-0 2018-12-01 822 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 Grouping1 2018-12-01 691 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 CONVERTER_gz_to_uncompressed 2018-12-01 643 join1 2018-12-01 641 toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.4.2 2018-12-01 619 comp1 2018-12-01 584 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 cat1 2018-12-01 480 toolshed.g2.bx.psu.edu/repos/devteam/vcffilter/vcffilter2/1.0.0_rc1+galaxy1 2018-12-01 471 toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.4.3.1 2018-12-01 456 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 toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.1.0 2018-12-01 357 sort1 2018-12-01 329 toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.2 2018-12-01 326 toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.1.0+galaxy3 2018-12-01 323 CONVERTER_interval_to_bedstrict_0 2018-12-01 312 Show beginning1 2018-12-01 299 toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.1 2018-12-01 294 CONVERTER_interval_to_bed_0 2018-12-01 222 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 toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idposteriorerrorprobability/IDPosteriorErrorProbability/2.3.0 2018-12-01 208 ebi_sra_main 2018-12-01 196 toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/3.2 2018-12-01 195 toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.1 2018-12-01 194 toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.4.1 2018-12-01 191 toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.27.0.2 2018-12-01 190 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 CONVERTER_bam_to_qname_sorted_bam 2018-12-01 8 toolshed.g2.bx.psu.edu/repos/iuc/mothur_align_seqs/mothur_align_seqs/1.39.5.0 2018-12-01 8 __IMPORT_HISTORY__ 2018-12-01 8 toolshed.g2.bx.psu.edu/repos/bgruening/augustus/augustus/3.2.3 2018-12-01 8 toolshed.g2.bx.psu.edu/repos/devteam/fastq_to_tabular/fastq_to_tabular/1.1.0 2018-12-01 8 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 toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicbuildmatrix/hicexplorer_hicbuildmatrix/2.1.2.0 2018-12-01 7 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 __FLATTEN__ 2018-12-01 6 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 toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_subtractbed/2.27.0.0 2018-12-01 6 CONVERTER_bz2_to_uncompressed 2018-12-01 6 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 echo_main_env 2018-12-01 5 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 __UNZIP_COLLECTION__ 2018-12-01 5 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 toolshed.g2.bx.psu.edu/repos/peterjc/seq_filter_by_mapping/seq_filter_by_mapping/0.0.6 2018-12-01 5 toolshed.g2.bx.psu.edu/repos/iuc/mothur_sub_sample/mothur_sub_sample/1.39.5.0 2018-12-01 5 CONVERTER_len_to_linecount 2018-12-01 5 toolshed.g2.bx.psu.edu/repos/iuc/metagenomeseq_normalization/metagenomeseq_normalizaton/1.16.0-0.0.1 2018-12-01 5 toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_profile/deeptools_plot_profile/3.0.2.0 2018-12-01 5 sklearn_numeric_clustering 2018-12-01 5 toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.3.1 2018-12-01 5 CONVERTER_fasta_to_len 2018-12-01 5 toolshed.g2.bx.psu.edu/repos/devteam/pileup_parser/pileup_parser/1.0.2 2018-12-01 5 mosaik_wrapper 2018-12-01 5 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 toolshed.g2.bx.psu.edu/repos/iuc/mothur_remove_groups/mothur_remove_groups/1.39.5.0 2018-12-01 5 toolshed.g2.bx.psu.edu/repos/iuc/qiime_pick_closed_reference_otus/qiime_pick_closed_reference_otus/1.9.1.0 2018-12-01 5 toolshed.g2.bx.psu.edu/repos/anton/vcfcombine/vcfcombine/0.0.1 2018-12-01 4 CONVERTER_vcf_to_tabix_0 2018-12-01 4 toolshed.g2.bx.psu.edu/repos/iuc/metaphlan2krona/metaphlan2krona/2.6.0.0 2018-12-01 4 toolshed.g2.bx.psu.edu/repos/iuc/qiime_core_diversity/qiime_core_diversity/1.9.1.0 2018-12-01 4 toolshed.g2.bx.psu.edu/repos/chemteam/bio3d_pca/bio3d_pca/2.3 2018-12-01 4 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 toolshed.g2.bx.psu.edu/repos/devteam/xy_plot/XY_Plot_1/1.0.2 2018-12-01 4 toolshed.g2.bx.psu.edu/repos/galaxyp/thermo_raw_file_converter/thermo_raw_file_converter/0.0.1 2018-12-01 4 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 toolshed.g2.bx.psu.edu/repos/iuc/mothur_summary_single/mothur_summary_single/1.39.5.0 2018-12-01 4 toolshed.g2.bx.psu.edu/repos/devteam/samtools_calmd/samtools_calmd/2.0.2 2018-12-01 4 toolshed.g2.bx.psu.edu/repos/iuc/varscan_mpileup/varscan_mpileup/2.4.3.1 2018-12-01 4 toolshed.g2.bx.psu.edu/repos/rnateam/peakachu/peakachu/0.1.0.1 2018-12-01 4 toolshed.g2.bx.psu.edu/repos/iuc/trinity_analyze_diff_expr/trinity_analyze_diff_expr/2.8.4 2018-12-01 4 toolshed.g2.bx.psu.edu/repos/iuc/msaboot/msaboot/0.1.2 2018-12-01 4 toolshed.g2.bx.psu.edu/repos/peterjc/tmhmm_and_signalp/wolf_psort/0.0.11 2018-12-01 4 __DATA_FETCH__ 2018-12-01 4 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 toolshed.g2.bx.psu.edu/repos/iuc/qiime_summarize_taxa_through_plots/qiime_summarize_taxa_through_plots/1.9.1.0 2018-12-01 4 toolshed.g2.bx.psu.edu/repos/galaxyp/openms_mascotadapter/MascotAdapter/2.3.0 2018-12-01 4 toolshed.g2.bx.psu.edu/repos/peterjc/blast_rbh/blast_reciprocal_best_hits/0.1.11 2018-12-01 4 toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FastqToSam/2.18.2.1 2018-12-01 4 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 toolshed.g2.bx.psu.edu/repos/iuc/qiime_validate_mapping_file/qiime_validate_mapping_file/1.9.1.0 2018-12-01 4 toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_filtering/cardinal_filtering/1.12.1.0 2018-12-01 4 toolshed.g2.bx.psu.edu/repos/iuc/qiime_pick_open_reference_otus/qiime_pick_open_reference_otus/1.9.1.0 2018-12-01 4 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 __RELABEL_FROM_FILE__ 2018-12-01 3 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 __SORTLIST__ 2018-12-01 2 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 toolshed.g2.bx.psu.edu/repos/rnateam/mirdeep2_mapper/rbc_mirdeep2_mapper/2.0.0 2018-12-01 1 toolshed.g2.bx.psu.edu/repos/iuc/column_order_header_sort/column_order_header_sort/0.0.1 2018-12-01 1 toolshed.g2.bx.psu.edu/repos/rnateam/viennarna_rnafold/viennarna_rnafold/2.2.10.0 2018-12-01 1 toolshed.g2.bx.psu.edu/repos/galaxyp/msi_qualitycontrol/mass_spectrometry_imaging_qc/1.10.0.7 2018-12-01 1 toolshed.g2.bx.psu.edu/repos/iuc/meme_dreme/meme_dreme/4.11.2.0 2018-12-01 1 toolshed.g2.bx.psu.edu/repos/iuc/mothur_merge_files/mothur_merge_files/1.39.5.0 2018-12-01 1 toolshed.g2.bx.psu.edu/repos/gga/apollo_list_organism/list_organism/3.1 2018-12-01 1 toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fastq/tabular_to_fastq/1.0.0 2018-12-01 1 toolshed.g2.bx.psu.edu/repos/iuc/meme_chip/meme_chip/4.11.2 2018-12-01 1 toolshed.g2.bx.psu.edu/repos/iuc/gemini_mendel_errors/gemini_mendel_errors/0.18.1.1 2018-12-01 1 solid_qual_boxplot 2018-12-01 1 toolshed.g2.bx.psu.edu/repos/galaxyp/openms_openswathmzmlfilecacher/OpenSwathMzMLFileCacher/2.3.0 2018-12-01 1 toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.0.0 2018-12-01 1 toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: geecee41/5.0.0 2018-12-01 1 toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_fingerprint/deeptools_plot_fingerprint/2.5.7.0 2018-12-01 1 toolshed.g2.bx.psu.edu/repos/iuc/gemini_query/gemini_query/0.18.1.1 2018-12-01 1 toolshed.g2.bx.psu.edu/repos/jjohnson/translate_bed_sequences/translate_bed_sequences/0.0.1 2018-12-01 1 Count1 2018-12-01 1 toolshed.g2.bx.psu.edu/repos/rnateam/chipseeker/chipseeker/1.14.2 2018-12-01 1 toolshed.g2.bx.psu.edu/repos/bgruening/split_file_on_column/tp_split_on_column/0.2 2018-12-01 1 toolshed.g2.bx.psu.edu/repos/devteam/fastx_collapser/cshl_fastx_collapser/1.0.1 2018-12-01 1 toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_annotate/4.3.0 2018-12-01 1 toolshed.g2.bx.psu.edu/repos/rnateam/viennarna_rnacofold/viennarna_rnacofold/2.2.10.0 2018-12-01 1 toolshed.g2.bx.psu.edu/repos/rnateam/viennarna_rnaalifold/viennarna_rnaalifold/2.2.10.1 2018-12-01 1 toolshed.g2.bx.psu.edu/repos/peterjc/blastxml_to_top_descr/blastxml_to_top_descr/0.1.1 2018-12-01 1 toolshed.g2.bx.psu.edu/repos/rnateam/structure_to_gspan/structure_to_gspan/0.4 2018-12-01 1 toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_refinepeak/2.1.1.20160309.0 2018-12-01 1 toolshed.g2.bx.psu.edu/repos/iuc/plasflow/PlasFlow/1.0 2018-12-01 1 toolshed.g2.bx.psu.edu/repos/iuc/gffcompare/gffcompare/0.9.8 2018-12-01 1 toolshed.g2.bx.psu.edu/repos/devteam/scatterplot/scatterplot_rpy/1.0.3 2018-12-01 1 toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_nn_classifier/sklearn_nn_classifier/0.9 2018-12-01 1 toolshed.g2.bx.psu.edu/repos/peterjc/blast2go/blast2go/0.0.9 2018-12-01 1 toolshed.g2.bx.psu.edu/repos/iuc/poretools_extract/poretools_extract/0.6.1a1.0 2018-12-01 1 toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.0.0 2018-12-01 1 toolshed.g2.bx.psu.edu/repos/devteam/cuffdiff/cuffdiff/2.2.1.3 2018-12-01 1 toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_int/4.3+t.galaxy0 2018-12-01 1 toolshed.g2.bx.psu.edu/repos/galaxyp/openms_simplesearchengine/SimpleSearchEngine/2.3.0 2018-12-01 1 toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/0.9.1 2018-12-01 1 toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_clusterbed/2.27.0.0 2018-12-01 1 toolshed.g2.bx.psu.edu/repos/galaxyp/openms_demeanderize/DeMeanderize/2.3.0 2018-12-01 1 toolshed.g2.bx.psu.edu/repos/galaxyp/msi_filtering/mass_spectrometry_imaging_filtering/1.7.0.1 2018-12-01 1 toolshed.g2.bx.psu.edu/repos/iuc/poretools_yield_plot/poretools_yield_plot/0.6.1a1.0 2018-12-01 1 toolshed.g2.bx.psu.edu/repos/devteam/bam_to_sam/bam_to_sam/2.0 2018-12-01 1 toolshed.g2.bx.psu.edu/repos/nml/spades/spades/3.11.1+galaxy1 2018-12-01 1 toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/1.3.0 2018-12-01 1 toolshed.g2.bx.psu.edu/repos/devteam/fastx_reverse_complement/cshl_fastx_reverse_complement/1.0.2 2018-12-01 1 toolshed.g2.bx.psu.edu/repos/devteam/t_test_two_samples/t_test_two_samples/1.0.1 2018-12-01 1 toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.1.8.3 2018-12-01 1 toolshed.g2.bx.psu.edu/repos/iuc/trinity/trinity/2.4.0.2 2018-12-01 1 toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_complementbed/2.27.0.0 2018-12-01 1 toolshed.g2.bx.psu.edu/repos/lparsons/fastq_join/fastq_join/1.1.2-806 2018-12-01 1 sequence_convert 2018-12-01 1 __EXTRACT_DATASET__ 2018-12-01 1 toolshed.g2.bx.psu.edu/repos/galaxyp/quantp/quantp/1.0.0 2018-12-01 1 toolshed.g2.bx.psu.edu/repos/iuc/dexseq/dexseq/1.26.0.0 2018-12-01 1 __BUILD_LIST__ 2018-12-01 1 toolshed.g2.bx.psu.edu/repos/iuc/qiime_align_seqs/qiime_align_seqs/1.9.1.0 2018-12-01 1 toolshed.g2.bx.psu.edu/repos/galaxyp/openms_ticcalculator/TICCalculator/2.3.0 2018-12-01 1 toolshed.g2.bx.psu.edu/repos/iuc/qiime_alpha_rarefaction/qiime_alpha_rarefaction/1.9.1.0 2018-12-01 1 toolshed.g2.bx.psu.edu/repos/iuc/khmer_partition/khmer_partition/2.0.0 2018-12-01 1 toolshed.g2.bx.psu.edu/repos/galaxyp/openms_metaprosip/MetaProSIP/2.3.0 2018-12-01 1 toolshed.g2.bx.psu.edu/repos/galaxyp/openms_masstraceextractor/MassTraceExtractor/2.2.0 2018-12-01 1 toolshed.g2.bx.psu.edu/repos/devteam/samtools_split/samtools_split/1.3.1 2018-12-01 1 toolshed.g2.bx.psu.edu/repos/devteam/samtools_flagstat/samtools_flagstat/2.0 2018-12-01 1 toolshed.g2.bx.psu.edu/repos/rnateam/rnashapes/RNAshapes/3.3.0 2018-12-01 1 toolshed.g2.bx.psu.edu/repos/iuc/qiime_count_seqs/qiime_count_seqs/1.9.1.0 2018-12-01 1 toolshed.g2.bx.psu.edu/repos/devteam/varscan_version_2/varscan/0.1 2018-12-01 1 toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectGcBiasMetrics/2.18.2.1 2018-12-01 1 toolshed.g2.bx.psu.edu/repos/iuc/qiime_filter_samples_from_otu_table/qiime_filter_samples_from_otu_table/1.9.1.0 2018-12-01 1 toolshed.g2.bx.psu.edu/repos/galaxyp/openms_mapstatistics/MapStatistics/2.3.0 2018-12-01 1 toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.12.5+galaxy1 2018-12-01 1 bigwig_to_bedgraph 2018-12-01 1 toolshed.g2.bx.psu.edu/repos/rnateam/rcas/rcas/1.1.1 2018-12-01 1 toolshed.g2.bx.psu.edu/repos/iuc/disco/disco/1.2.0 2018-12-01 1 toolshed.g2.bx.psu.edu/repos/iuc/trinity_gene_to_trans_map/trinity_gene_to_trans_map/2.8.4 2018-12-01 1 toolshed.g2.bx.psu.edu/repos/iuc/qiime_make_otu_table/qiime_make_otu_table/1.9.1.0 2018-12-01 1 toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.12.5+galaxy2 2018-12-01 1 toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_subtractbed/2.27.1 2018-12-01 1 toolshed.g2.bx.psu.edu/repos/iuc/qiime_make_phylogeny/qiime_make_phylogeny/1.9.1.0 2018-12-01 1 toolshed.g2.bx.psu.edu/repos/iuc/bctools_extract_crosslinked_nucleotides/bctools_extract_crosslinked_nucleotides/@VERSION+galaxy1 2018-12-01 1 toolshed.g2.bx.psu.edu/repos/devteam/freebayes_wrapper/freebayes_wrapper/0.5.0 2018-12-01 1 toolshed.g2.bx.psu.edu/repos/galaxyp/openms_inspectadapter/InspectAdapter/2.3.0 2018-12-01 1 toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicsummatrices/hicexplorer_hicsummatrices/2.1.4.0 2018-12-01 1 toolshed.g2.bx.psu.edu/repos/iuc/trinity_contig_exn50_statistic/trinity_contig_exn50_statistic/2.8.4 2018-12-01 1 toolshed.g2.bx.psu.edu/repos/iuc/rnaspades/rnaspades/3.9.0.1 2018-12-01 1 toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicplotdistvscounts/hicexplorer_hicplotdistvscounts/2.1.4.0 2018-12-01 1 toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicplotmatrix/hicexplorer_hicplotmatrix/1.8.0 2018-12-01 1 toolshed.g2.bx.psu.edu/repos/bgruening/nn_classifier/nn_classifier/0.9 2018-12-01 1 toolshed.g2.bx.psu.edu/repos/iuc/fasta_nucleotide_color_plot/fasta_nucleotide_color_plot/1.0.1 2018-12-01 1 toolshed.g2.bx.psu.edu/repos/crs4/ssake/ssake/0.0.10 2018-12-01 1 toolshed.g2.bx.psu.edu/repos/iuc/bctools_extract_barcodes/bctools_extract_barcodes/0.2.2 2018-12-01 1 toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/0.8.1+galaxy0 2018-12-01 1 toolshed.g2.bx.psu.edu/repos/earlhaminst/treebest_best/treebest_best/1.9.2 2018-12-01 1 toolshed.g2.bx.psu.edu/repos/bgruening/trna_prediction/trnascan/0.4 2018-12-01 1 toolshed.g2.bx.psu.edu/repos/iuc/humann2_renorm_table/humann2_renorm_table/0.11.1.0 2018-12-01 1 toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_quality_report/cardinal_quality_report/1.12.1.0 2018-12-01 1 toolshed.g2.bx.psu.edu/repos/rnateam/peakachu/peakachu/0.1.0.0 2018-12-01 1 toolshed.g2.bx.psu.edu/repos/devteam/megablast_xml_parser/megablast_xml_parser/1.0.0 2018-12-01 1 toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_data_exporter/cardinal_data_exporter/1.12.1.0 2018-12-01 1 toolshed.g2.bx.psu.edu/repos/iuc/qiime_summarize_taxa/qiime_summarize_taxa/1.9.1.0 2018-12-01 1 toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_nucbed/2.27.0.1 2018-12-01 1 toolshed.g2.bx.psu.edu/repos/rnateam/mirdeep2_quantifier/rbc_mirdeep2_quantifier/2.0.0 2018-12-01 1 toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/0.8.1+galaxy0 2018-12-01 1 toolshed.g2.bx.psu.edu/repos/bgruening/wtdbg/wtdbg/1.2.8.1 2018-12-01 1 toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: newcpgseek58/5.0.0.1 2018-12-01 1 toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: newcpgreport57/5.0.0.1 2018-12-01 1 toolshed.g2.bx.psu.edu/repos/devteam/dna_filtering/histogram_rpy/1.0.3 2018-12-01 1 toolshed.g2.bx.psu.edu/repos/iuc/bcftools_norm/bcftools_norm/1.4.0.0 2018-12-01 1 toolshed.g2.bx.psu.edu/repos/galaxyp/msi_classification/mass_spectrometry_imaging_classification/1.10.0.0 2018-12-01 1 toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed/2.27.1 2018-12-01 1 toolshed.g2.bx.psu.edu/repos/iuc/mummer_delta_filter/mummer_delta_filter/4.0.0beta2 2018-12-01 1 toolshed.g2.bx.psu.edu/repos/iuc/mummer_dnadiff/mummer_dnadiff/4.0.0beta2 2018-12-01 1 toolshed.g2.bx.psu.edu/repos/peterjc/tmhmm_and_signalp/signalp3/0.0.19 2018-12-01 1 CONVERTER_Bam_Bai_0 2018-12-01 1 toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_gc_bias/deeptools_compute_gc_bias/2.5.7.0 2018-12-01 1 toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: cpgplot15/5.0.0 2018-12-01 1 toolshed.g2.bx.psu.edu/repos/iuc/metaphlan_hclust_heatmap/metaphlan_hclust_heatmap/2.6.0.0 2018-12-01 1 CONVERTER_sam_to_unsorted_bam 2018-12-01 1 toolshed.g2.bx.psu.edu/repos/iuc/gemini_dump/gemini_dump/0.18.1.1 2018-12-01 1 toolshed.g2.bx.psu.edu/repos/iuc/ncbi_eutils_efetch/ncbi_eutils_efetch/1.1 2018-12-01 1 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 Filter1 2018-11-01 1421 toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.36.5 2018-11-01 1418 echo_main_handler2 2018-11-01 1110 echo_main_handler1 2018-11-01 1110 echo_main_handler0 2018-11-01 1110 echo_main_handler5 2018-11-01 1109 echo_main_handler3 2018-11-01 1109 echo_main_handler4 2018-11-01 1109 echo_main_handler8 2018-11-01 1108 echo_main_handler6 2018-11-01 1108 echo_main_handler7 2018-11-01 1108 echo_main_handler9 2018-11-01 1108 echo_main_handler10 2018-11-01 1107 echo_main_drmaa 2018-11-01 1107 echo_main_handler11 2018-11-01 1107 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 toolshed.g2.bx.psu.edu/repos/devteam/tophat2/tophat2/2.1.1 2018-11-01 986 toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.1.0.46-0 2018-11-01 986 __SET_METADATA__ 2018-11-01 986 toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/0.11.2 2018-11-01 974 toolshed.g2.bx.psu.edu/repos/devteam/vcffilter/vcffilter2/1.0.0_rc1+galaxy1 2018-11-01 953 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 toolshed.g2.bx.psu.edu/repos/rnateam/graphclust_mlocarna/locarna_best_subtree/0.3 2018-11-01 845 toolshed.g2.bx.psu.edu/repos/rnateam/graphclust_cmfinder/cmFinder/0.3 2018-11-01 845 comp1 2018-11-01 728 Cut1 2018-11-01 691 toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/1.6.3 2018-11-01 687 CONVERTER_gz_to_uncompressed 2018-11-01 618 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 toolshed.g2.bx.psu.edu/repos/iuc/trinity_align_and_estimate_abundance/trinity_align_and_estimate_abundance/2.8.4 2018-11-01 472 ebi_sra_main 2018-11-01 464 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 Remove beginning1 2018-11-01 373 ucsc_table_direct1 2018-11-01 333 toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.4 2018-11-01 326 toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_compare/deeptools_bam_compare/3.0.2.0 2018-11-01 321 join1 2018-11-01 320 toolshed.g2.bx.psu.edu/repos/devteam/samtools_flagstat/samtools_flagstat/2.0.2 2018-11-01 312 CONVERTER_bam_to_coodinate_sorted_bam 2018-11-01 295 toolshed.g2.bx.psu.edu/repos/iuc/scpipe/scpipe/1.0.0 2018-11-01 291 cat1 2018-11-01 283 toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.2 2018-11-01 279 CONVERTER_bed_gff_or_vcf_to_bigwig_0 2018-11-01 270 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 CONVERTER_bed_to_bgzip_0 2018-11-01 261 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 CONVERTER_interval_to_bed_0 2018-11-01 155 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 addValue 2018-11-01 119 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 ChangeCase 2018-11-01 109 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 sort1 2018-11-01 83 Convert characters1 2018-11-01 83 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 secure_hash_message_digest 2018-11-01 68 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 Show tail1 2018-11-01 61 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 Show beginning1 2018-11-01 52 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 __IMPORT_HISTORY__ 2018-11-01 26 toolshed.g2.bx.psu.edu/repos/rnateam/blockbuster/blockbuster/0.1.1.1 2018-11-01 26 __RELABEL_FROM_FILE__ 2018-11-01 26 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 CONVERTER_interval_to_bed12_0 2018-11-01 16 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 __ZIP_COLLECTION__ 2018-11-01 8 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 __FILTER_FROM_FILE__ 2018-11-01 8 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 __APPLY_RULES__ 2018-11-01 5 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 toolshed.g2.bx.psu.edu/repos/iuc/mothur_get_communitytype/mothur_get_communitytype/1.36.1.0 2018-11-01 3 __DATA_FETCH__ 2018-11-01 3 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 __UNZIP_COLLECTION__ 2018-11-01 3 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 __FLATTEN__ 2018-11-01 1 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 toolshed.g2.bx.psu.edu/repos/nml/spades/spades/3.11.1+galaxy1 2018-11-01 1 toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastp_wrapper/0.2.00 2018-11-01 1 toolshed.g2.bx.psu.edu/repos/bgruening/rnaz/rnaz/2.1.1 2018-11-01 1 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 toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hiccorrelate/hicexplorer_hiccorrelate/2.1.4.0 2018-11-01 1 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 toolshed.g2.bx.psu.edu/repos/devteam/fastq_quality_boxplot/cshl_fastq_quality_boxplot/1.0.1 2018-11-01 1 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 toolshed.g2.bx.psu.edu/repos/iuc/qiime_make_otu_table/qiime_make_otu_table/1.9.1.0 2018-11-01 1 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 toolshed.g2.bx.psu.edu/repos/devteam/fastq_to_tabular/fastq_to_tabular/1.1.0 2018-11-01 1 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 toolshed.g2.bx.psu.edu/repos/iuc/bcftools_cnv/bcftools_cnv/1.4.0.0 2018-11-01 1 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 echo_main_handler1 2018-10-01 2975 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 __SET_METADATA__ 2018-10-01 1486 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 Filter1 2018-10-01 1020 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 Convert characters1 2018-10-01 574 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 Remove beginning1 2018-10-01 447 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 join1 2018-10-01 302 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 Show beginning1 2018-10-01 134 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 __ZIP_COLLECTION__ 2018-10-01 98 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 Show tail1 2018-10-01 67 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 toolshed.g2.bx.psu.edu/repos/iuc/mothur_get_communitytype/mothur_get_communitytype/1.36.1.0 2018-10-01 1 toolshed.g2.bx.psu.edu/repos/bebatut/format_cd_hit_output/format_cd_hit_output/1.0.0 2018-10-01 1 toolshed.g2.bx.psu.edu/repos/iuc/mothur_classify_otu/mothur_classify_otu/1.36.1.0 2018-10-01 1 toolshed.g2.bx.psu.edu/repos/iuc/mothur_get_groups/mothur_get_groups/1.36.1.0 2018-10-01 1 toolshed.g2.bx.psu.edu/repos/galaxyp/openms_peakpickerwavelet/PeakPickerWavelet/2.3.0 2018-10-01 1 toolshed.g2.bx.psu.edu/repos/miller-lab/genome_diversity/gd_new_oscar/1.0.0 2018-10-01 1 toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_bdgcmp/2.1.1.20160309.0 2018-10-01 1 toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_fingerprint/deeptools_plot_fingerprint/2.5.1.1.0 2018-10-01 1 toolshed.g2.bx.psu.edu/repos/iuc/mothur_count_seqs/mothur_count_seqs/1.36.1.0 2018-10-01 1 toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_filtering/cardinal_filtering/1.12.1.1 2018-10-01 1 toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.19.3.3 2018-10-01 1 toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_compound_convert/openbabel_compound_convert/2.4.1.0 2018-10-01 1 toolshed.g2.bx.psu.edu/repos/wolma/mimodd_main/mimodd_vcf_filter/0.1.8_1 2018-10-01 1 toolshed.g2.bx.psu.edu/repos/devteam/vcfsort/vcfsort/1.0.0_rc1+galaxy0 2018-10-01 1 methtools_plot 2018-10-01 1 CONVERTER_picard_interval_list_to_bed6 2018-10-01 1 toolshed.g2.bx.psu.edu/repos/iuc/mothur_venn/mothur_venn/1.36.1.0 2018-10-01 1 toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_annotatebed/2.27.0.0 2018-10-01 1 toolshed.g2.bx.psu.edu/repos/bgruening/glimmer3/glimmer_build-icm/0.2 2018-10-01 1 toolshed.g2.bx.psu.edu/repos/iuc/hmmer3/hmmer_hmmscan/0.1.0 2018-10-01 1 toolshed.g2.bx.psu.edu/repos/devteam/vcf2pgsnp/vcf2pgSnp/1.0.0 2018-10-01 1 gtf_filter_by_attribute_values_list 2018-10-01 1 toolshed.g2.bx.psu.edu/repos/iuc/mothur_dist_shared/mothur_dist_shared/1.36.1.0 2018-10-01 1 toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.38 2018-10-01 1 toolshed.g2.bx.psu.edu/repos/iuc/bcftools/bcfview/0.1.19 2018-10-01 1 modENCODEfly 2018-10-01 1 toolshed.g2.bx.psu.edu/repos/galaxyp/openms_consensusmapnormalizer/ConsensusMapNormalizer/2.3.0 2018-10-01 1 toolshed.g2.bx.psu.edu/repos/galaxyp/cardinal_mz_images/cardinal_mz_images/1.12.1.1 2018-10-01 1 gtf2bedgraph 2018-10-01 1 toolshed.g2.bx.psu.edu/repos/iuc/mothur_chimera_uchime/mothur_chimera_uchime/1.36.1.0 2018-10-01 1 CONVERTER_interval_to_bed6_0 2018-10-01 1 toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_bdgdiff/2.1.1.20160309.1 2018-10-01 1 toolshed.g2.bx.psu.edu/repos/bgruening/nanopolish_methylation/nanopolish_methylation/0.1.0 2018-10-01 1 toolshed.g2.bx.psu.edu/repos/iuc/picrust_metagenome_contributions/picrust_metagenome_contributions/1.1.1.0 2018-10-01 1 toolshed.g2.bx.psu.edu/repos/bgruening/nanopolish_eventalign/nanopolish_eventalign/0.1.0 2018-10-01 1 __FILTER_FAILED_DATASETS__ 2018-10-01 1 toolshed.g2.bx.psu.edu/repos/iuc/kallisto_quant/kallisto_quant/0.43.1.3 2018-10-01 1 toolshed.g2.bx.psu.edu/repos/devteam/ctd_batch/ctdBatch_1/1.0.0 2018-10-01 1 toolshed.g2.bx.psu.edu/repos/iuc/valet/valet/1.0.0 2018-10-01 1 toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.63 2018-10-01 1 toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/0.0.1 2018-10-01 1 toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_segmasker_wrapper/0.3.1 2018-10-01 1 toolshed.g2.bx.psu.edu/repos/iuc/picrust_categorize/picrust_categorize/1.1.1.0 2018-10-01 1 toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_annotate/4.3+t.galaxy0 2018-10-01 1 toolshed.g2.bx.psu.edu/repos/iuc/mothur_align_seqs/mothur_align_seqs/1.36.1.0 2018-10-01 1 toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/1.1.2 2018-10-01 1 toolshed.g2.bx.psu.edu/repos/devteam/data_manager_build_kraken_database/kraken_database_builder/1.1 2018-10-01 1 toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/search_gui/3.2.13.3 2018-10-01 1 toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_retcor/abims_xcms_retcor/2.1.0 2018-10-01 1 toolshed.g2.bx.psu.edu/repos/iuc/mothur_summary_single/mothur_summary_single/1.36.1.0 2018-10-01 1 toolshed.g2.bx.psu.edu/repos/rnateam/splitfasta/rbc_splitfasta/0.2.0 2018-10-01 1 toolshed.g2.bx.psu.edu/repos/iuc/bcftools_call/bcftools_call/1.4.0 2018-10-01 1 toolshed.g2.bx.psu.edu/repos/iuc/mothur_lefse/mothur_lefse/1.36.1.0 2018-10-01 1 toolshed.g2.bx.psu.edu/repos/devteam/data_manager_fetch_genome_dbkeys_all_fasta/data_manager_fetch_genome_all_fasta_dbkey/0.0.1 2018-10-01 1 toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_shufflebed/2.27.0.0 2018-10-01 1 toolshed.g2.bx.psu.edu/repos/iuc/gatk2/gatk2_haplotype_caller/2.8.0 2018-10-01 1 toolshed.g2.bx.psu.edu/repos/iuc/vsearch/vsearch_chimera_detection/2.8.3.0 2018-10-01 1 toolshed.g2.bx.psu.edu/repos/devteam/data_manager_twobit_builder/twobit_builder_data_manager/0.0.2 2018-10-01 1 toolshed.g2.bx.psu.edu/repos/iuc/pick_open_reference_otus/pick_open_reference_otus/1.9.1.0 2018-10-01 1 convert_bc_to_binary_RY.py 2018-10-01 1 toolshed.g2.bx.psu.edu/repos/iuc/gatk2/gatk2_variant_validate/2.8.0 2018-10-01 1 toolshed.g2.bx.psu.edu/repos/crs4/prokka/prokka/1.12.0 2018-10-01 1 toolshed.g2.bx.psu.edu/repos/galaxyp/msconvert/msconvert_nix/3.0.0 2018-10-01 1 toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_biom/mothur_make_biom/1.39.5.0 2018-10-01 1 toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.1.8.0 2018-10-01 1 toolshed.g2.bx.psu.edu/repos/gbcs-embl-heidelberg/je_demultiplex_illu/je_demultiplex_illu/1.2.1 2018-10-01 1 CONVERTER_sdf_to_smiles 2018-10-01 1 toolshed.g2.bx.psu.edu/repos/iuc/abricate/abricate/0.8 2018-10-01 1 toolshed.g2.bx.psu.edu/repos/iuc/gatk2/gatk2_indel_realigner/2.8.0 2018-10-01 1 toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.1.8.3 2018-10-01 1 toolshed.g2.bx.psu.edu/repos/bgruening/bismark/bismark_deduplicate/0.20.0 2018-10-01 1 toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/1.0.0 2018-10-01 1 toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_contigs/mothur_make_contigs/1.36.1.0 2018-10-01 1 toolshed.g2.bx.psu.edu/repos/iuc/gatk2/gatk2_indel_realigner/0.0.7 2018-10-01 1 toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_regression_metrics/sklearn_regression_metrics/0.9 2018-10-01 1 toolshed.g2.bx.psu.edu/repos/iuc/mothur_sub_sample/mothur_sub_sample/1.36.1.0 2018-10-01 1 upload1 2018-09-01 8512 cat1 2018-09-01 6988 echo_main_handler0 2018-09-01 3049 echo_main_handler1 2018-09-01 3048 echo_main_handler2 2018-09-01 3044 echo_main_handler3 2018-09-01 3042 echo_main_handler4 2018-09-01 3038 echo_main_handler5 2018-09-01 3036 echo_main_handler6 2018-09-01 3035 echo_main_handler7 2018-09-01 3034 echo_main_handler8 2018-09-01 3034 echo_main_handler9 2018-09-01 3033 echo_main_handler10 2018-09-01 3032 echo_main_handler11 2018-09-01 3029 echo_main_drmaa 2018-09-01 3028 echo_main_condor 2018-09-01 3026 toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.71 2018-09-01 2135 toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_xcmsset/abims_xcms_xcmsSet/2.1.1 2018-09-01 1540 toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_heatmap/deeptools_plot_heatmap/3.0.2.0 2018-09-01 1292 toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/1.6.2 2018-09-01 1107 toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/deeptools_compute_matrix/3.0.2.0 2018-09-01 1103 __SET_METADATA__ 2018-09-01 1072 toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.4.2 2018-09-01 818 toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.4.3.1 2018-09-01 775 Filter1 2018-09-01 749 Cut1 2018-09-01 746 ucsc_table_direct1 2018-09-01 706 toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.1 2018-09-01 636 toolshed.g2.bx.psu.edu/repos/devteam/fastqtofasta/fastq_to_fasta_python/1.0.0 2018-09-01 593 toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.1.0 2018-09-01 519 toolshed.g2.bx.psu.edu/repos/galaxyp/msi_filtering/mass_spectrometry_imaging_filtering/1.10.0.6 2018-09-01 491 toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.0.2.0 2018-09-01 458 toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.36.5 2018-09-01 429 toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.2 2018-09-01 425 toolshed.g2.bx.psu.edu/repos/galaxyp/openms_msgfplusadapter/MSGFPlusAdapter/2.3.0 2018-09-01 418 toolshed.g2.bx.psu.edu/repos/lparsons/htseq_count/htseq_count/0.9.1 2018-09-01 418 toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/1.1.0 2018-09-01 409 toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/1.1.0 2018-09-01 403 wig_to_bigWig 2018-09-01 390 toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.6.0b-1 2018-09-01 387 toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.2 2018-09-01 360 toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.6 2018-09-01 357 toolshed.g2.bx.psu.edu/repos/mvdbeek/add_input_name_as_column/addName/0.1.1 2018-09-01 356 toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.5.2b-2 2018-09-01 351 toolshed.g2.bx.psu.edu/repos/bgruening/pileometh/pileometh/0.3.0.1 2018-09-01 342 toolshed.g2.bx.psu.edu/repos/galaxyp/msi_qualitycontrol/mass_spectrometry_imaging_qc/1.10.0.7 2018-09-01 339 toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_searchcv/sklearn_searchcv/0.9 2018-09-01 321 toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed_bedgraph/2.19.0 2018-09-01 314 toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1 2018-09-01 307 Remove beginning1 2018-09-01 299 toolshed.g2.bx.psu.edu/repos/galaxyp/msi_spectra_plot/mass_spectrometry_imaging_mzplots/1.10.0.6 2018-09-01 285 toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.1.0 2018-09-01 278 toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.36.0 2018-09-01 272 toolshed.g2.bx.psu.edu/repos/galaxyp/msi_preprocessing/mass_spectrometry_imaging_preprocessing/1.10.0.6 2018-09-01 264 join1 2018-09-01 259 toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72 2018-09-01 257 toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.3 2018-09-01 242 toolshed.g2.bx.psu.edu/repos/devteam/intersect/gops_intersect_1/1.0.0 2018-09-01 231 toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.1.1.20160309.4 2018-09-01 231 toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_intersectbed/2.27.0.2 2018-09-01 229 ebi_sra_main 2018-09-01 227 CONVERTER_gz_to_uncompressed 2018-09-01 217 toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_group/abims_xcms_group/2.1.1 2018-09-01 212 toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_coveragebed/2.27.0.2 2018-09-01 210 CONVERTER_interval_to_bedstrict_0 2018-09-01 206 toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.0.0 2018-09-01 204 toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/column_remove_by_header/0.0.1 2018-09-01 197 toolshed.g2.bx.psu.edu/repos/galaxyp/openms_falsediscoveryrate/FalseDiscoveryRate/2.3.0 2018-09-01 193 toolshed.g2.bx.psu.edu/repos/iuc/bwameth/bwameth/0.2.0.4 2018-09-01 191 toolshed.g2.bx.psu.edu/repos/galaxyp/msi_preprocessing/mass_spectrometry_imaging_preprocessing/1.10.0.7 2018-09-01 189 toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_retcor/abims_xcms_retcor/2.1.1 2018-09-01 188 toolshed.g2.bx.psu.edu/repos/crs4/bwa_mem/bwa_mem/0.8.0 2018-09-01 186 toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.67 2018-09-01 185 toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.5.2b-1 2018-09-01 184 Grouping1 2018-09-01 184 toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicplotmatrix/hicexplorer_hicplotmatrix/2.1.4.0 2018-09-01 178 toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/1.3.4 2018-09-01 171 toolshed.g2.bx.psu.edu/repos/bgruening/plotly_parallel_coordinates_plot/plotly_parallel_coordinates_plot/0.1 2018-09-01 166 Show beginning1 2018-09-01 164 toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.0 2018-09-01 161 toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0 2018-09-01 160 toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_heatmap2/ggplot2_heatmap2/2.2.1 2018-09-01 159 Grep1 2018-09-01 159 comp1 2018-09-01 156 toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.1 2018-09-01 154 toolshed.g2.bx.psu.edu/repos/galaxyp/msi_qualitycontrol/mass_spectrometry_imaging_qc/1.10.0.4 2018-09-01 154 toolshed.g2.bx.psu.edu/repos/galaxyp/msi_classification/mass_spectrometry_imaging_classification/1.10.0.0 2018-09-01 153 toolshed.g2.bx.psu.edu/repos/galaxyp/openms_peptideindexer/PeptideIndexer/2.3.0 2018-09-01 152 toolshed.g2.bx.psu.edu/repos/devteam/join/gops_join_1/1.0.0 2018-09-01 147 toolshed.g2.bx.psu.edu/repos/iuc/pear/iuc_pear/0.9.6.1 2018-09-01 145 toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/1.0.0 2018-09-01 143 toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/2.8.1.3 2018-09-01 143 CONVERTER_interval_to_bed_0 2018-09-01 141 toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_correlation/deeptools_plot_correlation/3.0.2.0 2018-09-01 139 toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idmerger/IDMerger/2.3.0 2018-09-01 137 toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idmapper/IDMapper/2.3.0 2018-09-01 136 toolshed.g2.bx.psu.edu/repos/galaxyp/openms_consensusid/ConsensusID/2.3.0 2018-09-01 132 toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.0 2018-09-01 129 toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.4.3.0 2018-09-01 129 toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idconflictresolver/IDConflictResolver/2.3.0 2018-09-01 129 toolshed.g2.bx.psu.edu/repos/galaxyp/openms_isobaricanalyzer/IsobaricAnalyzer/2.3.0 2018-09-01 129 toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.1 2018-09-01 129 toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_compare/deeptools_bam_compare/3.0.2.0 2018-09-01 125 toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/0.11.2 2018-09-01 123 toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.1.0+galaxy3 2018-09-01 120 addValue 2018-09-01 120 toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_infer_experiment/2.6.4.1 2018-09-01 118 toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicbuildmatrix/hicexplorer_hicbuildmatrix/2.1.4.0 2018-09-01 116 toolshed.g2.bx.psu.edu/repos/iuc/graphlan/graphlan/1.0.0.0 2018-09-01 115 toolshed.g2.bx.psu.edu/repos/galaxyp/proteomics_moff/proteomics_moff/1.2.1.1 2018-09-01 114 toolshed.g2.bx.psu.edu/repos/iuc/ngsutils_bam_filter/ngsutils_bam_filter/0.5.9 2018-09-01 112 toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hiccorrectmatrix/hicexplorer_hiccorrectmatrix/2.1.4.0 2018-09-01 111 toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1 2018-09-01 111 toolshed.g2.bx.psu.edu/repos/lparsons/htseq_count/htseq_count/0.6.1galaxy2 2018-09-01 110 wc_gnu 2018-09-01 109 toolshed.g2.bx.psu.edu/repos/devteam/fastqtofasta/fastq_to_fasta_python/1.1.1 2018-09-01 108 toolshed.g2.bx.psu.edu/repos/galaxyp/thermo_raw_file_converter/thermo_raw_file_converter/0.0.1 2018-09-01 108 ChangeCase 2018-09-01 103 toolshed.g2.bx.psu.edu/repos/iuc/export2graphlan/export2graphlan/0.19 2018-09-01 101 toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtofastq/2.27.0.0 2018-09-01 101 toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/search_gui/3.3.3.0 2018-09-01 101 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 __DATA_FETCH__ 2018-09-01 4 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 __FILTER_FROM_FILE__ 2018-09-01 3 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 toolshed.g2.bx.psu.edu/repos/devteam/fastq_quality_filter/cshl_fastq_quality_filter/1.0.2 2018-09-01 1 toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fastq/tabular_to_fastq/1.0.0 2018-09-01 1 __ZIP_COLLECTION__ 2018-09-01 1 toolshed.g2.bx.psu.edu/repos/jjohnson/query_tabular/filter_tabular/5.0.0 2018-09-01 1 toolshed.g2.bx.psu.edu/repos/jjohnson/cdhit/cd_hit_est/1.2 2018-09-01 1 toolshed.g2.bx.psu.edu/repos/iuc/zerone/zerone/1.0 2018-09-01 1 toolshed.g2.bx.psu.edu/repos/devteam/tables_arithmetic_operations/tables_arithmetic_operations/1.0.0 2018-09-01 1 gff_filter_by_attribute 2018-09-01 1 toolshed.g2.bx.psu.edu/repos/iuc/mageck_count/mageck_count/0.5.7.4 2018-09-01 1 toolshed.g2.bx.psu.edu/repos/iuc/vsearch/vsearch_chimera_detection/1.9.7.0 2018-09-01 1 toolshed.g2.bx.psu.edu/repos/iuc/meme_chip/meme_chip/4.11.2 2018-09-01 1 toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastx_wrapper/0.2.01 2018-09-01 1 hgv_david 2018-09-01 1 toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_convert2blastmask_wrapper/0.3.0 2018-09-01 1 toolshed.g2.bx.psu.edu/repos/gbcs-embl-heidelberg/je_markdupes/je_markdupes/1.2.1 2018-09-01 1 toolshed.g2.bx.psu.edu/repos/galaxyp/openms_decharger/Decharger/2.3.0 2018-09-01 1 toolshed.g2.bx.psu.edu/repos/iuc/merge_metaphlan_tables/merge_metaphlan_tables/2.6.0.0 2018-09-01 1 toolshed.g2.bx.psu.edu/repos/devteam/fastq_quality_boxplot/cshl_fastq_quality_boxplot/1.0.1 2018-09-01 1 toolshed.g2.bx.psu.edu/repos/iuc/mothur_align_seqs/mothur_align_seqs/1.36.1.0 2018-09-01 1 toolshed.g2.bx.psu.edu/repos/galaxyp/openms_digestor/Digestor/2.3.0 2018-09-01 1 toolshed.g2.bx.psu.edu/repos/iuc/mothur_chimera_slayer/mothur_chimera_slayer/1.39.5.0 2018-09-01 1 toolshed.g2.bx.psu.edu/repos/iuc/mothur_chimera_uchime/mothur_chimera_uchime/1.36.1.0 2018-09-01 1 toolshed.g2.bx.psu.edu/repos/iuc/mothur_classify_otu/mothur_classify_otu/1.36.1.0 2018-09-01 1 toolshed.g2.bx.psu.edu/repos/iuc/trinity_super_transcripts/trinity_super_transcripts/2.8.3 2018-09-01 1 toolshed.g2.bx.psu.edu/repos/iuc/mothur_classify_rf/mothur_classify_rf/1.36.1.0 2018-09-01 1 toolshed.g2.bx.psu.edu/repos/iuc/mothur_classify_seqs/mothur_classify_seqs/1.36.1.0 2018-09-01 1 toolshed.g2.bx.psu.edu/repos/iuc/mothur_cluster/mothur_cluster/1.36.1.0 2018-09-01 1 toolshed.g2.bx.psu.edu/repos/iuc/mothur_cluster_split/mothur_cluster_split/1.36.1.0 2018-09-01 1 toolshed.g2.bx.psu.edu/repos/iuc/trinity_run_de_analysis/trinity_run_de_analysis/2.8.3 2018-09-01 1 toolshed.g2.bx.psu.edu/repos/iuc/trinity_gene_to_trans_map/trinity_gene_to_trans_map/2.8.3 2018-09-01 1 toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_svm_classifier/sklearn_svm_classifier/0.9 2018-09-01 1 toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_ensemble/sklearn_ensemble/0.9 2018-09-01 1 toolshed.g2.bx.psu.edu/repos/iuc/mothur_count_seqs/mothur_count_seqs/1.36.1.0 2018-09-01 1 toolshed.g2.bx.psu.edu/repos/bgruening/sklearn_discriminant_classifier/sklearn_discriminant_classifier/0.9 2018-09-01 1 toolshed.g2.bx.psu.edu/repos/iuc/mothur_dist_seqs/mothur_dist_seqs/1.36.1.0 2018-09-01 1 toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0.1 2018-09-01 1 toolshed.g2.bx.psu.edu/repos/iuc/mothur_dist_shared/mothur_dist_shared/1.36.1.0 2018-09-01 1 methtools_plot 2018-09-01 1 toolshed.g2.bx.psu.edu/repos/iuc/trinity_analyze_diff_expr/trinity_analyze_diff_expr/2.8.3 2018-09-01 1 toolshed.g2.bx.psu.edu/repos/iuc/mothur_filter_seqs/mothur_filter_seqs/1.36.1.0 2018-09-01 1 toolshed.g2.bx.psu.edu/repos/galaxyp/proteomics_moff/proteomics_moff/1.2 2018-09-01 1 toolshed.g2.bx.psu.edu/repos/iuc/trinity_align_and_estimate_abundance/trinity_align_and_estimate_abundance/2.6.6 2018-09-01 1 toolshed.g2.bx.psu.edu/repos/iuc/mothur_get_communitytype/mothur_get_communitytype/1.36.1.0 2018-09-01 1 toolshed.g2.bx.psu.edu/repos/iuc/mothur_get_coremicrobiome/mothur_get_coremicrobiome/1.39.5.0 2018-09-01 1 toolshed.g2.bx.psu.edu/repos/iuc/mothur_get_groups/mothur_get_groups/1.36.1.0 2018-09-01 1 toolshed.g2.bx.psu.edu/repos/bgruening/numeric_clustering/numeric_clustering/0.9 2018-09-01 1 toolshed.g2.bx.psu.edu/repos/iuc/mothur_get_rabund/mothur_get_rabund/1.39.5.0 2018-09-01 1 toolshed.g2.bx.psu.edu/repos/iuc/mothur_get_relabund/mothur_get_relabund/1.39.5.0 2018-09-01 1 toolshed.g2.bx.psu.edu/repos/wolma/mimodd_main/mimodd_vcf_filter/0.1.8_1 2018-09-01 1 toolshed.g2.bx.psu.edu/repos/bgruening/nanopolish_methylation/nanopolish_methylation/0.1.0 2018-09-01 1 random_lines1 2018-09-01 1 toolshed.g2.bx.psu.edu/repos/iuc/mothur_lefse/mothur_lefse/1.36.1.0 2018-09-01 1 toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_contigs/mothur_make_contigs/1.36.1.0 2018-09-01 1 __RELABEL_FROM_FILE__ 2018-09-01 1 toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sra_pileup/2.9.1.2 2018-09-01 1 toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/2.9.1.3 2018-09-01 1 toolshed.g2.bx.psu.edu/repos/iuc/mothur_metastats/mothur_metastats/1.36.1.0 2018-09-01 1 secure_hash_message_digest 2018-09-01 1 toolshed.g2.bx.psu.edu/repos/devteam/picard/PicardInsertSize/1.56.0 2018-09-01 1 toolshed.g2.bx.psu.edu/repos/iuc/mothur_otu_hierarchy/mothur_otu_hierarchy/1.39.5.0 2018-09-01 1 toolshed.g2.bx.psu.edu/repos/iuc/mothur_parse_list/mothur_parse_list/1.39.5.0 2018-09-01 1 toolshed.g2.bx.psu.edu/repos/iuc/mothur_pre_cluster/mothur_pre_cluster/1.36.1.0 2018-09-01 1 toolshed.g2.bx.psu.edu/repos/galaxyp/openms_filefilter/FileFilter/2.2.0 2018-09-01 1 toolshed.g2.bx.psu.edu/repos/iuc/sqlite_to_tabular/sqlite_to_tabular/2.0.0 2018-09-01 1 toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpsift_vartype/4.3.1 2018-09-01 1 toolshed.g2.bx.psu.edu/repos/iuc/mothur_remove_groups/mothur_remove_groups/1.36.1.0 2018-09-01 1 toolshed.g2.bx.psu.edu/repos/iuc/mothur_remove_lineage/mothur_remove_lineage/1.36.1.0 2018-09-01 1 __APPLY_RULES__ 2018-09-01 1 toolshed.g2.bx.psu.edu/repos/iuc/mothur_seq_error/mothur_seq_error/1.36.1.0 2018-09-01 1 toolshed.g2.bx.psu.edu/repos/iuc/snpsift_dbnsfp_generic/snpSift_dbnsfp_generic/4.1.1 2018-09-01 1 toolshed.g2.bx.psu.edu/repos/iuc/mothur_sub_sample/mothur_sub_sample/1.36.1.0 2018-09-01 1 toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hiccorrectmatrix/hicexplorer_hiccorrectmatrix/1.8.0 2018-09-01 1 toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeSamFiles/2.7.1.0 2018-09-01 1 toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hiccomparematrices/hicexplorer_hiccomparematrices/2.1.4.0 2018-09-01 1 toolshed.g2.bx.psu.edu/repos/galaxyp/openms_qcimporter/QCImporter/2.3.0 2018-09-01 1 toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_databases/4.3r.1 2018-09-01 1 toolshed.g2.bx.psu.edu/repos/iuc/mothur_summary_single/mothur_summary_single/1.36.1.0 2018-09-01 1 toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_databases/4.0.0 2018-09-01 1 toolshed.g2.bx.psu.edu/repos/galaxyp/openms_qcembedder/QCEmbedder/2.3.0 2018-09-01 1 toolshed.g2.bx.psu.edu/repos/iuc/mothur_summary_single/mothur_summary_single/1.39.5.0 2018-09-01 1 toolshed.g2.bx.psu.edu/repos/galaxyp/openms_highresprecursormasscorrector/HighResPrecursorMassCorrector/2.2.0 2018-09-01 1 toolshed.g2.bx.psu.edu/repos/bgruening/graphmap_align/graphmap_align/0.5.2 2018-09-01 1 toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReorderSam/2.18.2.1 2018-09-01 1 toolshed.g2.bx.psu.edu/repos/bebatut/cdhit/cd_hit_est/1.3 2018-09-01 1 toolshed.g2.bx.psu.edu/repos/iuc/mothur_venn/mothur_venn/1.36.1.0 2018-09-01 1 toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idfileconverter/IDFileConverter/2.1.0 2018-09-01 1 toolshed.g2.bx.psu.edu/repos/bgruening/diamond/bg_diamond_makedb/0.8.24 2018-09-01 1 toolshed.g2.bx.psu.edu/repos/galaxyp/openms_idfileconverter/IDFileConverter/2.2.0 2018-09-01 1 toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/3.4 2018-09-01 1 toolshed.g2.bx.psu.edu/repos/bgruening/augustus/augustus/3.2.3 2018-09-01 1 toolshed.g2.bx.psu.edu/repos/iuc/ncbi_eutils_einfo/ncbi_eutils_einfo/1.1 2018-09-01 1 toolshed.g2.bx.psu.edu/repos/bgruening/bismark/bismark_deduplicate/0.16.3 2018-09-01 1 toolshed.g2.bx.psu.edu/repos/devteam/picard/rgPicFixMate/1.56.0 2018-09-01 1 toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_mergepe/1.2.0 2018-09-01 1 toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_fqchk/1.2.0 2018-09-01 1 toolshed.g2.bx.psu.edu/repos/iuc/raceid_diffgene/raceid_diffgene/1.0.0 2018-09-01 1 toolshed.g2.bx.psu.edu/repos/iuc/qiime_assign_taxonomy/qiime_assign_taxonomy/1.9.1.0 2018-09-01 1