EMBL-EBI Interproscan 5 Java Client:

Protein function analysis with Interproscan 5.

[Required (for job submission)]
  --email               E-mail address.
  --sequence            Your protein sequence can be entered directly into this form
                        in GCG, FASTA, EMBL, PIR, NBRF or UniProtKB/Swiss-Prot
                        format. A partially formatted sequence is not accepted.
                        Adding a return to the end of the sequence may help certain
                        applications understand the input. Note that directly using
                        data from word processors may yield unpredictable results as
                        hidden/control characters may be present.
  --asequence           Undocumented, use with --bsequence.
  --bsequence           Undocumented, use with --asequence.


[Optional]
  --goterms             Switch on look-up of corresponding Gene Ontology annotations.

  --pathways            Switch on look-up of corresponding pathway annotations.

  --appl                A number of different protein sequence applications are
                        launched. These applications search against specific
                        databases and have preconfigured cut off thresholds.


[General]
  -h, --help            Show this help message and exit.
  --asyncjob            Forces to make an asynchronous query.
  --title               Title for job.
  --status              Get job status.
  --resultTypes         Get available result types for job.
  --polljob             Poll for the status of a job.
  --pollFreq            Poll frequency in seconds (default 3s).
  --jobid               JobId that was returned when an asynchronous job was submitted.
  --outfile             File name for results (default is JobId; for STDOUT).
  --outformat           Result format(s) to retrieve. It accepts comma-separated values.
  --params              List input parameters.
  --paramDetail         Display details for input parameter.
  --verbose             Increase output.
  --version             Prints out the version of the Client and exit.
  --quiet               Decrease output.
  --baseUrl             Base URL. Defaults to:
                        https://www.ebi.ac.uk/Tools/services/rest/iprscan5

Synchronous job:
  The results/errors are returned as soon as the job is finished.
  Usage: java -jar iprscan5.jar --email <your@email.com> [options...] <SeqFile|SeqID(s)>
  Returns: results as an attachment

Asynchronous job:
  Use this if you want to retrieve the results at a later time. The results
  are stored for up to 24 hours.
  Usage: java -jar iprscan5.jar --asyncjob --email <your@email.com> [options...] <SeqFile|SeqID(s)>
  Returns: jobid

Check status of Asynchronous job:
   Usage: java -jar iprscan5.jar --status --jobid <jobId>

Retrieve job data:
  Use the jobid to query for the status of the job. If the job is finished,
  it also returns the results/errors.
  Usage: java -jar iprscan5.jar --polljob --jobid <jobId> [--outfile string]
  Returns: string indicating the status of the job and if applicable, results
  as an attachment.

Further information:
  https://www.ebi.ac.uk/Tools/webservices and
    https://github.com/ebi-wp/webservice-clients

Support/Feedback:
  https://www.ebi.ac.uk/support/";
