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#!/usr/bin/env cwl-runner
# This CWL file was automatically generated using CTDConverter.
# Visit https://github.com/WorkflowConversion/CTDConverter for more information.
baseCommand: lambda_indexer
class: CommandLineTool
cwlVersion: v1.0
doc: "Lambda is a local aligner optimized for many query sequences and searches in\
\ protein space. It is compatible to BLAST, but much faster than BLAST and many\
\ other comparable tools.\nDetailed information is available in the wiki: <https://github.com/seqan/lambda/wiki>\n\
This is the indexer_binary for creating lambda-compatible databases.\n\n\n\nFor\
\ more information, visit http://www.seqan.de"
inputs:
- default: 'false'
doc: Display the help message with advanced options.
id: param_full-help
inputBinding:
prefix: -full-help
label: Display the help message with advanced options.
type:
- 'null'
- string
- default: '1'
doc: 'Turn this option off to disable version update notifications of the application. '
id: param_version-check
inputBinding:
prefix: -version-check
label: 'Turn this option off to disable version update notifications of the application. '
type:
- 'null'
- string
- default: 'false'
doc: Display long copyright information.
id: param_copyright
inputBinding:
prefix: -copyright
label: Display long copyright information.
type:
- 'null'
- string
- default: '1'
doc: 'Display more/less diagnostic output during operation: 0 [only errors]; 1 [default];
2 [+run-time, options and statistics].'
id: param_verbosity
inputBinding:
prefix: -verbosity
label: 'Display more/less diagnostic output during operation: 0 [only errors]; 1
[default]; 2 [+run-time, options and statistics].'
type:
- 'null'
- int
- doc: Database sequences.
id: param_database
inputBinding:
prefix: -database
label: Database sequences.
type: File
- doc: SEG intervals for database(optional).
id: param_segfile
inputBinding:
prefix: -segfile
label: SEG intervals for database(optional).
type:
- 'null'
- File
- default: fm
doc: Suffix array or full-text minute space.
id: param_db-index-type
inputBinding:
prefix: -db-index-type
label: Suffix array or full-text minute space.
type:
- 'null'
- string
- default: 'on'
doc: Truncate IDs at first whitespace. This saves a lot of space and is irrelevant
for all LAMBDA output formats other than BLAST Pairwise (.m0).
id: param_truncate-ids
inputBinding:
prefix: -truncate-ids
label: Truncate IDs at first whitespace. This saves a lot of space and is irrelevant
for all LAMBDA output formats other than BLAST Pairwise (.m0).
type:
- 'null'
- string
- default: blastx
doc: Blast Operation Mode.
id: param_program
inputBinding:
prefix: -program
label: Blast Operation Mode.
type:
- 'null'
- string
- default: '1'
doc: The translation table to use (not for BlastN, BlastP). See https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=c
for ids (default is generic).
id: param_genetic-code
inputBinding:
prefix: -genetic-code
label: The translation table to use (not for BlastN, BlastP). See https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=c
for ids (default is generic).
type:
- 'null'
- int
- default: murphy10
doc: Alphabet Reduction for seeding phase (ignored for BLASTN).
id: param_alphabet-reduction
inputBinding:
prefix: -alphabet-reduction
label: Alphabet Reduction for seeding phase (ignored for BLASTN).
type:
- 'null'
- string
- default: radixsort
doc: Algorithm for SA construction (also used for FM; see Memory Requirements below!).
id: param_algorithm
inputBinding:
prefix: -algorithm
label: Algorithm for SA construction (also used for FM; see Memory Requirements
below!).
type:
- 'null'
- string
- default: '8'
doc: number of threads to run concurrently (ignored if a == skew7ext).
id: param_threads
inputBinding:
prefix: -threads
label: number of threads to run concurrently (ignored if a == skew7ext).
type:
- 'null'
- int
- default: /home/mcrusoe/debian/lambda-align
doc: temporary directory used by skew, defaults to working directory.
id: param_tmp-dir
inputBinding:
prefix: -tmp-dir
label: temporary directory used by skew, defaults to working directory.
type:
- 'null'
- string
label: indexer for creating lambda-compatible databases
|
