| Next changeset 1:eb12db502d3c (2013-07-10) |
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interproscan.xml readme.rst |
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| diff -r 000000000000 -r c10e37cca7e3 interproscan.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/interproscan.xml Tue Jun 25 06:29:45 2013 -0400 |
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| b'@@ -0,0 +1,239 @@\n+<tool id="interproscan" name="Interproscan functional predictions of ORFs" version="1.2">\n+ <description>Interproscan functional predictions of ORFs</description>\n+ <command>\n+## The command is a Cheetah template which allows some Python based syntax.\n+## Lines starting hash hash are comments. Galaxy will turn newlines into spaces\n+\n+## create temp directory\n+#import tempfile, os\n+#set $tfile = tempfile.mkstemp()[1]\n+\n+sed \'s/ /_/g\' $input > $tfile;\n+\n+## Hack, because interproscan does not seem to produce gff output even if it is configured\n+#if str($oformat) == "gff":\n+ #set $tfile2 = tempfile.mkstemp()[1]\n+ iprscan -cli -nocrc -i $tfile -o $tfile2 -goterms -seqtype p -altjobs -format raw -appl $appl 2>&1;\n+ converter.pl -format gff3 -input $tfile2 -output $output;\n+ rm $tfile2;\n+#else\n+ iprscan -cli -nocrc -i $tfile -o $output -goterms -seqtype p -altjobs -format $oformat -appl $appl 2>&1;\n+#end if\n+\n+rm $tfile\n+\n+ </command>\n+ <inputs>\n+ <param name="input" type="data" format="fasta" label="Protein Fasta File"/>\n+\n+ <param name="appl" type="select" format="text" label="Applications to run" help="Select your programm.">\n+ <option value="blastprodom+coils+gene3d+hamap+hmmpanther+hmmpir+hmmpfam+hmmsmart+hmmtigr+fprintscan+patternscan+profilescan+superfamily+seg+signalp+tmhmm" selected="true">all</option>\n+ <option value="seg">seg</option>\n+ <option value="signalp">signalp</option>\n+ <option value="tmhmm">tmhmm</option>\n+ <option value="fprintscan">fprintscan</option>\n+ <option value="patternscan">patternscan</option>\n+ <option value="profilescan">profilescan</option>\n+ <option value="superfamily">superfamily</option>\n+ <option value="hmmpir">hmmpir</option>\n+ <option value="hmmpfam">hmmpfam</option>\n+ <option value="hmmsmart">hmmsmart</option>\n+ <option value="hmmtigr">hmmtigr</option>\n+ <option value="hmmpanther">hmmpanther</option>\n+ <option value="hamap">hamap</option>\n+ <option value="gene3d">gene3d</option>\n+ <option value="coils">coils</option>\n+ <option value="blastprodom">blastprodom</option>\n+ </param>\n+\n+ <param name="oformat" type="select" label="Output format" help="Please select a output format.">\n+ <option value="gff">gff</option>\n+ <option value="raw" selected="true">raw</option>\n+ <option value="txt">txt</option>\n+ <option value="html">html</option>\n+ <option value="xml">xml</option>\n+ <option value="ebixml">EBI header on top of xml</option>\n+ </param>\n+\n+ </inputs>\n+ <outputs>\n+\n+ <data format="txt" name="output" label="Interproscan calculation on ${on_string}">\n+ <change_format>\n+ <when input="oformat" value="html" format="html"/>\n+ <when input="oformat" value="xml" format="xml"/>\n+ <when input="oformat" value="ebixml" format="xml"/>\n+ <when input="oformat" value="gff" format="gff"/>\n+ </change_format>\n+ </data>\n+\n+ </outputs>\n+ <requirements>\n+ </requirements>\n+ <help>\n+**What it does**\n+\n+Interproscan is a batch tool to query the Interpro database. It provides annotations based on multiple searches of profile and other functional databases. \n+These include SCOP, CATH, PFAM and SUPERFAMILY.\n+\n+**Input**\n+\n+Required is a FASTA file containing ORF predictions. This file must NOT contain any spaces in the FASTA headers - any spaces will be convereted to underscores ``_`` by this tool before running with Interproscan.\n+\n+**Output**\n+\n+Example for the raw format.\n+The output will consist of a tabular file in galaxy with 14 columns and can be eas'..b'sse beausse@toulouse.inra.fr)\n+ a wrapper on top of the Blast package (Altschul S.F. et al., 1997).\n+\n+**SMART**\n+ SMART (a Simple Modular Architecture Research Tool) allows the\n+ identification and annotation of genetically mobile domains and the\n+ analysis of domain architectures. These domains are extensively\n+ annotated with respect to phyletic distributions, functional class, tertiary\n+ structures and functionally important residues. SMART alignments are\n+ optimised manually and following construction of corresponding hidden Markov models (HMMs).\n+ hmmpfam from the HMMER2.3.2 package (by Sean Eddy,\n+ eddy@genetics.wustl.edu, http://hmmer.wustl.edu).\n+\n+**TIGRFAMs**\n+ TIGRFAMs are a collection of protein families featuring curated multiple\n+ sequence alignments, Hidden Markov Models (HMMs) and associated\n+ information designed to support the automated functional identification\n+ of proteins by sequence homology. Classification by equivalog family\n+ (see below), where achievable, complements classification by orthologs,\n+ superfamily, domain or motif. It provides the information best suited\n+ for automatic assignment of specific functions to proteins from large\n+ scale genome sequencing projects.\n+ hmmpfam from the HMMER2.3.2 package (by Sean Eddy,\n+ eddy@genetics.wustl.edu, http://hmmer.wustl.edu).\n+\n+**PIR SuperFamily**\n+ PIR SuperFamily (PIRSF) is a classification system based on evolutionary\n+ relationship of whole proteins.\n+ hmmpfam from the HMMER2.3.2 package (by Sean Eddy,\n+ eddy@genetics.wustl.edu, http://hmmer.wustl.edu).\n+\n+**SUPERFAMILY**\n+ SUPERFAMILY is a library of profile hidden Markov models that represent\n+ all proteins of known structure, based on SCOP.\n+ hmmpfam/hmmsearch from the HMMER2.3.2 package (by Sean Eddy,\n+ eddy@genetics.wustl.edu, http://hmmer.wustl.edu).\n+ Optionally, predictions for coiled-coil, signal peptide cleavage sites\n+ (SignalP v3) and TM helices (TMHMM v2) are supported (See the FAQs file for details).\n+\n+**GENE3D**\n+ Gene3D is supplementary to the CATH database. This protein sequence database\n+ contains proteins from complete genomes which have been clustered into protein\n+ families and annotated with CATH domains, Pfam domains and functional\n+ information from KEGG, GO, COG, Affymetrix and STRINGS.\n+ hmmpfam from the HMM2.3.2 package (by Sean Eddy,\n+ eddy@genetics.wustl.edu, http://hmmer.wustl.edu).\n+\n+**PANTHER**\n+ The PANTHER (Protein ANalysis THrough Evolutionary Relationships)\n+ Classification System was designed to classify proteins (and their genes)\n+ in order to facilitate high-throughput analysis.\n+ hmmsearch from the HMM2.3.2 package (by Sean Eddy,\n+ eddy@genetics.wustl.edu, http://hmmer.wustl.edu).\n+ and blastall from the Blast package (Altschul S.F. et al., 1997).\n+\n+----------\n+References\n+----------\n+\n+Zdobnov EM, Apweiler R (2001)\n+InterProScan an integration platform for the signature-recognition methods in InterPro.\n+Bioinformatics 17, 847-848.\n+http://dx.doi.org/10.1093/bioinformatics/17.9.847\n+\n+Quevillon E, Silventoinen V, Pillai S, Harte N, Mulder N, Apweiler R, Lopez R (2005)\n+InterProScan: protein domains identifier.\n+Nucleic Acids Research 33 (Web Server issue), W116-W120.\n+http://dx.doi.org/10.1093/nar/gki442\n+\n+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)\n+InterPro: the integrative protein signature database.\n+Nucleic Acids Research 37 (Database Issue), D224-228.\n+http://dx.doi.org/10.1093/nar/gkn785\n+\n+\n+**Galaxy Wrapper Author**::\n+\n+ * Bjoern Gruening, Pharmaceutical Bioinformatics, University of Freiburg\n+ * Konrad Paszkiewicz, Exeter Sequencing Service, University of Exeter\n+\n+ </help>\n+</tool>\n' |
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| diff -r 000000000000 -r c10e37cca7e3 readme.rst --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/readme.rst Tue Jun 25 06:29:45 2013 -0400 |
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| @@ -0,0 +1,88 @@ +================================================ +Galaxy wrapper for InterProScan prediction tools +================================================ + +InterProScan is a tool that combines different protein signature recognition methods native to the InterPro +member databases into one resource with look up of corresponding InterPro and GO annotation. + +This wrapper is copyright 2012-2013 by +* Bjoern Gruening, Pharmaceutical Bioinformatics, University of Freiburg +* Konrad Paszkiewicz, Exeter Sequencing Service, University of Exeter + + +This prepository contains wrapper for the InterProScan command line tool. +http://www.ebi.ac.uk/interpro/ + + +Zdobnov E.M. and Apweiler R. "InterProScan - an integration platform for the signature-recognition methods in InterPro" Bioinformatics, 2001, 17(9): p. 847-8. + + +============ +Installation +============ + +Please download install InterProScan according to: + +ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/Installing_InterProScan.txt + +Please see also: +ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/index.html + +And rebuild the indizes if necessary: + +index_data.pl -f interpro.xml -inx -v -bin -bforce +index_data.pl -f match_complete.xml -inx -v -bin -bforce +index_data.pl -f Pfam-A.seed -inx -v -bin -bforce +index_data.pl -f Pfam-C -inx -v -bin -bforce +index_data.pl -f prints.pval -inx -v -bin -bforce +index_data.pl -f sf.seq -inx -v -bin -bforce +index_data.pl -f sf_hmm -inx -v -bin -bforce +index_data.pl -f smart.HMMs -inx -v -bin -bforce +index_data.pl -f superfamily.hmm -inx -v -bin -bforce +index_data.pl -f TIGRFAMs_HMM.LIB -inx -v -bin -bforce + + +Add the tool definition to your tool_conf.xml file under Galaxy root. + <tool file="iprscan/interproscan.xml" /> + +============= +Input formats +============= + +The standard interproscan input is either genomic or protein sequences. In the case of genomic sequences Interproscan will run an ORF +prediction tool. However this tends to lose the ORF information (e.g. start/end co-ordinates) from the header. As such the requirement here is to input ORF +sequences (e.g. from EMBOSS getorf) and to then replace any spaces in the FASTA header with underscores. This workaround generally preserves the relevant +positional information. + + +======= +History +======= + +interproscan: +- v1.1: Initial public release +- v1.2: Merge with Konrad Paszkiewicz repository + + +=============================== +Wrapper Licence (MIT/BSD style) +=============================== + +Permission to use, copy, modify, and distribute this software and its +documentation with or without modifications and for any purpose and +without fee is hereby granted, provided that any copyright notices +appear in all copies and that both those copyright notices and this +permission notice appear in supporting documentation, and that the +names of the contributors or copyright holders not be used in +advertising or publicity pertaining to distribution of the software +without specific prior permission. + +THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL +WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED +WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE +CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT +OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS +OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE +OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE +OR PERFORMANCE OF THIS SOFTWARE. + |