annotate iprscan/interproscan.xml @ 5:a3f43bb03458 draft default tip

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<tool id="interproscan" name="Interproscan functional predictions of ORFs"  version="1.1">
	<description>Interproscan functional predictions of ORFs</description>
    <command>
## The command is a Cheetah template which allows some Python based syntax.
## Lines starting hash hash are comments. Galaxy will turn newlines into spaces

## create temp directory
#import tempfile, os
#set $tfile = tempfile.mkstemp()[1]

sed 's/ /_/g' $input > $tfile;

## Hack, because interproscan does not seem to produce gff output even if it is configured
#if str($oformat)=="gff":
    #set $tfile2 = tempfile.mkstemp()[1]
    /home/katrien/iprscan/bin/iprscan -cli -nocrc -i $tfile -o $tfile2 -goterms -iprlookup -seqtype p -altjobs -format raw -appl $appl > /dev/null 2> /dev/null;
    /home/katrien/iprscan/bin/converter.pl -format gff3 -input $tfile2 -output $output
    rm $tfile2
#else
    /home/katrien/iprscan/bin/iprscan -cli -nocrc -i $tfile -o $output -goterms -iprlookup -seqtype p -altjobs -format $oformat 
    #if not isinstance( $appl.value, list ):
    	#set $args = [ $appl.value ]
    #else:
        #set $args = $appl.value
    #end if
    ## loop through the applications which were checked by the user
    #for $application in $args:
    	-appl $application 
    #end for
    > /dev/null 2> /dev/null
#end if


rm $tfile

	</command>
        <inputs>
            <param name="input" type="data" format="fasta" label="Protein Fasta File"/>
    	    <param name="appl" type="select" multiple="True" display="checkboxes" label="Applications to run ..." help="Select your program.">
                <option value="seg">seg</option>
                <option value="profilescan">profilescan</option>
                <option value="fprintscan">fprintscan</option>
                <option value="patternscan">patternscan</option>
                <option value="superfamily">superfamily</option>
                <option value="hmmpir">hmmpir</option>
                <option value="hmmpfam">hmmpfam</option>
                <option value="hmmsmart">hmmsmart</option>
                <option value="hmmtigr">hmmtigr</option>
                <option value="hmmpanther">hmmpanther</option>
                <option value="hamap">hamap</option>
                <option value="gene3d">gene3d</option>
                <option value="coils">coils</option>
                <option value="blastprodom">blastprodom</option>
            </param>
            <param name="oformat" type="select" label="Output format" help="Please select a output format.">
                <option value="gff">gff</option>
                <option value="raw">raw</option>
                <option value="txt">txt</option>
                <option value="html">html</option>
                <option value="xml" selected="true">xml</option>
                <option value="ebixml">EBI header on top of xml</option>
            </param>

        </inputs>
    <outputs>
	<data format="txt" name="output" label="Interproscan calculation on ${on_string}">
            <change_format>
		<when input="oformat" value="raw" format="raw"/>
                <when input="oformat" value="html" format="html"/>
                <when input="oformat" value="xml" format="xml"/>
                <when input="oformat" value="ebixml" format="xml"/>
                <when input="oformat" value="gff" format="gff"/>
            </change_format>
        </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. 
These include SCOP, CATH, PFAM and SUPERFAMILY.

This Galaxy wrapper for InterProScan is based on the version of Bjoern Gruening (http://toolshed.g2.bx.psu.edu/repos/bjoern-gruening/iprscan), but is extended with the possibility to select several applications at once via checkboxes.

**Input**

A FASTA file containing ORF predictions is required. This file must NOT contain any spaces in the FASTA headers - any spaces will be convereted to underscores (_) by this tool before submission to Interproscan.

**Output**

Example for the raw format.
This is a basic tab delimited format useful for uploading the data into a relational database or concatenation of different runs. 
is all on one line. 

====== ================================================================ ======================================================================
column example                                                          description
====== ================================================================ ======================================================================
c1     NF00181542                                                       the id of the input sequence.
c2     27A9BBAC0587AB84                                                 the crc64 (checksum) of the protein sequence (supposed to be unique).
c3     272                                                              the length of the sequence (in AA). 
c4     HMMPIR                                                           the anaysis method launched. 
c5     PIRSF001424                                                      the database members entry for this match. 
c6     Prephenate dehydratase                                           the database member description for the entry. 
c7     1                                                                the start of the domain match. 
c8     270                                                              the end of the domain match. 
c9     6.5e-141                                                         the evalue of the match (reported by member database method). 
c10    T                                                                the status of the match (T: true, ?: unknown). 
c11    06-Aug-2005                                                      the date of the run. 
c12    IPR008237                                                        the corresponding InterPro entry (if iprlookup requested by the user).
c13    Prephenate dehydratase with ACT region                           the description of the InterPro entry.
c14    Molecular Function:prephenate dehydratase activity (GO:0004664)  the GO (gene ontology) description for the InterPro entry. 
====== ================================================================ ======================================================================


**Database updates**

Typically these take place 2-3 times a year.


**Tools**

PROSITE patterns

::

 Some biologically significant amino acid patterns can be summarised in
 the form of regular expressions.
 ScanRegExp (by [e-mail]),

PROSITE profiles

::

 There are a number of protein families as well as functional or
 structural domains that cannot be detected using patterns due to their extreme
 sequence divergence, so the use of techniques based on weight matrices
 (also known as profiles) allows the detection of such proteins or domains.
 A profile is a table of position-specific amino acid weights and gap costs.
 The profile structure used in PROSITE is similar to but slightly more general
 (Bucher P. et al., 1996 [7]) than the one introduced by M. Gribskov and
 co-workers.
 pfscan from the Pftools package (by [e-mail]).

PRINTS

::

 The PRINTS database houses a collection of protein family fingerprints.
 These are groups of motifs that together are diagnostically more
 powerful than single motifs by making use of the biological context inherent in a
 multiple-motif method. The fingerprinting method arose from the need for
 a reliable technique for detecting members of large, highly divergent
 protein super-families.
 FingerPRINTScan (Scordis P. et al., 1999 [8]).

PFAM

::

 Pfam is a database of protein domain families. Pfam contains curated
 multiple sequence alignments for each family and corresponding hidden
 Markov models (HMMs) (Eddy S.R., 1998 [9]). 
 Profile hidden Markov models are statistical models of the primary
 structure consensus of a sequence family. The construction and use
 of Pfam is tightly tied to the HMMER software package.
 hmmpfam from the HMMER2.3.2 package (by Sean Eddy,
 [e-mail], http://hmmer.wustl.edu).

PRODOM

::


 ProDom is a database of protein domain families obtained by automated
 analysis of the SWISS-PROT and TrEMBL protein sequences. It is useful
 for analysing the domain arrangements of complex protein families and the
 homology relationships in modular proteins. ProDom families are built by
 an automated process based on a recursive use of PSI-BLAST homology
 searches.
 ProDomBlast3i.pl (by Emmanuel Courcelle [e-mail]
 and Yoann Beausse [e-mail])
 a wrapper on top of the Blast package (Altschul S.F. et al., 1997 [10]).


SMART

::

 SMART (a Simple Modular Architecture Research Tool) allows the
 identification and annotation of genetically mobile domains and the
 analysis of domain architectures. These domains are extensively
 annotated with respect to phyletic distributions, functional class, tertiary
 structures and functionally important residues. SMART alignments are
 optimised manually and following construction of corresponding hidden Markov models (HMMs).
 hmmpfam from the HMMER2.3.2 package (by Sean Eddy,
 [e-mail], http://hmmer.wustl.edu).


TIGRFAMs

::

 TIGRFAMs are a collection of protein families featuring curated multiple
 sequence alignments, Hidden Markov Models (HMMs) and associated
 information designed to support the automated functional identification
 of proteins by sequence homology. Classification by equivalog family
 (see below), where achievable, complements classification by orthologs,
 superfamily, domain or motif. It provides the information best suited
 for automatic assignment of specific functions to proteins from large
 scale genome sequencing projects.
 hmmpfam from the HMMER2.3.2 package (by Sean Eddy,
 [e-mail], http://hmmer.wustl.edu).

PIR SuperFamily

::

 PIR SuperFamily (PIRSF) is a classification system based on evolutionary
 relationship of whole proteins.
 hmmpfam from the HMMER2.3.2 package (by Sean Eddy,
 [e-mail], http://hmmer.wustl.edu).

SUPERFAMILY

::

 SUPERFAMILY is a library of profile hidden Markov models that represent
 all proteins of known structure, based on SCOP.
 hmmpfam/hmmsearch from the HMMER2.3.2 package (by Sean Eddy,
 [e-mail], http://hmmer.wustl.edu).
 Optionally, predictions for coiled-coil, signal peptide cleavage sites
 (SignalP v3) and TM helices (TMHMM v2) are supported (See the FAQs file
 for details).


GENE3D

::

 Gene3D is supplementary to the CATH database. This protein sequence database
 contains proteins from complete genomes which have been clustered into protein
 families and annotated with CATH domains, Pfam domains and functional
 information from KEGG, GO, COG, Affymetrix and STRINGS.
 hmmpfam from the HMM2.3.2 package (by Sean Eddy,
 [e-mail], http://hmmer.wustl.edu).


PANTHER

::

 The PANTHER (Protein ANalysis THrough Evolutionary Relationships)
 Classification System was designed to classify proteins (and their genes)
 in order to facilitate high-throughput analysis.
 hmmsearch from the HMM2.3.2 package (by Sean Eddy,
 [e-mail], http://hmmer.wustl.edu).
 and blastall from the Blast package (Altschul S.F. et al., 1997 [10]).


**Author and affiliation**

Katrien Bernaerts and Domantas Motiejunas, 12/07/2012

Corresponding author: domantas dot motiejunas at cropdesign dot com



Affiliation: CropDesign N.V., a BASF Plant Science Company - Technologiepark 3, 9052 Zwijnaarde - Belgium


**Terms of use**

Galaxy wrapper for InterProScan – sequence annotation tool - Copyright (C) 2012 CropDesign N.V. - this software may be used, copied and redistributed, with or without modification freely, without advance permission, provided that the above Copyright statement is reproduced with each copy. 
THIS SOFTWARE IS PROVIDED "AS IS" WITHOUT ANY EXPRESS OR IMPLIED WARRANTIES. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE (INCLUDING NEGLIGENCE OR OTHERWISE).


**References**

Quevillon E., Silventoinen V., Pillai S., Harte N., Mulder N., Apweiler R., Lopez R. 
InterProScan: protein domains identifier (2005). 
Nucleic Acids Res. 33 (Web Server issue) :W116-W120 

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. 
InterPro: the integrative protein signature database (2009). 
Nucleic Acids Res. 37 (Database Issue) :D224-228 

Previous Galaxy wrapper authors:

*  Bjoern Gruening, Pharmaceutical Bioinformatics, University of Freiburg
*  Konrad Paszkiewicz, Exeter Sequencing Service, University of Exeter



	</help>
</tool>