An efficient way to access JSON file, no need to convert a JSON into a
Tool or Flow object before access, directly operate on a
list parsed from JSON file. Compare to convert_app, it is much faster.
Arguments
- from
JSON file path
- new.order
a vector of column orders by default for input it's
"id","label","type","required","prefix","fileTypes"; For output it's"id","label","type","fileTypes"- required
logical value, show requried input node only or not.
Examples
tool.in <- system.file("extdata/app", "tool_unpack_fastq.json", package = "sevenbridges")
flow.in <- system.file("extdata/app", "flow_star.json", package = "sevenbridges")
input_matrix(tool.in)
#> id label type required prefix
#> 1 #input_archive_file Input archive file File TRUE --input_archive_file
#> fileTypes
#> 1 TAR, TAR.GZ, TGZ, TAR.BZ2, TBZ2, GZ, BZ2, ZIP
input_matrix(tool.in, required = TRUE)
#> id label type required prefix
#> 1 #input_archive_file Input archive file File TRUE --input_archive_file
#> fileTypes
#> 1 TAR, TAR.GZ, TGZ, TAR.BZ2, TBZ2, GZ, BZ2, ZIP
input_matrix(flow.in)
#> id label type required
#> 1 #sjdbGTFfile sjdbGTFfile File... FALSE
#> 2 #fastq fastq File... TRUE
#> 3 #genomeFastaFiles genomeFastaFiles File TRUE
#> 4 #sjdbGTFtagExonParentTranscript Exons' parents name string FALSE
#> 5 #sjdbGTFtagExonParentGene Gene name string FALSE
#> 6 #winAnchorMultimapNmax Max loci anchors int FALSE
#> 7 #winAnchorDistNbins Max bins between anchors int FALSE
#> fileTypes
#> 1 null
#> 2 null
#> 3 null
#> 4 null
#> 5 null
#> 6 null
#> 7 null
input_matrix(flow.in, c("id", "type"))
#> id type
#> 1 #sjdbGTFfile File...
#> 2 #fastq File...
#> 3 #genomeFastaFiles File
#> 4 #sjdbGTFtagExonParentTranscript string
#> 5 #sjdbGTFtagExonParentGene string
#> 6 #winAnchorMultimapNmax int
#> 7 #winAnchorDistNbins int
input_matrix(flow.in, required = TRUE)
#> id label type required fileTypes
#> 2 #fastq fastq File... TRUE null
#> 3 #genomeFastaFiles genomeFastaFiles File TRUE null
tool.in <- system.file("extdata/app", "tool_unpack_fastq.json", package = "sevenbridges")
flow.in <- system.file("extdata/app", "flow_star.json", package = "sevenbridges")
output_matrix(tool.in)
#> id label type fileTypes
#> 1 #output_fastq_files Output FASTQ files File... FASTQ
output_matrix(flow.in)
#> id label type fileTypes
#> 1 #unmapped_reads unmapped_reads File... null
#> 2 #transcriptome_aligned_reads transcriptome_aligned_reads File null
#> 3 #splice_junctions splice_junctions File null
#> 4 #reads_per_gene reads_per_gene File null
#> 5 #log_files log_files File... null
#> 6 #chimeric_junctions chimeric_junctions File null
#> 7 #intermediate_genome intermediate_genome File null
#> 8 #chimeric_alignments chimeric_alignments File null
#> 9 #sorted_bam sorted_bam File null
#> 10 #result result File null