cwlVersion: v1.0
class: CommandLineTool
baseCommand: awe_blat_prot.py

hints:
  DockerRequirement:
    dockerPull: mgrast/pipeline:cwl

label: "aa sims blat"

requirements:
  - class: InlineJavascriptRequirement
  - class: InitialWorkDirRequirement
    listing:
      -     $(inputs.nr_dir.listing)
      # - entryname: userattr.json
 #        entry: |
 #         {
 #           "stage_id": "650",
 #           "stage_name": "protein.sims",
 #           "m5nr_sims_version": $(inputs.nr_version)",
 #           "data_type": "similarity",
 #           "file_format": "blast m8",
 #           "sim_type": "protein"
 #         }
      
     


inputs:
  input:
    type: File
    inputBinding:
      prefix: -i
  output:
    type: string
    inputBinding:
      prefix: -o
  nr_prefix:
    type: string
    doc: prefix for nr, expects *.1 and *.2
    default: md5nr
  nr_dir:
    type: Directory
    doc: Directory containing the db with prefix nr_prefix
  sort_dir:
    type: string?
    inputBinding:
      prefix: -d  
  nr_version:
    type: string
        
                 
  
                        
outputs:
  sims:
    type: File
    outputBinding:
      glob: $(inputs.output)
  userattr:
    type: File
    outputBinding:
      glob: userattr.json
 
        
cwlVersion: v1.0
class: CommandLineTool
baseCommand: awe_blat_prot.py

hints:
  DockerRequirement:
    dockerPull: mgrast/pipeline:cwl

requirements:
  - class: InlineJavascriptRequirement
  - class: InitialWorkDirRequirement
    listing: 
      - $(inputs.nr_part_1)
      - $(inputs.nr_part_2)
      - entryname: userattr.json
        entry: |
          {
            "stage_id": "650",
            "stage_name": "protein.sims",
            "m5nr_sims_version": $(inputs.nr_version)",
            "data_type": "similarity",
            "file_format": "blast m8",
            "sim_type": "protein"
          }
    
label: "aa sims blat"
    
stdout: out.log
stderr: error.log

inputs:
  input:
    type: File
    inputBinding:
      prefix: -i
  output:
    type: string
    inputBinding:
      prefix: -o
  nr_prefix:
    type: string
    doc: prefix for nr, expects *.1 and *.2
    default: md5nr
  nr_dir:
    type: Directory
    doc: Directory containing the db with prefix nr_prefix
  sort_dir:
    type: string?
    inputBinding:
      prefix: -d  
  nr_version:
    type: string
  nr_part_1:
    type: File
    doc: Filename prefix has to match nr_prefix    
  nr_part_2:
    type: File
    doc: Filename prefix has to match nr_prefix           
                 
  
                        
outputs:
  sims:
    type: File
    outputBinding:
      glob: $(inputs.output)
  stdout:
    type: stdout
  error: 
    type: stderr    
 
        
Add part files for reference DB explicitly
Add part files for reference DB explicitly
