# HG changeset patch
# User mkh
# Date 1454951424 18000
# Node ID 1d6b3be059c8695bc522d35c599754911e391cd8
# Parent f2153ec1ccfd7b52c1e0913ab89fdee10d505b9c
Name change. Removed redundant tool def.
diff -r f2153ec1ccfd -r 1d6b3be059c8 interproscan5/interproscan.xml
--- a/interproscan5/interproscan.xml Fri Feb 05 13:18:41 2016 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,285 +0,0 @@
-
- Interproscan functional predictions of ORFs
-
-
- INTERPROSCAN_SCRIPT_PATH
-
-
-
- #import os
- \$IPS_HOME/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
- $mode
-
- #if str($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.
-
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-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
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-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 f2153ec1ccfd -r 1d6b3be059c8 interproscan5/ips5.xml
--- a/interproscan5/ips5.xml Fri Feb 05 13:18:41 2016 -0500
+++ b/interproscan5/ips5.xml Mon Feb 08 12:10:24 2016 -0500
@@ -1,4 +1,4 @@
-
+Interproscan functional predictions of ORFs.