CWL Workflow: blastp_wnode_struct

Note that the tools invoked by the workflow may have separate licenses.

Inputs

ID	Type	Title	Doc
ids	File[]
seg	String
lds2	File
ofmt	String
taxid	Integer
dbsize	String
evalue	Float (Optional)
blastdb	String[]
compart	Boolean
affinity	String
max_jobs	Integer
no_merge	Boolean
proteins	File
taxon_db	File
asn_cache	Directory[]
nogenbank	Boolean
threshold	Integer
word_size	Integer
batch-size	Integer (Optional)
blast_type	String (Optional)
genus_list	Integer[]
blastdb_dir	Directory
align_filter	String
soft_masking	String
top_by_score	Integer
extra_coverage	Integer (Optional)
max_target_seqs	Integer
blast_hits_cache	File (Optional)
comp_based_stats	String
max_batch_length	Integer
allow_intersection	Boolean
scatter_gather_nchunks	String

ID	Runs	Label	Doc
split_jobs	../split_jobs/split.cwl (CommandLineTool)	cwl split wrapper
gpx_qsubmit	../progs/gpx_qsubmit.cwl (CommandLineTool)	gpx_qsubmit	This workflow is specialized for the case when there is an LDS2 input LDS2 is a _reference_ object, the kind that CWL does not like we need to provide actual input: proteins which matches the name of ASN.1 object references in LDS2 Another limitation is that it can handle no more than two item arrays in blastdb_dir and asn_cache Workaround used so far: in: proteins: default: class: File path: '/dev/null' basename: 'null' contents: ''
collect_aligns	../split_jobs/cat_array_of_files.cwl (CommandLineTool)	file concatenation
cluster_and_qdump	tt_cluster_and_qdump.cwl (Workflow)	cluster_blastp_wnode and gpx_qdump combined

ID	Type	Label	Doc
blast_align	File[]