Mercurial > repos > si-datascience > genome_tools
changeset 2:5a720d9e7071 draft default tip
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/interproscan5-e32f2ea6a139/create_index.py Thu May 24 14:39:59 2018 -0400 @@ -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()
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/interproscan5-e32f2ea6a139/interproscan.xml Thu May 24 14:39:59 2018 -0400 @@ -0,0 +1,268 @@ +<tool id="interproscan" name="Interproscan functional predictions of ORFs" version="5.0.0"> + <description>Interproscan functional predictions of ORFs</description> + <requirements> + <requirement type="package">signalp</requirement> + <requirement type="package">phobius</requirement> + <requirement type="package">tmhmm</requirement> + <requirement type="set_environment">INTERPROSCAN_SCRIPT_PATH</requirement> + </requirements> + <command> + + #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 + + </command> + <inputs> + <param name="infile" type="data" format="fasta" label="Protein Fasta File"/> + + <param name="seqtype" type="select" label="Type of the input sequences" help=""> + <option value="p" selected="true">Protein</option> + <option value="n">DNA / RNA</option> + </param> + + <param name="appl" type="select" multiple="True" display="checkboxes" label="Applications to run" help="Select your programm."> + <option value="TIGRFAM" selected="true">TIGRFAM: protein families based on Hidden Markov Models or HMMs</option> + <option value="PIRSF" selected="true">PIRSF: non-overlapping clustering of UniProtKB sequences into a hierarchical order (evolutionary relationships)</option> + <option value="ProDom" selected="true">ProDom: set of protein domain families generated from the UniProtKB</option> + <option value="Panther" selected="true">Panther: Protein ANalysis THrough Evolutionary Relationships</option> + <option value="SMART" selected="true">SMART: identification and analysis of domain architectures based on Hidden Markov Models or HMMs</option> + <option value="PrositeProfiles" selected="true">PROSITE Profiles: protein domains, families and functional sites as well as associated profiles to identify them</option> + <option value="PrositePatterns" selected="true">PROSITE Pattern: protein domains, families and functional sites as well as associated patterns to identify them</option> + <option value="HAMAP" selected="true">HAMAP: High-quality Automated Annotation of Microbial Proteomes</option> + <option value="PfamA" selected="true">PfamA: protein families, each represented by multiple sequence alignments and hidden Markov models</option> + <option value="PRINTS" selected="true">PRINTS: group of conserved motifs (fingerprints) used to characterise a protein family</option> + <option value="SuperFamily" selected="true">SUPERFAMILY: database of structural and functional annotation</option> + <option value="Coils" selected="true">Coils: Prediction of Coiled Coil Regions in Proteins</option> + <option value="Gene3d" selected="true">Gene3d: Structural assignment for whole genes and genomes using the CATH domain structure database</option> + <option value="SignalP-GRAM_POSITIVE" selected="false">SignalP Gram Positive Bacteria</option> + <option value="SignalP-GRAM_NEGATIVE" selected="false">SignalP Gram Negative Bacteria</option> + <option value="SignalP-EUK" selected="true">SignalP Eukaryotic Bacteria</option> + <option value="Phobius" selected="true">Phobius: combined transmembrane topology and signal peptide predictor</option> + <option value="TMHMM" selected="true">TMHMM: Prediction of transmembrane helices in proteins</option> + </param> + + <param name="pathways" truevalue="--pathways" falsevalue="" checked="True" type="boolean" label="Include pathway information" + help="Option that provides mappings from matches to pathway information, which is based on the matched manually curated InterPro entries. (--pathways)"/> + <param name="goterms" truevalue="--goterms" falsevalue="" checked="True" type="boolean" label="Include Gene Ontology (GO) mappings" + help="Look up of corresponding Gene Ontology annotation. Implies -iprlookup option. (--goterms)"/> + <param name="iprlookup" truevalue="--iprlookup" falsevalue="" checked="False" type="boolean" + label="Provide additional mappings" help="Provide mappings from matched member database signatures to the InterPro entries that they are integrated into (--iprlookup)"/> + + <param name="oformat" type="select" label="Output format" help="Please select a output format."> + <option value="TSV" selected="true">Tab-separated values format (TSV)</option> + <option value="GFF3">GFF3</option> + <option value="SVG">SVG</option> + <option value="HTML">HTML</option> + <option value="XML">XML</option> + </param> + + </inputs> + <outputs> + + <data format="tabular" name="outfile" label="Interproscan calculation on ${on_string}"> + <change_format> + <when input="oformat" value="HTML" format="html"/> + <when input="oformat" value="XML" format="xml"/> + <when input="oformat" value="SVG" format="html"/> + <when input="oformat" value="GFF3" 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. + + +##### +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 + + </help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/interproscan5-e32f2ea6a139/readme.rst Thu May 24 14:39:59 2018 -0400 @@ -0,0 +1,83 @@ +================================================== +Galaxy wrapper for InterProScan 5 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 a 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 + + +============= +Licence (MIT) +============= + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in +all copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN +THE SOFTWARE. +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/interproscan5-e32f2ea6a139/tool_dependencies.xml Thu May 24 14:39:59 2018 -0400 @@ -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> + + +