annotate interproscan5/ips5.xml @ 1:e2d4343d73ad draft

Minor fixes.

<tool id="ips5" name="Interproscan functional predictions of ORFs" version="5.0.0mkh">
    <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
        echo "Start timestamp: $(date)";
        \$IPS_HOME/interproscan.sh
            ## disables the precalculated lookup service, all calculation will be run locally
            -dp
            --input $infile
            --seqtype $seqtype
            -f $output_types
            --applications $appl

            $pathways
            $goterms
            $iprlookup
            $mode
            --output-file-base __base__
            2>&#38;1;

        #if 'tsv' in str($output_types):
            mv __base__.tsv $tsv_file;
        #end if

        #if 'gff3' in str($output_types):
            mv __base__.gff3 $gff3_file;
        #end if

        #if 'xml' in str($output_types):
            mv __base__.xml $xml_file;
        #end if

         #if 'html' in str($output_types):
            mkdir -p $html_file.files_path;
            #set temp_archive_file = '__base__.html.tar.gz'
            tar -C $html_file.files_path -xvmzf $temp_archive_file;
            python \$INTERPROSCAN_SCRIPT_PATH/interproscan5/create_index.py $html_file $html_file.files_path;
            rm $temp_archive_file;
        #end if

         #if 'svg' in str($output_types):
            mkdir -p $svg_file.files_path;
            #set temp_archive_file = '__base__.svg.tar.gz'
            tar -C $svg_file.files_path -xvmzf $temp_archive_file;
            python \$INTERPROSCAN_SCRIPT_PATH/interproscan5/create_index.py $svg_file $svg_file.files_path;
            rm $temp_archive_file;
        #end if

        echo "End timestamp: $(date)"
    </command>

    <inputs>
        <param name="infile" type="data" format="fasta" label="Sequence 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="mode" type="boolean" label="Run on cluster?" help="Check to submit job to cluster."
               truevalue="--mode=cluster --clusterrunid=gtdi-ips-analysis"
               falsevalue=""/>

        <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="false">SignalP Eukaryotic Bacteria</option>
            <option value="Phobius" selected="false">Phobius: combined transmembrane topology and signal peptide predictor</option>
            <option value="TMHMM" selected="false">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="output_types" type="select" display="checkboxes" multiple="true" label="Output formats"
               help="Select the output formats to generate (at least one)">
            <option value="tsv" selected="true">Raw (TSV)</option>
            <option value="html" selected="true">HTML (Graphical)</option>
            <option value="svg" selected="false">SVG (Scalable Vector Graphics)</option>
            <option value="gff3" selected="true">GFF3</option>
            <option value="xml" selected="false">XML</option>
        </param>
    </inputs>

    <outputs>
        <data format="tabular" name="tsv_file" label="Interproscan TSV on ${on_string}">
            <filter>'tsv' in output_types</filter>
        </data>
        <data format="html" name="html_file" label="Interproscan HTML on ${on_string}">
            <filter>'html' in output_types</filter>
        </data>
        <data format="html" name="svg_file" label="Interproscan SVG on ${on_string}">
            <filter>'svg' in output_types</filter>
        </data>
        <data format="gff3" name="gff3_file" label="Interproscan GFF3 on ${on_string}">
            <filter>'gff3' in output_types</filter>
        </data>
        <data format="xml" name="xml_file" label="Interproscan XML on ${on_string}">
            <filter>'xml' in output_types</filter>
        </data>
    </outputs>

    <requirements>
    </requirements>

    <help>

**What it does**

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>