Get input/output matrix out of JSON CWL file directly

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.

input_matrix(
  from,
  new.order = c("id", "label", "type", "required", "prefix", "fileTypes"),
  required = NULL
)

output_matrix(from, new.order = c("id", "label", "type", "fileTypes"))

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.

Value

A data frame of input/output information.

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