tool_list.yaml

---
# This is a sample file to be used as a reference for populating a list of
# tools that you wish to install into Galaxy from a Tool Shed via the
# `install_tool_shed_tools.py` script.
#
# For each tool you want to install, you must provide the following keys:
#  * name: this is is the name of the tool to install
#  * owner: owner of the Tool Shed repository from where the tools is being
#           installed
# Further, you need to provide **one** of the following two keys:
#  * tool_panel_section_id: ID of the tool panel section where you want the
#                           tool to be installed. The section ID can be found
#                           in Galaxy's `shed_tool_conf.xml` config file. Note
#                           that the specified section must exist in this file.
#                           Otherwise, the tool will be installed outside any
#                           section.
#  * tool_panel_section_label: Display label of a tool panel section where
#                              you want the tool to be installed. If it does not
#                              exist, this section will be created on the target
#                              Galaxy instance (note that this is different than
#                              when using the ID).
#                              Multi-word labels need to be placed in quotes.
#                              Each label will have a corresponding ID created;
#                              the ID will be an all lowercase version of the
#                              label, with multiple words joined with
#                              underscores (e.g., 'BED tools' -> 'bed_tools').
#
# You can also specify the following optional keys to further define the
# installation properties:
#  * tool_shed_url: the URL of the Tool Shed from where the tool should be
#                   installed. (default: https://toolshed.g2.bx.psu.edu)
#  * revisions: a list of revisions of the tool, all of which will attempt to
#               be installed. (default: latest)
#  * install_tool_dependencies: True or False - whether to install classic galaxy 
#                               Tool Shed dependencies or not. (default: True)
#  * install_repository_dependencies: True or False - whether to install classic
#                               Galaxy Tool Shed repo dependencies or not. 
#                               (default: True)
#  * install_resolver_dependencies: True or False - whether to install dependencies
#                                through a resolver (e.g Conda). (default: False)
api_key: <Admin user API key from galaxy_instance>
galaxy_instance: <Galaxy instance IP>
tools:
#################
## Data managers
#################
- name: ctat_centrifuge_indexes_data_manager
  owner: trinity_ctat
  tool_panel_section_label: 'CTAT Metagenomics Tools'
  tool_shed_url: https://toolshed.g2.bx.psu.edu
  revisions:
  - b4d4f0d76e94
- name: ctat_genome_resource_libs_data_manager
  owner: trinity_ctat
  tool_panel_section_label: 'CTAT Assembly Tools'
  tool_shed_url: https://toolshed.g2.bx.psu.edu
  revisions:
  - da7f50809820
- name: ctat_lncrna_annotations_data_manager
  owner: trinity_ctat
  tool_panel_section_label: 'CTAT lncRNA Tools'
  tool_shed_url: https://toolshed.g2.bx.psu.edu
  revisions:
  - a3aa3f9e1702
#
#################
## Helpers
#################
- name: ctat_clean_headers
  owner: trinity_ctat
  tool_panel_section_label: 'CTAT Helper Tools'
  tool_shed_url: https://toolshed.g2.bx.psu.edu
  revisions:
  - 67e77c325002
- name: ctat_concatenate
  owner: trinity_ctat
  tool_panel_section_label: 'CTAT Helper Tools'
  tool_shed_url: https://toolshed.g2.bx.psu.edu
  revisions:
  - 702a3586942a
#
#################
## Metagenomics
#################
- name: ctat_metagenomics
  owner: trinity_ctat
  tool_panel_section_label: 'CTAT Metagenomics Tools'
  tool_shed_url: https://toolshed.g2.bx.psu.edu
  revisions:
  - f92fcdde48fc
#
########################
## long non-coding RNA
########################
- name: ctat_lncrna
  owner: trinity_ctat
  tool_panel_section_label: 'CTAT lncRNA Tools'
  tool_shed_url: https://toolshed.g2.bx.psu.edu
  revisions:
  - a940c4a36a43
#
#################
## Assemblers
#################
- name: ctat_trinity_rnaseq
  owner: trinity_ctat
  tool_panel_section_label: 'CTAT Assembly Tools'
  tool_shed_url: https://toolshed.g2.bx.psu.edu
  revisions:
  - 045dadbbb0a2
#
######################
## RNA-Seq Protocol
######################
- name: ctat_abundance_estimation_to_matrix
  owner: trinity_ctat
  tool_panel_section_label: 'CTAT RNA-Seq Protocol'
  tool_shed_url: https://toolshed.g2.bx.psu.edu
  revisions:
  - 5eca0c75b178
- name: ctat_analyze_differential_expression
  owner: trinity_ctat
  tool_panel_section_label: 'CTAT RNA-Seq Protocol'
  tool_shed_url: https://toolshed.g2.bx.psu.edu
  revisions:
  - 2ca97cd84ce3
- name: ctat_edger_differential_expression
  owner: trinity_ctat
  tool_panel_section_label: 'CTAT RNA-Seq Protocol'
  tool_shed_url: https://toolshed.g2.bx.psu.edu
  revisions:
  - f36264827fb4
- name: ctat_rsem_align_and_estimate_abundance
  owner: trinity_ctat
  tool_panel_section_label: 'CTAT RNA-Seq Protocol'
  tool_shed_url: https://toolshed.g2.bx.psu.edu
  revisions:
  - 8605f8570c77
#
#################
## Fusion Tools
#################
- name: ctat_star_fusion
  owner: trinity_ctat
  tool_panel_section_label: 'CTAT Fusion Tools'
  tool_shed_url: https://toolshed.g2.bx.psu.edu
  revisions:
  - a530fa18e9e8
- name: ctat_discasm
  owner: trinity_ctat
  tool_panel_section_label: 'CTAT Fusion Tools'
  tool_shed_url: https://toolshed.g2.bx.psu.edu
  revisions:
  - a772e555b5a1
- name: ctat_gmap_fusion
  owner: trinity_ctat
  tool_panel_section_label: 'CTAT Fusion Tools'
  tool_shed_url: https://toolshed.g2.bx.psu.edu
  revisions:
  - 966ea55e1aae
- name: ctat_fusion_inspector
  owner: trinity_ctat
  tool_panel_section_label: 'CTAT Fusion Tools'
  tool_shed_url: https://toolshed.g2.bx.psu.edu/
  revisions:
  - 1a7ec343001c
#
###################
## Mutation Tools
###################
#Coming soon