api_key: 'd223b6821fd95b7f9558a771ef1a8931' galaxy_instance: 127.0.0.1:8080 tools: - name: 'column_maker' owner: 'devteam' tool_panel_section_id: 'textutil' revisions: - '08a01b2ce4cd' # v1.1.0 - name: 'tabular_to_fasta' owner: 'devteam' tool_panel_section_id: 'convert' revisions: - '0b4e36026794' # v1.1.0 - name: 'fasta_to_tabular' owner: 'devteam' tool_panel_section_id: 'convert' revisions: - '9d189d08f2ad' # v1.1.0 - name: 'fastqtofasta' owner: 'devteam' tool_panel_section_id: 'convert' revisions: - '3571553aeb20' # v1.0.0 - name: 'dna_filtering' owner: 'devteam' tool_panel_section_id: 'filter' revisions: - 'a6f0d355b05f' # v1.0.3 - name: 'subtract_query' owner: 'devteam' tool_panel_section_id: 'group' revisions: - '5f6ebef89722' # v0.1 - name: 'fastqc' owner: 'devteam' tool_panel_section_id: 'cshl_library_information' revisions: - '8c650f7f76e9' # v0.63 - 'e28c965eeed4' # v0.52 - name: 'short_reads_trim_seq' owner: 'devteam' tool_panel_section_id: 'cshl_library_information' revisions: - 'f17a1585733b' - name: 'short_reads_figure_score' owner: 'devteam' tool_panel_section_id: 'cshl_library_information' revisions: - 'b52b9c7aabd9' - name: 'fastq_quality_boxplot' owner: 'devteam' tool_panel_section_id: 'cshl_library_information' revisions: - 'f95284aa2946' - name: 'fastq_quality_converter' owner: 'devteam' tool_panel_section_id: 'cshl_library_information' revisions: - 'b87c74b61d81' - name: 'fastq_quality_filter' owner: 'devteam' tool_panel_section_id: 'cshl_library_information' revisions: - '57adb07cccfc' - name: 'fastx_artifacts_filter' owner: 'devteam' tool_panel_section_id: 'cshl_library_information' revisions: - 'c8808979ba33' - name: 'fastx_barcode_splitter' owner: 'devteam' tool_panel_section_id: 'cshl_library_information' revisions: - 'c46a5807f2b6' - name: 'fastx_clipper' owner: 'devteam' tool_panel_section_id: 'cshl_library_information' revisions: - '8192b4014977' - name: 'fastx_collapser' owner: 'devteam' tool_panel_section_id: 'cshl_library_information' revisions: - '13c2d9e8c6d5' - name: 'fastx_nucleotides_distribution' owner: 'devteam' tool_panel_section_id: 'cshl_library_information' revisions: - '9353010b95df' - name: 'fastx_quality_statistics' owner: 'devteam' tool_panel_section_id: 'cshl_library_information' revisions: - 'c2af34024061' - name: 'fastx_renamer' owner: 'devteam' tool_panel_section_id: 'cshl_library_information' revisions: - 'd7bce63e6e09' - name: 'fastx_reverse_complement' owner: 'devteam' tool_panel_section_id: 'cshl_library_information' revisions: - '5bd826723d61' - name: 'fastx_trimmer' owner: 'devteam' tool_panel_section_id: 'cshl_library_information' revisions: - 'd77c9c6ecf68' - name: 'fastq_combiner' owner: 'devteam' tool_panel_section_id: 'cshl_library_information' revisions: - '94306bdd58f7' - name: 'fastq_filter' owner: 'devteam' tool_panel_section_id: 'cshl_library_information' revisions: - '30d9ece6c752' - name: 'fastq_groomer' owner: 'devteam' tool_panel_section_id: 'cshl_library_information' revisions: - '1298445c852b' - name: 'fastq_manipulation' owner: 'devteam' tool_panel_section_id: 'cshl_library_information' revisions: - '5d1e9e13e8db' - name: 'fastq_masker_by_quality' owner: 'devteam' tool_panel_section_id: 'cshl_library_information' revisions: - '5a7b5751617b' - name: 'fastq_paired_end_joiner' owner: 'devteam' tool_panel_section_id: 'cshl_library_information' revisions: - '270a8ed8a300' - name: 'fastq_paired_end_splitter' owner: 'devteam' tool_panel_section_id: 'cshl_library_information' revisions: - 'c549e99026db' - name: 'fastq_stats' owner: 'devteam' tool_panel_section_id: 'cshl_library_information' revisions: - '9b7b4e0ca9db' - name: 'fastq_to_tabular' owner: 'devteam' tool_panel_section_id: 'cshl_library_information' revisions: - 'bc9269529e88' - name: 'fastq_trimmer' owner: 'devteam' tool_panel_section_id: 'cshl_library_information' revisions: - '0b9feb0ed628' - name: 'fastq_trimmer_by_quality' owner: 'devteam' tool_panel_section_id: 'cshl_library_information' revisions: - '1cdcaf5fc1da' - name: 'tabular_to_fastq' owner: 'devteam' tool_panel_section_id: 'cshl_library_information' revisions: - 'b334cd1095ea' - name: 'bowtie2' owner: 'devteam' tool_panel_section_id: 'ngs_mapping' revisions: - 'ceb6467e276c' # v0.4 - 'c1ec08cb34f9' # v0.3 - 'a54de7e658f7' # v0.2 - name: 'bwa' owner: 'devteam' tool_panel_section_id: 'ngs_mapping' revisions: - 'c71dd035971e' # v0.1 - 'ac30bfd3e2a8' # v0.2.2 & v0.2.3 - name: 'megablast_xml_parser' owner: 'devteam' tool_panel_section_id: 'ngs_mapping' revisions: - '03ca082aeb2e' # v1.0.0 - name: 'megablast_wrapper' owner: 'devteam' tool_panel_section_id: 'ngs_mapping' revisions: - 'dc7b4acb3fa6' # v1.2.0 - name: 'bwa_wrappers' owner: 'devteam' tool_panel_section_id: 'ngs_mapping' revisions: - 'b4427dbb6ced' # v1.0.2 & v1.2.3 - name: 'lastz' owner: 'devteam' tool_panel_section_id: 'ngs_mapping' revisions: - 'd054d95585b1' # v1.2.2 - name: 'bamtools' owner: 'devteam' tool_panel_section_id: 'ngs:_bam_tools' revisions: - '76b2f1eee508' # v0.0.1 - name: 'bamtools_filter' owner: 'devteam' tool_panel_section_id: 'ngs:_bam_tools' revisions: - 'd64c7e752f4d' # v0.0.1 - name: 'bamtools_split' owner: 'devteam' tool_panel_section_id: 'ngs:_bam_tools' revisions: - '71dd32fb0b0a' # v0.0.1 - name: 'picard' owner: 'devteam' tool_panel_section_id: 'ngs:_picard' revisions: - '379fdf4c41ac' # v1.126.0 - name: 'vcfgeno2haplo' owner: 'anton' tool_panel_section_id: 'ngs:_vcf_manipulation' revisions: - 'd6fd217a1f90' - name: 'vcfgeno2haplo' owner: 'devteam' tool_panel_section_id: 'ngs:_vcf_manipulation' revisions: - '2bdb74ab3270' - name: 'vcfcombine' owner: 'devteam' tool_panel_section_id: 'ngs:_vcf_manipulation' revisions: - 'da419f5ed589' - name: 'vcffilter' owner: 'devteam' tool_panel_section_id: 'ngs:_vcf_manipulation' revisions: - '34c3b846e0b6' - name: 'vcf2tsv' owner: 'devteam' tool_panel_section_id: 'ngs:_vcf_manipulation' revisions: - 'd6c944f1581a' - name: 'vcfallelicprimitives' owner: 'devteam' tool_panel_section_id: 'ngs:_vcf_manipulation' revisions: - '3f4fefbc52c8' - name: 'vcfbreakcreatemulti' owner: 'devteam' tool_panel_section_id: 'ngs:_vcf_manipulation' revisions: - 'f0dae4ac267e' - name: 'vcfrandomsample' owner: 'devteam' tool_panel_section_id: 'ngs:_vcf_manipulation' revisions: - 'd9efe7842413' - name: 'vcfflatten' owner: 'devteam' tool_panel_section_id: 'ngs:_vcf_manipulation' revisions: - '38d93ca9c0f0' - name: 'vcfselectsamples' owner: 'devteam' tool_panel_section_id: 'ngs:_vcf_manipulation' revisions: - '88fd8ef7e4af' - name: 'vcfcheck' owner: 'devteam' tool_panel_section_id: 'ngs:_vcf_manipulation' revisions: - 'd7d4d88ae84d' - name: 'vcfgenotypes' owner: 'devteam' tool_panel_section_id: 'ngs:_vcf_manipulation' revisions: - '1673e7848bf4' - name: 'vcfvcfintersect' owner: 'devteam' tool_panel_section_id: 'ngs:_vcf_manipulation' revisions: - 'b29dbe1270b5' - name: 'vcfhethom' owner: 'devteam' tool_panel_section_id: 'ngs:_vcf_manipulation' revisions: - '586d614a4c2d' - name: 'vcfleftalign' owner: 'devteam' tool_panel_section_id: 'ngs:_vcf_manipulation' revisions: - '3e3d0dffeb1f' - name: 'vcfaddinfo' owner: 'devteam' tool_panel_section_id: 'ngs:_vcf_manipulation' revisions: - '4d4b16af67aa' - name: 'vcfsort' owner: 'devteam' tool_panel_section_id: 'ngs:_vcf_manipulation' revisions: - '433d50620231' - name: 'vcfprimers' owner: 'devteam' tool_panel_section_id: 'ngs:_vcf_manipulation' revisions: - '67a4da1a4df3' - name: 'vcfannotategenotypes' owner: 'devteam' tool_panel_section_id: 'ngs:_vcf_manipulation' revisions: - 'c6be83b8883d' - name: 'vcffixup' owner: 'devteam' tool_panel_section_id: 'ngs:_vcf_manipulation' revisions: - 'a03f346b6aae' - name: 'vcfbedintersect' owner: 'devteam' tool_panel_section_id: 'ngs:_vcf_manipulation' revisions: - '8a482a9aa45d' - name: 'vcfdistance' owner: 'devteam' tool_panel_section_id: 'ngs:_vcf_manipulation' revisions: - '6e0fc18309f4' - name: 'vcfcommonsamples' owner: 'devteam' tool_panel_section_id: 'ngs:_vcf_manipulation' revisions: - 'f27d6187d808' - name: 'annotation_profiler' owner: 'devteam' tool_panel_section_id: 'bxops' revisions: - '3b33da018e74' - name: 'merge' owner: 'devteam' tool_panel_section_id: 'bxops' revisions: - '1bc76ceffa7f' # v1.0.0 - name: 'flanking_features' owner: 'devteam' tool_panel_section_id: 'bxops' revisions: - '90100b587723' # v4.0.1 - name: 'concat' owner: 'devteam' tool_panel_section_id: 'bxops' revisions: - '855580142a12' #v1.0.1 - name: 'get_flanks' owner: 'devteam' tool_panel_section_id: 'bxops' revisions: - '4b14d0e3a837' #v1.0.0 - name: 'coverage' owner: 'devteam' tool_panel_section_id: 'bxops' revisions: - '16b62a897aac' #v1.0.0 - name: 'cluster' owner: 'devteam' tool_panel_section_id: 'bxops' revisions: - '520de69b107a' #v1.0.0 - name: 'basecoverage' owner: 'devteam' tool_panel_section_id: 'bxops' revisions: - 'b8a9e718caa3' #v1.0.0 - name: join owner: devteam tool_panel_section_id: bxops revisions: - 'de21bdbb8d28' # v1.0.0 - name: annotation_profiler owner: devteam tool_panel_section_id: bxops revisions: - '3b33da018e74' # v1.0.0 - name: subtract owner: devteam tool_panel_section_id: bxops revisions: - 'c19a2a29c561' #v1.0.0 - name: intersect owner: devteam tool_panel_section_id: bxops revisions: - '77641d5731c8' # v1.0.0 - name: complement owner: devteam tool_panel_section_id: bxops revisions: - '2221cf5f59aa' # v1.0.0 - name: 'plot_from_lda' owner: 'devteam' tool_panel_section_id: 'stats' revisions: - 'c5ab37076128' - name: 'lda_analysis' owner: 'devteam' tool_panel_section_id: 'stats' revisions: - 'f38763b52f33' - name: 'generate_pc_lda_matrix' owner: 'devteam' tool_panel_section_id: 'stats' revisions: - '04cdbd00dcec' - name: 'correlation' owner: 'devteam' tool_panel_section_id: 'stats' revisions: - '24e01abf9e34' - name: 'ucsc_custom_track' owner: 'devteam' tool_panel_section_id: 'plots' revisions: - '618e56c3109b' - name: 'scatterplot' owner: 'devteam' tool_panel_section_id: 'plots' revisions: - 'c12b0759203b' - name: 'histogram' owner: 'devteam' tool_panel_section_id: 'plots' revisions: - '6ff47de059a0' - name: 'xy_plot' owner: 'devteam' tool_panel_section_id: 'plots' revisions: - '1a73a2406edc' - name: 'gmaj' owner: 'devteam' tool_panel_section_id: 'plots' revisions: - '2cd5ee197ec7' - name: 'vcf2pgsnp' owner: 'devteam' tool_panel_section_id: 'hgv' revisions: - '5fca46616675' - name: 'snpfreq' owner: 'devteam' tool_panel_section_id: 'hgv' revisions: - '72ea0d13dd66' - name: 'ctd_batch' owner: 'devteam' tool_panel_section_id: 'hgv' revisions: - '4a32700dcaa2' - name: 'divide_pg_snp' owner: 'devteam' tool_panel_section_id: 'hgv' revisions: - 'f74fdfc17143' - name: 'hgv_fundo' owner: 'devteam' tool_panel_section_id: 'hgv' revisions: - '64133669255f' - name: 'hgv_hilbertvis' owner: 'devteam' tool_panel_section_id: 'hgv' revisions: - 'e1a9ad05dced' - name: 'freebayes_wrapper' owner: 'devteam' tool_panel_section_id: 'hgv' revisions: - '33a0e6aca936' - name: 'dgidb_annotator' owner: 'devteam' tool_panel_section_id: 'hgv' revisions: - 'c5bb987015c5' - name: 'snpeff' owner: 'pcingola' tool_panel_section_id: 'snpeff' revisions: - 'c052639fa666' - name: 'check_snpeff_candidates' owner: 'gregory-minevich' tool_panel_section_id: 'snpeff' revisions: - 'f20585ccbf05' - name: 'bedtools' owner: 'aaronquinlan' tool_panel_section_id: 'bedtools' revisions: - '41bba3e648d1' # Broken install # - name: 'genome_diversity' # owner: 'miller-lab' # tool_panel_section_id: 'genome_diversity' # tool_shed_url: https://toolshed.g2.bx.psu.edu - name: 'emboss_5' owner: 'devteam' tool_panel_section_id: 'EMBOSSLite' revisions: - 'ce22ceec214a' - name: 'linear_regression' owner: 'devteam' tool_panel_section_id: 'regVar' revisions: - 'cf431604ec3e' - name: 'logistic_regression_vif' owner: 'devteam' tool_panel_section_id: 'regVar' revisions: - 'bd196d7c1ca9' - name: 'partialr_square' owner: 'devteam' tool_panel_section_id: 'regVar' revisions: - '88ef41de020d' - name: 'rcve' owner: 'devteam' tool_panel_section_id: 'regVar' revisions: - '7740956d197b' - name: 'substitution_rates' owner: 'devteam' tool_panel_section_id: 'regVar' revisions: - 'd1b35bcdaacc' - name: 'substitutions' owner: 'devteam' tool_panel_section_id: 'regVar' revisions: - 'c54f5d0bbb58' - name: 'weightedaverage' owner: 'devteam' tool_panel_section_id: 'regVar' revisions: - '90611e86a998' - name: 'canonical_correlation_analysis' owner: 'devteam' tool_panel_section_id: 'regVar' revisions: - '9bc0c48a027f' - name: 'kernel_canonical_correlation_analysis' owner: 'devteam' tool_panel_section_id: 'regVar' revisions: - '7a092113eb8c' - name: 'kernel_principal_component_analysis' owner: 'devteam' tool_panel_section_id: 'regVar' revisions: - 'e9ebd4bfbdfc' - name: 'indels_3way' owner: 'devteam' tool_panel_section_id: 'regVar' revisions: - '5ad24b81dd10' - name: 'featurecounter' owner: 'devteam' tool_panel_section_id: 'regVar' revisions: - 'ac6218e2b686' - name: 'getindelrates_3way' owner: 'devteam' tool_panel_section_id: 'regVar' revisions: - 'd427e5acb9ee' - name: 'maf_cpg_filter' owner: 'devteam' tool_panel_section_id: 'regVar' revisions: - '7f2a12cb047d' - name: 'microsats_mutability' owner: 'devteam' tool_panel_section_id: 'regVar' revisions: - '4aa1ee5d8510' - name: 'best_regression_subsets' owner: 'devteam' tool_panel_section_id: 'regVar' revisions: - '4f33ec73e445' - name: 'getindels_2way' owner: 'devteam' tool_panel_section_id: 'regVar' revisions: - 'f1dc6f5fce6e' - name: 'microsats_alignment_level' owner: 'devteam' tool_panel_section_id: 'regVar' revisions: - 'ad471b193191' - name: 'windowsplitter' owner: 'devteam' tool_panel_section_id: 'regVar' revisions: - '75abda2290cc' - name: 'karyotype_plot' owner: 'guru-ananda' tool_panel_section_id: 'regVar' revisions: - 'd810aa84ee6a' - name: 'rhmm' owner: 'guru-ananda' tool_panel_section_id: 'regVar' revisions: - '38f5cd46ffd3' - name: 'heatmap' owner: 'guru-ananda' tool_panel_section_id: 'regVar' revisions: - 'dbd447fcd3e4' - name: 'fasta_filter_by_length' owner: 'devteam' tool_panel_section_id: 'fasta_manipulation' revisions: - '16679a7f554a' - name: 'fasta_concatenate_by_species' owner: 'devteam' tool_panel_section_id: 'fasta_manipulation' revisions: - '717aee069681' - name: 'fasta_compute_length' owner: 'devteam' tool_panel_section_id: 'fasta_manipulation' revisions: - '1dbb5181c327' - name: 'fasta_formatter' owner: 'devteam' tool_panel_section_id: 'fasta_manipulation' revisions: - '1dbb5181c327' - name: 'fasta_nucleotide_changer' owner: 'devteam' tool_panel_section_id: 'fasta_manipulation' revisions: - '2f868bfbe9de' - name: 'mutate_snp_codon' owner: 'devteam' tool_panel_section_id: 'hyphy' revisions: - '8f0af7251167' - name: 'clustalw' owner: 'devteam' tool_panel_section_id: 'clustal' revisions: - 'acf51ff24c7d' - name: 'find_diag_hits' owner: 'devteam' tool_panel_section_id: 'tax_manipulation' revisions: - 'acf51ff24c7d' - name: 'gi2taxonomy' owner: 'devteam' tool_panel_section_id: 'tax_manipulation' revisions: - '7b1b03c4465d' - name: 'lca_wrapper' owner: 'devteam' tool_panel_section_id: 'tax_manipulation' revisions: - '33e8ed5a4601' - name: 'poisson2test' owner: 'devteam' tool_panel_section_id: 'tax_manipulation' revisions: - '8cd5945559b8' - name: 't2ps' owner: 'devteam' tool_panel_section_id: 'tax_manipulation' revisions: - 'dee81096ec71' - name: 't2t_report' owner: 'devteam' tool_panel_section_id: 'tax_manipulation' revisions: - '592acb9505fc' - name: 'weblogo3' owner: 'devteam' tool_panel_section_id: 'motifs' revisions: - 'a10f9ed463ae' # v0.4 - name: 'bam_to_sam' owner: 'devteam' tool_panel_section_id: 'samtools' revisions: - 'af7c50162f0b' # v2.0 - 'dc20f447c0e2' # v1.0.3 - name: 'pileup_interval' owner: 'devteam' tool_panel_section_id: 'samtools' revisions: - 'a110f9d6ae24' # v1.0.0 - name: 'pileup_parser' owner: 'devteam' tool_panel_section_id: 'samtools' revisions: - '1670f0565000' # v1.0.2 - name: 'sam2interval' owner: 'devteam' tool_panel_section_id: 'samtools' revisions: - '8c737b8ddc45' # v1.0.1 - name: 'sam_bitwise_flag_filter' owner: 'devteam' tool_panel_section_id: 'samtools' revisions: - '0b2424a404d9' # v1.0.0 - name: 'sam_merge' owner: 'devteam' tool_panel_section_id: 'samtools' revisions: - 'a7a49d31c5cf' # v1.1.2 - name: 'sam_pileup' owner: 'devteam' tool_panel_section_id: 'samtools' revisions: - '890d97772e2a' # v1.1.2 - '95612c159681' # v1.1.1 - name: 'sam_to_bam' owner: 'devteam' tool_panel_section_id: 'samtools' revisions: - 'd04d9f1c6791' - name: 'samtools_flagstat' owner: 'devteam' tool_panel_section_id: 'samtools' revisions: - '0072bf593791' - name: 'samtools_mpileup' owner: 'devteam' tool_panel_section_id: 'samtools' revisions: - 'aa0ef6f0ee89' # v2.0 - '44a18a94d7a9' # v0.0.1 - name: 'samtools_rmdup' owner: 'devteam' tool_panel_section_id: 'samtools' revisions: - '3735f950b2f5' - name: 'samtool_filter2' owner: 'devteam' tool_panel_section_id: 'samtools' revisions: - '2d4ae2f8231e' - name: 'bcftools_view' owner: 'gregory-minevich' tool_panel_section_id: 'samtools' revisions: - '6572c40a8505' - name: 'samtools_slice_bam' owner: 'devteam' tool_panel_section_id: 'samtools' revisions: - '2b474ebbfc7d' # v2.0 - '68ba55e96489' # v0.0.1 - name: 'sam_merge' owner: 'devteam' tool_panel_section_id: 'samtools' revisions: - '1f18d80df2a5' - 'a7a49d31c5cf' - name: 'samtools_idxstats' owner: 'devteam' tool_panel_section_id: 'samtools' revisions: - '87398ae795c7' - name: 'samtools_bedcov' owner: 'devteam' tool_panel_section_id: 'samtools' revisions: - '8c3472790020' - name: 'samtools_calmd' owner: 'devteam' tool_panel_section_id: 'samtools' revisions: - '1ebb4ecdc1ef' - name: 'samtools_sort' owner: 'devteam' tool_panel_section_id: 'samtools' revisions: - 'a430da4f04cd' - name: 'samtools_stats' owner: 'devteam' tool_panel_section_id: 'samtools' revisions: - '0d71d9467847' - name: 'samtools_split' owner: 'devteam' tool_panel_section_id: 'samtools' revisions: - '57f3e32f809d' - name: 'samtools_reheader' owner: 'devteam' tool_panel_section_id: 'samtools' revisions: - '020e144b5f78' - name: 'macs' owner: 'devteam' tool_panel_section_id: 'peak_calling' revisions: - 'ae2ec275332a' # v1.0.1 - name: 'sicer' owner: 'devteam' tool_panel_section_id: 'peak_calling' revisions: - '82a8234e03f2' # v0.0.1 - name: 'naive_variant_caller' owner: 'blankenberg' tool_panel_section_id: 'variant_detection' revisions: - '907b40517289' # v0.0.1 - name: 'ems_variant_density_mapping' owner: 'gregory-minevich' tool_panel_section_id: 'variant_detection' revisions: - 'ddfef7773c2d' # v1.0.0 - name: 'snp_mapping_using_wgs' owner: 'gregory-minevich' tool_panel_section_id: 'variant_detection' revisions: - '7fb9d1e732a0' # v1.0.0 - name: 'cloudmap_variant_discovery_mapping' owner: 'gregory-minevich' tool_panel_section_id: 'variant_detection' revisions: - 'c80c0aabc869' # v1.0.0 - name: 'cloudmap_in_silico_complementation' owner: 'gregory-minevich' tool_panel_section_id: 'variant_detection' revisions: - '5389dc5a0be3' # v1.0.0 - name: 'allele_counts' owner: 'nick' tool_panel_section_id: 'variant_detection' revisions: - '31361191d2d2' # v1.1 - name: 'getalleleseq' owner: 'boris' tool_panel_section_id: 'variant_detection' revisions: - '5a89151b5e82' # v0.0.1 - name: 'varscan_version_2' owner: 'devteam' tool_panel_section_id: 'variant_detection' revisions: - '6f8cead3dc93' # v0.1 - name: 'table_annovar' owner: 'devteam' tool_panel_section_id: 'variant_detection' revisions: - '091154194ce8' # v0.1 - name: 'vcftools_annotate' owner: 'devteam' tool_panel_section_id: 'variant_detection' revisions: - '57a6550df582' # v0.1 - name: 'vcftools_slice' owner: 'devteam' tool_panel_section_id: 'variant_detection' revisions: - '1363e5d4a8b8' # v0.1 - name: 'tophat2' owner: 'devteam' tool_panel_section_id: 'ngs-rna-tools' revisions: - '5c5517d2a9e9' # v0.9 - '6242cda7e278' # v0.7 - 'ae06af1118dc' # v0.6 - name: 'cuffcompare' owner: 'devteam' tool_panel_section_id: 'ngs-rna-tools' revisions: - '8e534225baa9' # v2.2.1.0 - '8b22e9adae34' # v0.0.6 - '7fb01ea4a641' # v0.0.5 - name: 'cufflinks' owner: 'devteam' tool_panel_section_id: 'ngs-rna-tools' revisions: - '64698e16f4a6' # v2.2.1.0 - '9aab29e159a7' # v0.0.7 - '7498f5a8fe06' # v0.0.6 - name: 'cuffmerge' owner: 'devteam' tool_panel_section_id: 'ngs-rna-tools' revisions: - 'b6e3849293b1' # v2.2.1.0 - '424d49834830' # v0.0.6 - 'aa209d311ece' # v0.0.5 - name: 'filter_transcripts_via_tracking' owner: 'devteam' tool_panel_section_id: 'ngs-rna-tools' revisions: - '31154ff9f5e1' # v0.1 - name: 'cuffdiff' owner: 'devteam' tool_panel_section_id: 'ngs-rna-tools' revisions: - '4e6f043995ff' # v2.2.1.2 - 'db57b46b05bf' # v2.2.1.1 - '604fa75232a2' # v0.0.7 - '2d6a90609943' # v0.0.6 - name: 'tophat_fusion_post' owner: 'devteam' tool_panel_section_id: 'ngs-rna-tools' revisions: - 'f83394a2c2da' # v0.1 - name: 'gffread' owner: 'devteam' tool_panel_section_id: 'ngs-rna-tools' revisions: - '5f6e6582c01d' # v2.2.1.0 - name: 'cuffnorm' owner: 'devteam' tool_panel_section_id: 'ngs-rna-tools' revisions: - 'a26af05ac218' # v2.2.1.0 - name: 'cuffquant' owner: 'devteam' tool_panel_section_id: 'ngs-rna-tools' revisions: - '5d8b9dcaf17d' # v2.2.1.0 - name: stringtie owner: 'iuc' tool_panel_section_id: 'ngs-rna-tools' revisions: - '48b891c1c2aa' # v1.0.3 - name: 'variants_validate' owner: 'devteam' tool_panel_section_id: 'gatk' revisions: - '7e1ecaa64370' - name: 'variant_select' owner: 'devteam' tool_panel_section_id: 'gatk' revisions: - '135e8721ffc5' - name: 'variant_recalibrator' owner: 'devteam' tool_panel_section_id: 'gatk' revisions: - 'cb7cf57397a7' - name: 'variant_filtration' owner: 'devteam' tool_panel_section_id: 'gatk' revisions: - 'da6e2503c62d' - name: 'variant_eval' owner: 'devteam' tool_panel_section_id: 'gatk' revisions: - 'fbca1c0956d2' - name: 'variant_combine' owner: 'devteam' tool_panel_section_id: 'gatk' revisions: - '1a6e16391727' - name: 'variant_apply_recalibration' owner: 'devteam' tool_panel_section_id: 'gatk' revisions: - '350a4d0d1678' - name: 'variant_annotator' owner: 'devteam' tool_panel_section_id: 'gatk' revisions: - 'ae9d0a543e9b' - name: 'unified_genotyper' owner: 'devteam' tool_panel_section_id: 'gatk' revisions: - '66dd4d4c1743' - name: 'realigner_target_creator' owner: 'devteam' tool_panel_section_id: 'gatk' revisions: - '5b8eaae854da' - name: 'print_reads' owner: 'devteam' tool_panel_section_id: 'gatk' revisions: - 'e768f4851646' - name: 'indel_realigner' owner: 'devteam' tool_panel_section_id: 'gatk' revisions: - 'bb0beda6cf83' - name: 'depth_of_coverage' owner: 'devteam' tool_panel_section_id: 'gatk' revisions: - 'c3f08370fc82' - name: 'count_covariates' owner: 'devteam' tool_panel_section_id: 'gatk' revisions: - '14e304b70425' - name: 'analyze_covariates' owner: 'devteam' tool_panel_section_id: 'gatk' revisions: - '738bc749f9a3' - name: 'table_recalibration' owner: 'devteam' tool_panel_section_id: 'gatk' revisions: - '30e1dd77e99c' # Cloud-only tools - name: ncbi_sra_toolkit owner: 'matt-shirley' tool_panel_section_id: convert tool_shed_url: https://toolshed.g2.bx.psu.edu - name: htseq_bams_to_count_matrix owner: fubar tool_panel_section_id: ngs-rna-tools tool_shed_url: https://testtoolshed.g2.bx.psu.edu # Data Managers - name: data_manager_snpeff owner: iuc tool_shed_url: https://toolshed.g2.bx.psu.edu - name: data_manager_bwa_index_builder owner: devteam tool_shed_url: https://toolshed.g2.bx.psu.edu - name: data_manager_gatk_picard_index_builder owner: devteam tool_shed_url: https://toolshed.g2.bx.psu.edu - name: data_manager_sam_fasta_index_builder owner: devteam tool_shed_url: https://toolshed.g2.bx.psu.edu - name: data_manager_fetch_genome_dbkeys_all_fasta owner: devteam tool_shed_url: https://toolshed.g2.bx.psu.edu - name: data_manager_fetch_genome_all_fasta owner: devteam tool_shed_url: https://toolshed.g2.bx.psu.edu - name: data_manager_rsync_g2 owner: blankenberg tool_shed_url: https://testtoolshed.g2.bx.psu.edu - name: data_manager_bowtie2_index_builder owner: devteam tool_shed_url: https://toolshed.g2.bx.psu.edu - name: data_manager_bwa_mem_index_builder owner: devteam tool_shed_url: https://toolshed.g2.bx.psu.edu - name: data_manager_picard_index_builder owner: devteam tool_shed_url: https://testtoolshed.g2.bx.psu.edu