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createOrganism.cwl
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createOrganism.cwl
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#!/usr/bin/env cwl-runner
cwlVersion: v1.2
class: CommandLineTool
requirements:
- class: InlineJavascriptRequirement
baseCommand: [createOrganism.py]
$namespaces:
cwltool: "http://commonwl.org/cwltool#"
hints:
cwltool:LoadListingRequirement:
loadListing: shallow_listing
arguments:
- position: 1
prefix: -host
valueFrom: $(inputs.host[0])
- position: 3
prefix: -organism
valueFrom: $(inputs.scientific_name[0])_$(inputs.scientific_name[1])
- position: 5
prefix: -genus
valueFrom: $(inputs.scientific_name[0])
- position: 7
prefix: -species
valueFrom: $(inputs.scientific_name[1])
- position: 9
prefix: -directory
valueFrom: $(inputs.PATH[0])/$(inputs.tree[0])/$(inputs.tree[1])/$(inputs.deepPATH_apollo2_data[0])
- position: 11
prefix: -blatdb
valueFrom: $(inputs.PATH[2])/$(inputs.tree[0])/$(inputs.genome_fasta_name[0]).2bi
- position: 13
prefix: -username
valueFrom: $(inputs.login_apollo2[0])
- position: 15
prefix: -password
valueFrom: $(inputs.login_apollo2[1])
- position: 17
valueFrom: -publicMode
inputs:
host:
type: string[]
scientific_name:
type: string[]
PATH:
type: string[]
tree:
type: string[]
deepPATH_apollo2_data:
type: string[]
login_apollo2:
type: string[]
genome_fasta_name:
type: string[]
outputs:
out_createOrganism_log:
type: stdout
stdout: createOrganism.log