-
Notifications
You must be signed in to change notification settings - Fork 2
/
.schema.yaml
140 lines (140 loc) · 8.3 KB
/
.schema.yaml
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
---
type: map
mapping:
"install_repository_dependencies":
type: bool
default: false
"install_resolver_dependencies":
type: bool
default: false
"install_tool_dependencies":
type: bool
default: false
"tools":
type: seq
sequence:
- type: map
mapping:
"name":
type: str
required: true
"owner":
type: str
required: true
"tool_panel_section_label":
type: str
enum: [
'Get Data', 'Send Data', 'Collection Operations', 'Expression Tools', 'Data and Metadata Management',
'Text Manipulation', 'Filter and Sort', 'Join, Subtract and Group',
'Convert Formats', 'FASTA/FASTQ', 'FASTQ Quality Control', 'SAM/BAM', 'BED',
'VCF/BCF', 'Nanopore', 'Operate on Genomic Intervals', 'Fetch Sequences / Alignments',
'Annotation', 'Ontology', 'Assembly', 'Mapping', 'Variant Calling', 'Genome editing',
'RNA-Seq', 'Peak Calling', 'Epigenetics', 'Phylogenetics', 'Phenotype Association',
'Single-cell', 'Get scRNAseq data', 'Seurat', 'SC3', 'Scanpy', 'Monocl3', 'SCMap',
'SCCAF', 'Single Cell Utils and Viz', 'Picard', 'deepTools', 'Gemini', 'EMBOSS',
'GATK Tools', 'NCBI Blast', 'HiCExplorer', 'RAD-seq', 'GraphClust' , 'MiModD',
'Metagenomic Analysis', 'Qiime' , 'Mothur' , 'DNA Metabarcoding' , 'Proteomics', 'Metabolomics',
'ChemicalToolBox', 'Statistics', 'Graph/Display Data' , 'Evolution', 'Motif Tools', "Machine Learning",
'Test Tools', 'GIS Data Handling', 'Animal Detection on Acoustic Recordings', 'Compute indicators for satellite remote sensing', 'Imaging', 'Virology',
'Regional Variation' , 'Genome Diversity' , 'Deprecated', 'Interactive tools', 'Apollo', 'Quality Control',
'Multiple Alignments', 'Climate Analysis', 'RNA Analysis', 'Data Managers', 'Extract Features', 'Other Tools',
'Species abundance', 'Biodiversity data exploration', 'Sanger Sequencing', 'Spatial Omics', 'Muon Spectroscopy',
'Compute indicators for turnover boulders fields', 'QIIME 2', 'Astronomy', 'Ecoregionalization', 'Indicators from geometric mean',
'Imaging - ImageJ2',
'Sequence Analysis - bbtools',
'Exposomics - recetox',
'Phyloseq',
'Testing',
'Qiime2',
'Proteomics - ProteomIQon',
'Sequence Analysis - Stacks',
'Data Source',
'Amplicon Analysis',
'Metagenomics',
'Proteomics - ProteoRE',
'Data Export',
'Sequence Analysis',
'Proteomics - OpenMS',
'Computational chemistry - Open Babel',
'Genomic Interval Operations',
'Genome Annotation',
'Sequence Analysis - RSeQC',
'Transcriptomics',
'Assembly - Trinity',
'Sequence Analysis - Stacks2',
'Fastq Manipulation',
'Metabolomics - W4M',
'SAM - Tools for manipulating alignments in the SAM format',
'Next Gen Mappers',
'Fasta Manipulation',
'Metagenomics - mothur',
'RNA - Utilities for RNA',
'Amplicon Analysis - ampvis2',
'Run CellProfiler pipeline',
'Visualization',
'Amplicon Analysis - dada2',
'Sequence Analysis (BLAST)',
'Sequence Analysis (EMBOSS)',
'BED tools',
'Computational chemistry',
'Computational chemistry - Ball',
'Toxicology'
]
"tool_panel_section_id":
type: str
enum: [
"get_data", "send_data", "collection_operations", "expression_tools", "text_manipulation", "data_and_metadata_management",
"filter_and_sort", "join__subtract_and_group", "convert_formats", "fasta_fastq", "fastq_quality_control",
"sam_bam", "bed", "vcf_bcf", "nanopore", "operate_on_genomic_intervals", "fetch_sequences___alignments",
"annotation", "ontology", "assembly", "mapping", "variant_calling", "genome_editing", "rna_seq",
"peak_calling", "epigenetics", "phylogenetics", "phenotype_association", "single-cell",
"hca_sc_get-scrna", "hca_sc_seurat_tools", "hca_sc_sc3_tools", "hca_sc_scanpy_tools", "qiime_2",
"hca_sc_label_analysis_tools", "hca_sc_garnett_tools", "hca_sc_scpred_tools", "hca_sc_scater_tools", "machine_learning",
"hca_sc_monocle3_tools", "hca_sc_scmap_tools", "hca_sc_sccaf_tools", "hca_sc_utils_viz", "picard", "compute_indicators_for_satellite_remote_sensing",
"deeptools", "gemini", "emboss", "gatk_tools", "ncbi_blast", "hicexplorer", "rad_seq", "graphclust",
"mimodd", "metagenomic_analysis", "qiime", "mothur", "dna_metabarcoding" , "proteomics", "metabolomics", "chemicaltoolbox",
"statistics", "graph_display_data", "evolution", "motif_tools", "test_tools", "gis_data_handling", "quality_control",
"animal_detection_on_acoustic_recordings", "regional_variation", "genome_diversity", 'apollo', 'imaging', 'virology',
"deprecated", "interactivetools", "multiple_alignments", "climate_analysis", "rna_analysis", "species_abundance",
"biodiversity_data_exploration", "sanger_sequencing", "spatial_omics", "muon_spectroscopy", "compute_indicators_for_turnover_boulders_fields",
"astronomy", "ecoregionalization", "geom_mean",
"imaging_-_imagej2",
"sequence_analysis_-_bbtools",
"exposomics_-_recetox",
"phyloseq",
"testing",
"qiime2",
"proteomics_-_proteomiqon",
"sequence_analysis_-_stacks",
"data_source",
"amplicon_analysis",
"metagenomics",
"proteomics_-_proteore",
"data_export",
"sequence_analysis",
"proteomics_-_openms",
"computational_chemistry_-_open_babel",
"genomic_interval_operations",
"genome_annotation",
"sequence_analysis_-_rseqc",
"transcriptomics",
"assembly_-_trinity",
"sequence_analysis_-_stacks2",
"fastq_manipulation",
"metabolomics_-_w4m",
"sam_-_tools_for_manipulating_alignments_in_the_sam_format",
"next_gen_mappers",
"fasta_manipulation",
"metagenomics_-_mothur",
"rna_-_utilities_for_rna",
"amplicon_analysis_-_ampvis2",
"run_cellprofiler_pipeline",
"visualization",
"amplicon_analysis_-_dada2",
"sequence_analysis_(blast)",
"sequence_analysis_(emboss)",
"bed_tools",
"computational_chemistry",
"computational_chemistry_ball",
"toxicology"
]