| Next changeset 1:e32f2ea6a139 (2013-10-08) |
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Commit message:
Initial interproscan5 wrapper. |
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added:
create_index.py interproscan.xml readme.rst static/images/P51587.svg.png static/images/example_xml_output.png tool_dependencies.xml |
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| diff -r 000000000000 -r 82547f0d3a29 create_index.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/create_index.py Tue Oct 08 09:18:17 2013 -0400 |
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| @@ -0,0 +1,15 @@ +#!/usr/bin/env python + +import os +import sys + +o = open( sys.argv[1], 'w+' ) + + +o.write('<html> <body> <h1> InterProScan result summary page </h1> <ul>' ) + +for filename in [f for f in os.listdir( sys.argv[2] ) if os.path.isfile( os.path.join( sys.argv[2], f) )]: + o.write( '<li><a href="%s"> %s </a></li>' % ( filename, os.path.splitext( filename )[0] ) ) + +o.write( '</ul></body></html>' ) +o.close() |
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| 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 |
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| b'@@ -0,0 +1,268 @@\n+<tool id="interproscan" name="Interproscan functional predictions of ORFs" version="5.0.0">\n+ <description>Interproscan functional predictions of ORFs</description>\n+ <requirements>\n+ <requirement type="package">signalp</requirement>\n+ <requirement type="package">phobius</requirement>\n+ <requirement type="package">tmhmm</requirement>\n+ <requirement type="set_environment">INTERPROSCAN_SCRIPT_PATH</requirement>\n+ </requirements>\n+ <command>\n+\n+ #import os\n+ interproscan.sh \n+ ## disables the precalculated lookup service, all calculation will be run locally\n+ -dp \n+ --input $infile \n+ --seqtype $seqtype \n+ -f $oformat \n+ --applications $appl \n+ --tempdir \\$TEMP\n+\n+ $pathways\n+ $goterms\n+ $iprlookup\n+\n+ #if str($oformat) in [\'SVG\', \'HTML\']:\n+ --output-file-base $outfile\n+ 2>&1;\n+ mkdir -p $outfile.files_path;\n+ #set temp_archive_file = str($outfile) + \'.\' + str($oformat).lower() + \'.tar.gz\'\n+ tar -C $outfile.files_path -xvmzf $temp_archive_file;\n+ python \\$INTERPROSCAN_SCRIPT_PATH/create_index.py $outfile $outfile.files_path;\n+ rm $temp_archive_file\n+ #else:\n+ -o $outfile\n+ 2>&1\n+ #end if \n+\n+ </command>\n+ <inputs>\n+ <param name="infile" type="data" format="fasta" label="Protein Fasta File"/>\n+\n+ <param name="seqtype" type="select" label="Type of the input sequences" help="">\n+ <option value="p" selected="true">Protein</option>\n+ <option value="n">DNA / RNA</option>\n+ </param>\n+\n+ <param name="appl" type="select" multiple="True" display="checkboxes" label="Applications to run" help="Select your programm.">\n+ <option value="TIGRFAM" selected="true">TIGRFAM: protein families based on Hidden Markov Models or HMMs</option>\n+ <option value="PIRSF" selected="true">PIRSF: non-overlapping clustering of UniProtKB sequences into a hierarchical order (evolutionary relationships)</option>\n+ <option value="ProDom" selected="true">ProDom: set of protein domain families generated from the UniProtKB</option>\n+ <option value="Panther" selected="true">Panther: Protein ANalysis THrough Evolutionary Relationships</option>\n+ <option value="SMART" selected="true">SMART: identification and analysis of domain architectures based on Hidden Markov Models or HMMs</option>\n+ <option value="PrositeProfiles" selected="true">PROSITE Profiles: protein domains, families and functional sites as well as associated profiles to identify them</option>\n+ <option value="PrositePatterns" selected="true">PROSITE Pattern: protein domains, families and functional sites as well as associated patterns to identify them</option>\n+ <option value="HAMAP" selected="true">HAMAP: High-quality Automated Annotation of Microbial Proteomes</option>\n+ <option value="PfamA" selected="true">PfamA: protein families, each represented by multiple sequence alignments and hidden Markov models</option>\n+ <option value="PRINTS" selected="true">PRINTS: group of conserved motifs (fingerprints) used to characterise a protein family</option>\n+ <option value="SuperFamily" selected="true">SUPERFAMILY: database of structural and functional annotation</option>\n+ <option value="Coils" selected="true">Coils: Prediction of Coiled Coil Regions in Proteins</option>\n+ <option value="Gene3d" selected="true">Gene3d: Structural assignment for whole genes and genomes using the CATH domain structure database</option>\n+ <option value="SignalP-GRAM_POSITIVE" selected="false">SignalP Gram Positive Bacteria</option>\n+ <'..b'of all the columns and attributes used on [http://www.sequenceontology.org/gff3.shtml].\n+\n+Example Output\n+--------------\n+\n+::\n+\n+ ##gff-version 3\n+ ##feature-ontology http://song.cvs.sourceforge.net/viewvc/song/ontology/sofa.obo?revision=1.269\n+ ##sequence-region AACH01000027 1 1347\n+ ##seqid|source|type|start|end|score|strand|phase|attributes\n+ AACH01000027 provided_by_user nucleic_acid 1 1347 . + . Name=AACH01000027;md5=b2a7416cb92565c004becb7510f46840;ID=AACH01000027\n+ AACH01000027 getorf ORF 1 1347 . + . Name=AACH01000027.2_21;Target=pep_AACH01000027_1_1347 1 449;md5=b2a7416cb92565c004becb7510f46840;ID=orf_AACH01000027_1_1347\n+ AACH01000027 getorf polypeptide 1 449 . + . md5=fd0743a673ac69fb6e5c67a48f264dd5;ID=pep_AACH01000027_1_1347\n+ 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"\n+ ##sequence-region 2\n+ ...\n+ >pep_AACH01000027_1_1347\n+ LVLLAAFDCIDDTKLVKQIIISEIINSLPNIVNDKYGRKVLLYLLSPRDPAHTVREIIEV\n+ LQKGDGNAHSKKDTEIRRREMKYKRIVFKVGTSSLTNEDGSLSRSKVKDITQQLAMLHEA\n+ GHELILVSSGAIAAGFGALGFKKRPTKIADKQASAAVGQGLLLEEYTTNLLLRQIVSAQI\n+ LLTQDDFVDKRRYKNAHQALSVLLNRGAIPIINENDSVVIDELKVGDNDTLSAQVAAMVQ\n+ ADLLVFLTDVDGLYTGNPNSDPRAKRLERIETINREIIDMAGGAGSSNGTGGMLTKIKAA\n+ TIATESGVPVYICSSLKSDSMIEAAEETEDGSYFVAQEKGLRTQKQWLAFYAQSQGSIWV\n+ DKGAAEALSQYGKSLLLSGIVEAEGVFSYGDIVTVFDKESGKSLGKGRVQFGASALEDML\n+ RSQKAKGVLIYRDDWISITPEIQLLFTEF\n+ ...\n+ >match$8_84_314\n+ KRIVFKVGTSSLTNEDGSLSRSKVKDITQQLAMLHEAGHELILVSSGAIAAGFGALGFKK\n+ RPTKIADKQASAAVGQGLLLEEYTTNLLLRQIVSAQILLTQDDFVDKRRYKNAHQALSVL\n+ LNRGAIPIINENDSVVIDELKVGDNDTLSAQVAAMVQADLLVFLTDVDGLYTGNPNSDPR\n+ AKRLERIETINREIIDMAGGAGSSNGTGGMLTKIKAATIATESGVPVYICS\n+ \n+\n+Scalable Vector Graphics (SVG) and HyperText Markup Language (HTML)\n+====================================================================\n+\n+InterProScan_ 5 outputs a single HTML/SVG file for each protein sequence analysed. \n+\n+\n+Example Output\n+--------------\n+\n+.. image:: $PATH_TO_IMAGES/P51587.svg.png\n+\n+.. _InterProScan: http://www.ebi.ac.uk/interpro\n+\n+\n+----------\n+References\n+----------\n+\n+\n+If you use this Galaxy tool in work leading to a scientific publication please\n+cite the following papers:\n+\n+Peter J.A. Cock, Bj\xc3\xb6rn A. Gr\xc3\xbcning, Konrad Paszkiewicz and Leighton Pritchard (2013).\n+Galaxy tools and workflows for sequence analysis with applications\n+in molecular plant pathology. PeerJ 1:e167\n+http://dx.doi.org/10.7717/peerj.167\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+This wrapper is available to install into other Galaxy Instances via the Galaxy Tool Shed at\n+http://toolshed.g2.bx.psu.edu/view/bgruening/interproscan5\n+\n+\n+**Galaxy Wrapper Author**::\n+\n+ * Bjoern Gruening, University of Freiburg\n+ * Konrad Paszkiewicz, University of Exeter\n+\n+ </help>\n+</tool>\n' |
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| 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 |
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| @@ -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. + |
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| 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 |
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| @@ -0,0 +1,9 @@ +<?xml version="1.0"?> +<tool_dependency> + <set_environment version="1.0"> + <environment_variable name="INTERPROSCAN_SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable> + </set_environment> +</tool_dependency> + + + |
