diff --git a/regalaxy_tool_list.yaml b/regalaxy_tool_list.yaml index f37991f..cb7230e 100644 --- a/regalaxy_tool_list.yaml +++ b/regalaxy_tool_list.yaml @@ -1,302 +1,365 @@ tools: +- name: ncbi_datasets + owner: iuc + revisions: + - 198c75abbf55 + tool_panel_section_id: getext + tool_panel_section_label: Get Data + tool_shed_url: toolshed.g2.bx.psu.edu +- name: repeatexplorer2_testing + owner: petr-novak + revisions: + - 3d0ba5734776 + - 4308d3e572ee + - 792914356c37 + - 20ef42e81eeb + - 5cca2c9aa4ad + - a27646c27090 + tool_panel_section_id: repeatexplorer + tool_panel_section_label: RepeatExplorer + tool_shed_url: toolshed.g2.bx.psu.edu +- name: dante + owner: petr-novak + revisions: + - 8f2bd3cae2de + - f0663cdbae66 + tool_panel_section_id: dante + tool_panel_section_label: DANTE + tool_shed_url: toolshed.g2.bx.psu.edu +- name: dante_ltr + owner: petr-novak + revisions: + - e61f06df42b9 + - 08b5e23859ed + - 27e5f58763f2 + - 8224e3d7b03a + - d5508ce50c49 + tool_panel_section_id: dante_ltr + tool_panel_section_label: DANTE_LTR + tool_shed_url: toolshed.g2.bx.psu.edu +- name: tidecluster + owner: petr-novak + revisions: + - 440796be7576 + - a0f57cfa1bb7 + - 971dbc97e607 + - 30a8a954dd93 + tool_panel_section_id: tidecluster + tool_panel_section_label: TideCluster + tool_shed_url: toolshed.g2.bx.psu.edu - name: repeat_annotation_pipeline3 owner: petr-novak revisions: - 755a4d643184 + - 5366d5ea04bc + tool_panel_section_id: assembly_annotation_tools tool_panel_section_label: Assembly annotation tools tool_shed_url: toolshed.g2.bx.psu.edu +- name: re_utils + owner: petr-novak + revisions: + - 91996b991991 + tool_panel_section_id: repeatexplorer_utilities + tool_panel_section_label: RepeatExplorer utilities + tool_shed_url: toolshed.g2.bx.psu.edu +- name: long_reads_sampling + owner: petr-novak + revisions: + - 060fc04af21c + tool_panel_section_id: repeatexplorer_utilities + tool_panel_section_label: RepeatExplorer utilities + tool_shed_url: toolshed.g2.bx.psu.edu +- name: fastqc + owner: devteam + revisions: + - 5ec9f6bceaee + tool_panel_section_id: ngs:_qc_and_manipulation + tool_panel_section_label: 'NGS: QC and manipulation' + tool_shed_url: toolshed.g2.bx.psu.edu +- name: fastq_groomer + owner: devteam + revisions: + - 47e5dbc3e790 + tool_panel_section_id: ngs:_qc_and_manipulation + tool_panel_section_label: 'NGS: QC and manipulation' + tool_shed_url: toolshed.g2.bx.psu.edu +- name: fastq_paired_end_splitter + owner: devteam + revisions: + - e39cc71d3ed6 + tool_panel_section_id: ngs:_qc_and_manipulation + tool_panel_section_label: 'NGS: QC and manipulation' + tool_shed_url: toolshed.g2.bx.psu.edu +- name: fastq_stats + owner: devteam + revisions: + - f0e7deab6518 + tool_panel_section_id: ngs:_qc_and_manipulation + tool_panel_section_label: 'NGS: QC and manipulation' + tool_shed_url: toolshed.g2.bx.psu.edu +- name: fastx_barcode_splitter + owner: devteam + revisions: + - 0b7ec11b3c7c + tool_panel_section_id: ngs:_qc_and_manipulation + tool_panel_section_label: 'NGS: QC and manipulation' + tool_shed_url: toolshed.g2.bx.psu.edu +- name: fastx_artifacts_filter + owner: devteam + revisions: + - 529bccd5e4a1 + tool_panel_section_id: ngs:_qc_and_manipulation + tool_panel_section_label: 'NGS: QC and manipulation' + tool_shed_url: toolshed.g2.bx.psu.edu +- name: fastx_nucleotides_distribution + owner: devteam + revisions: + - b6b54ba71bd8 + tool_panel_section_id: ngs:_qc_and_manipulation + tool_panel_section_label: 'NGS: QC and manipulation' + tool_shed_url: toolshed.g2.bx.psu.edu +- name: fastx_quality_statistics + owner: devteam + revisions: + - cc0fd298cc17 + tool_panel_section_id: ngs:_qc_and_manipulation + tool_panel_section_label: 'NGS: QC and manipulation' + tool_shed_url: toolshed.g2.bx.psu.edu +- name: fastq_quality_boxplot + owner: devteam + revisions: + - 867ab348287d + tool_panel_section_id: ngs:_qc_and_manipulation + tool_panel_section_label: 'NGS: QC and manipulation' + tool_shed_url: toolshed.g2.bx.psu.edu +- name: fastq_quality_converter + owner: devteam + revisions: + - 045f0e1043f7 + tool_panel_section_id: ngs:_qc_and_manipulation + tool_panel_section_label: 'NGS: QC and manipulation' + tool_shed_url: toolshed.g2.bx.psu.edu +- name: fastq_quality_filter + owner: devteam + revisions: + - 64e9a6afdd0c + tool_panel_section_id: ngs:_qc_and_manipulation + tool_panel_section_label: 'NGS: QC and manipulation' + tool_shed_url: toolshed.g2.bx.psu.edu +- name: multiqc + owner: iuc + revisions: + - abfd8a6544d7 + tool_panel_section_id: ngs:_qc_and_manipulation + tool_panel_section_label: 'NGS: QC and manipulation' + tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_compute_length owner: devteam revisions: - 7d37cfda8e00 + tool_panel_section_id: fasta/fastq_manipulation tool_panel_section_label: FASTA/FASTQ manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_to_tabular owner: devteam revisions: - e7ed3c310b74 + tool_panel_section_id: fasta/fastq_manipulation tool_panel_section_label: FASTA/FASTQ manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_formatter owner: devteam revisions: - 516b97a23d7e + tool_panel_section_id: fasta/fastq_manipulation tool_panel_section_label: FASTA/FASTQ manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_reverse_complement owner: devteam revisions: - 177f0621c266 + tool_panel_section_id: fasta/fastq_manipulation tool_panel_section_label: FASTA/FASTQ manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_trimmer owner: devteam revisions: - 73194cdd4f57 + tool_panel_section_id: fasta/fastq_manipulation tool_panel_section_label: FASTA/FASTQ manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: fastx_renamer owner: devteam revisions: - f984bb114520 + tool_panel_section_id: fasta/fastq_manipulation tool_panel_section_label: FASTA/FASTQ manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: tabular_to_fasta owner: devteam revisions: - 0a7799698fe5 + tool_panel_section_id: fasta/fastq_manipulation tool_panel_section_label: FASTA/FASTQ manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: tabular_to_fastq owner: devteam revisions: - 2dcfbbf9071a + tool_panel_section_id: fasta/fastq_manipulation tool_panel_section_label: FASTA/FASTQ manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_to_tabular owner: devteam revisions: - 4b347702c4aa + tool_panel_section_id: fasta/fastq_manipulation tool_panel_section_label: FASTA/FASTQ manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: fastqtofasta owner: devteam revisions: - 297962e79f39 + tool_panel_section_id: fasta/fastq_manipulation tool_panel_section_label: FASTA/FASTQ manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_paired_end_deinterlacer owner: devteam revisions: - f3936d0632cb + tool_panel_section_id: fasta/fastq_manipulation tool_panel_section_label: FASTA/FASTQ manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: fastq_paired_end_interlacer owner: devteam revisions: - 2ccb8dcabddc + tool_panel_section_id: fasta/fastq_manipulation tool_panel_section_label: FASTA/FASTQ manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: fasta_filter_by_length owner: devteam revisions: - 8cacfcf96a52 + tool_panel_section_id: fasta/fastq_manipulation tool_panel_section_label: FASTA/FASTQ manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: ucsc_fasplit owner: iuc revisions: - bf04bd405d5b + tool_panel_section_id: fasta/fastq_manipulation tool_panel_section_label: FASTA/FASTQ manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: trimmomatic owner: pjbriggs revisions: - 32f1f56bd970 + tool_panel_section_id: fasta/fastq_manipulation tool_panel_section_label: FASTA/FASTQ manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: trim_galore owner: bgruening revisions: - cd7e644cae1d + tool_panel_section_id: fasta/fastq_manipulation tool_panel_section_label: FASTA/FASTQ manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: seqkit_stats owner: iuc revisions: - 54a954ee64d4 + tool_panel_section_id: fasta/fastq_manipulation tool_panel_section_label: FASTA/FASTQ manipulation tool_shed_url: toolshed.g2.bx.psu.edu - name: seqtk owner: iuc revisions: - 4b494533146a + tool_panel_section_id: fasta/fastq_manipulation tool_panel_section_label: FASTA/FASTQ manipulation tool_shed_url: toolshed.g2.bx.psu.edu -- name: long_reads_sampling - owner: petr-novak - revisions: - - 060fc04af21c - tool_panel_section_label: RepeatExplorer utilities - tool_shed_url: toolshed.g2.bx.psu.edu -- name: re_utils - owner: petr-novak - revisions: - - 91996b991991 - tool_panel_section_label: RepeatExplorer utilities - tool_shed_url: toolshed.g2.bx.psu.edu -- name: repeatexplorer2_testing - owner: petr-novak - revisions: - - a27646c27090 # revision 25 - tool version 2.3.11.1 -# - 84106349d4b1 # revision 21 - tool version 2.3.10.1 - - 3d0ba5734776 # revision 19 - tool version 2.3.9.1 - - 4308d3e572ee # revision 18 - tool version 2.3.9.1/2.3.8.3 - - 5cca2c9aa4ad # revision 17 - tool version 2.3.8.4/2.3.8.3 - - 20ef42e81eeb # revision 16 - tool version 2.3.8.3 - tool_panel_section_label: RepeatExplorer - tool_shed_url: toolshed.g2.bx.psu.edu -- name: dante - owner: petr-novak - revisions: - - 8f2bd3cae2de - tool_panel_section_label: DANTE - tool_shed_url: toolshed.g2.bx.psu.edu -- name: dante_ltr - owner: petr-novak - revisions: - - 27e5f58763f2 - tool_panel_section_label: DANTE_LTR - tool_shed_url: toolshed.g2.bx.psu.edu -- name: tidecluster +- name: various_galaxy_tools owner: petr-novak revisions: - - 440796be7576 - tool_panel_section_label: TideCluster - tool_shed_url: toolshed.g2.bx.psu.edu -- name: jbrowse - owner: iuc - revisions: - - a6e57ff585c0 - tool_panel_section_label: Jbrowse - tool_shed_url: toolshed.g2.bx.psu.edu -- name: fastq_groomer - owner: devteam - revisions: - - 47e5dbc3e790 - tool_panel_section_label: 'NGS: QC and manipulation' - tool_shed_url: toolshed.g2.bx.psu.edu -- name: fastq_paired_end_splitter - owner: devteam - revisions: - - e39cc71d3ed6 - tool_panel_section_label: 'NGS: QC and manipulation' - tool_shed_url: toolshed.g2.bx.psu.edu -- name: fastq_stats - owner: devteam - revisions: - - f0e7deab6518 - tool_panel_section_label: 'NGS: QC and manipulation' - tool_shed_url: toolshed.g2.bx.psu.edu -- name: fastx_barcode_splitter - owner: devteam - revisions: - - 0b7ec11b3c7c - tool_panel_section_label: 'NGS: QC and manipulation' - tool_shed_url: toolshed.g2.bx.psu.edu -- name: fastx_artifacts_filter - owner: devteam - revisions: - - 529bccd5e4a1 - tool_panel_section_label: 'NGS: QC and manipulation' - tool_shed_url: toolshed.g2.bx.psu.edu -- name: fastx_nucleotides_distribution - owner: devteam - revisions: - - b6b54ba71bd8 - tool_panel_section_label: 'NGS: QC and manipulation' - tool_shed_url: toolshed.g2.bx.psu.edu -- name: fastx_quality_statistics - owner: devteam - revisions: - - cc0fd298cc17 - tool_panel_section_label: 'NGS: QC and manipulation' - tool_shed_url: toolshed.g2.bx.psu.edu -- name: fastq_quality_boxplot - owner: devteam - revisions: - - 867ab348287d - tool_panel_section_label: 'NGS: QC and manipulation' - tool_shed_url: toolshed.g2.bx.psu.edu -- name: fastq_quality_converter - owner: devteam - revisions: - - 045f0e1043f7 - tool_panel_section_label: 'NGS: QC and manipulation' - tool_shed_url: toolshed.g2.bx.psu.edu -- name: fastq_quality_filter - owner: devteam - revisions: - - 64e9a6afdd0c - tool_panel_section_label: 'NGS: QC and manipulation' - tool_shed_url: toolshed.g2.bx.psu.edu -- name: multiqc - owner: iuc - revisions: - - abfd8a6544d7 - tool_panel_section_label: 'NGS: QC and manipulation' - tool_shed_url: toolshed.g2.bx.psu.edu -- name: fastqc - owner: devteam - revisions: - - 5ec9f6bceaee - tool_panel_section_label: 'NGS: QC and manipulation' + - 1069776f7ae2 + tool_panel_section_id: genomic_file_utilities + tool_panel_section_label: Genomic file utilities tool_shed_url: toolshed.g2.bx.psu.edu - name: gffread owner: devteam revisions: - 3e436657dcd0 + tool_panel_section_id: bed tool_panel_section_label: BED tool_shed_url: toolshed.g2.bx.psu.edu - name: bedtools owner: iuc revisions: - a1a923cd89e8 + tool_panel_section_id: bed tool_panel_section_label: BED tool_shed_url: toolshed.g2.bx.psu.edu +- name: jbrowse + owner: iuc + revisions: + - a6e57ff585c0 + tool_panel_section_id: jbrowse + tool_panel_section_label: Jbrowse + tool_shed_url: toolshed.g2.bx.psu.edu - name: krona_text owner: petr-novak revisions: - 04021cfd5170 + tool_panel_section_id: visualisation tool_panel_section_label: Visualisation tool_shed_url: toolshed.g2.bx.psu.edu - name: histogram owner: devteam revisions: - 6f134426c2b0 + tool_panel_section_id: visualisation tool_panel_section_label: Visualisation tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_point owner: iuc revisions: - 3b12bf9b4b87 + tool_panel_section_id: visualisation tool_panel_section_label: Visualisation tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_histogram owner: iuc revisions: - b0d96516e6a5 + tool_panel_section_id: visualisation tool_panel_section_label: Visualisation tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_violin owner: iuc revisions: - 0e7290688b50 + tool_panel_section_id: visualisation tool_panel_section_label: Visualisation tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_pca owner: iuc revisions: - b1268b7544d3 + tool_panel_section_id: visualisation tool_panel_section_label: Visualisation tool_shed_url: toolshed.g2.bx.psu.edu - name: ggplot2_heatmap owner: iuc revisions: - 10515715c940 + tool_panel_section_id: visualisation tool_panel_section_label: Visualisation tool_shed_url: toolshed.g2.bx.psu.edu - name: text_processing owner: bgruening revisions: - d698c222f354 + tool_panel_section_id: text_manipulation tool_panel_section_label: Text manipulation tool_shed_url: toolshed.g2.bx.psu.edu -- name: various_galaxy_tools - owner: petr-novak - revisions: - - 1069776f7ae2 - tool_panel_section_label: Genomic file utilities - tool_shed_url: toolshed.g2.bx.psu.edu - -