bgruening.yaml

---
install_repository_dependencies: true
install_resolver_dependencies: true
install_tool_dependencies: false

tools:

# BioModels

  - name: biomodels_biomd0000001066
    owner: bgruening
    tool_panel_section_label: Machine Learning

  - name: biomodels_biomd0000001076
    owner: bgruening
    tool_panel_section_label: Machine Learning

# "CONVERT FORMATS"

  - name: glimmer_glimmer_to_gff
    owner: bgruening
    tool_panel_section_label: "Convert Formats"

  - name: graphicsmagick_image_convert
    owner: bgruening
    tool_panel_section_label: "Convert Formats"

  - name: graphicsmagick_image_montage
    owner: bgruening
    tool_panel_section_label: "Convert Formats"

  - name: graphicsmagick_image_compare
    owner: bgruening
    tool_panel_section_label: "Convert Formats"

  - name: hictk
    owner: bgruening
    tool_panel_section_label: "Convert Formats"

  - name: uniprot_rest_interface
    owner: bgruening
    tool_panel_section_label: Convert Formats

# SAM/BAM

  - name: sambamba_flagstat
    owner: bgruening
    tool_panel_section_label: SAM/BAM

  - name: sambamba_markdup
    owner: bgruening
    tool_panel_section_label: SAM/BAM

  - name: sambamba_merge
    owner: bgruening
    tool_panel_section_label: SAM/BAM

  - name: sambamba_sort
    owner: bgruening
    tool_panel_section_label: SAM/BAM

# ANNOTATION

  - name: antismash
    owner: bgruening
    tool_panel_section_label: Annotation

  - name: agat
    owner: bgruening
    tool_panel_section_label: Annotation

  - name: cpat
    owner: bgruening
    tool_panel_section_label: Annotation

  - name: edta
    owner: bgruening
    tool_panel_section_label: Annotation

  - name: netboxr
    owner: bgruening
    tool_panel_section_label: Annotation

  - name: pfamscan
    owner: bgruening
    tool_panel_section_label: Annotation

  - name: tapscan
    owner: bgruening
    tool_panel_section_label: Annotation

# ASSEMBLY

  - name: blobtoolkit
    owner: bgruening
    tool_panel_section_label: Assembly

  - name: canu
    owner: bgruening
    tool_panel_section_label: Assembly

  - name: flye
    owner: bgruening
    tool_panel_section_label: Assembly

  - name: instagraal
    owner: bgruening
    tool_panel_section_label: Assembly

  - name: minipolish
    owner: bgruening
    tool_panel_section_label: Assembly

  - name: mitohifi
    owner: bgruening
    tool_panel_section_label: Assembly

  - name: nextdenovo
    owner: bgruening
    tool_panel_section_label: Assembly

  - name: racon
    owner: bgruening
    tool_panel_section_label: Assembly

  - name: reago
    owner: bgruening
    tool_panel_section_label: Assembly

  - name: tgsgapcloser
    owner: bgruening
    tool_panel_section_label: Assembly

  - name: wtdbg
    owner: bgruening
    tool_panel_section_label: Assembly

  - name: erga_ear
    owner: bgruening
    tool_panel_section_label: Assembly
  

# COLLECTION OPERATIONS

  - name: split_file_to_collection
    owner: bgruening
    tool_panel_section_label: Collection Operations


# FASTA/FASTQ

  - name: gfastats
    owner: bgruening
    tool_panel_section_label: FASTA/FASTQ

  - name: trim_galore
    owner: bgruening
    tool_panel_section_label: FASTA/FASTQ

  - name: mgnify_seqprep
    owner: bgruening
    tool_panel_section_label: FASTA/FASTQ


# Get Data

  - name: mavedb_importer
    owner: bgruening
    tool_panel_section_label: Get Data

# GRAPH/DISPLAY DATA

  - name: jbrowse2
    owner: fubar
    tool_panel_section_label: Graph/Display Data

  - name: plotly_ml_performance_plots
    owner: bgruening
    tool_panel_section_label: Graph/Display Data

  - name: plotly_regression_performance_plots
    owner: bgruening
    tool_panel_section_label: Graph/Display Data

# IMAGING

  - name: cellpose
    owner: bgruening
    tool_panel_section_label: Imaging

  - name: bioimage_inference
    owner: bgruening
    tool_panel_section_label: Imaging

  - name: woundhealing_scratch_assay
    owner: bgruening
    tool_panel_section_label: Imaging

# MACHINE LEARNING

  - name: keras_batch_models
    owner: bgruening
    tool_panel_section_label: Machine Learning

  - name: keras_model_builder
    owner: bgruening
    tool_panel_section_label: Machine Learning

  - name: keras_model_config
    owner: bgruening
    tool_panel_section_label: Machine Learning

  - name: keras_train_and_eval
    owner: bgruening
    tool_panel_section_label: Machine Learning

  - name: ml_visualization_ex
    owner: bgruening
    tool_panel_section_label: Machine Learning

  - name: model_prediction
    owner: bgruening
    tool_panel_section_label: Machine Learning

#  - name: run_jupyter_job
#    owner: bgruening
#    tool_panel_section_label: Machine Learning

  - name: sklearn_build_pipeline
    owner: bgruening
    tool_panel_section_label: Machine Learning

  - name: sklearn_clf_metrics
    owner: bgruening
    tool_panel_section_label: Machine Learning

  - name: sklearn_data_preprocess
    owner: bgruening
    tool_panel_section_label: Machine Learning

  - name: sklearn_discriminant_classifier
    owner: bgruening
    tool_panel_section_label: Machine Learning

  - name: sklearn_ensemble
    owner: bgruening
    tool_panel_section_label: Machine Learning

  - name: sklearn_estimator_attributes
    owner: bgruening
    tool_panel_section_label: Machine Learning

  - name: sklearn_feature_selection
    owner: bgruening
    tool_panel_section_label: Machine Learning

  - name: sklearn_fitted_model_eval
    owner: bgruening
    tool_panel_section_label: Machine Learning

  - name: sklearn_generalized_linear
    owner: bgruening
    tool_panel_section_label: Machine Learning

  - name: sklearn_label_encoder
    owner: bgruening
    tool_panel_section_label: Machine Learning

  - name: sklearn_lightgbm
    owner: bgruening
    tool_panel_section_label: Machine Learning

  - name: sklearn_model_fit
    owner: bgruening
    tool_panel_section_label: Machine Learning

  - name: sklearn_model_validation
    owner: bgruening
    tool_panel_section_label: Machine Learning

  - name: sklearn_nn_classifier
    owner: bgruening
    tool_panel_section_label: Machine Learning

  - name: sklearn_numeric_clustering
    owner: bgruening
    tool_panel_section_label: Machine Learning

  - name: sklearn_pairwise_metrics
    owner: bgruening
    tool_panel_section_label: Machine Learning

  - name: sklearn_pca
    owner: bgruening
    tool_panel_section_label: Machine Learning

  - name: sklearn_regression_metrics
    owner: bgruening
    tool_panel_section_label: Machine Learning

  - name: sklearn_sample_generator
    owner: bgruening
    tool_panel_section_label: Machine Learning

  - name: sklearn_searchcv
    owner: bgruening
    tool_panel_section_label: Machine Learning

  - name: sklearn_stacking_ensemble_models
    owner: bgruening
    tool_panel_section_label: Machine Learning

  - name: sklearn_svm_classifier
    owner: bgruening
    tool_panel_section_label: Machine Learning

  - name: sklearn_to_categorical
    owner: bgruening
    tool_panel_section_label: Machine Learning

  - name: sklearn_train_test_eval
    owner: bgruening
    tool_panel_section_label: Machine Learning

  - name: sklearn_train_test_split
    owner: bgruening
    tool_panel_section_label: Machine Learning

  - name: whisper
    owner: bgruening
    tool_panel_section_label: Machine Learning

  - name: flexynesis
    owner: bgruening
    tool_panel_section_label: Machine Learning

  - name: chatgpt_openai_api
    owner: bgruening
    tool_panel_section_label: Machine Learning

  - name: black_forest_labs_flux
    owner: bgruening
    tool_panel_section_label: Machine Learning

# MAPPING

  - name: graphmap_align
    owner: bgruening
    tool_panel_section_label: Mapping

  - name: graphmap_overlap
    owner: bgruening
    tool_panel_section_label: Mapping


# METAGENOMIC ANALYSIS

  - name: combine_metaphlan2_humann2
    owner: bebatut
    tool_panel_section_label: Metagenomic Analysis

  - name: compare_humann2_output
    owner: bebatut
    tool_panel_section_label: Metagenomic Analysis

  - name: format_cd_hit_output
    owner: bebatut
    tool_panel_section_label: Multiple Alignments

  - name: format_metaphlan2_output
    owner: bebatut
    tool_panel_section_label: Metagenomic Analysis

  - name: itsx
    owner: bgruening
    tool_panel_section_label: Metagenomic Analysis

  - name: motus
    owner: bgruening
    tool_panel_section_label: Metagenomic Analysis

  - name: data_manager_motus
    owner: bgruening
 
  - name: tiara
    owner: bgruening
    tool_panel_section_label: Metagenomic Analysis


# MULTIPLE ALIGNMENTS

  - name: mafft
    owner: rnateam
    tool_panel_section_label: Multiple Alignments


# NANOPORE

  - name: nanopolish_eventalign
    owner: bgruening
    tool_panel_section_label: Nanopore

  - name: nanopolish_methylation
    owner: bgruening
    tool_panel_section_label: Nanopore

  - name: nanopolish_polya
    owner: bgruening
    tool_panel_section_label: Nanopore

  - name: nanopolish_variants
    owner: bgruening
    tool_panel_section_label: Nanopore


# PEAK CALLING

  - name: dewseq
    owner: rnateam
    tool_panel_section_label: Peak Calling

  - name: htseq_clip
    owner: rnateam
    tool_panel_section_label: Peak Calling


# QUALITY CONTROL

  - name: fastq_info
    owner: bgruening
    tool_panel_section_label: Quality Control


# SINGLE-CELL

  - name: 10x_bamtofastq
    owner: bgruening
    tool_panel_section_label: Single-cell

  - name: music_compare
    owner: bgruening
    tool_panel_section_label: Single-cell

  - name: music_construct_eset
    owner: bgruening
    tool_panel_section_label: Single-cell

  - name: music_deconvolution
    owner: bgruening
    tool_panel_section_label: Single-cell

  - name: music_inspect_eset
    owner: bgruening
    tool_panel_section_label: Single-cell

  - name: music_manipulate_eset
    owner: bgruening
    tool_panel_section_label: Single-cell


# STATISTICS

  - name: bg_statistical_hypothesis_testing
    owner: bgruening
    tool_panel_section_label: Statistics

  - name: create_tool_recommendation_model
    owner: bgruening
    tool_panel_section_label: Statistics

  - name: pandas_rolling_window
    owner: bgruening
    tool_panel_section_label: Statistics

  - name: scipy_sparse
    owner: bgruening
    tool_panel_section_label: Statistics


# TEXT MANIPULATION

  - name: add_line_to_file
    owner: bgruening
    tool_panel_section_label: Text Manipulation

  - name: diff
    owner: bgruening
    tool_panel_section_label: Text Manipulation

  - name: replace_column_by_key_value_file
    owner: bgruening
    tool_panel_section_label: Text Manipulation


# VARIANT CALLING

  - name: pharmcat
    owner: bgruening
    tool_panel_section_label: Variant Calling