fetch_data.cwl

id: fetchdata
label: fetch_data
class: CommandLineTool
cwlVersion: v1.1
inputs: 
  - id: surl_link
    type: string
    inputBinding:
      position: 0
    
outputs: 
  - id: uncompressed
    type: Directory
    outputBinding:
      glob: 'out/*'
baseCommand: 
 - 'bash'
 - 'fetch.sh'
doc: 'Untar a compressed file'
requirements:
  InlineJavascriptRequirement: {}
  InitialWorkDirRequirement:
    listing:
      - entryname: 'fetch.sh' 
        entry: |
          #!/bin/bash
          mkdir out
          cd out
          if [[ $1 == *"sara.nl"* ]]; then
            turl=`echo $1 | awk '{gsub("srm://srm.grid.sara.nl[:0-9]*","gsiftp://gridftp.grid.sara.nl"); print}'`
            echo "Downloading $turl with globus-url-copy"
            globus-url-copy $turl - | tar -xvf -
          else
            echo "Downloading $1 with srmcp"
            srmcp $1 file:////`pwd`/\$(basename $1)
            tar -xvf \$(basename $1)
          fi