psiblast.cwl

#!/usr/bin/env cwl-runner

# Copyright (C) 2019 - 2024 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: CommandLineTool
label: "PSI-Blast"
id: "psiblast"
baseCommand: python

inputs:
  # Web Service Clients: Common Entries
  command:
    type: File
    inputBinding:
      position: 0
    default:
      class: File
      location: ../../webservice-clients/python/psiblast.py

  email:
    type: string?
    doc: "E-mail address"
    inputBinding:
      prefix: --email
      position: 2

  title:
    type: string?
    doc: "Job title"
    inputBinding:
      prefix: --title
      position: 3

  jobid:
    type: string?
    doc: "Job identifier"
    inputBinding:
      prefix: --jobid
      position: 1

  polljob:
    type: boolean?
    doc: "Get job result"
    inputBinding:
      prefix: --polljob
      position: 2

  outfile:
    type: string?
    doc: "File name for results"
    inputBinding:
      prefix: --outfile
      position: 4

  outformat:
    type: string?
    doc: "Output format for results"
    inputBinding:
      prefix: --outformat
      position: 5

  pollfreq:
    type: int?
    doc: "Poll frequency in seconds (default 3s)"
    inputBinding:
      prefix: --pollFreq
      position: 6

  params:
    type: boolean?
    doc: "List input parameters"
    inputBinding:
      prefix: --params
      position: 1

  paramdetails:
    type: string?
    doc: "Get details for parameter"
    inputBinding:
      prefix: --paramDetail
      position: 1

  resultTypes:
    type: string?
    doc: "Get result types"
    inputBinding:
      prefix: --resultTypes
      position: 1

  asyncjob:
    type: boolean?
    doc: "Asynchronous mode"
    inputBinding:
      prefix: --asyncjob
      position: 2

  status:
    type: boolean?
    doc: "Get job status"
    inputBinding:
      prefix: --status
      position: 2

  version:
    type: boolean?
    doc: "Prints out the version of the Client and exit"
    inputBinding:
      prefix: --version
      position: 1

  baseUrl:
    type: string?
    doc: "Base URL for service"
    inputBinding:
      prefix: --baseUrl
      position: 7


  multifasta:
    type: boolean?
    doc: "Treat input as a set of fasta formatted sequences"
    inputBinding:
      prefix: --multifasta
      position: 8

  useSeqId:
    type: boolean?
    doc: "Use sequence identifiers for output filenames. Only available in multi-fasta and multi-identifier modes"
    inputBinding:
      prefix: --useSeqId
      position: 9

  maxJobs:
    type: int?
    doc: "Maximum number of concurrent jobs. Only available in multifasta or list file modes (default 20 jobs)"
    inputBinding:
      prefix: --maxJobs
      position: 10

  # Web Service Clients: Different Entries
  sequence_file:
    type: File?
    label: "Input sequence"
    doc: "Sequence filename or ID"
    inputBinding:
      prefix: --sequence
      position: 8

  sequence_string:
    type: string?
    label: "Input sequence"
    doc: "Sequence filename or ID"
    inputBinding:
      prefix: --sequence
      position: 8

  matrix:
    type: string?
    label: Matrix
    doc: "The comparison matrix to be used to score alignments when searching the database"
    inputBinding:
      prefix: --matrix
      position: 9
    default: "BLOSUM62"

  gapopen:
    type: string?
    label: Gap open
    doc: "Penalty taken away from the score when a gap is created in sequence. Increasing the gap openning penalty will decrease the number of gaps in the final alignment."
    inputBinding:
      prefix: --gapopen
      position: 10
    default: "11"

  gapext:
    type: string?
    label: Gap extend
    doc: "Penalty taken away from the score for each base or residue in the gap. Increasing the gap extension penalty favors short gaps in the final alignment, conversly decreasing the gap extension penalty favors long gaps in the final alignment."
    inputBinding:
      prefix: --gapext
      position: 11
    default: "1"

  expthr:
    type: string?
    label: Results E() Limit
    doc: "Limits the number of scores and alignments reported based on the expectation value. This is the maximum number of times the match is expected to occur by chance."
    inputBinding:
      prefix: --expthr
      position: 12
    default: "10.0"

  psithr:
    type: string?
    label: PSSM E-Value cut-off
    doc: "Expectation value threshold for automatic selection of matched sequences for inclusion in PSSM at each iteration."
    inputBinding:
      prefix: --psithr
      position: 13
    default: "1.0e-3"

  scores:
    type: string?
    label: Scores
    doc: "Maximum number of match score summaries reported in the result output."
    inputBinding:
      prefix: --scores
      position: 14
    default: "500"

  alignments:
    type: string?
    label: Alignments
    doc: "Maximum number of match alignments reported in the result output."
    inputBinding:
      prefix: --alignments
      position: 15
    default: "500"

  alignView:
    type: string?
    label: Align views
    doc: "Formating for the alignments"
    inputBinding:
      prefix: --alignView
      position: 16
    default: "0"

  dropoff:
    type: string?
    label: Dropoff
    doc: "The amount a score can drop before extension of word hits is halted"
    inputBinding:
      prefix: --dropoff
      position: 17
    default: "15"

  finaldropoff:
    type: string?
    label: Final Dropoff
    doc: "Dropoff value for final gapped alignment"
    inputBinding:
      prefix: --finaldropoff
      position: 18
    default: "25"

  filter:
    type: string?
    label: Filter
    doc: "Filter regions of low sequence complexity. This can avoid issues with low complexity sequences where matches are found due to composition rather than meaningful sequence similarity. However in some cases filtering also masks regions of interest and so should be used with caution."
    inputBinding:
      prefix: --filter
      position: 19
    default: "no"

  seqrange:
    type: string?
    label: Sequence range
    doc: "Specify a range or section of the input sequence to use in the search. Example: Specifying '34-89' in an input sequence of total length 100, will tell BLAST to only use residues 34 to 89, inclusive."
    inputBinding:
      prefix: --seqrange
      position: 20

  database:
    type: string?
    label: Database
    doc: "The databases to run the sequence similarity search against. Multiple databases can be used at the same time"
    inputBinding:
      prefix: --database
      position: 21

  previousjobid:
    type: string?
    label: Previous Iteration Job Id
    doc: "The job identifier for the previous PSI-BLAST iteration."
    inputBinding:
      prefix: --previousjobid
      position: 22

  selectedHits:
    type: string?
    label: Selected Hits
    doc: "List of identifiers of the hits from the previous iteration to use to construct the search PSSM for this iteration."
    inputBinding:
      prefix: --selectedHits
      position: 23

  cpfile:
    type: string?
    label: Checkpoint File
    doc: "Checkpoint file from the previous iteration. Must be in ASN.1 Binary Format."
    inputBinding:
      prefix: --cpfile
      position: 24

  patfile:
    type: string?
    label: Pattern File
    doc: "Pattern file for PHI-BLAST functionality. This file needs to be in the style of a prosite entry file, with at least an ID line, PA line and optional HI line."
    inputBinding:
      prefix: --patfile
      position: 25


outputs:
  all:
    type: File[]
    streamable: true
    outputBinding:
      glob: "*"


$schemas:
  - https://schema.org/version/latest/schemaorg-current-https.rdf

$namespaces:
  s: http://schema.org/
  edam: http://edamontology.org/

s:author:
  - class: s:Person
    s:identifier: https://orcid.org/0000-0001-8728-9449
    s:email: mailto:www-prod@ebi.ac.uk
    s:name: Fábio Madeira (Web Production)
    s:worksFor:
    - class: s:Organization
      s:name: EMBL - European Bioinformatics Institute
      s:location: Hinxton, Cambridgeshire, CB10 1SD, UK
      s:department:
      - class: s:Organization
        s:name: Web Production

# s:citation: https://dx.doi.org/10.6084/m9.figshare.3115156.v2
# s:codeRepository: https://github.com/common-workflow-language/common-workflow-language
s:dateCreated: "2018-08-03"

# s:license:
s:license:
  - https://www.apache.org/licenses/LICENSE-2.0
  - https://spdx.org/licenses/Apache-2.0

s:copyrightHolder: "EMBL - European Bioinformatics Institute"