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changeset 0:98c6e970cbc1 draft

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author bgruening
date Thu, 22 Aug 2013 08:07:13 -0400
parents
children 2d56d3ae499c
files create_index.py interproscan.xml readme.rst static/images/P51587.svg.png static/images/example_xml_output.png tool_dependencies.xml
diffstat 6 files changed, 367 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/create_index.py	Thu Aug 22 08:07:13 2013 -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/interproscan.xml	Thu Aug 22 08:07:13 2013 -0400
@@ -0,0 +1,274 @@
+<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 -dp --fasta $infile --seqtype $seqtype -f $oformat --applications $appl --tempdir \$TEMP
+
+        $pathways
+        $goterms
+        $iprlookup
+
+         #if str($oformat) in ['SVG', 'HTML']:
+            --output-file-base $outfile
+            2>&#38;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>&#38;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."/>
+            <param name="goterms" truevalue="--goterms" falsevalue="" checked="True" type="boolean" label="Include Gene Ontology (GO) mappings" />
+            <param name="iprlookup" truevalue="--iprlookup" falsevalue="" checked="False" type="boolean" label="Provide mappings from matched member database signatures to the InterPro entries that they are integrated into" />
+
+            <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
+
+
+.. _`GFF3 3.0`: http://gmod.org/wiki/GFF#GFF3_Format
+.. _here: http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5
+
+
+Previous versions of InterProScan_ 5 (I5RC1 - I5RC6) could only output data for nucleotide sequences in XML and GFF3. This has now changed and InterProScan_ 5 can output results for nucleotide sequences in all formats. *Please note* you can only trace protein match positions to the original nucleotide sequence with GFF3 and XML.
+
+You can override the default output formats using the *-f* option, e.g.::
+
+  ./interproscan.sh -f XML -f HTML -i /path/to/sequences.fasta -b /path/to/output_file
+
+or
+
+::
+
+  ./interproscan.sh -f XML, HTML -i /path/to/sequences.fasta -b /path/to/output_file
+
+
+These two equivalent commands will output the results in XML and HTML format.
+
+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.  The HTML/SVG file(s) are compressed into a single gzipped tar archive (or "tarball") that includes the resources (images, Javascript, style etc) to render the pages/images in a browser or image viewer.  (Note that from version 5RC4, the SVG format has no external dependencies.)
+
+The tarball will be named something similar to::
+
+  base_output_file_name.html.tar.gz OR base_output_file_name.svg.tar.gz
+
+
+  To access the HTML pages/SVG images, unzip the tarball using a command like:
+
+  tar -xvzf base_output_file_name.html(svg).tar.gz
+
+You can then open the unzipped HTML/SVG files in any browser or image viewer (for SVG).
+
+Example Output
+--------------
+
+.. image:: $PATH_TO_IMAGES/P51587.svg.png
+
+.. _InterProScan: http://www.ebi.ac.uk/interpro
+
+
+----------
+References
+----------
+
+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/interproscan
+
+
+**Galaxy Wrapper Author**::
+
+    *  Bjoern Gruening, Pharmaceutical Bioinformatics, University of Freiburg
+    *  Konrad Paszkiewicz, Exeter Sequencing Service, University of Exeter
+
+    </help>
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/readme.rst	Thu Aug 22 08:07:13 2013 -0400
@@ -0,0 +1,69 @@
+================================================
+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/
+
+
+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:
+
+https://code.google.com/p/interproscan/wiki/i5RC7HowToObtainingACopy
+
+
+
+=============
+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.
+
Binary file static/images/P51587.svg.png has changed
Binary file static/images/example_xml_output.png has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Thu Aug 22 08:07:13 2013 -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>
+
+
+