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changeset 1:94745fda6aff draft

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Uploaded
author bjoern-gruening
date Sun, 23 Jun 2013 07:38:53 -0400
parents 341830c8cd37
children 99517734aa65
files interproscan.xml readme.rst readme.txt
diffstat 3 files changed, 171 insertions(+), 181 deletions(-) [+]
line wrap: on
line diff
--- a/interproscan.xml	Tue Jan 24 07:35:10 2012 -0500
+++ b/interproscan.xml	Sun Jun 23 07:38:53 2013 -0400
@@ -1,5 +1,5 @@
-<tool id="interproscan" name="Interproscan functional predictions of ORFs"  version="1.1">
-	<description>Interproscan functional predictions of ORFs</description>
+<tool id="interproscan" name="Interproscan functional predictions of ORFs"  version="1.2">
+    <description>Interproscan functional predictions of ORFs</description>
     <command>
 ## The command is a Cheetah template which allows some Python based syntax.
 ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces
@@ -11,23 +11,22 @@
 sed 's/ /_/g' $input > $tfile;
 
 ## Hack, because interproscan does not seem to produce gff output even if it is configured
-#if str($oformat)=="gff":
+#if str($oformat) == "gff":
     #set $tfile2 = tempfile.mkstemp()[1]
-    iprscan -cli -nocrc -i $tfile -o $tfile2 -goterms -seqtype p -altjobs -format raw -appl $appl > /dev/null 2> /dev/null;
-    converter.pl -format gff3 -input $tfile2 -output $output
-    rm $tfile2
+    iprscan -cli -nocrc -i $tfile -o $tfile2 -goterms -seqtype p -altjobs -format raw -appl $appl 2>&#38;1;
+    converter.pl -format gff3 -input $tfile2 -output $output;
+    rm $tfile2;
 #else
-    iprscan -cli -nocrc -i $tfile -o $output -goterms -seqtype p -altjobs -format $oformat -appl $appl > /dev/null 2> /dev/null;
+    iprscan -cli -nocrc -i $tfile -o $output -goterms -seqtype p -altjobs -format $oformat -appl $appl 2>&#38;1;
 #end if
 
-rm $tfile;
+rm $tfile
 
-	</command>
+    </command>
         <inputs>
             <param name="input" type="data" format="fasta" label="Protein Fasta File"/>
 
-            <param name="appl" type="select" format="text" help="Select your programm.">
-                <label>Applications to run ...</label>
+            <param name="appl" type="select" format="text" label="Applications to run" help="Select your programm.">
                 <option value="blastprodom+coils+gene3d+hamap+hmmpanther+hmmpir+hmmpfam+hmmsmart+hmmtigr+fprintscan+patternscan+profilescan+superfamily+seg+signalp+tmhmm" selected="true">all</option>
                 <option value="seg">seg</option>
                 <option value="signalp">signalp</option>
@@ -45,11 +44,11 @@
                 <option value="gene3d">gene3d</option>
                 <option value="coils">coils</option>
                 <option value="blastprodom">blastprodom</option>
-            </param> 
+            </param>
 
             <param name="oformat" type="select" label="Output format" help="Please select a output format.">
-                <option value="gff" selected="true">gff</option>
-                <option value="raw">raw</option>
+                <option value="gff">gff</option>
+                <option value="raw" selected="true">raw</option>
                 <option value="txt">txt</option>
                 <option value="html">html</option>
                 <option value="xml">xml</option>
@@ -72,60 +71,54 @@
     <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. 
 These include SCOP, CATH, PFAM and SUPERFAMILY.
 
 **Input**
-A FASTA file containing ORF predictions is required. This file must NOT contain any spaces in the FASTA headers - any spaces will be convereted to underscores (_) by this tool before submission to Interproscan.
+
+Required is a FASTA file containing ORF predictions. This file must NOT contain any spaces in the FASTA headers - any spaces will be convereted to underscores ``_`` by this tool before running with Interproscan.
 
 **Output**
 
 Example for the raw format.
-This is a basic tab delimited format useful for uploading the data into a relational database or concatenation of different runs. 
-is all on one line. 
+The output will consist of a tabular file in galaxy with 14 columns and can be easily concatenated or filtered.
 
 ====== ================================================================ ======================================================================
 column example                                                          description
 ====== ================================================================ ======================================================================
-c1     NF00181542                                                       the id of the input sequence.
-c2     27A9BBAC0587AB84                                                 the crc64 (checksum) of the protein sequence (supposed to be unique).
-c3     272                                                              the length of the sequence (in AA). 
+c1     NF00181542                                                       the id of the input sequence
+c2     27A9BBAC0587AB84                                                 the crc64 (checksum) of the protein sequence (supposed to be unique)
+c3     272                                                              the length of the sequence (in AA)
 c4     HMMPIR                                                           the anaysis method launched. 
-c5     PIRSF001424                                                      the database members entry for this match. 
-c6     Prephenate dehydratase                                           the database member description for the entry. 
-c7     1                                                                the start of the domain match. 
-c8     270                                                              the end of the domain match. 
-c9     6.5e-141                                                         the evalue of the match (reported by member database method). 
-c10    T                                                                the status of the match (T: true, ?: unknown). 
+c5     PIRSF001424                                                      the database members entry for this match
+c6     Prephenate dehydratase                                           the database member description for the entry
+c7     1                                                                the start of the domain match 
+c8     270                                                              the end of the domain match
+c9     6.5e-141                                                         the evalue of the match (reported by member database method) 
+c10    T                                                                the status of the match (T: true, ?: unknown) 
 c11    06-Aug-2005                                                      the date of the run. 
-c12    IPR008237                                                        the corresponding InterPro entry (if iprlookup requested by the user).
-c13    Prephenate dehydratase with ACT region                           the description of the InterPro entry.
-c14    Molecular Function:prephenate dehydratase activity (GO:0004664)  the GO (gene ontology) description for the InterPro entry. 
+c12    IPR008237                                                        the corresponding InterPro entry (if iprlookup requested by the user)
+c13    Prephenate dehydratase with ACT region                           the description of the InterPro entry
+c14    Molecular Function:prephenate dehydratase activity (GO:0004664)  the GO (gene ontology) description for the InterPro entry 
 ====== ================================================================ ======================================================================
 
-
 **Database updates**
 
-Typically these take place 2-3 times a year.
-
+Typically these take place 2-3 times a year. Please contact your Galaxy administrator to update the databases.
 
-**Tools**
+-----
+Tools
+-----
 
-PROSITE patterns
-
-::
+**PROSITE patterns**::
 
  Some biologically significant amino acid patterns can be summarised in
  the form of regular expressions.
- ScanRegExp (by Wolfgang.Fleischmann@ebi.ac.uk),
+ ScanRegExp (by Wolfgang.Fleischmann@ebi.ac.uk).
 
-PROSITE profiles
-
-::
+**PROSITE profiles**::
 
  There are a number of protein families as well as functional or
  structural domains that cannot be detected using patterns due to their extreme
@@ -133,13 +126,11 @@
  (also known as profiles) allows the detection of such proteins or domains.
  A profile is a table of position-specific amino acid weights and gap costs.
  The profile structure used in PROSITE is similar to but slightly more general
- (Bucher P. et al., 1996 [7]) than the one introduced by M. Gribskov and
+ (Bucher P. et al., 1996) than the one introduced by M. Gribskov and
  co-workers.
  pfscan from the Pftools package (by Philipp.Bucher@isrec.unil.ch).
 
-PRINTS
-
-::
+**PRINTS**::
 
  The PRINTS database houses a collection of protein family fingerprints.
  These are groups of motifs that together are diagnostically more
@@ -147,25 +138,20 @@
  multiple-motif method. The fingerprinting method arose from the need for
  a reliable technique for detecting members of large, highly divergent
  protein super-families.
- FingerPRINTScan (Scordis P. et al., 1999 [8]).
+ FingerPRINTScan (Scordis P. et al., 1999).
 
-PFAM
-
-::
+**PFAM**::
 
  Pfam is a database of protein domain families. Pfam contains curated
  multiple sequence alignments for each family and corresponding hidden
- Markov models (HMMs) (Eddy S.R., 1998 [9]). 
+ Markov models (HMMs) (Eddy S.R., 1998). 
  Profile hidden Markov models are statistical models of the primary
  structure consensus of a sequence family. The construction and use
  of Pfam is tightly tied to the HMMER software package.
  hmmpfam from the HMMER2.3.2 package (by Sean Eddy,
  eddy@genetics.wustl.edu, http://hmmer.wustl.edu).
 
-PRODOM
-
-::
-
+**PRODOM**::
 
  ProDom is a database of protein domain families obtained by automated
  analysis of the SWISS-PROT and TrEMBL protein sequences. It is useful
@@ -175,12 +161,9 @@
  searches.
  ProDomBlast3i.pl (by Emmanuel Courcelle emmanuel.courcelle@toulouse.inra.fr
  and Yoann Beausse beausse@toulouse.inra.fr)
- a wrapper on top of the Blast package (Altschul S.F. et al., 1997 [10]).
-
+ a wrapper on top of the Blast package (Altschul S.F. et al., 1997).
 
-SMART
-
-::
+**SMART**::
 
  SMART (a Simple Modular Architecture Research Tool) allows the
  identification and annotation of genetically mobile domains and the
@@ -191,10 +174,7 @@
  hmmpfam from the HMMER2.3.2 package (by Sean Eddy,
  eddy@genetics.wustl.edu, http://hmmer.wustl.edu).
 
-
-TIGRFAMs
-
-::
+**TIGRFAMs**::
 
  TIGRFAMs are a collection of protein families featuring curated multiple
  sequence alignments, Hidden Markov Models (HMMs) and associated
@@ -207,18 +187,14 @@
  hmmpfam from the HMMER2.3.2 package (by Sean Eddy,
  eddy@genetics.wustl.edu, http://hmmer.wustl.edu).
 
-PIR SuperFamily
-
-::
+**PIR SuperFamily**::
 
  PIR SuperFamily (PIRSF) is a classification system based on evolutionary
  relationship of whole proteins.
  hmmpfam from the HMMER2.3.2 package (by Sean Eddy,
  eddy@genetics.wustl.edu, http://hmmer.wustl.edu).
 
-SUPERFAMILY
-
-::
+**SUPERFAMILY**::
 
  SUPERFAMILY is a library of profile hidden Markov models that represent
  all proteins of known structure, based on SCOP.
@@ -228,48 +204,48 @@
  (SignalP v3) and TM helices (TMHMM v2) are supported (See the FAQs file
  for details).
 
+**GENE3D**::
 
-GENE3D
+  Gene3D is supplementary to the CATH database. This protein sequence database
+  contains proteins from complete genomes which have been clustered into protein
+  families and annotated with CATH domains, Pfam domains and functional
+  information from KEGG, GO, COG, Affymetrix and STRINGS.
+  hmmpfam from the HMM2.3.2 package (by Sean Eddy,
+  eddy@genetics.wustl.edu, http://hmmer.wustl.edu).
 
-::
+**PANTHER**::
+
+  The PANTHER (Protein ANalysis THrough Evolutionary Relationships)
+  Classification System was designed to classify proteins (and their genes)
+  in order to facilitate high-throughput analysis.
+  hmmsearch from the HMM2.3.2 package (by Sean Eddy,
+  eddy@genetics.wustl.edu, http://hmmer.wustl.edu).
+  and blastall from the Blast package (Altschul S.F. et al., 1997).
 
- Gene3D is supplementary to the CATH database. This protein sequence database
- contains proteins from complete genomes which have been clustered into protein
- families and annotated with CATH domains, Pfam domains and functional
- information from KEGG, GO, COG, Affymetrix and STRINGS.
- hmmpfam from the HMM2.3.2 package (by Sean Eddy,
- eddy@genetics.wustl.edu, http://hmmer.wustl.edu).
+----------
+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
 
 
-PANTHER
-
-::
-
- The PANTHER (Protein ANalysis THrough Evolutionary Relationships)
- Classification System was designed to classify proteins (and their genes)
- in order to facilitate high-throughput analysis.
- hmmsearch from the HMM2.3.2 package (by Sean Eddy,
- eddy@genetics.wustl.edu, http://hmmer.wustl.edu).
- and blastall from the Blast package (Altschul S.F. et al., 1997 [10]).
-
-
-
-**References**
+**Galaxy Wrapper Author**::
 
-Quevillon E., Silventoinen V., Pillai S., Harte N., Mulder N., Apweiler R., Lopez R. 
-InterProScan: protein domains identifier (2005). 
-Nucleic Acids Res. 33 (Web Server issue) :W116-W120 
-
-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. 
-InterPro: the integrative protein signature database (2009). 
-Nucleic Acids Res. 37 (Database Issue) :D224-228 
+    *  Bjoern Gruening, Pharmaceutical Bioinformatics, University of Freiburg
+    *  Konrad Paszkiewicz, Exeter Sequencing Service, University of Exeter
 
-Galaxy Wrapper Author:
-
-*  Bjoern Gruening, Pharmaceutical Bioinformatics, University of Freiburg
-*  Konrad Paszkiewicz, Exeter Sequencing Service, University of Exeter
-
-
-
-	</help>
+    </help>
 </tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/readme.rst	Sun Jun 23 07:38:53 2013 -0400
@@ -0,0 +1,88 @@
+================================================
+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 2012-2013 by
+*  Bjoern Gruening, Pharmaceutical Bioinformatics, University of Freiburg
+*  Konrad Paszkiewicz, Exeter Sequencing Service, University of Exeter
+
+
+This prepository contains wrapper for the InterProScan command line tool.
+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:
+
+ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/Installing_InterProScan.txt
+
+Please see also:
+ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/index.html
+
+And rebuild the indizes if necessary:
+
+index_data.pl -f interpro.xml -inx -v -bin -bforce
+index_data.pl -f match_complete.xml -inx -v -bin -bforce
+index_data.pl -f Pfam-A.seed -inx -v -bin -bforce
+index_data.pl -f Pfam-C -inx -v -bin -bforce
+index_data.pl -f prints.pval -inx -v -bin -bforce
+index_data.pl -f sf.seq -inx -v -bin -bforce
+index_data.pl -f sf_hmm -inx -v -bin -bforce
+index_data.pl -f smart.HMMs -inx -v -bin -bforce
+index_data.pl -f superfamily.hmm -inx -v -bin -bforce
+index_data.pl -f TIGRFAMs_HMM.LIB -inx -v -bin -bforce
+
+
+Add the tool definition to your tool_conf.xml file under Galaxy root.
+	<tool file="iprscan/interproscan.xml" />
+
+=============
+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. However this tends to lose the ORF information (e.g. start/end co-ordinates) from the header. As such the requirement here is to input ORF 
+sequences (e.g. from EMBOSS getorf) and to then replace any spaces in the FASTA header with underscores. This workaround generally preserves the relevant 
+positional information. 
+
+
+=======
+History
+=======
+
+interproscan:
+- v1.1: Initial public release
+- v1.2: Merge with Konrad Paszkiewicz repository
+
+
+===============================
+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.
+
--- a/readme.txt	Tue Jan 24 07:35:10 2012 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,74 +0,0 @@
-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 2012 by
-*  Bjoern Gruening, Pharmaceutical Bioinformatics, University of Freiburg
-*  Konrad Paszkiewicz, Exeter Sequencing Service, University of Exeter
-
-
-This prepository contains wrapper for the InterProScan command line tool.
-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:
-
-ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/Installing_InterProScan.txt
-
-Please see also:
-ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/index.html
-
-And rebuild the indizes if necessary:
-
-index_data.pl -f interpro.xml -inx -v -bin -bforce
-index_data.pl -f match_complete.xml -inx -v -bin -bforce
-index_data.pl -f Pfam-A.seed -inx -v -bin -bforce
-index_data.pl -f Pfam-C -inx -v -bin -bforce
-index_data.pl -f prints.pval -inx -v -bin -bforce
-index_data.pl -f sf.seq -inx -v -bin -bforce
-index_data.pl -f sf_hmm -inx -v -bin -bforce
-index_data.pl -f smart.HMMs -inx -v -bin -bforce
-index_data.pl -f superfamily.hmm -inx -v -bin -bforce
-index_data.pl -f TIGRFAMs_HMM.LIB -inx -v -bin -bforce
-
-<tool file="iprscan/interproscan.xml" />
-
-
-
-History
-=======
-
-interproscan:
-v0.1 - initial commit
-
-
-
-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.
-