<commit_before>cwlVersion: v1.0
class: CommandLineTool
baseCommand: awe_filter_feature.pl

hints:
  DockerRequirement:
    dockerPull: mgrast/pipeline:cwl

label: "aa filtering"

requirements:
  InitialWorkDirRequirement:
    listing:
      - entryname: userattr.json
        entry: |
          {
            "stage_id": "375",
            "stage_name": "filtering",
            "data_type": "sequence",
            "file_format": "fasta",
            "seq_format": "aa",
            "overlap": "$(inputs.overlap)"
          }

inputs:
  in_clust:
    type: File
    inputBinding:
      prefix: -in_clust
  in_sim:
    type: File
    inputBinding:
      prefix: -in_sim
  in_seq:
    type: File
    inputBinding:
      prefix: -in_seq
  output:
    type: string
    inputBinding:
      prefix: -output
  memory:
    type: int
    default: 10
    inputBinding:
      prefix: -memory
  overlap:
    type: int?
    default: 10
    inputBinding:
      prefix: -overlap
  tool_help:
    type: boolean?
    inputBinding:
      prefix: -help    
                                            
outputs:
  output:
    type: File
    outputBinding:
      glob: $(inputs.output)
  userattr:
    type: File
    outputBinding:
      glob: $(inputs.output).json<commit_msg>Changed output file tag<commit_after>cwlVersion: v1.0
class: CommandLineTool
baseCommand: awe_filter_feature.pl

hints:
  DockerRequirement:
    dockerPull: mgrast/pipeline:cwl

label: "aa filtering"

requirements:
  InitialWorkDirRequirement:
    listing:
      - entryname: userattr.json
        entry: |
          {
            "stage_id": "375",
            "stage_name": "filtering",
            "data_type": "sequence",
            "file_format": "fasta",
            "seq_format": "aa",
            "overlap": "$(inputs.overlap)"
          }

inputs:
  in_clust:
    type: File
    inputBinding:
      prefix: -in_clust
  in_sim:
    type: File
    inputBinding:
      prefix: -in_sim
  in_seq:
    type: File
    inputBinding:
      prefix: -in_seq
  output:
    type: string
    inputBinding:
      prefix: -output
  memory:
    type: int
    default: 10
    inputBinding:
      prefix: -memory
  overlap:
    type: int?
    default: 10
    inputBinding:
      prefix: -overlap
  tool_help:
    type: boolean?
    inputBinding:
      prefix: -help    
                                            
outputs:
  filtered:
    type: File
    outputBinding:
      glob: $(inputs.output)
  userattr:
    type: File
    outputBinding:
      glob: $(inputs.output).json
{'fraction_non_alphanumeric': 0.09738717339667459, 'fraction_numerical': 0.007125890736342043, 'mean_word_length': 1.9045977011494253, 'pattern_counts': {'":': 12, '<': 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': 2, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '509838', 'n_tokens_mistral': 816, 'n_tokens_neox': 795, 'n_words': 184}