NGS_1.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').
#
# Tou 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: sra_tools
  owner: iuc
  tool_panel_section_id: 'getext'
  
- name: fetch_fasta_from_ncbi
  owner: drosofff
  tool_panel_section_id: 'getext'
  
- name: text_processing
  owner: bgruening
  tool_panel_section_id: 'textutil'
  
- name: regex_find_replace
  owner: jjohnson
  tool_panel_section_id: 'textutil'
  
- name: collapse_collections
  owner: nml
  tool_panel_section_id: 'collection_operations'
  
- name: ncbi_blast_plus
  owner: devteam
  tool_panel_section_label: "BLAST"
  
- name: fasta_compute_length
  owner: devteam
  tool_panel_section_label: "FASTA Tools"

- name: fasta_formatter
  owner: devteam
  tool_panel_section_label: "FASTA Tools"

- name: fasta_nucleotide_changer
  owner: devteam
  tool_panel_section_label: "FASTA Tools"

- name: fasta_to_tabular
  owner: devteam
  tool_panel_section_label: "FASTA Tools"

- name: tabular_to_fasta
  owner: devteam
  tool_panel_section_label: "FASTA Tools"
  
- name: xy_plot
  owner: devteam
  tool_panel_section_label: "Visualisation"

- name: newick_display
  owner: dcorreia
  tool_panel_section_label: "Visualisation"

- name: krona_text
  owner: saskia-hiltemann
  tool_panel_section_label: "Visualisation"
  
- name: ireport
  owner: saskia-hiltemann
  tool_panel_section_label: "Visualisation"

- name: plot_barplot
  owner: bebatut
  tool_panel_section_label: "Visualisation"
  
- name: msp_sr_readmap_and_size_histograms
  owner: drosofff
  tool_panel_section_label: "Visualisation"
  
- name: newick_utils
  owner: iuc
  tool_panel_section_label: "Visualisation"
  
- name: taxonomy_krona_chart
  owner: crs4
  tool_panel_section_label: "Visualisation"
  
- name: fastqc
  owner: devteam
  tool_panel_section_label: "NGS Quality Control"

- name: multiqc
  owner: iuc
  tool_panel_section_label: "NGS Quality Control"
  
- name: bowtie2
  owner: devteam
  tool_panel_section_label: "NGS Mapping"

- name: bwa
  owner: devteam
  tool_panel_section_label: "NGS Mapping"
  
- name: bowtie_wrappers
  owner: devteam
  tool_panel_section_label: "NGS Mapping"
  
- name: msp_sr_bowtie
  owner: drosofff
  tool_panel_section_label: "NGS Mapping"

- name: data_manager_bowtie2_index_builder
  owner: devteam

- name: data_manager_fetch_genome_dbkeys_all_fasta
  owner: devteam

- name: data_manager_bowtie_index_builder
  owner: iuc

- name: data_manager_bwa_mem_index_builder
  owner: devteam
  
- name: trim_galore
  owner: bgruening
  tool_panel_section_label: "NGS pre-processing tools"
  tool_shed_url: https://toolshed.g2.bx.psu.edu
  
- name: cutadapt
  owner: lparsons
  tool_panel_section_label: "NGS pre-processing tools"
  
- name: trimmomatic
  owner: pjbriggs
  tool_panel_section_label: "NGS pre-processing tools"
  
- name: fastx_collapser
  owner: devteam
  tool_panel_section_label: "NGS pre-processing tools"
  
- name: fastq_collapser
  owner: kaymccoy
  tool_panel_section_label: "NGS pre-processing tools"
   
- name: fastx_clipper
  owner: devteam
  tool_panel_section_label: "NGS pre-processing tools"
  
- name: fastq_to_fasta
  owner: devteam
  tool_panel_section_label: "NGS pre-processing tools"
   
- name: pear
  owner: iuc
  tool_panel_section_label: "NGS pre-processing tools"
  
- name: fastq_paired_end_interlacer
  owner: devteam
  tool_panel_section_label: "NGS pre-processing tools"
  
- name: fastx_collapser
  owner: devteam
  tool_panel_section_label: "NGS pre-processing tools"
  
- name: fastq_groomer
  owner: devteam
  tool_panel_section_label: "NGS pre-processing tools"
  
- name: data_manager_sam_fasta_index_builder
  owner: devteam
  tool_panel_section_label: "NGS SAM/BAM tools"

- name: bam_to_sam
  owner: devteam
  tool_panel_section_label: "NGS SAM/BAM tools"

- name: sam_to_bam
  owner: devteam
  tool_panel_section_label: "NGS SAM/BAM tools"

- name: samtools_bedcov
  owner: devteam
  tool_panel_section_label: "NGS SAM/BAM tools"

- name: samtools_calmd
  owner: devteam
  tool_panel_section_label: "NGS SAM/BAM tools"

- name: samtools_flagstat
  owner: devteam
  tool_panel_section_label: "NGS SAM/BAM tools"

- name: samtools_idxstats
  owner: devteam
  tool_panel_section_label: "NGS SAM/BAM tools"

- name: samtools_mpileup
  owner: devteam
  tool_panel_section_label: "NGS SAM/BAM tools"

- name: samtools_reheader
  owner: devteam
  tool_panel_section_label: "NGS SAM/BAM tools"

- name: samtools_rmdup
  owner: devteam
  tool_panel_section_label: "NGS SAM/BAM tools"

- name: samtools_slice_bam
  owner: devteam
  tool_panel_section_label: "NGS SAM/BAM tools"

- name: samtools_sort
  owner: devteam
  tool_panel_section_label: "NGS SAM/BAM tools"

- name: samtools_split
  owner: devteam
  tool_panel_section_label: "NGS SAM/BAM tools"

- name: samtools_stats
  owner: devteam
  tool_panel_section_label: "NGS SAM/BAM tools"