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#!/usr/bin/env cwl-runner
# Copyright (C) 2018 EMBL - European Bioinformatics Institute
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# http://www.apache.org/licenses/LICENSE-2.0
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
cwlVersion: v1.0
class: Workflow
inputs:
email: string
sequence: string
program: string
database: string
type: string
method: string
domain: string
referencedDomain: string
fields: string
outputs:
workflow_output:
type: File
outputSource: ebeye_step/ebeye_out
pdbe_output:
type:
type: array
items: File
outputSource: pdbe_step/pdbe_info
steps:
ncbiblast_step:
run: 'ncbiblast.cwl'
in:
email: email
sequence_string: sequence
program: program
database: database
type: type
out: [blast_ids]
# converts blast output into usable input format for EBI search
conversion_step:
run: 'conversion.cwl'
in:
idFile: ncbiblast_step/blast_ids
out: [idstring]
ebeye_step:
run: 'ebeye.cwl'
in:
method: method
domain: domain
entryids: conversion_step/idstring
referencedDomain: referencedDomain
fields: fields
out: [ebeye_out]
# search the ids in the pdbe database to learn more about them
pdbe_step:
run: 'pdbe_API.cwl'
in:
ids: ebeye_step/ebeye_out
out: [pdbe_info]