<commit_before>cwlVersion: v1.0
class: CommandLineTool
baseCommand: ["awe_search_rna.pl"]

hints:
  DockerRequirement:
    dockerPull: mgrast/pipeline:cwl

label: "rna detection"

requirements:
  InitialWorkDirRequirement:
    listing:
      - entryname: userattr.json
        entry: |
          {
                "stage_id": "425",
                "stage_name": "rna.filter",
                "data_type": "sequence",
                "file_format": "fasta",
                "seq_format": "bp" ,
          }
      - entry: $(inputs.input)

inputs:
  input:
    type: File
    inputBinding:
      prefix: -input
      valueFrom: $(inputs.input.basename)
  output:
    type: string
    inputBinding:
      prefix: -output 
  rna_nr:
    type: File
    inputBinding:
      prefix: -rna_nr
  size:
    type: int
    default: 100
    inputBinding:
      prefix: -size
  proc:
    type: int
    default: 8
    inputBinding:
      prefix: -proc          
  
                        
outputs:
 fasta:
   type: File
   outputBinding:
     glob: $(inputs.output)
 userattr:
   type: File
   outputBinding:
     glob: userattr.json<commit_msg>Changed output tag name from fasta to rna<commit_after>cwlVersion: v1.0
class: CommandLineTool
baseCommand: ["awe_search_rna.pl"]

hints:
  DockerRequirement:
    dockerPull: mgrast/pipeline:cwl

label: "rna detection"

requirements:
  InitialWorkDirRequirement:
    listing:
      - entryname: userattr.json
        entry: |
          {
                "stage_id": "425",
                "stage_name": "rna.filter",
                "data_type": "sequence",
                "file_format": "fasta",
                "seq_format": "bp" ,
          }
      - entry: $(inputs.input)

inputs:
  input:
    type: File
    inputBinding:
      prefix: -input
      valueFrom: $(inputs.input.basename)
  output:
    type: string
    inputBinding:
      prefix: -output 
  rna_nr:
    type: File
    inputBinding:
      prefix: -rna_nr
  size:
    type: int
    default: 100
    inputBinding:
      prefix: -size
  proc:
    type: int
    default: 8
    inputBinding:
      prefix: -proc          
  
                        
outputs:
 rna:
   type: File
   outputBinding:
     glob: $(inputs.output)
 userattr:
   type: File
   outputBinding:
     glob: userattr.json
{'fraction_non_alphanumeric': 0.10052447552447552, 'fraction_numerical': 0.007867132867132868, 'mean_word_length': 1.86125, 'pattern_counts': {'":': 10, '<': 3, '<?xml version=': 0, '>': 3, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '2211709', 'n_tokens_mistral': 760, 'n_tokens_neox': 731, 'n_words': 168}