# HG changeset patch
# User bgruening
# Date 1381238083 14400
# Node ID 2d56d3ae499c64a2825a22f49dbeb586ce0b20bd
# Parent  98c6e970cbc1abb241def96a3af6a2c07b3c523c
Uploaded

diff -r 98c6e970cbc1 -r 2d56d3ae499c interproscan.xml
--- a/interproscan.xml	Thu Aug 22 08:07:13 2013 -0400
+++ b/interproscan.xml	Tue Oct 08 09:14:43 2013 -0400
@@ -7,8 +7,16 @@
         <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
+        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
@@ -57,9 +65,12 @@
                 <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="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>
@@ -111,24 +122,10 @@
  * SVG: An Scalable Vector Graphics representation of the protein matches
 
 
-.. _`GFF3 3.0`: http://gmod.org/wiki/GFF#GFF3_Format
+.. _`GFF 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)
 =================================
@@ -174,8 +171,6 @@
 Example Output
 --------------
 
-::
-
 .. image:: $PATH_TO_IMAGES/example_xml_output.png
 
 
@@ -220,19 +215,9 @@
 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
+InterProScan_ 5 outputs a single HTML/SVG file for each protein sequence analysed. 
 
 
-  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
 --------------
 
@@ -245,6 +230,15 @@
 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.
@@ -262,13 +256,13 @@
 
 
 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
+http://toolshed.g2.bx.psu.edu/view/bgruening/interproscan5
 
 
 **Galaxy Wrapper Author**::
 
-    *  Bjoern Gruening, Pharmaceutical Bioinformatics, University of Freiburg
-    *  Konrad Paszkiewicz, Exeter Sequencing Service, University of Exeter
+    *  Bjoern Gruening, University of Freiburg
+    *  Konrad Paszkiewicz, University of Exeter
 
     </help>
 </tool>
diff -r 98c6e970cbc1 -r 2d56d3ae499c readme.rst
--- a/readme.rst	Thu Aug 22 08:07:13 2013 -0400
+++ b/readme.rst	Tue Oct 08 09:14:43 2013 -0400
@@ -12,10 +12,10 @@
 
 This prepository contains wrapper for the InterProScan_ command line tool.
 
-.. _InterProScan: http://www.ebi.ac.uk/interpro/
+.. _InterProScan: http://www.ebi.ac.uk/interpro/interproscan.html
 
 
-Zdobnov E.M. and Apweiler R. "InterProScan - an integration platform for the signature-recognition methods in InterPro" Bioinformatics, 2001, 17(9): p. 847-8.
+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
 
 
 ============
@@ -24,8 +24,22 @@
 
 Please download install InterProScan according to:
 
-https://code.google.com/p/interproscan/wiki/i5RC7HowToObtainingACopy
+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.
 
 
 =============
@@ -33,7 +47,7 @@
 =============
 
 The standard interproscan input is either genomic or protein sequences. 
-In the case of genomic sequences Interproscan will run an ORF prediction tool. 
+In the case of genomic sequences Interproscan will run an ORF prediction tool.
 
 
 =======