' )
+o.close()
diff -r 000000000000 -r 82547f0d3a29 interproscan.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/interproscan.xml Tue Oct 08 09:18:17 2013 -0400
@@ -0,0 +1,268 @@
+
+ Interproscan functional predictions of ORFs
+
+ signalp
+ phobius
+ tmhmm
+ INTERPROSCAN_SCRIPT_PATH
+
+
+
+ #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>&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>&1
+ #end if
+
+
+
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+
+
+
+**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
+
+
+
diff -r 000000000000 -r 82547f0d3a29 readme.rst
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/readme.rst Tue Oct 08 09:18:17 2013 -0400
@@ -0,0 +1,83 @@
+================================================
+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 2013 by:
+ * Bjoern Gruening
+ * Konrad Paszkiewicz
+
+
+This prepository contains wrapper for the InterProScan_ command line tool.
+
+.. _InterProScan: http://www.ebi.ac.uk/interpro/interproscan.html
+
+
+Quevillon E., Silventoinen V., Pillai S., Harte N., Mulder N., Apweiler R., Lopez R. (2005). InterProScan: protein domains identifier. Nucleic Acids Res. 33 (Web Server issue): W116-W120
+
+
+============
+Installation
+============
+
+Please download install InterProScan according to:
+
+https://code.google.com/p/interproscan/wiki/HowToDownload
+
+
+========
+Citation
+========
+
+If you use this Galaxy tool in work leading to a scientific
+publication, in addition to citing the invididual underlying tools, please cite:
+
+Peter Cock, Bjoern Gruening, 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
+
+Full reference information is included in the help text.
+
+
+=============
+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.
+
+
+=======
+History
+=======
+
+interproscan:
+
+ - v5.0: Initial public release of version 5.0
+
+
+===============================
+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.
+
diff -r 000000000000 -r 82547f0d3a29 static/images/P51587.svg.png
Binary file static/images/P51587.svg.png has changed
diff -r 000000000000 -r 82547f0d3a29 static/images/example_xml_output.png
Binary file static/images/example_xml_output.png has changed
diff -r 000000000000 -r 82547f0d3a29 tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Tue Oct 08 09:18:17 2013 -0400
@@ -0,0 +1,9 @@
+
+
+
+ $REPOSITORY_INSTALL_DIR
+
+
+
+
+