comparison interproscan5/interproscan.xml @ 0:f41c8f299270 draft default tip

Untested version

0:f41c8f299270

<tool id="interproscan" name="Interproscan functional predictions of ORFs" version="5.0.1">
    <description>Interproscan functional predictions of ORFs</description>
    <requirements>
        <requirement type="package">signalp</requirement>
        <requirement type="package">phobius</requirement>
        <requirement type="package">tmhmm</requirement>
        <requirement type="set_environment">INTERPROSCAN_SCRIPT_PATH</requirement>
    </requirements>

    <command>
        #import os
        interproscan.sh
        ## disables the precalculated lookup service, all calculation will be run locally
        -dp
        --input $infile
        --seqtype $seqtype
        -f $oformat
        --applications $appl
        --tempdir \$TEMP

        $pathways
        $goterms
        $iprlookup

        #if str($oformat) in ['SVG', 'HTML']:
        --output-file-base $outfile
        2>&#38;1;
        mkdir -p $outfile.files_path;
        #set temp_archive_file = str($outfile) + '.' + str($oformat).lower() + '.tar.gz'
        tar -C $outfile.files_path -xvmzf $temp_archive_file;
        python \$INTERPROSCAN_SCRIPT_PATH/create_index.py $outfile $outfile.files_path;
        rm $temp_archive_file
        #else:
        -o $outfile
        2>&#38;1
        #end if
    </command>

    <inputs>
        <param name="infile" type="data" format="fasta" label="Protein Fasta File"/>

        <param name="seqtype" type="select" label="Type of the input sequences" help="">
            <option value="p" selected="true">Protein</option>
            <option value="n">DNA / RNA</option>
        </param>

        <param name="appl" type="select" multiple="True" display="checkboxes" label="Applications to run"
               help="Select your programm.">
            <option value="TIGRFAM" selected="true">TIGRFAM: protein families based on Hidden Markov Models or HMMs
            </option>
            <option value="PIRSF" selected="true">PIRSF: non-overlapping clustering of UniProtKB sequences into a
                hierarchical order (evolutionary relationships)
            </option>
            <option value="ProDom" selected="true">ProDom: set of protein domain families generated from the UniProtKB
            </option>
            <option value="Panther" selected="true">Panther: Protein ANalysis THrough Evolutionary Relationships
            </option>
            <option value="SMART" selected="true">SMART: identification and analysis of domain architectures based on
                Hidden Markov Models or HMMs
            </option>
            <option value="PrositeProfiles" selected="true">PROSITE Profiles: protein domains, families and functional
                sites as well as associated profiles to identify them
            </option>
            <option value="PrositePatterns" selected="true">PROSITE Pattern: protein domains, families and functional
                sites as well as associated patterns to identify them
            </option>
            <option value="HAMAP" selected="true">HAMAP: High-quality Automated Annotation of Microbial Proteomes
            </option>
            <option value="PfamA" selected="true">PfamA: protein families, each represented by multiple sequence
                alignments and hidden Markov models
            </option>
            <option value="PRINTS" selected="true">PRINTS: group of conserved motifs (fingerprints) used to characterise
                a protein family
            </option>
            <option value="SuperFamily" selected="true">SUPERFAMILY: database of structural and functional annotation
            </option>
            <option value="Coils" selected="true">Coils: Prediction of Coiled Coil Regions in Proteins</option>
            <option value="Gene3d" selected="true">Gene3d: Structural assignment for whole genes and genomes using the
                CATH domain structure database
            </option>
            <option value="SignalP-GRAM_POSITIVE" selected="false">SignalP Gram Positive Bacteria</option>
            <option value="SignalP-GRAM_NEGATIVE" selected="false">SignalP Gram Negative Bacteria</option>
            <option value="SignalP-EUK" selected="true">SignalP Eukaryotic Bacteria</option>
            <option value="Phobius" selected="true">Phobius: combined transmembrane topology and signal peptide
                predictor
            </option>
            <option value="TMHMM" selected="true">TMHMM: Prediction of transmembrane helices in proteins</option>
        </param>

        <param name="pathways" truevalue="--pathways" falsevalue="" checked="True" type="boolean"
               label="Include pathway information"
               help="Option that provides mappings from matches to pathway information, which is based on the matched manually curated InterPro entries. (--pathways)"/>
        <param name="goterms" truevalue="--goterms" falsevalue="" checked="True" type="boolean"
               label="Include Gene Ontology (GO) mappings"
               help="Look up of corresponding Gene Ontology annotation. Implies -iprlookup option. (--goterms)"/>
        <param name="iprlookup" truevalue="--iprlookup" falsevalue="" checked="False" type="boolean"
               label="Provide additional mappings"
               help="Provide mappings from matched member database signatures to the InterPro entries that they are integrated into (--iprlookup)"/>

        <param name="oformat" type="select" label="Output format" help="Please select a output format.">
            <option value="TSV" selected="true">Tab-separated values format (TSV)</option>
            <option value="GFF3">GFF3</option>
            <option value="SVG">SVG</option>
            <option value="HTML">HTML</option>
            <option value="XML">XML</option>
        </param>
    </inputs>

    <outputs>
        <data format="tabular" name="outfile" label="Interproscan calculation on ${on_string}">
            <change_format>
                <when input="oformat" value="HTML" format="html"/>
                <when input="oformat" value="XML" format="xml"/>
                <when input="oformat" value="SVG" format="html"/>
                <when input="oformat" value="GFF3" format="gff"/>
            </change_format>
        </data>

    </outputs>

    <requirements>
    </requirements>

    <help>
        **What it does and does not do**

        Interproscan is a batch tool to query the Interpro database. It provides annotations based on multiple searches
        of profile and other functional databases.


        #####
        Input
        #####

        Required is a FASTA file containing protein or nucleotide sequences.


        ######
        Output
        ######

        In this version of InterProScan_, you can retrieve output in any of the following five formats:

        * TSV: a simple tab-delimited file format
        * XML: the new "IMPACT" XML format (XSD available here_).
        * GFF: The `GFF 3.0`_ format
        * HTML: An HTML representation of the protein matches
        * SVG: An Scalable Vector Graphics representation of the protein matches


        .. _`GFF 3.0`: http://gmod.org/wiki/GFF#GFF3_Format
        .. _here: http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5


        Tab-separated values format (TSV)
        =================================

        Basic tab delimited format.


        Example Output
        --------------

        ::

        P51587 14086411a2cdf1c4cba63020e1622579 3418 Pfam PF09103 BRCA2, oligonucleotide/oligosaccharide-binding, domain
        1 2670 2799 7.9E-43 T 15-03-2013
        P51587 14086411a2cdf1c4cba63020e1622579 3418 ProSiteProfiles PS50138 BRCA2 repeat profile. 1002 1036 0.0 T
        18-03-2013 IPR002093 BRCA2 repeat GO:0005515|GO:0006302
        P51587 14086411a2cdf1c4cba63020e1622579 3418 Gene3D G3DSA:2.40.50.140 2966 3051 3.1E-52 T 15-03-2013
        ...


        The TSV format presents the match data in columns as follows:

        - Protein Accession (e.g. P51587)
        - Sequence MD5 digest (e.g. 14086411a2cdf1c4cba63020e1622579)
        - Sequence Length (e.g. 3418)
        - Analysis (e.g. Pfam / PRINTS / Gene3D)
        - Signature Accession (e.g. PF09103 / G3DSA:2.40.50.140)
        - Signature Description (e.g. BRCA2 repeat profile)
        - Start location
        - Stop location
        - Score - is the e-value of the match reported by member database method (e.g. 3.1E-52)
        - Status - is the status of the match (T: true)
        - Date - is the date of the run
        - (InterProScan_ annotations - accession (e.g. IPR002093) - optional column; only displayed if -iprscan option
        is switched on)
        - (InterProScan_ annotations - description (e.g. BRCA2 repeat) - optional column; only displayed if -iprscan
        option is switched on)
        - (GO annotations (e.g. GO:0005515) - optional column; only displayed if --goterms option is switched on)
        - (Pathways annotations (e.g. REACT_71) - optional column; only displayed if --pathways option is switched on)


        Extensible Markup Language (XML)
        ================================

        XML representation of the matches - this is the richest form of the data. The XML Schema Definition (XSD) is
        available [http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5 here].

        Example Output
        --------------

        .. image:: $PATH_TO_IMAGES/example_xml_output.png


        Generic Feature Format Version 3 (GFF3)
        =======================================

        The GFF3 format is a flat tab-delimited file, which is much richer then the TSV output format. It allows you to
        trace back from matches to predicted proteins and to nucleic acid sequences. It also contains a FASTA format
        representation of the predicted protein sequences and their matches. You will find a documentation of all the
        columns and attributes used on [http://www.sequenceontology.org/gff3.shtml].

        Example Output
        --------------

        ::

        ##gff-version 3
        ##feature-ontology http://song.cvs.sourceforge.net/viewvc/song/ontology/sofa.obo?revision=1.269
        ##sequence-region AACH01000027 1 1347
        ##seqid|source|type|start|end|score|strand|phase|attributes
        AACH01000027 provided_by_user nucleic_acid 1 1347 . + .
        Name=AACH01000027;md5=b2a7416cb92565c004becb7510f46840;ID=AACH01000027
        AACH01000027 getorf ORF 1 1347 . + . Name=AACH01000027.2_21;Target=pep_AACH01000027_1_1347 1
        449;md5=b2a7416cb92565c004becb7510f46840;ID=orf_AACH01000027_1_1347
        AACH01000027 getorf polypeptide 1 449 . + . md5=fd0743a673ac69fb6e5c67a48f264dd5;ID=pep_AACH01000027_1_1347
        AACH01000027 Pfam protein_match 84 314 1.2E-45 + . Name=PF00696;signature_desc=Amino acid kinase
        family;Target=null 84
        314;status=T;ID=match$8_84_314;Ontology_term="GO:0008652";date=15-04-2013;Dbxref="InterPro:IPR001048","Reactome:REACT_13"
        ##sequence-region 2
        ...
        >pep_AACH01000027_1_1347
        LVLLAAFDCIDDTKLVKQIIISEIINSLPNIVNDKYGRKVLLYLLSPRDPAHTVREIIEV
        LQKGDGNAHSKKDTEIRRREMKYKRIVFKVGTSSLTNEDGSLSRSKVKDITQQLAMLHEA
        GHELILVSSGAIAAGFGALGFKKRPTKIADKQASAAVGQGLLLEEYTTNLLLRQIVSAQI
        LLTQDDFVDKRRYKNAHQALSVLLNRGAIPIINENDSVVIDELKVGDNDTLSAQVAAMVQ
        ADLLVFLTDVDGLYTGNPNSDPRAKRLERIETINREIIDMAGGAGSSNGTGGMLTKIKAA
        TIATESGVPVYICSSLKSDSMIEAAEETEDGSYFVAQEKGLRTQKQWLAFYAQSQGSIWV
        DKGAAEALSQYGKSLLLSGIVEAEGVFSYGDIVTVFDKESGKSLGKGRVQFGASALEDML
        RSQKAKGVLIYRDDWISITPEIQLLFTEF
        ...
        >match$8_84_314
        KRIVFKVGTSSLTNEDGSLSRSKVKDITQQLAMLHEAGHELILVSSGAIAAGFGALGFKK
        RPTKIADKQASAAVGQGLLLEEYTTNLLLRQIVSAQILLTQDDFVDKRRYKNAHQALSVL
        LNRGAIPIINENDSVVIDELKVGDNDTLSAQVAAMVQADLLVFLTDVDGLYTGNPNSDPR
        AKRLERIETINREIIDMAGGAGSSNGTGGMLTKIKAATIATESGVPVYICS


        Scalable Vector Graphics (SVG) and HyperText Markup Language (HTML)
        ====================================================================

        InterProScan_ 5 outputs a single HTML/SVG file for each protein sequence analysed.


        Example Output
        --------------

        .. image:: $PATH_TO_IMAGES/P51587.svg.png

        .. _InterProScan: http://www.ebi.ac.uk/interpro


        ----------
        References
        ----------


        If you use this Galaxy tool in work leading to a scientific publication please
        cite the following papers:

        Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013).
        Galaxy tools and workflows for sequence analysis with applications
        in molecular plant pathology. PeerJ 1:e167
        http://dx.doi.org/10.7717/peerj.167

        Zdobnov EM, Apweiler R (2001)
        InterProScan an integration platform for the signature-recognition methods in InterPro.
        Bioinformatics 17, 847-848.
        http://dx.doi.org/10.1093/bioinformatics/17.9.847

        Quevillon E, Silventoinen V, Pillai S, Harte N, Mulder N, Apweiler R, Lopez R (2005)
        InterProScan: protein domains identifier.
        Nucleic Acids Research 33 (Web Server issue), W116-W120.
        http://dx.doi.org/10.1093/nar/gki442

        Hunter S, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bork P, Das U, Daugherty L, Duquenne L, Finn
        RD, Gough J, Haft D, Hulo N, Kahn D, Kelly E, Laugraud A, Letunic I, Lonsdale D, Lopez R, Madera M, Maslen J,
        McAnulla C, McDowall J, Mistry J, Mitchell A, Mulder N, Natale D, Orengo C, Quinn AF, Selengut JD, Sigrist CJ,
        Thimma M, Thomas PD, Valentin F, Wilson D, Wu CH, Yeats C. (2009)
        InterPro: the integrative protein signature database.
        Nucleic Acids Research 37 (Database Issue), D224-228.
        http://dx.doi.org/10.1093/nar/gkn785


        This wrapper is available to install into other Galaxy Instances via the Galaxy Tool Shed at
        http://toolshed.g2.bx.psu.edu/view/bgruening/interproscan5


        **Galaxy Wrapper Author**::

        * Bjoern Gruening, University of Freiburg
        * Konrad Paszkiewicz, University of Exeter

    </help>
</tool>