galaxyp.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 tool
#                               dependencies or not. (default: True)
#  * install_repository_dependencies: True or False - whether to install repo
#                               dependencies or not. (default: True)

api_key: admin
galaxy_instance: http://localhost:8080
install_resolver_dependencies: true
install_tool_dependencies: false
tools:
- name: text_processing
  owner: bgruening
  tool_panel_section_id: "textutil"

- name: column_maker
  owner: devteam
  tool_panel_section_id: "textutil"

- name: translate_bed_sequences
  owner: jjohnson
  tool_panel_section_label: "BED Tools"

- name: filter_bed_on_splice_junctions
  owner: jjohnson
  tool_panel_section_label: "BED Tools"

- name: suite_openms
  owner: galaxyp
  tool_panel_section_label: "OpenMS"

- name: peptideshaker
  owner: galaxyp
  tool_panel_section_label: "PeptideShaker"
  revisions:
    - a72c48001f7c

- name: dbbuilder
  owner: galaxyp
  tool_panel_section_id: getext

- name: blastxml_to_tabular_selectable
  owner: galaxyp
  tool_panel_section_label: "BLAST"

- name: mgf_formatter
  owner: galaxyp
  tool_panel_section_id: convert

- name: directag_and_tagrecon
  owner: galaxyp
  tool_panel_section_label: Bumbershoot

- name: idpqonvert
  owner: galaxyp
  tool_panel_section_label: Bumbershoot

- name: ltq_iquant_cli
  owner: galaxyp
  tool_panel_section_id: utils

- name: mgf_formatter
  owner: galaxyp
  tool_panel_section_id: utils

- name: msconvert
  owner: galaxyp
  tool_panel_section_id: utils

- name: ms_data_converter
  owner: galaxyp
  tool_panel_section_id: utils

- name: peptide_to_gff
  owner: galaxyp
  tool_panel_section_id: utils

- name: pepxml_to_xls
  owner: galaxyp
  tool_panel_section_id: utils

- name: protxml_to_xls
  owner: galaxyp
  tool_panel_section_id: utils

- name: psm_eval
  owner: galaxyp
  tool_panel_section_id: utils

- name: percolator
  owner: galaxyp
  tool_panel_section_label: Percolator

- name: unipept
  owner: galaxyp
  tool_panel_section_id: utils

- name: query_tabular
  owner: iuc
  tool_panel_section_id: utils

- name: sqlite_to_tabular
  owner: iuc
  tool_panel_section_id: utils