tools.yaml

api_key: admin
galaxy_instance: http://localhost:8080
install_repository_dependencies: true
install_resolver_dependencies: true
install_tool_dependencies: false

tools:

# Quality Control

- name: fastqc
  owner: devteam
  tool_panel_section_label: "Quality Control"
  revisions:
  - 'e7b2202befea'

- name: cutadapt
  owner: lparsons
  tool_panel_section_label: "Quality Control"
  revisions:
  - 'e4691e1589d3'

- name: trim_galore
  owner: bgruening
  tool_panel_section_label: "Quality Control"
  revisions:
  - '084bbd8ba7b8'

- name: trimmomatic
  owner: pjbriggs
  tool_panel_section_label: "Quality Control"
  revisions:
  - '898b67846b47'

- name: prinseq
  owner: iuc
  tool_panel_section_label: "Quality Control"
  revisions:
  - '02befcb391f5'

# Utilities

- name: samtool_filter2
  owner: devteam
  tool_panel_section_label: "Utilities"
  revisions:
  - 'a7add3e93cc5'

- name: samtools_sort
  owner: devteam
  tool_panel_section_label: "Utilities"
  revisions:
  - 'e613c1ad4c4c'

- name: samtools_flagstat
  owner: devteam
  tool_panel_section_label: "Utilities"
  revisions:
  - 'db17d5321bad'

- name: samtools_fixmate
  owner: iuc
  tool_panel_section_label: "Utilities"
  revisions:
  - 'bc0cc7bfbfe9'

- name: samtools_markdup
  owner: iuc
  tool_panel_section_label: "Utilities"
  revisions:
  - '83b8e36e9cbe'

- name: bedtools
  owner: iuc
  tool_panel_section_label: "Utilities"
  revisions:
  - 'dde39ba9c031'

- name: picard
  owner: devteam
  tool_panel_section_label: "Utilities"
  revisions:
  - 'a1f0b3f4b781'

# Text processing

- name: text_processing
  owner: bgruening
  tool_panel_section_label: "Text processing"
  revisions:
  - '0a8c6b61f0f4'

- name: replace_column_by_key_value_file
  owner: bgruening
  tool_panel_section_label: "Text processing"
  revisions:
  - 'd533e4b75800'

- name: column_maker
  owner: devteam
  tool_panel_section_label: "Text processing"
  revisions:
  - '464b9305180e'

# RNA-Seq

- name: hisat2
  owner: iuc
  tool_panel_section_label: "RNA-Seq"
  revisions:
  - '3fb01a8c902d'

- name: segemehl
  owner: rnateam
  tool_panel_section_label: "RNA-Seq"
  revisions:
  - '9c0d4ec99ba9'

- name: bwa
  owner: devteam
  tool_panel_section_label: "RNA-Seq"
  revisions:
  - '01ac0a5fedc3'

- name: featurecounts
  owner: iuc
  tool_panel_section_label: "RNA-Seq"
  revisions:
  - '9301937c9037'

- name: deseq2
  owner: iuc
  tool_panel_section_label: "RNA-Seq"
  revisions:
  - '0696db066a5b'

- name: htseq_count
  owner: lparsons
  tool_panel_section_label: "RNA-Seq"
  revisions:
  - '7f5a8d427b39'

- name: rseqc
  owner: nilesh
  tool_panel_section_label: "RNA-Seq"
  revisions:
  - 'f437057e46f1'

- name: sortmerna
  owner: rnateam
  tool_panel_section_label: "RNA-Seq"
  revisions:
  - 'eb35257d2e29'

- name: data_manager_sortmerna_database_downloader
  owner: rnateam
  install_resolver_dependencies: false
  revisions:
  - '7d2252852f96'

- name: rcorrector
  owner: iuc
  tool_panel_section_label: "RNA-Seq"
  revisions:
  - '9a0b65ad3c84'

- name: rgrnastar
  owner: iuc
  tool_panel_section_label: "RNA-Seq"
  revisions:
  - '0a563fd2f22e'

# BS/RRBS-Seq

- name: bismark
  owner: bgruening
  tool_panel_section_label: "BS/RRBS-Seq"
  revisions:
  - 'b6aa3b6ba129'

- name: pileometh
  owner: bgruening
  tool_panel_section_label: "BS/RRBS-Seq"
  revisions:
  - '183cb55b1729'

- name: segemehl
  owner: rnateam
  tool_panel_section_label: "BS/RRBS-Seq"
  revisions:
  - '9c0d4ec99ba9'

- name: bwameth
  owner: iuc
  tool_panel_section_label: "BS/RRBS-Seq"
  revisions:
  - '29bdbc353f20'

# Annotation

- name: gtftobed12
  owner: iuc
  tool_panel_section_label: "Annotation"
  revisions:
  - '57d45064f114'

# Peak Calling

- name: macs2
  owner: iuc
  tool_panel_section_label: "Peak Calling"
  revision:
  - '424aefbd7777'

- name: idr
  owner: iuc
  tool_panel_section_label: "Peak Calling"
  revisions:
  - 'd3ebbf39b1c5'