From 06abf9e7a6d6853b44f11be3201802d8583fd055 Mon Sep 17 00:00:00 2001
From: martindemko <325073@mail.muni.cz>
Date: Wed, 6 Nov 2024 14:23:11 +0100
Subject: [PATCH] update of regalaxy tool list

---
 regalaxy_tool_list.yaml | 311 ++++++++++++++++++++++++----------------
 1 file changed, 187 insertions(+), 124 deletions(-)

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
-
-