Get label for inputs

get_inputs_label(inputs)

Arguments

inputs	Parsed inputs

Value

Vector of input labels

Examples

# inputs represented by a dictionary
system.file("cwl/sbg/workflow/rnaseq-salmon.json", package = "tidycwl") %>%
  read_cwl_json() %>%
  parse_inputs() %>%
  get_inputs_label()
#>  [1] "Transcriptome FASTA or Salmon index archive"
#>  [2] "FASTQ Read Files"                           
#>  [3] "Gene map or GTF file"                       
#>  [4] "Maximum number of parallel jobs"            
#>  [5] "K-mer length"                               
#>  [6] "GENCODE FASTA"                              
#>  [7] "Keep duplicates"                            
#>  [8] "Write unmapped names"                       
#>  [9] "Write mappings"                             
#> [10] "VBEM prior"                                 
#> [11] "Use Variational Bayesian optimization"      
#> [12] "Thinning factor"                            
#> [13] "Strict intersect"                           
#> [14] "Sequence-specific bias correction"          
#> [15] "Reduce GC memory"                           
#> [16] "Range factorization bins"                   
#> [17] "Quasi coverage"                             
#> [18] "Position bias"                              
#> [19] "Per transcript prior"                       
#> [20] "Number of pre auxiliary model samples"      
#> [21] "Number of Gibbs samples"                    
#> [22] "Number of bootstraps"                       
#> [23] "Number of bias samples"                     
#> [24] "Number of auxiliary model samples"          
#> [25] "No length correction"                       
#> [26] "No fragment length distribution"            
#> [27] "No effective length correction"             
#> [28] "No bias length threshold"                   
#> [29] "Minimum assigned fragments"                 
#> [30] "Meta"                                       
#> [31] "Maximum read occurence"                     
#> [32] "Maximum (S)MEM occurance"                   
#> [33] "Initialize uniform parameters"              
#> [34] "Incompatible prior probability"             
#> [35] "GC size sample"                             
#> [36] "GC bias correction"                         
#> [37] "Forgetting factor"                          
#> [38] "Fragment length standard deviation"         
#> [39] "Mean fragment length"                       
#> [40] "Maximum fragment length"                    
#> [41] "Faster mapping"                             
#> [42] "Dump equivalence class weights"             
#> [43] "Dump equivalence class counts"              
#> [44] "Discard orphans in Quasi-mapping mode"      
#> [45] "Consistent hits"                            
#> [46] "Bias speed sample"                          
#> [47] "Alternative initialization mode"            
#> [48] "Allow orphans in FMD mode"                  

# inputs represented by a list
system.file("cwl/sbg/workflow/rnaseq-salmon.cwl", package = "tidycwl") %>%
  read_cwl_yaml() %>%
  parse_inputs() %>%
  get_inputs_label()
#>  [1] "Transcriptome FASTA or Salmon index archive"
#>  [2] "FASTQ Read Files"                           
#>  [3] "Gene map or GTF file"                       
#>  [4] "Maximum number of parallel jobs"            
#>  [5] "K-mer length"                               
#>  [6] "GENCODE FASTA"                              
#>  [7] "Keep duplicates"                            
#>  [8] "Write unmapped names"                       
#>  [9] "Write mappings"                             
#> [10] "VBEM prior"                                 
#> [11] "Use Variational Bayesian optimization"      
#> [12] "Thinning factor"                            
#> [13] "Strict intersect"                           
#> [14] "Sequence-specific bias correction"          
#> [15] "Reduce GC memory"                           
#> [16] "Range factorization bins"                   
#> [17] "Quasi coverage"                             
#> [18] "Position bias"                              
#> [19] "Per transcript prior"                       
#> [20] "Number of pre auxiliary model samples"      
#> [21] "Number of Gibbs samples"                    
#> [22] "Number of bootstraps"                       
#> [23] "Number of bias samples"                     
#> [24] "Number of auxiliary model samples"          
#> [25] "No length correction"                       
#> [26] "No fragment length distribution"            
#> [27] "No effective length correction"             
#> [28] "No bias length threshold"                   
#> [29] "Minimum assigned fragments"                 
#> [30] "Meta"                                       
#> [31] "Maximum read occurence"                     
#> [32] "Maximum (S)MEM occurance"                   
#> [33] "Initialize uniform parameters"              
#> [34] "Incompatible prior probability"             
#> [35] "GC size sample"                             
#> [36] "GC bias correction"                         
#> [37] "Forgetting factor"                          
#> [38] "Fragment length standard deviation"         
#> [39] "Mean fragment length"                       
#> [40] "Maximum fragment length"                    
#> [41] "Faster mapping"                             
#> [42] "Dump equivalence class weights"             
#> [43] "Dump equivalence class counts"              
#> [44] "Discard orphans in Quasi-mapping mode"      
#> [45] "Consistent hits"                            
#> [46] "Bias speed sample"                          
#> [47] "Alternative initialization mode"            
#> [48] "Allow orphans in FMD mode"