InterProScan_4.7.yaml

!mobyle/program
name: InterProScan
version: '4.7'
title: InterProScan (4.7)
description: InterProScan - Signature Recognition Search Against the Integrated Resource
    of Protein Domains and Functional Sites
authors: <html:span xmlns:html="http://www.w3.org/1999/xhtml">Zdobnov E.M. and Apweiler
    R.</html:span>
inputs: !mobyle/inputparagraph
    children:
    - !mobyle/inputprogramparagraph
        prompt: Input data
        name: input
        children:
        - !mobyle/inputprogramparameter
            prompt: iprscan initiation
            format: '"iprscan_launcher.sh"'
            argpos: -2
            name: iprscan_init
            command: true
            hidden: true
            type: !mobyle/stringtype {}
        - !mobyle/inputprogramparameter
            comment: Sequence where to look for some known motifs.
            prompt: Query (-i)
            format: '" -i "+ str(query_seq)'
            simple: true
            mandatory: true
            name: query_seq
            command: false
            type: !mobyle/formattedtype
                format_terms: ['EDAM_format:2200']
                data_terms: ['EDAM_data:2044']
        - !mobyle/inputprogramparameter
            comment: Select the type of sequence corresponding to the one entered
                above.
            prompt: Sequence type
            format: '" -seqtype "+ str(value)'
            simple: true
            mandatory: true
            name: seqtype
            command: false
            type: !mobyle/stringtype
                default: p
                options:
                - {label: Nucleic, value: n}
                - {label: Proteic, value: p}
    - !mobyle/inputprogramparagraph
        prompt: InterProScan options
        name: options
        children:
        - !mobyle/inputprogramparameter
            prompt: Switch on the InterPro lookup for results.
            format: ("" , " -iprlookup")[bool(value)]
            name: iprlookup
            command: false
            type: !mobyle/booleantype {default: false}
        - !mobyle/inputprogramparameter
            prompt: Show GO terms if iprlookup option is also given.
            format: ("" , " -goterms")[bool(value)]
            name: goterms
            command: false
            type: !mobyle/booleantype {default: false}
        - !mobyle/inputprogramparameter {comment: Select the applications that will
                perform the search in InterPro member databases., prompt: Applications
                to launch, format: '" -appl "+ str(value)', simple: true, mandatory: true,
            name: applications, command: false}
        - !mobyle/inputprogramparameter
            comment: Select the type of sequence corresponding to the one entered
                above.
            prompt: Output format
            format: '" -format "+ str(value)'
            simple: true
            mandatory: true
            name: output_format
            command: false
            type: !mobyle/stringtype
                default: txt
                options:
                - {label: Raw, value: raw}
                - {label: Txt, value: txt}
                - {label: Html, value: html}
                - {label: Xml, value: xml}
                - {label: EBI header on top of xml, value: ebixml}
                - {label: GFF, value: gff}
    - !mobyle/inputprogramparameter
        prompt: InterProScan results
        format: '" -o "+value'
        argpos: 0
        name: outputFile
        command: false
        hidden: true
        type: !mobyle/stringtype {default: interpro_results}
    - !mobyle/inputprogramparameter
        prompt: Some constant options
        format: '" -cli"'
        argpos: -1
        name: configStuff
        command: false
        hidden: true
        type: !mobyle/stringtype {}
outputs: !mobyle/outputparagraph
    children:
    - !mobyle/outputprogramparameter {prompt: The output file where to write results,
        filenames: outputFile, name: outputFilePath}
    - !mobyle/outputprogramparameter
        prompt: Standard output
        filenames: '"InterProScan.out"'
        name: stdout
        output_type: stdout
        type: !mobyle/formattedtype
            data_terms: ['EDAM_data:2048']
    - !mobyle/outputprogramparameter
        prompt: Standard error
        filenames: '"InterProScan.err"'
        name: stderr
        type: !mobyle/formattedtype
            data_terms: ['EDAM_data:2048']
references:
- {doi: null, label: '<html:span xmlns:html="http://www.w3.org/1999/xhtml">Zdobnov
        E.M. and Apweiler R. "InterProScan - an integration platform for the signature-recognition
        methods in InterPro" Bioinformatics, 2001, 17(9): p. 847-8.</html:span>',
    url: null}
documentation_links: ['http://www.ebi.ac.uk/Tools/InterProScan/help.html']
env: {}