List possible linking methods
link_what(from, to, ...) # S4 method for Tool,Tool link_what(from, to) # S4 method for Tool,SBGWorkflow link_what(from, to) # S4 method for SBGWorkflow,Tool link_what(from, to) # S4 method for SBGWorkflow,SBGWorkflow link_what(from, to)
| from | either Tool App or SBGWorkflow object |
|---|---|
| to | either Tool App or Workflow object |
| ... | more auguments |
A Workflow object
Given two object of Tool, Flow or App, list all possible input/output match.
t1 <- system.file("extdata/app", "tool_unpack_fastq.json", package = "sevenbridges") t2 <- system.file("extdata/app", "tool_star.json", package = "sevenbridges") t1 <- convert_app(t1) t2 <- convert_app(t2) # check possible link link_what(t1, t2)#> $File... #> $File...$from #> id label type fileTypes full.name #> 1 #output_fastq_files Output FASTQ files File... FASTQ #SBG_Unpack_FASTQs #> #> $File...$to #> id label type required prefix #> 1 #reads Read sequence File... TRUE <NA> #> 95 #sjdbGTFfile Splice junction file File... FALSE <NA> #> fileTypes full.name #> 1 FASTA, FASTQ, FA, FQ, FASTQ.GZ, FQ.GZ, FASTQ.BZ2, FQ.BZ2 #STAR #> 95 GTF, GFF, TXT #STAR #> #>tool.in <- system.file("extdata/app", "tool_unpack_fastq.json", package = "sevenbridges") flow.in <- system.file("extdata/app", "flow_star.json", package = "sevenbridges") t1 <- convert_app(tool.in) f2 <- convert_app(flow.in) link_what(t1, f2)#> $File... #> $File...$from #> id label type fileTypes #> 1 #output_fastq_files Output FASTQ files File... FASTQ #> #> $File...$to #> id label type required fileTypes #> 1 #sjdbGTFfile sjdbGTFfile File... FALSE null #> 2 #fastq fastq File... TRUE null #> link_to #> 1 #STAR_Genome_Generate.sjdbGTFfile | #STAR.sjdbGTFfile #> 2 #SBG_FASTQ_Quality_Detector.fastq #> #>tool.in <- system.file("extdata/app", "tool_unpack_fastq.json", package = "sevenbridges") flow.in <- system.file("extdata/app", "flow_star.json", package = "sevenbridges") t1 <- convert_app(tool.in) f2 <- convert_app(flow.in) link_what(f2, t1)#> $File #> $File$from #> id label type required #> 2 #transcriptome_aligned_reads transcriptome_aligned_reads File FALSE #> 3 #splice_junctions splice_junctions File FALSE #> 4 #reads_per_gene reads_per_gene File FALSE #> 6 #chimeric_junctions chimeric_junctions File FALSE #> 7 #intermediate_genome intermediate_genome File FALSE #> 8 #chimeric_alignments chimeric_alignments File FALSE #> 9 #sorted_bam sorted_bam File FALSE #> 10 #result result File FALSE #> fileTypes link_to #> 2 null #STAR.transcriptome_aligned_reads #> 3 null #STAR.splice_junctions #> 4 null #STAR.reads_per_gene #> 6 null #STAR.chimeric_junctions #> 7 null #STAR.intermediate_genome #> 8 null #STAR.chimeric_alignments #> 9 null #Picard_SortSam.sorted_bam #> 10 null #SBG_FASTQ_Quality_Detector.result #> #> $File$to #> 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 #> #>