Commit 17d9987e authored by Hervé  MENAGER's avatar Hervé MENAGER

localy modified Diamond cwl with tweaked gx types for tests

parent 28aa4903
class: CommandLineTool
cwlVersion: v1.0
$namespaces:
gx: "http://galaxyproject.org/cwl#"
edam: 'http://edamontology.org/'
s: 'http://schema.org/'
baseCommand:
- diamond
- makedb
inputs:
- format: 'edam:format_1929'
id: inputRefDBFile
type: File
inputBinding:
position: 0
prefix: '--in'
label: Input protein reference database file
doc: >
Path to the input protein reference database file in FASTA format (may be
gzip compressed).
If this parameter is omitted, the input will be read from stdin.
- id: taxonMapFile
type: File?
inputBinding:
position: 0
prefix: '--taxonmap'
label: Protein accession to taxon identifier NCBI mapping file
doc: >
Path to mapping file that maps NCBI protein accession numbers to taxon ids
(gzip compressed).
This parameter is optional and needs to be supplied in order to provide
taxonomy features.
The file can be downloaded from NCBI:
ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/accession2taxid/prot.accession2taxid.gz.
- id: taxonNodesFiles
type: File?
inputBinding:
position: 0
prefix: '--taxonnodes'
label: Nodes.dmp file from the NCBI taxonomy
doc: >
Path to the nodes.dmp file from the NCBI taxonomy. This parameter is
optional and needs to be supplied in order to provide taxonomy features. The file is contained within this
archive downloadable at NCBI:
ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdmp.zip
- id: threads
type: int?
inputBinding:
position: 0
prefix: '--threads'
label: Number of CPU threads
doc: >
Number of CPU threads. By default, the program will auto-detect and use
all available virtual cores on the machine.
outputs:
- id: diamondDatabaseFile
type: File
outputBinding:
glob: $(inputs.inputRefDBFile.nameroot).dmnd
format: 'edam:format_2333'
doc: |
DIAMOND is a sequence aligner for protein and translated DNA searches,
designed for high performance analysis of big sequence data.
The key features are:
+ Pairwise alignment of proteins and translated DNA at 500x-20,000x speed of BLAST.
+ Frameshift alignments for long read analysis.
+ Low resource requirements and suitable for running on standard desktops or laptops.
+ Various output formats, including BLAST pairwise, tabular and XML, as well as taxonomic classification.
Please visit https://github.com/bbuchfink/diamond for full documentation.
Releases can be downloaded from https://github.com/bbuchfink/diamond/releases
label: >-
diamond makedb: Sets up a reference protein database (in binary file format)
for DIAMOND
arguments:
- position: 0
prefix: '--db'
valueFrom: $(inputs.inputRefDBFile.nameroot).dmnd
requirements:
- class: ResourceRequirement
ramMin: 1024
- class: InlineJavascriptRequirement
hints:
- class: DockerRequirement
dockerPull: 'buchfink/diamond:version0.9.21'
- class: gx:interface
gx:inputs:
- gx:name: inputRefDBFile
gx:type: data
gx:format: 'fasta'
- gx:name: taxonMapFile
gx:type: data
gx:format: 'txt'
gx:optional: True
- gx:name: taxonNodesFiles
gx:type: data
gx:format: 'txt'
gx:optional: True
- gx:name: threads
gx:type: integer
gx:optional: True
$schemas:
- 'http://edamontology.org/EDAM_1.20.owl'
- 'https://schema.org/docs/schema_org_rdfa.html'
s:license: "https://www.apache.org/licenses/LICENSE-2.0"
s:copyrightHolder: "EMBL - European Bioinformatics Institute, 2018"
s:author: "Arnaud Meng, Maxim Scheremetjew"
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment