# HG changeset patch
# User peterjc
# Date 1379929858 14400
# Node ID 872cf247c899798a1ce27eead0b67fed5bd21572
# Parent  e4419efbefad36dfc4c9894f84191e4eeda4ca8c
Uploaded v0.0.8, auto-installation, RST README, MIT licence, citation information, development moved to GitHub, split out XML formatter into standalone script

diff -r e4419efbefad -r 872cf247c899 blast2go/README.rst
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/blast2go/README.rst	Mon Sep 23 05:50:58 2013 -0400
@@ -0,0 +1,208 @@
+Galaxy wrapper for Blast2GO for pipelines, b2g4pipe
+===================================================
+
+This wrapper is copyright 2011-2013 by Peter Cock, The James Hutton Institute
+(formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
+See the licence text below (MIT licence).
+
+This is a wrapper for the command line Java tool b2g4pipe v2.5,
+Blast2GO for pipelines. It is available from the Galaxy Tool Shed at:
+http://toolshed.g2.bx.psu.edu/view/peterjc/blast2go
+
+
+References
+==========
+
+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
+
+S. Geotz et al. (2008).
+High-throughput functional annotation and data mining with the Blast2GO suite.
+Nucleic Acids Res. 36(10):3420-3435.
+http://dx.doi.org/10.1093/nar/gkn176
+
+A. Conesa and S. Geotz (2008).
+Blast2GO: A Comprehensive Suite for Functional Analysis in Plant Genomics.
+International Journal of Plant Genomics. 619832.
+http://dx.doi.org/10.1155/2008/619832
+
+A. Conesa et al. (2005).
+Blast2GO: A universal tool for annotation, visualization and analysis in functional genomics research.
+Bioinformatics 21:3674-3676.
+http://dx.doi.org/10.1093/bioinformatics/bti610
+
+See also http://www.blast2go.com/
+
+
+Automated Installation
+======================
+
+Installation via the Galaxy Tool Shed should take care of the Galaxy side of
+things, including the dependency on 'blast_datatypes' which defines the
+'blastxml' file format. However, you will also probably need to configure
+the Blast2GO property file(s), for example if you have a local Blast2GO
+database (which we recommend for speed).
+
+
+Manual Installation
+===================
+
+The main dependency is b2g4pipe which must be installed manually. Also we
+strongly recommend installing a local Blast2GO database as well (see the
+intructions below about the blast2go.loc file). At the time of writing,
+the current version is b2g4pipe v2.5 which is available here:
+
+* http://www.blast2go.com/data/blast2go/b2g4pipe_v2.5.zip
+
+You can change the path by setting the B2G4PIPE environement variable to
+the desired folder, but by default the script looks for the JAR file here::
+
+    /opt/b2g4pipe_v2.5/blast2go.jar
+
+To install the wrapper manually, first install 'blast_datatypes', then
+copy or move the following files under the Galaxy tools folder, e.g. in a
+tools/blast2go/ folder:
+
+* blast2go.xml (the Galaxy tool definition)
+* blast2go.py (the Python wrapper script)
+* massage_xml_for_blast2go.py (Python XML reformatting script)
+* README.rst (this file)
+
+For a manual installation of the wrapper you will also need to modify the
+tools_conf.xml file to tell Galaxy to offer the tool. We suggest putting
+it next to the NCBI BLAST+ wrappers. Just add the line::
+
+  <tool file="blast2go/blast2go.xml" />
+
+If you wish to run the unit tests, also add this to tools_conf.xml.sample
+and move/copy the test-data files under Galaxy's test-data folder. Then::
+
+    $ ./run_functional_tests.sh -id blast2go
+
+
+Configuration
+=============
+
+As part of setting up b2g4pipe you will need to setup one or more Blast2GO
+property files which tell the tool which database to use etc. The example
+b2gPipe.properties provided with b2g4pipe is often out of date. The current
+server IP address and database name may given on the Blast2GO website, or
+can be found by running the latest GUI version via Java web-start, and
+looking under the tools/options menu. These property files can be anywhere
+accessable to the Galaxy Unix user, we put them with the JAR file etc.
+
+You must tell Galaxy about these Blast2GO property files so that they can be
+offered to the user. Copy file blast2go.loc.sample to tool-data/blast2go.loc
+under the Galaxy folder and edit this to match your installation. This must
+be plain text, tab separated, with three columns:
+
+1. ID for the setup, e.g. Spain_2012_August
+2. Description for the setup, e.g. Database in Spain (August 2012)
+3. Properties filename for the setup, e.g. Spain_2012_August.properties
+   relative to the main JAR file, or with a full path
+   e.g. /opt/b2g4pipe/Spain_2012_August.properties
+
+Avoid including "Blast2GO" in the description (column 2) as this text will be
+included in the automatically assigned output dataset name. The blast2go.loc
+file allows you to customise the database setup. If for example you have a local
+Blast2GO server running (which we recommend for speed), and you want this to be
+the default setting, include it as the first line in your blast2go.loc file.
+
+Consult the Blast2GO documentation for details about the property files and
+setting up a local MySQL Blast2GO database.
+
+
+History
+=======
+
+======= ======================================================================
+Version Changes
+------- ----------------------------------------------------------------------
+v0.0.1  - Initial public release
+v0.0.2  - Documentation clarifications, e.g. concatenated BLAST XML is allowed.
+        - Fixed error handler in wrapper script (for when b2g4pipe fails).
+        - Reformats the XML to use old NCBI-style concatenated BLAST XML since
+          b2g4pipe crashes with heap space error on with large files using
+          current NCBI output.
+v0.0.3  - Include sample loc file, tool-data/blast2go.loc.sample
+v0.0.4  - Include repository_dependencies.xml file for 'blastxml' format
+          (previously included in the core Galaxy installation)
+v0.0.5  - Quote arguments in case of spaces in filenames (internal change)
+        - Last release supporting b2g4pipe v2.3.5
+v0.0.6  - Support for b2g4pipe v2.5 instead of v2.3.5
+
+          - Now invoked with a class path and es.blast2go.prog.B2GAnnotPipe
+            rather then simply calling the jar file
+          - Now uses the switch -annot instead of -a (this change breaks
+            support for b2g4pipe v2.3.5 unfortunately)
+
+        - Catch a few error messages and treat them explicitly as errors.
+v0.0.7  - Update output description in XML file (b2g4pipe v2.3.5 included
+          the sequence description, b2g4pipe v2.5 omits this).
+v0.0.8  - Automated installation via the Galaxy Tool Shed.
+        - Added unit test.
+        - Explain how to load the tabular file into the Blast2GO GUI.
+        - Link to Tool Shed added to help text and this documentation.
+        - Switch to standard MIT licence.
+        - Use reStructuredText for this README file.
+        - Updated citation information (Cock et al. 2013).
+        - Development moved to GitHub, https://github.com/peterjc/galaxy_blast
+        - Split out massage_xml_for_blast2go.py as a standalone file.
+======= ======================================================================
+
+
+Developers
+==========
+
+This script and related tools were originally developed on the 'tools' branch
+of the following BitBucket Mercurial repository:
+https://bitbucket.org/peterjc/galaxy-central/
+
+As of September 2013, development is continuing on a dedicated GitHub repository:
+https://github.com/peterjc/galaxy_blast
+
+For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball I use
+the following command from the Galaxy root folder::
+
+    $ tar -czf blast2go.tar.gz blast2go/README.rst blast2go/blast2go.xml blast2go/blast2go.py blast2go/massage_xml_for_blast2go.py blast2go/repository_dependencies.xml blast2go/tool_dependencies.xml tool-data/blast2go.loc.sample test-data/blastp_sample.xml test-data/blastp_sample.blast2go.tabular
+
+Check this worked::
+
+    $ tar -tzf blast2go.tar.gz
+    blast2go/README.rst
+    blast2go/blast2go.xml
+    blast2go/blast2go.py
+    blast2go/massage_xml_for_blast2go.py
+    blast2go/repository_dependencies.xml
+    blast2go/tool_dependencies.xml
+    tool-data/blast2go.loc.sample
+    test-data/blastp_sample.xml
+    test-data/blastp_sample.blast2go.tabular
+
+
+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.
+
+
+NOTE: This is the licence for the Galaxy Wrapper only. Blast2GO and
+associated data files are available and licenced separately.
diff -r e4419efbefad -r 872cf247c899 blast2go/blast2go.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/blast2go/blast2go.py	Mon Sep 23 05:50:58 2013 -0400
@@ -0,0 +1,134 @@
+#!/usr/bin/env python
+"""Galaxy wrapper for Blast2GO for pipelines, b2g4pipe v2.5.
+
+This script takes exactly three command line arguments:
+ * Input BLAST XML filename
+ * Blast2GO properties filename (settings file)
+ * Output tabular filename
+
+The properties filename can be a fully qualified path, but if not
+this will look next to the blast2go.jar file.
+
+Sadly b2g4pipe (at least v2.3.5 to v2.5.0) cannot cope with current
+style large BLAST XML files (e.g. from BLAST 2.2.25+), so we reformat
+these to avoid it crashing with a Java heap space OutOfMemoryError.
+
+As part of this reformatting, we check for BLASTP or BLASTX output
+(otherwise raise an error), and print the query count.
+
+It then calls the Java command line tool, and moves the output file to
+the location Galaxy is expecting, and removes the tempory XML file.
+
+This script is called from my Galaxy wrapper for Blast2GO for pipelines,
+available from the Galaxy Tool Shed here:
+http://toolshed.g2.bx.psu.edu/view/peterjc/blast2go
+
+This script is under version control here:
+https://github.com/peterjc/galaxy_blast/tree/master/blast2go
+"""
+import sys
+import os
+import subprocess
+
+#You may need to edit this to match your local setup,
+blast2go_dir = os.environ.get("B2G4PIPE", "/opt/b2g4pipe_v2.5/")
+blast2go_jar = os.path.join(blast2go_dir, "blast2go.jar")
+
+def stop_err(msg, error_level=1):
+    """Print error message to stdout and quit with given error level."""
+    sys.stderr.write("%s\n" % msg)
+    sys.exit(error_level)
+
+try:
+    from massage_xml_for_blast2go import prepare_xml
+except ImportError:
+    stop_err("Missing sister file massage_xml_for_blast2go.py")
+
+if len(sys.argv) != 4:
+    stop_err("Require three arguments: XML filename, properties filename, output tabular filename")
+
+xml_file, prop_file, tabular_file = sys.argv[1:]
+
+#We should have write access here:
+tmp_xml_file = tabular_file + ".tmp.xml"
+
+if not os.path.isfile(blast2go_jar):
+    stop_err("Blast2GO JAR file not found: %s" % blast2go_jar)
+
+if not os.path.isfile(xml_file):
+    stop_err("Input BLAST XML file not found: %s" % xml_file)
+
+if not os.path.isfile(prop_file):
+    tmp = os.path.join(os.path.split(blast2go_jar)[0], prop_file)
+    if os.path.isfile(tmp):
+        #The properties file seems to have been given relative to the JAR
+        prop_file = tmp
+    else:
+        stop_err("Blast2GO configuration file not found: %s" % prop_file)
+    del tmp
+
+
+def run(cmd):
+    #Avoid using shell=True when we call subprocess to ensure if the Python
+    #script is killed, so too is the child process.
+    try:
+        child = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+    except Exception, err:
+        stop_err("Error invoking command:\n%s\n\n%s\n" % (" ".join(cmd), err))
+    #Use .communicate as can get deadlocks with .wait(),
+    stdout, stderr = child.communicate()
+    return_code = child.returncode
+
+    #keep stdout minimal as shown prominently in Galaxy
+    #Record it in case a silent error needs diagnosis
+    if stdout:
+        sys.stderr.write("Standard out:\n%s\n\n" % stdout)
+    if stderr:
+        sys.stderr.write("Standard error:\n%s\n\n" % stderr)
+
+    error_msg = None
+    if return_code:
+        cmd_str = " ".join(cmd)
+        error_msg = "Return code %i from command:\n%s" % (return_code, cmd_str)
+    elif "Database or network connection (timeout) error" in stdout+stderr:
+        error_msg = "Database or network connection (timeout) error"
+    elif "Annotation of 0 seqs with 0 annots finished." in stdout+stderr:
+        error_msg = "No sequences processed!"
+
+    if error_msg:
+        print error_msg
+        stop_err(error_msg)
+
+
+blast2go_classpath = os.path.split(blast2go_jar)[0]
+assert os.path.isdir(blast2go_classpath)
+blast2go_classpath = "%s/*:%s/ext/*:" % (blast2go_classpath, blast2go_classpath)
+
+prepare_xml(xml_file, tmp_xml_file)
+#print "XML file prepared for Blast2GO"
+
+#We will have write access wherever the output should be,
+#so we'll ask Blast2GO to use that as the stem for its output
+#(it will append .annot to the filename)
+cmd = ["java", "-cp", blast2go_classpath, "es.blast2go.prog.B2GAnnotPipe",
+       "-in", tmp_xml_file,
+       "-prop", prop_file,
+       "-out", tabular_file, #Used as base name for output files
+       "-annot", # Generate *.annot tabular file
+       #NOTE: For v2.3.5 must use -a, for v2.5 must use -annot instead
+       #"-img", # Generate images, feature not in v2.3.5
+       ]
+#print " ".join(cmd)
+run(cmd)
+
+#Remove the temp XML file
+os.remove(tmp_xml_file)
+
+out_file = tabular_file + ".annot"
+if not os.path.isfile(out_file):
+    stop_err("ERROR - No output annotation file from Blast2GO")
+
+#Move the output file where Galaxy expects it to be:
+os.rename(out_file, tabular_file)
+
+print "Done"
diff -r e4419efbefad -r 872cf247c899 blast2go/blast2go.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/blast2go/blast2go.xml	Mon Sep 23 05:50:58 2013 -0400
@@ -0,0 +1,118 @@
+<tool id="blast2go" name="Blast2GO" version="0.0.8">
+    <description>Maps BLAST results to GO annotation terms</description>
+    <requirements>
+        <requirement type="package" version="2.5">b2g4pipe</requirement>
+    </requirements>
+    <command interpreter="python">
+        blast2go.py "${xml}" "${prop.fields.path}" "${tab}"
+    </command>
+    <stdio>
+        <!-- Wrapper ensures anything other than zero is an error -->
+        <exit_code range="1:" />
+        <exit_code range=":-1" />
+    </stdio>
+    <inputs>
+        <param name="xml" type="data" format="blastxml" label="BLAST XML results" description="You must have run BLAST against a protein database such as the NCBI non-redundant (NR) database. Use BLASTX for nucleotide queries, BLASTP for protein queries." /> 
+        <param name="prop" type="select" label="Blast2GO settings" description="One or more configurations can be setup, such as using the Blast2GO team's server in Spain, or a local database.">
+             <options from_file="blast2go.loc">
+                 <column name="value" index="0"/>
+                 <column name="name" index="1"/>
+                 <column name="path" index="2"/>
+             </options>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="tab" format="tabular" label="Blast2GO ${prop.fields.name}" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="xml" value="blastp_sample.xml" ftype="blastxml"/>
+            <param name="prop" value="Spain_2011_June"/>
+            <output name="tab" file="blastp_sample.blast2go.tabular" ftype="tabular"/>
+        </test>
+    </tests>
+    <help>
+.. class:: warningmark
+
+**Note**. Blast2GO may take a substantial amount of time, especially if
+running against the public server in Spain. For large input datasets it
+is advisable to allow overnight processing, or consider subdividing.
+
+-----
+
+**What it does**
+
+This runs b2g4Pipe v2.5, which is the command line (no GUI) version of
+Blast2GO designed for use in pipelines.
+
+It takes as input BLAST XML results against a protein database, typically
+the NCBI non-redundant (NR) database. This tool will accept concatenated
+BLAST XML files (although they are technically invalid XML), which is very
+useful if you have sub-divided your protein FASTA files and run BLAST on
+them in batches.
+
+The BLAST matches are used to assign Gene Ontology (GO) annotation terms
+to each query sequence.
+
+The output from this tool is a tabular file containing three columns, with
+the order taken from query order in the original BLAST XML file:
+
+====== ====================
+Column Description
+------ --------------------
+     1 ID of query sequence
+     2 GO term
+     3 GO description
+====== ====================
+
+Note that if no GO terms are assigned to a sequence (e.g. if it had no
+BLAST matches), then it will not be present in the output file.
+
+This tabular file is called an "Annotation File" in the Blast2GO GUI.
+If you download the tabular file, and rename it to use the extension
+".annot", then it can be opened with the Blast2GO GUI via the "File",
+"Load Annotation (.annot)" menu (keyboard shortcut ALT+L). You can
+then run some of the interactive analyses offered in the GUI tool.
+
+
+**Advanced Settings**
+
+Blast2GO has a properties setting file which includes which database
+server to connect to (e.g. the public server in Valencia, Spain, or a
+local server), as well as more advanced options such as thresholds and
+evidence code weights. To change these settings, your Galaxy administrator
+must create a new properties file, and add it to the drop down menu above.
+
+
+**References**
+
+If you use this Galaxy tool in work leading to a scientific publication please
+cite the following papers:
+
+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
+
+S. Götz et al. (2008).
+High-throughput functional annotation and data mining with the Blast2GO suite.
+Nucleic Acids Res. 36(10):3420–3435.
+http://dx.doi.org/10.1093/nar/gkn176
+
+A. Conesa and S. Götz (2008).
+Blast2GO: A Comprehensive Suite for Functional Analysis in Plant Genomics.
+International Journal of Plant Genomics. 619832.
+http://dx.doi.org/10.1155/2008/619832
+
+A. Conesa et al. (2005).
+Blast2GO: A universal tool for annotation, visualization and analysis in functional genomics research.
+Bioinformatics 21:3674-3676.
+http://dx.doi.org/10.1093/bioinformatics/bti610
+
+See also http://www.blast2go.com/
+
+This wrapper is available to install into other Galaxy Instances via the Galaxy
+Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/blast2go
+
+    </help>
+</tool>
diff -r e4419efbefad -r 872cf247c899 blast2go/massage_xml_for_blast2go.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/blast2go/massage_xml_for_blast2go.py	Mon Sep 23 05:50:58 2013 -0400
@@ -0,0 +1,92 @@
+#!/usr/bin/env python
+"""Script for reformatting Blast XML to suite Blast2GO.
+
+This script takes exactly two command line arguments:
+ * Input BLAST XML filename
+ * Output BLAST XML filename
+
+Sadly b2g4pipe (at least v2.3.5 to v2.5.0) cannot cope with current
+style large BLAST XML files (e.g. from BLAST 2.2.25+), so we reformat
+these to avoid it crashing with a Java heap space OutOfMemoryError.
+
+As part of this reformatting, we check for BLASTP or BLASTX output
+(otherwise raise an error), and print the query count.
+
+This script is called from my Galaxy wrapper for Blast2GO for pipelines,
+available from the Galaxy Tool Shed here:
+http://toolshed.g2.bx.psu.edu/view/peterjc/blast2go 
+
+This script is under version control here:
+https://github.com/peterjc/galaxy_blast/tree/master/blast2go
+"""
+import sys
+import os
+import subprocess
+
+def stop_err(msg, error_level=1):
+    """Print error message to stdout and quit with given error level."""
+    sys.stderr.write("%s\n" % msg)
+    sys.exit(error_level)
+
+def prepare_xml(original_xml, mangled_xml):
+    """Reformat BLAST XML to suit Blast2GO.
+
+    Blast2GO can't cope with 1000s of <Iteration> tags within a
+    single <BlastResult> tag, so instead split this into one
+    full XML record per interation (i.e. per query). This gives
+    a concatenated XML file mimicing old versions of BLAST.
+
+    This also checks for BLASTP or BLASTX output, and outputs
+    the number of queries. Galaxy will show this as "info".
+    """
+    in_handle = open(original_xml)
+    footer = "  </BlastOutput_iterations>\n</BlastOutput>\n"
+    header = ""
+    while True:
+        line = in_handle.readline()
+        if not line:
+            #No hits?
+            stop_err("Problem with XML file?")
+        if line.strip() == "<Iteration>":
+            break
+        header += line
+
+    if "<BlastOutput_program>blastx</BlastOutput_program>" in header:
+        print "BLASTX output identified"
+    elif "<BlastOutput_program>blastp</BlastOutput_program>" in header:
+        print "BLASTP output identified"
+    else:
+        in_handle.close()
+        stop_err("Expect BLASTP or BLASTX output")
+
+    out_handle = open(mangled_xml, "w")
+    out_handle.write(header)
+    out_handle.write(line)
+    count = 1
+    while True:
+        line = in_handle.readline()
+        if not line:
+            break
+        elif line.strip() == "<Iteration>":
+           #Insert footer/header
+           out_handle.write(footer)
+           out_handle.write(header)
+           count += 1
+        out_handle.write(line)
+
+    out_handle.close()
+    in_handle.close()
+    print "Input has %i queries" % count
+
+
+if __name__ == "__main__":
+    # Run the conversion...
+    if len(sys.argv) != 3:
+        stop_err("Require two arguments: XML input filename, XML output filename")
+
+    xml_file, out_xml_file = sys.argv[1:]
+
+    if not os.path.isfile(xml_file):
+        stop_err("Input BLAST XML file not found: %s" % xml_file)
+
+    prepare_xml(xml_file, out_xml_file)
diff -r e4419efbefad -r 872cf247c899 blast2go/repository_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/blast2go/repository_dependencies.xml	Mon Sep 23 05:50:58 2013 -0400
@@ -0,0 +1,4 @@
+<?xml version="1.0"?>
+<repositories description="Requires BLAST XML and database datatype definitions.">
+<repository changeset_revision="a44a7a5456e1" name="blast_datatypes" owner="devteam" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+</repositories>
diff -r e4419efbefad -r 872cf247c899 blast2go/tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/blast2go/tool_dependencies.xml	Mon Sep 23 05:50:58 2013 -0400
@@ -0,0 +1,32 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="b2g4pipe" version="2.5">
+        <install version="1.0">
+            <actions>
+                <!-- If used, download_by_url must be the first action -->	
+                <!-- The ZIP file decompresses to give a folder b2g4pipe -->
+                <action type="download_by_url">http://www.blast2go.com/data/blast2go/b2g4pipe_v2.5.zip</action>
+		<!-- Galaxy moves into the unzipped folder b2g4pipe -->
+                <action type="shell_command">
+cp b2gPipe.properties Spain_2012_August.properties &amp;&amp;
+sed -i "s/Dbacces.dbname=b2g_apr12/Dbacces.dbname=b2g_aug12/g" Spain_2012_August.properties &amp;&amp;
+sed -i "s/Dbacces.dbhost=10.10.100.203/Dbacces.dbhost=publicdb.blast2go.com/g" Spain_2012_August.properties
+                </action>
+                <action type="shell_command">
+cp b2gPipe.properties Spain_2011_June.properties &amp;&amp;
+sed -i "s/Dbacces.dbname=b2g_apr12/Dbacces.dbname=b2g_jun11/g" Spain_2011_June.properties &amp;&amp;
+sed -i "s/Dbacces.dbhost=10.10.100.203/Dbacces.dbhost=publicdb.blast2go.com/g" Spain_2011_June.properties
+                </action>
+                <action type="move_directory_files"><source_directory>.</source_directory><destination_directory>$INSTALL_DIR/</destination_directory></action>
+                <!-- Set environment variable $B2G4PIPE so Python script knows where to look -->
+                <action type="set_environment">
+                    <environment_variable name="B2G4PIPE" action="set_to">$INSTALL_DIR</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>
+Downloads b2g4pipe v2.5
+        </readme>
+    </package>
+</tool_dependency>
+
diff -r e4419efbefad -r 872cf247c899 test-data/blastp_sample.blast2go.tabular
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/blastp_sample.blast2go.tabular	Mon Sep 23 05:50:58 2013 -0400
@@ -0,0 +1,1 @@
+Sample	GO:0005488	tail tape measure protein
diff -r e4419efbefad -r 872cf247c899 test-data/blastp_sample.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/blastp_sample.xml	Mon Sep 23 05:50:58 2013 -0400
@@ -0,0 +1,293 @@
+<?xml version="1.0"?>
+<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "NCBI_BlastOutput.dtd">
+<BlastOutput>
+  <BlastOutput_program>blastp</BlastOutput_program>
+  <BlastOutput_version>BLASTP 2.2.24+</BlastOutput_version>
+  <BlastOutput_reference>Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&amp;auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), &quot;Gapped BLAST and PSI-BLAST: a new generation of protein database search programs&quot;, Nucleic Acids Res. 25:3389-3402.</BlastOutput_reference>
+  <BlastOutput_db>nr</BlastOutput_db>
+  <BlastOutput_query-ID>Query_1</BlastOutput_query-ID>
+  <BlastOutput_query-def>Sample</BlastOutput_query-def>
+  <BlastOutput_query-len>516</BlastOutput_query-len>
+  <BlastOutput_param>
+    <Parameters>
+      <Parameters_matrix>BLOSUM62</Parameters_matrix>
+      <Parameters_expect>1e-30</Parameters_expect>
+      <Parameters_gap-open>11</Parameters_gap-open>
+      <Parameters_gap-extend>1</Parameters_gap-extend>
+      <Parameters_filter>F</Parameters_filter>
+    </Parameters>
+  </BlastOutput_param>
+  <BlastOutput_iterations>
+    <Iteration>
+      <Iteration_iter-num>1</Iteration_iter-num>
+      <Iteration_query-ID>Query_1</Iteration_query-ID>
+      <Iteration_query-def>Sample</Iteration_query-def>
+      <Iteration_query-len>516</Iteration_query-len>
+      <Iteration_hits>
+        <Hit>
+          <Hit_num>1</Hit_num>
+          <Hit_id>gi|119953746|ref|YP_950551.1|</Hit_id>
+          <Hit_def>tail tape measure protein [Streptococcus phage SMP] &gt;gi|118430558|gb|ABK91882.1| tail tape measure protein [Streptococcus suis phage SMP]</Hit_def>
+          <Hit_accession>YP_950551</Hit_accession>
+          <Hit_len>659</Hit_len>
+          <Hit_hsps>
+            <Hsp>
+              <Hsp_num>1</Hsp_num>
+              <Hsp_bit-score>949.117592429394</Hsp_bit-score>
+              <Hsp_score>2452</Hsp_score>
+              <Hsp_evalue>0</Hsp_evalue>
+              <Hsp_query-from>1</Hsp_query-from>
+              <Hsp_query-to>516</Hsp_query-to>
+              <Hsp_hit-from>27</Hsp_hit-from>
+              <Hsp_hit-to>542</Hsp_hit-to>
+              <Hsp_query-frame>0</Hsp_query-frame>
+              <Hsp_hit-frame>0</Hsp_hit-frame>
+              <Hsp_identity>500</Hsp_identity>
+              <Hsp_positive>500</Hsp_positive>
+              <Hsp_gaps>0</Hsp_gaps>
+              <Hsp_align-len>516</Hsp_align-len>
+              <Hsp_qseq>FHLLNSGGSALSVMFAKLVGIIAGISAPIWXXXXXXXXXXXXXXXXYNTNEEFRTKVQAAWEAIKSAISTAVEAVVSFVMDLWGQMVAWWNENQELIRQTAETVWNAIRTVVETVMTALIPIVQTAWDLILAVVTTVLNVIKTVVDTGLKVVLGIIKAVMQMINGDWSGAWETLKGVAGTIWEGIKSLVQVAIDGLVQIFQTGLAFLKSIWDTVWGTIMAVVGPIWDWIKTTVSNAITAVWEIIQNIMTSIQTTWDTVWNAISTVASNIWTAISTTVMSVLTTIWGYIQTYLELIKTVWSAAWEIIKAVFAAILLTIVGLVTGNFDLIKQAISNAWEIIKTKTSEIWNAITTFLSGIWEGIKTAASTAWEWIKTTISNVMTTIKSNIETAWNNIKTSISNALNNIKSAAENAWNNIKSAISTAIENIKSTVSNGWNNLVSTVTNAGPRIVSAVRTGFDNAVNAARNFISNAISVGGDLINGFVEGVKGAAGRLIDAVGGAVSGAIDWAKGLLGIKS</Hsp_qseq>
+              <Hsp_hseq>FHLLNSGGSALSVMFAKLVGIIAGISAPIWAVIGVIAALVAGFVLLYNTNEEFRTKVQAAWEAIKSAISTAVEAVVSFVMDLWGQMVAWWNENQELIRQTAETVWNAIRTVVETVMTALIPIVQTAWDLILAVVTTVLNVIKTVVDTGLKVVLGIIKAVMQMINGDWSGAWETLKGVAGTIWEGIKSLVQVAIDGLVQIFQTGLAFLKSIWDTVWGTIMAVVGPIWDWIKTTVSNAITAVWEIIQNIMTSIQTTWDTVWNAISTVASNIWTAISTTVMSVLTTIWGYIQTYLELIKTVWSAAWEIIKAVFAAILLTIVGLVTGNFDLIKQAISNAWEIIKTKTSEIWNAITTFLSGIWEGIKTAASTAWEWIKTTISNVMTTIKSNIETAWNNIKTSISNALNNIKSAAENAWNNIKSAISTAIENIKSTVSNGWNNLVSTVTNAGPRIVSAVRTGFDNAVNAARNFISNAISVGGDLINGFVEGVKGAAGRLIDAVGGAVSGAIDWAKGLLGIKS</Hsp_hseq>
+              <Hsp_midline>FHLLNSGGSALSVMFAKLVGIIAGISAPIW                YNTNEEFRTKVQAAWEAIKSAISTAVEAVVSFVMDLWGQMVAWWNENQELIRQTAETVWNAIRTVVETVMTALIPIVQTAWDLILAVVTTVLNVIKTVVDTGLKVVLGIIKAVMQMINGDWSGAWETLKGVAGTIWEGIKSLVQVAIDGLVQIFQTGLAFLKSIWDTVWGTIMAVVGPIWDWIKTTVSNAITAVWEIIQNIMTSIQTTWDTVWNAISTVASNIWTAISTTVMSVLTTIWGYIQTYLELIKTVWSAAWEIIKAVFAAILLTIVGLVTGNFDLIKQAISNAWEIIKTKTSEIWNAITTFLSGIWEGIKTAASTAWEWIKTTISNVMTTIKSNIETAWNNIKTSISNALNNIKSAAENAWNNIKSAISTAIENIKSTVSNGWNNLVSTVTNAGPRIVSAVRTGFDNAVNAARNFISNAISVGGDLINGFVEGVKGAAGRLIDAVGGAVSGAIDWAKGLLGIKS</Hsp_midline>
+            </Hsp>
+          </Hit_hsps>
+        </Hit>
+        <Hit>
+          <Hit_num>2</Hit_num>
+          <Hit_id>gi|148986157|ref|ZP_01819143.1|</Hit_id>
+          <Hit_def>unknown phage protein [Streptococcus pneumoniae SP3-BS71] &gt;gi|147921871|gb|EDK72998.1| unknown phage protein [Streptococcus pneumoniae SP3-BS71]</Hit_def>
+          <Hit_accession>ZP_01819143</Hit_accession>
+          <Hit_len>1031</Hit_len>
+          <Hit_hsps>
+            <Hsp>
+              <Hsp_num>1</Hsp_num>
+              <Hsp_bit-score>174.481245259597</Hsp_bit-score>
+              <Hsp_score>441</Hsp_score>
+              <Hsp_evalue>1.54640812741294e-41</Hsp_evalue>
+              <Hsp_query-from>49</Hsp_query-from>
+              <Hsp_query-to>300</Hsp_query-to>
+              <Hsp_hit-from>679</Hsp_hit-from>
+              <Hsp_hit-to>897</Hsp_hit-to>
+              <Hsp_query-frame>0</Hsp_query-frame>
+              <Hsp_hit-frame>0</Hsp_hit-frame>
+              <Hsp_identity>104</Hsp_identity>
+              <Hsp_positive>148</Hsp_positive>
+              <Hsp_gaps>33</Hsp_gaps>
+              <Hsp_align-len>252</Hsp_align-len>
+              <Hsp_qseq>TNEEFRTKVQAAWEAIKSAISTAVEAVVSFVMDLWGQMVAWWNENQELIRQTAETVWNAIRTVVETVMTALIPIVQTAWDLILAVVTTVLNVIKTVVDTGLKVVLGIIKAVMQMINGDWSGAWETLKGVAGTIWEGIKSLVQVAIDGLVQIFQTGLAFLKSIWDTVWGTIMAVVGPIWDWIKTTVSNAITAVWEIIQNIMTSIQTTWDTVWNAISTVASNIWTAISTTVMSVLTTIWGYIQTYLELIKTVWS</Hsp_qseq>
+              <Hsp_hseq>TNEGFRDAVTTVWNAILEVINAVVSEISNFVMSIFGTVVTWWTENQELIRTSAETVWNAIYTVISTILDILGPLLQAGWDNIQLIITTTWEIIKIVVETAINVVLGVIQAVMQIITGDWSGAWETIKGVFSTVWQAIQSIVQT-------IFSAIQSYISNILNGISGT----VSNIWNSIKDTVSN----------------------VLNAISSTVSSVWEGIKSTISSAINGARDAVSSAIEAIKGLFN</Hsp_hseq>
+              <Hsp_midline>TNE FR  V   W AI   I+  V  + +FVM ++G +V WW ENQELIR +AETVWNAI TV+ T++  L P++Q  WD I  ++TT   +IK VV+T + VVLG+I+AVMQ+I GDWSGAWET+KGV  T+W+ I+S+VQ        IF    +++ +I + + GT    V  IW+ IK TVSN                      V NAIS+  S++W  I +T+ S +      + + +E IK +++</Hsp_midline>
+            </Hsp>
+          </Hit_hsps>
+        </Hit>
+        <Hit>
+          <Hit_num>3</Hit_num>
+          <Hit_id>gi|77411259|ref|ZP_00787609.1|</Hit_id>
+          <Hit_def>tail tape meausure protein [Streptococcus agalactiae CJB111] &gt;gi|77162685|gb|EAO73646.1| tail tape meausure protein [Streptococcus agalactiae CJB111]</Hit_def>
+          <Hit_accession>ZP_00787609</Hit_accession>
+          <Hit_len>1039</Hit_len>
+          <Hit_hsps>
+            <Hsp>
+              <Hsp_num>1</Hsp_num>
+              <Hsp_bit-score>165.621655013498</Hsp_bit-score>
+              <Hsp_score>418</Hsp_score>
+              <Hsp_evalue>7.61538823982138e-39</Hsp_evalue>
+              <Hsp_query-from>50</Hsp_query-from>
+              <Hsp_query-to>310</Hsp_query-to>
+              <Hsp_hit-from>655</Hsp_hit-from>
+              <Hsp_hit-to>904</Hsp_hit-to>
+              <Hsp_query-frame>0</Hsp_query-frame>
+              <Hsp_hit-frame>0</Hsp_hit-frame>
+              <Hsp_identity>107</Hsp_identity>
+              <Hsp_positive>158</Hsp_positive>
+              <Hsp_gaps>11</Hsp_gaps>
+              <Hsp_align-len>261</Hsp_align-len>
+              <Hsp_qseq>NEEFRTKVQAAWEAIKSAISTAVEAVVSFVMDLWGQMVAWWNENQELIRQTAETVWNAIRTVVETVMTALIPIVQTAWDLILAVVTTVLNVIKTVVDTGLKVVLGIIKAVMQMINGDWSGAWETLKGVAGTIWEGIKSLVQVAIDGLVQIFQTGLAFLKSIWDTVWGTIMAVVGPIWDWIKTTVSNAITAVWEIIQNIMTSIQTTWDTVWNAISTVASNIWTAISTTVMSVLTTIWGYIQTYLELIKTVWSAAWEIIKAVF</Hsp_qseq>
+              <Hsp_hseq>HEGFRTAVTEIWNAIYAFLSVIIQQISSFVMSIWGTLTTWWTENQQLILNAANTVWTAISTVIQTIMTILGPYLQASWENIKLIITTAWDIIKVVVETAINVVLGIIKAVMQIITGDWSGAWETIKQVVSTVWEAIKSLISIVLSAIAQ-------FISNSWNGIKGTMTNLL----NSIKSVVSNVWNSIKSTISSILSSIGSTVSSVWNGMKATISGVLSGISNTVSSVWNGVKSTITNAINGAKNAVSSAINAIKNLF</Hsp_hseq>
+              <Hsp_midline>+E FRT V   W AI + +S  ++ + SFVM +WG +  WW ENQ+LI   A TVW AI TV++T+MT L P +Q +W+ I  ++TT  ++IK VV+T + VVLGIIKAVMQ+I GDWSGAWET+K V  T+WE IKSL+ + +  + Q       F+ + W+ + GT+  ++    + IK+ VSN   ++   I +I++SI +T  +VWN +    S + + IS TV SV   +   I   +   K   S+A   IK +F</Hsp_midline>
+            </Hsp>
+          </Hit_hsps>
+        </Hit>
+        <Hit>
+          <Hit_num>4</Hit_num>
+          <Hit_id>gi|76786754|ref|YP_329383.1|</Hit_id>
+          <Hit_def>prophage LambdaSa04, tail tape measure protein, TP901 family [Streptococcus agalactiae A909] &gt;gi|76561811|gb|ABA44395.1| prophage LambdaSa04, tail tape measure protein, TP901 family [Streptococcus agalactiae A909]</Hit_def>
+          <Hit_accession>YP_329383</Hit_accession>
+          <Hit_len>1039</Hit_len>
+          <Hit_hsps>
+            <Hsp>
+              <Hsp_num>1</Hsp_num>
+              <Hsp_bit-score>159.073262222903</Hsp_bit-score>
+              <Hsp_score>401</Hsp_score>
+              <Hsp_evalue>6.55719737745379e-37</Hsp_evalue>
+              <Hsp_query-from>50</Hsp_query-from>
+              <Hsp_query-to>310</Hsp_query-to>
+              <Hsp_hit-from>655</Hsp_hit-from>
+              <Hsp_hit-to>904</Hsp_hit-to>
+              <Hsp_query-frame>0</Hsp_query-frame>
+              <Hsp_hit-frame>0</Hsp_hit-frame>
+              <Hsp_identity>103</Hsp_identity>
+              <Hsp_positive>156</Hsp_positive>
+              <Hsp_gaps>11</Hsp_gaps>
+              <Hsp_align-len>261</Hsp_align-len>
+              <Hsp_qseq>NEEFRTKVQAAWEAIKSAISTAVEAVVSFVMDLWGQMVAWWNENQELIRQTAETVWNAIRTVVETVMTALIPIVQTAWDLILAVVTTVLNVIKTVVDTGLKVVLGIIKAVMQMINGDWSGAWETLKGVAGTIWEGIKSLVQVAIDGLVQIFQTGLAFLKSIWDTVWGTIMAVVGPIWDWIKTTVSNAITAVWEIIQNIMTSIQTTWDTVWNAISTVASNIWTAISTTVMSVLTTIWGYIQTYLELIKTVWSAAWEIIKAVF</Hsp_qseq>
+              <Hsp_hseq>HEGFRTAVTEIWNAIYAFLTVIIQQISSFVMSIWGTLITWWTENQQLILNATNTVWTAISTVIQTIMTILAPYLQASWENIKLIITTAWDIIKVVVETAINVVLGIIKAVMQIITGDWSGAWETIKQVVSTVWEVIKSLISIVLSAIAQ-------FISNSWNGIKGTMTNLL----NSIKGVVSNVWNGIKSTISSILSSIGSTVSSIWNGMKATISGVLSGISSTVSFVWNGVKSTITNAINGAKNAVSSAINAIKNLF</Hsp_hseq>
+              <Hsp_midline>+E FRT V   W AI + ++  ++ + SFVM +WG ++ WW ENQ+LI     TVW AI TV++T+MT L P +Q +W+ I  ++TT  ++IK VV+T + VVLGIIKAVMQ+I GDWSGAWET+K V  T+WE IKSL+ + +  + Q       F+ + W+ + GT+  ++    + IK  VSN    +   I +I++SI +T  ++WN +    S + + IS+TV  V   +   I   +   K   S+A   IK +F</Hsp_midline>
+            </Hsp>
+          </Hit_hsps>
+        </Hit>
+        <Hit>
+          <Hit_num>5</Hit_num>
+          <Hit_id>gi|153811333|ref|ZP_01964001.1|</Hit_id>
+          <Hit_def>hypothetical protein RUMOBE_01725 [Ruminococcus obeum ATCC 29174] &gt;gi|149832460|gb|EDM87544.1| hypothetical protein RUMOBE_01725 [Ruminococcus obeum ATCC 29174]</Hit_def>
+          <Hit_accession>ZP_01964001</Hit_accession>
+          <Hit_len>1228</Hit_len>
+          <Hit_hsps>
+            <Hsp>
+              <Hsp_num>1</Hsp_num>
+              <Hsp_bit-score>157.147264343316</Hsp_bit-score>
+              <Hsp_score>396</Hsp_score>
+              <Hsp_evalue>2.33083876931167e-36</Hsp_evalue>
+              <Hsp_query-from>3</Hsp_query-from>
+              <Hsp_query-to>516</Hsp_query-to>
+              <Hsp_hit-from>573</Hsp_hit-from>
+              <Hsp_hit-to>1059</Hsp_hit-to>
+              <Hsp_query-frame>0</Hsp_query-frame>
+              <Hsp_hit-frame>0</Hsp_hit-frame>
+              <Hsp_identity>167</Hsp_identity>
+              <Hsp_positive>247</Hsp_positive>
+              <Hsp_gaps>113</Hsp_gaps>
+              <Hsp_align-len>557</Hsp_align-len>
+              <Hsp_qseq>LLNSGGSALSVMFAKLVGIIAGISAPIWXXXXXXXXXXXXXXXXYNTNEEFRTKVQAAWEAIKSAISTAVEAVVSFVMDLWGQMVAWWNENQELIRQTAETVWNAIRTVVETVMTALIPIVQTAWDLILAVVTTVLNVIKTVVDTGLKVVLGIIKAVMQMINGDWSGAWETLKGVAGTIWEGIKSLVQV---AIDGLVQIFQTGLAFLKSIWDTVWGTIMAVVGPIWDWIKTTVSNAITAVWEIIQNIMTSIQTTWDTVWNAISTVASNIWTAISTTVMSVLTTIWGYIQTYLELIKTVWSAAWEIIKAVFAAILLTIVGLVTGNFDLI-----------KQAISNAWEIIKTKT-----------------------SEIWNAITTFLSGIWEGIKTAASTAWEWIKTT-ISNVMTTIKSNIETAWNNIKTSISNALNNIKSAAENAWNNIKSAISTAIEN-IKSTVSNGWNNL---VSTVTNAGPRIVSAVRTGFDNAVNAARNFISNAISVGGDLI-NGFVEGVKGAAGRLIDAVGGAVSGAIDWAKGLLGIKS</Hsp_qseq>
+              <Hsp_hseq>LVKAGG--FSGVFTKALGLI---TSPAAIVVGVIAAITAVIIHLWNTNEDFRNTITAIWQKIKDAFTT---------------FAAGISERLSALGITFSDVTSAIKTIWDGFCNLLAPVLEAAFSTIAIALQTAFNVI-----------LGIWDVFSAVFSGDWSGAWEAIKGIFSSIWDGLKEYFSTIIGAVKGVADVF---LGWFGTNWETVWNGVKTFFEGIW--------NGISSFFEGI--------------WNGISTFCTTVWNGIVTNVTAFCTTVHDTISTIFNAVKDVVSNVWETIKNVVQVAIMFIVEVVKAAFELITVPFRFIWENCRDTIISVWETIKSAVQTAINFVKDNIITPVMNAISATITTVWNAIQTTFTTVINAIKSAVQTAWNFMKDNVVTPVMNAISTTISTVWNTIKTTFTTVINAIKSAVQTAWNFMKNSVITPVMNGIKTVITTVWNAIKTAVQTVVNA---IKTTVQTVF-NAVKTTVTTIWNAIKTGTSTAWN----AVKTAVTTPINAAKSAVTSAIN------GIKS</Hsp_hseq>
+              <Hsp_midline>L+ +GG   S +F K +G+I   ++P                  +NTNE+FR  + A W+ IK A +T                 A  +E    +  T   V +AI+T+ +     L P+++ A+  I   + T  NVI           LGI      + +GDWSGAWE +KG+  +IW+G+K        A+ G+  +F   L +  + W+TVW  +      IW        N I++ +E I              WN IST  + +W  I T V +  TT+   I T    +K V S  WE IK V    ++ IV +V   F+LI           +  I + WE IK+                         + +WNAI T  + +   IK+A  TAW ++K   ++ VM  I + I T WN IKT+ +  +N IKSA + AWN +K+++ T + N IK+ ++  WN +   V TV NA   I + V+T F NAV      I NAI  G     N     VK A    I+A   AV+ AI+      GIKS</Hsp_midline>
+            </Hsp>
+          </Hit_hsps>
+        </Hit>
+        <Hit>
+          <Hit_num>6</Hit_num>
+          <Hit_id>gi|56962696|ref|YP_174422.1|</Hit_id>
+          <Hit_def>hypothetical protein ABC0922 [Bacillus clausii KSM-K16] &gt;gi|56908934|dbj|BAD63461.1| phage-related protein [Bacillus clausii KSM-K16]</Hit_def>
+          <Hit_accession>YP_174422</Hit_accession>
+          <Hit_len>593</Hit_len>
+          <Hit_hsps>
+            <Hsp>
+              <Hsp_num>1</Hsp_num>
+              <Hsp_bit-score>146.746875793547</Hsp_bit-score>
+              <Hsp_score>369</Hsp_score>
+              <Hsp_evalue>3.12404663750498e-33</Hsp_evalue>
+              <Hsp_query-from>48</Hsp_query-from>
+              <Hsp_query-to>433</Hsp_query-to>
+              <Hsp_hit-from>123</Hsp_hit-from>
+              <Hsp_hit-to>465</Hsp_hit-to>
+              <Hsp_query-frame>0</Hsp_query-frame>
+              <Hsp_hit-frame>0</Hsp_hit-frame>
+              <Hsp_identity>112</Hsp_identity>
+              <Hsp_positive>187</Hsp_positive>
+              <Hsp_gaps>49</Hsp_gaps>
+              <Hsp_align-len>389</Hsp_align-len>
+              <Hsp_qseq>NTNEEFRTKVQAAWEAIKSAISTAVEAVVSFVMDLWGQMVAWWNENQELIRQTAETVWNAIRTVVETVMTALIPIVQTAWDLILAVVTTVLNVIKTVVDTGLKVVLGIIKAVMQMINGDWSGAWETLKGVAGTIWEGIKSLVQVAIDGL---VQIFQTGLAFLKSIWDTVWGTIMAVVGPIWDWIKTTVSNAITAVWEIIQNIMTSIQTTWDTVWNAISTVASNIWTAISTTVMSVLTTIWGYIQTYLELIKTVWSAAWEIIKAVFAAILLTIVGLVTGNFDLIKQAISNAWEIIKTKTSEIWNAITTFLSGIWEGIKTAASTAWEWIKTTISNVMTTIKSNIETAWNNIKTSISNALNNIKSAAENAWNNIKSAISTAIENIKSTVSN</Hsp_qseq>
+              <Hsp_hseq>QTNETFRNGVIQAWEAIKTTMETVVATIVTFVSEKLAQIKAFWDEHGAAVMQAVTNIFNGIKSIIEPVMNGILAIMQFVWPFIVSLIQMVWGNIQGVISGALNIIMGLVKAFAGLFTGDFS-----------LMWEGIKQLFSGALEAIWNVVQLLLFGR--LLKIASSLFTGLMGVFSKMWGAISNLFLTALNGIRSFFSTIFTPIQ-------NVVMTVMGFIRNAISTG----LTTASNVVQTVLTAIRTVFLTVFNAVRNV-----------VTTAISFVQNFISTGISAARTAVTSALNAIKTTFTTIFNAVRSSVTTAMTNIKTAISN-------GIQSAWQ----AVLNFVGRFREAGKNIVNSIAEGITSAIGAVKNAISN</Hsp_hseq>
+              <Hsp_midline> TNE FR  V  AWEAIK+ + T V  +V+FV +   Q+ A+W+E+   + Q    ++N I++++E VM  ++ I+Q  W  I++++  V   I+ V+   L +++G++KA   +  GD+S            +WEGIK L   A++ +   VQ+   G   L  I  +++  +M V   +W  I      A+  +      I T IQ       N + TV   I  AIST     LTT    +QT L  I+TV+   +  ++ V           VT     ++  IS      +T  +   NAI T  + I+  ++++ +TA   IKT ISN        I++AW     ++ N +   + A +N  N+I   I++AI  +K+ +SN</Hsp_midline>
+            </Hsp>
+          </Hit_hsps>
+        </Hit>
+        <Hit>
+          <Hit_num>7</Hit_num>
+          <Hit_id>gi|50914476|ref|YP_060448.1|</Hit_id>
+          <Hit_def>unknown phage protein [Streptococcus pyogenes MGAS10394] &gt;gi|40218580|gb|AAR83234.1| prophage pi2 protein [Streptococcus pyogenes] &gt;gi|50261625|gb|AAT72393.1| unknown [Streptococcus pyogenes] &gt;gi|50903550|gb|AAT87265.1| unknown phage protein [Streptococcus pyogenes MGAS10394]</Hit_def>
+          <Hit_accession>YP_060448</Hit_accession>
+          <Hit_len>1039</Hit_len>
+          <Hit_hsps>
+            <Hsp>
+              <Hsp_num>1</Hsp_num>
+              <Hsp_bit-score>146.36167621763</Hsp_bit-score>
+              <Hsp_score>368</Hsp_score>
+              <Hsp_evalue>4.74132513340056e-33</Hsp_evalue>
+              <Hsp_query-from>50</Hsp_query-from>
+              <Hsp_query-to>227</Hsp_query-to>
+              <Hsp_hit-from>655</Hsp_hit-from>
+              <Hsp_hit-to>832</Hsp_hit-to>
+              <Hsp_query-frame>0</Hsp_query-frame>
+              <Hsp_hit-frame>0</Hsp_hit-frame>
+              <Hsp_identity>78</Hsp_identity>
+              <Hsp_positive>112</Hsp_positive>
+              <Hsp_gaps>0</Hsp_gaps>
+              <Hsp_align-len>178</Hsp_align-len>
+              <Hsp_qseq>NEEFRTKVQAAWEAIKSAISTAVEAVVSFVMDLWGQMVAWWNENQELIRQTAETVWNAIRTVVETVMTALIPIVQTAWDLILAVVTTVLNVIKTVVDTGLKVVLGIIKAVMQMINGDWSGAWETLKGVAGTIWEGIKSLVQVAIDGLVQIFQTGLAFLKSIWDTVWGTIMAVVGPIWD</Hsp_qseq>
+              <Hsp_hseq>NEGFRTAVIEIWNAIYAFISVIIQEISTFIMTIWGTLTTWWTENQALIQAAVETVWNAISTVIQTVMSLIGPYLEAAWANIQLIITTAWEIIKTVVETAITVVLGIIKAIMQAITGDWSGAWETIKGVLQRVWQAIQQIVTTILSAIGQFISNTWNGIKNTFSNILSAISGIVSSIWN</Hsp_hseq>
+              <Hsp_midline>NE FRT V   W AI + IS  ++ + +F+M +WG +  WW ENQ LI+   ETVWNAI TV++TVM+ + P ++ AW  I  ++TT   +IKTVV+T + VVLGIIKA+MQ I GDWSGAWET+KGV   +W+ I+ +V   +  + Q        +K+ +  +   I  +V  IW+</Hsp_midline>
+            </Hsp>
+          </Hit_hsps>
+        </Hit>
+        <Hit>
+          <Hit_num>8</Hit_num>
+          <Hit_id>gi|29374987|ref|NP_814140.1|</Hit_id>
+          <Hit_def>tail protein [Enterococcus faecalis V583] &gt;gi|29342445|gb|AAO80211.1| tail protein [Enterococcus faecalis V583]</Hit_def>
+          <Hit_accession>NP_814140</Hit_accession>
+          <Hit_len>1049</Hit_len>
+          <Hit_hsps>
+            <Hsp>
+              <Hsp_num>1</Hsp_num>
+              <Hsp_bit-score>139.0428842752</Hsp_bit-score>
+              <Hsp_score>349</Hsp_score>
+              <Hsp_evalue>6.84844401007043e-31</Hsp_evalue>
+              <Hsp_query-from>73</Hsp_query-from>
+              <Hsp_query-to>482</Hsp_query-to>
+              <Hsp_hit-from>545</Hsp_hit-from>
+              <Hsp_hit-to>920</Hsp_hit-to>
+              <Hsp_query-frame>0</Hsp_query-frame>
+              <Hsp_hit-frame>0</Hsp_hit-frame>
+              <Hsp_identity>110</Hsp_identity>
+              <Hsp_positive>196</Hsp_positive>
+              <Hsp_gaps>78</Hsp_gaps>
+              <Hsp_align-len>432</Hsp_align-len>
+              <Hsp_qseq>EAVVSFVMDLWGQMVAWWNENQELIRQ-------TAETVWNAIRTVVETVMTALIPIVQTAWDLILAVVTTVL----NVIKTVVDTGLKVVLGIIKAVMQMINGDWSGAWETLKGVAGTIWEGIKSLVQVAIDGLVQIFQTGLAFLKSIWDTVWGTIMAVVGPIWDWIKTTVSNAITAVWEIIQNIMTSIQTTWDTVWNAISTVASNIWTAISTTVMSVLTTIWGYIQTYLELIKTVWSAAWEIIKAVFAAILLTIVGLVTGNFDLIKQAISNAWEIIKTKTSEIWNAITTFLSGIWEGIKTAASTAWEWIKTTISNVMTTIKSNIETAWNNIKTSIS-----------NALNNIKSAAENAWNNIKSAISTAIENIKSTVSNGWNNLVSTVTNAGPRIVSAVRTGFDNAVNAARNFISNAISVGGDLINGF</Hsp_qseq>
+              <Hsp_hseq>DSIVKTASGLKGSLVKTWNDITAKVSEIWKKFTDAGKKTFDGFKKTVENVFNGIKNFLQTVWNVIYAVVGAIIVNTINIWKGIFDG--------FKAYFQYL-------WDLIKAIATGVWEKIGDTVTGIINGFIGVIKGIFDAFKTFFQQIWDAVVYSVTIAWNGIKNTVTSVSTAIKNFVTPIFNAIKTTITNVFNAIKNTATNVWNAIKTTISNVVQTILNF---------------------------------VTPIFNTMKNTITNIFNAIRNTASSVWNSIKTTISNIVTSVKNTVINIFNALKNSITNIFNAIRNTASTVWNSIKSTVSNIVSATVNTVKNLFNGMKNTVSSIWDGVRNTISNVVNAVKNTISNVWGGITGTVSN----IFNGVKNAIDGPMNAAKNLVKNVV----DAIKGF</Hsp_hseq>
+              <Hsp_midline>+++V     L G +V  WN+    + +         +  ++  +  VE V   +   +QT W++I AVV  ++    N+ K + D          KA  Q +       W+ +K +A  +WE I   V   I+G + + +      K+ +  +W  ++  V   W+ IK TV++  TA+   +  I  +I+TT   V+NAI   A+N+W AI TT+ +V+ TI  +                                 VT  F+ +K  I+N +  I+   S +WN+I T +S I   +K      +  +K +I+N+   I++   T WN+IK+++S           N  N +K+   + W+ +++ IS  +  +K+T+SN W  +  TV+N    I + V+   D  +NAA+N + N +    D I GF</Hsp_midline>
+            </Hsp>
+          </Hit_hsps>
+        </Hit>
+        <Hit>
+          <Hit_num>9</Hit_num>
+          <Hit_id>gi|163941333|ref|YP_001646217.1|</Hit_id>
+          <Hit_def>prophage LambdaBa01, membrane protein, putative [Bacillus weihenstephanensis KBAB4] &gt;gi|163863530|gb|ABY44589.1| prophage LambdaBa01, membrane protein, putative [Bacillus weihenstephanensis KBAB4]</Hit_def>
+          <Hit_accession>YP_001646217</Hit_accession>
+          <Hit_len>725</Hit_len>
+          <Hit_hsps>
+            <Hsp>
+              <Hsp_num>1</Hsp_num>
+              <Hsp_bit-score>138.657684699283</Hsp_bit-score>
+              <Hsp_score>348</Hsp_score>
+              <Hsp_evalue>8.15996781441799e-31</Hsp_evalue>
+              <Hsp_query-from>61</Hsp_query-from>
+              <Hsp_query-to>480</Hsp_query-to>
+              <Hsp_hit-from>142</Hsp_hit-from>
+              <Hsp_hit-to>560</Hsp_hit-to>
+              <Hsp_query-frame>0</Hsp_query-frame>
+              <Hsp_hit-frame>0</Hsp_hit-frame>
+              <Hsp_identity>118</Hsp_identity>
+              <Hsp_positive>203</Hsp_positive>
+              <Hsp_gaps>29</Hsp_gaps>
+              <Hsp_align-len>434</Hsp_align-len>
+              <Hsp_qseq>WEAIKSAISTAVEAVVSFVMDLWGQMVAWWNENQELIRQTAETVWNAIRTVVETVMTALIPIVQTAWDLILAVVTTVLNVIKTVVDTGLKVVLGIIK---AVMQMINGDWSGAWETLKGVAGTIWEGIKSLVQVAIDGLVQIFQTGLAFLKSIWDTVWGTIMAVVGPIWDWIKTTVSNAITAVWEIIQNIMTSIQTTWDTVWNAISTVASNIWTAISTTVMSVLTTIWGYIQTYLELIKT----VWS-------AAWEIIKAVFAAILLTIVGLVTGNFDLIKQAISNAWEIIKTKTSEIWNAITTFLSGIWEGIKTAASTAWEWIKTTISNVMTTIKSNIETAWNNIKTSISNALNNIKSAAENAWNNIKSAISTAIENIKSTVSNGWNNLVSTVTNAGPRIVSAVRTGFDNAVNAARNFISNAISVGGDLIN</Hsp_qseq>
+              <Hsp_hseq>WDAIKQWTIDAWNAIGEFLVGIWDGIVQWASEAWNSISESTSAVWNSIKEFLIGIWNGIVEFVVT-WGT--AILETYVGIWTSIFNFCMEIWNGIVEYLTSVLQGIATFFTEIWTSISTFFQEIWNGLVAFITPVLQGIADFFAM-----------IWNGISTVIQTVWNFITQYLQAIWTAILYFATPLFESIKNFISECWNKISSTTSLVWETIKNFLVSCWNGLVSFVTPIFEKIKSWIISVWDTISSATMAVWNAVKNFLQACWNGLVSIVTPIFDAIKNWIVNVWNAISSTTSAVWNAIKSYLSSLWNSIVSTASSIFNSIKSAISTVWNMISSASSSVWNGIKSTLSSIWNGIKSTASSVWNGLKDAIMTPVRWVTSAVSGAFNGMKSAVLGVWDGIKSGIRTAINGIIRIINKFI-DGFNTPAELLN</Hsp_hseq>
+              <Hsp_midline>W+AIK     A  A+  F++ +W  +V W +E    I ++   VWN+I+  +  +   ++  V T W    A++ T + +  ++ +  +++  GI++   +V+Q I   ++  W ++      IW G+ + +   + G+   F             +W  I  V+  +W++I   +    TA+      +  SI+      WN IS+  S +W  I   ++S    +  ++    E IK+    VW        A W  +K    A    +V +VT  FD IK  I N W  I + TS +WNAI ++LS +W  I + AS+ +  IK+ IS V   I S   + WN IK+++S+  N IKS A + WN +K AI T +  + S VS  +N + S V      I S +RT  +  +     FI +  +   +L+N</Hsp_midline>
+            </Hsp>
+          </Hit_hsps>
+        </Hit>
+      </Iteration_hits>
+      <Iteration_stat>
+        <Statistics>
+          <Statistics_db-num>6589360</Statistics_db-num>
+          <Statistics_db-len>-2041834015</Statistics_db-len>
+          <Statistics_hsp-len>0</Statistics_hsp-len>
+          <Statistics_eff-space>504129014857</Statistics_eff-space>
+          <Statistics_kappa>0.041</Statistics_kappa>
+          <Statistics_lambda>0.267</Statistics_lambda>
+          <Statistics_entropy>0.14</Statistics_entropy>
+        </Statistics>
+      </Iteration_stat>
+    </Iteration>
+  </BlastOutput_iterations>
+</BlastOutput>
diff -r e4419efbefad -r 872cf247c899 tool-data/blast2go.loc.sample
--- a/tool-data/blast2go.loc.sample	Fri Feb 22 08:47:27 2013 -0500
+++ b/tool-data/blast2go.loc.sample	Mon Sep 23 05:50:58 2013 -0400
@@ -6,19 +6,22 @@
 # Column 3 - Filename, Galaxy will use this when calling the tool
 #
 # Probably the most important setting in the properties file is the
-# Blast2GO database to use. Currently b2g4pipe v2.3.5 ships with an
-# old configuration so consult http://blast2go.org for the latest
-# public database they host in Spain. We also strongly recommend
+# Blast2GO database to use. Currently b2g4pipe v2.5 ships with an
+# old configuration so consult http://www.blast2go.com for the latest
+# public database they host in Spain (or find this by running the GUI
+# version of Blast2GO via Java Web Start under the menu entry "Tools",
+# "General Settings", "DataAccess setting"). We also strongly recommend
 # configuring a local Blast2GO database.
 #
-# The property filenames can be fullied qualified paths like
+# The property filenames can be fully qualified paths like
 # /opt/b2g4pipe/Spain_2012_August.properties or provided they are
 # in the same folder as the Blast2GO JAR file, just the filename
 # like Spain_2012_August.properties instead. This is intended to
-# make migrating between versions of Blast2GO easier (as the
+# make migrating between future versions of Blast2GO easier (as the
 # property files change between versions), and simpler overall.
 #
-Local_2011_May	Local database (May 2011)	Local_2011_May.properties
-Spain_2010_May	Database in Spain (May 2010)	Spain_2010_May.properties
+#Local_2011_May	Local database (May 2011)	Local_2011_May.properties
+#Spain_2010_May	Database in Spain (May 2010)	Spain_2010_May.properties
+Spain_2012_August	Database in Spain (August 2012)	Spain_2012_August.properties
 Spain_2011_June	Database in Spain (June 2011)	Spain_2011_June.properties
-Spain_2012_August	Database in Spain (August 2012)	Spain_2012_August.properties
+#default	Default settings	b2gPipe.properties
diff -r e4419efbefad -r 872cf247c899 tools/blast2go/blast2go.py
--- a/tools/blast2go/blast2go.py	Fri Feb 22 08:47:27 2013 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,173 +0,0 @@
-#!/usr/bin/env python
-"""Galaxy wrapper for Blast2GO for pipelines, b2g4pipe v2.5.
-
-This script takes exactly three command line arguments:
- * Input BLAST XML filename
- * Blast2GO properties filename (settings file)
- * Output tabular filename
-
-The properties filename can be a fully qualified path, but if not
-this will look next to the blast2go.jar file.
-
-Sadly b2g4pipe (at least v2.3.5 to v2.5.0) cannot cope with current
-style large BLAST XML files (e.g. from BLAST 2.2.25+), so we reformat
-these to avoid it crashing with a Java heap space OutOfMemoryError.
-
-As part of this reformatting, we check for BLASTP or BLASTX output
-(otherwise raise an error), and print the query count.
-
-It then calls the Java command line tool, and moves the output file to
-the location Galaxy is expecting, and removes the tempory XML file.
-"""
-import sys
-import os
-import subprocess
-
-#You may need to edit this to match your local setup,
-#blast2go_jar = "/opt/b2g4pipe/blast2go.jar"
-blast2go_jar = "/opt/b2g4pipe_v2.5/blast2go.jar"
-
-
-def stop_err(msg, error_level=1):
-    """Print error message to stdout and quit with given error level."""
-    sys.stderr.write("%s\n" % msg)
-    sys.exit(error_level)
-
-if len(sys.argv) != 4:
-    stop_err("Require three arguments: XML filename, properties filename, output tabular filename")
-
-xml_file, prop_file, tabular_file = sys.argv[1:]
-
-#We should have write access here:
-tmp_xml_file = tabular_file + ".tmp.xml"
-
-if not os.path.isfile(blast2go_jar):
-    stop_err("Blast2GO JAR file not found: %s" % blast2go_jar)
-
-if not os.path.isfile(xml_file):
-    stop_err("Input BLAST XML file not found: %s" % xml_file)
-
-if not os.path.isfile(prop_file):
-    tmp = os.path.join(os.path.split(blast2go_jar)[0], prop_file)
-    if os.path.isfile(tmp):
-        #The properties file seems to have been given relative to the JAR
-        prop_file = tmp
-    else:
-        stop_err("Blast2GO configuration file not found: %s" % prop_file)
-    del tmp
-
-def prepare_xml(original_xml, mangled_xml):
-    """Reformat BLAST XML to suit Blast2GO.
-
-    Blast2GO can't cope with 1000s of <Iteration> tags within a
-    single <BlastResult> tag, so instead split this into one
-    full XML record per interation (i.e. per query). This gives
-    a concatenated XML file mimicing old versions of BLAST.
-
-    This also checks for BLASTP or BLASTX output, and outputs
-    the number of queries. Galaxy will show this as "info".
-    """
-    in_handle = open(original_xml)
-    footer = "  </BlastOutput_iterations>\n</BlastOutput>\n"
-    header = ""
-    while True:
-        line = in_handle.readline()
-        if not line:
-            #No hits?
-            stop_err("Problem with XML file?")
-        if line.strip() == "<Iteration>":
-            break
-        header += line
-
-    if "<BlastOutput_program>blastx</BlastOutput_program>" in header:
-        print "BLASTX output identified"
-    elif "<BlastOutput_program>blastp</BlastOutput_program>" in header:
-        print "BLASTP output identified"
-    else:
-        in_handle.close()
-        stop_err("Expect BLASTP or BLASTX output")
-
-    out_handle = open(mangled_xml, "w")
-    out_handle.write(header)
-    out_handle.write(line)
-    count = 1
-    while True:
-        line = in_handle.readline()
-        if not line:
-            break
-        elif line.strip() == "<Iteration>":
-           #Insert footer/header
-           out_handle.write(footer)
-           out_handle.write(header)
-           count += 1
-        out_handle.write(line)
-
-    out_handle.close()
-    in_handle.close()
-    print "Input has %i queries" % count
-
-
-def run(cmd):
-    #Avoid using shell=True when we call subprocess to ensure if the Python
-    #script is killed, so too is the child process.
-    try:
-        child = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
-    except Exception, err:
-        stop_err("Error invoking command:\n%s\n\n%s\n" % (" ".join(cmd), err))
-    #Use .communicate as can get deadlocks with .wait(),
-    stdout, stderr = child.communicate()
-    return_code = child.returncode
-
-    #keep stdout minimal as shown prominently in Galaxy
-    #Record it in case a silent error needs diagnosis
-    if stdout:
-        sys.stderr.write("Standard out:\n%s\n\n" % stdout)
-    if stderr:
-        sys.stderr.write("Standard error:\n%s\n\n" % stderr)
-
-    error_msg = None
-    if return_code:
-        cmd_str = " ".join(cmd)
-        error_msg = "Return code %i from command:\n%s" % (return_code, cmd_str)
-    elif "Database or network connection (timeout) error" in stdout+stderr:
-        error_msg = "Database or network connection (timeout) error"
-    elif "Annotation of 0 seqs with 0 annots finished." in stdout+stderr:
-        error_msg = "No sequences processed!"
-
-    if error_msg:
-        print error_msg
-        stop_err(error_msg)
-
-
-blast2go_classpath = os.path.split(blast2go_jar)[0]
-assert os.path.isdir(blast2go_classpath)
-blast2go_classpath = "%s/*:%s/ext/*:" % (blast2go_classpath, blast2go_classpath)
-
-prepare_xml(xml_file, tmp_xml_file)
-#print "XML file prepared for Blast2GO"
-
-#We will have write access wherever the output should be,
-#so we'll ask Blast2GO to use that as the stem for its output
-#(it will append .annot to the filename)
-cmd = ["java", "-cp", blast2go_classpath, "es.blast2go.prog.B2GAnnotPipe",
-       "-in", tmp_xml_file,
-       "-prop", prop_file,
-       "-out", tabular_file, #Used as base name for output files
-       "-annot", # Generate *.annot tabular file
-       #NOTE: For v2.3.5 must use -a, for v2.5 must use -annot instead
-       #"-img", # Generate images, feature not in v2.3.5
-       ]
-#print " ".join(cmd)
-run(cmd)
-
-#Remove the temp XML file
-os.remove(tmp_xml_file)
-
-out_file = tabular_file + ".annot"
-if not os.path.isfile(out_file):
-    stop_err("ERROR - No output annotation file from Blast2GO")
-
-#Move the output file where Galaxy expects it to be:
-os.rename(out_file, tabular_file)
-
-print "Done"
diff -r e4419efbefad -r 872cf247c899 tools/blast2go/blast2go.txt
--- a/tools/blast2go/blast2go.txt	Fri Feb 22 08:47:27 2013 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,153 +0,0 @@
-Galaxy wrapper for Blast2GO for pipelines, b2g4pipe
-===================================================
-
-This wrapper is copyright 2011-2013 by Peter Cock, The James Hutton Institute
-(formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
-See the licence text below.
-
-This is a wrapper for the command line Java tool b2g4pipe v2.5,
-Blast2GO for pipelines. See:
-
-S. Götz et al.
-High-throughput functional annotation and data mining with the Blast2GO suite.
-Nucleic Acids Res. 36(10):3420–3435, 2008.
-http://dx.doi.org/10.1093/nar/gkn176
-
-A. Conesa and S. Götz.
-Blast2GO: A Comprehensive Suite for Functional Analysis in Plant Genomics.
-Int. J. Plant Genomics. 619832, 2008.
-http://dx.doi.org/10.1155/2008/619832
-
-A. Conesa et al.
-Blast2GO: A universal tool for annotation, visualization and analysis in functional genomics research.
-Bioinformatics 21:3674-3676, 2005.
-http://dx.doi.org/10.1093/bioinformatics/bti610
-
-http://www.blast2go.org/
-
-
-
-Installation
-============
-
-The main dependency is b2g4pipe which must be installed manually. Also we
-strongly recommend installing a local Blast2GO database as well (see the
-intructions below about the blast2go.loc file). At the time of writing,
-the current version is b2g4pipe v2.5 which is available here:
-
-http://www.blast2go.com/data/blast2go/b2g4pipe_v2.5.zip
-
-You can change the path by editing the definition near the start of the Python
-script blast2go.py, but by default it expects the underlying tool to be here:
-
-/opt/b2g4pipe_v2.5/blast2go.jar
-
-Installation of the Galaxy wrapper should work automatically via the Galaxy
-Tool Shed, including the dependency on 'blast_datatypes' for the 'blastxml'
-file format definition. To install the wrapper manually, first install
-'blast_datatypes', then copy or move the following files under the Galaxy
-tools folder, e.g. in a tools/blast2go/ folder:
-
-* blast2go.xml (the Galaxy tool definition)
-* blast2go.py (the Python wrapper script)
-* blast2go.txt (this README file)
-
-For a manual installation of the wrapper you will also need to modify the
-tools_conf.xml file to tell Galaxy to offer the tool. We suggest putting
-it next to the NCBI BLAST+ wrappers. Just add the line:
-
-<tool file="blast2go/blast2go.xml" />
-
-As part of setting up b2g4pipe you will need to setup one or more Blast2GO
-property files which tell the tool which database to use etc. The example
-b2gPipe.properties provided with b2g4pipe is often out of date. The current
-server IP address and database name may given on the Blast2GO website, or
-can be found by running the latest GUI version via Java web-start, and
-looking under the tools/options menu. These property files can be anywhere
-accessable to the Galaxy Unix user, we put them with the JAR file etc.
-
-You must tell Galaxy about these Blast2GO property files so that they can be
-offered to the user. Copy file blast2go.loc.sample to tool-data/blast2go.loc
-under the Galaxy folder and edit this to match your installation. This must
-be plain text, tab separated, with three columns:
-
-(1) ID for the setup, e.g. Spain_2012_August
-(2) Description for the setup, e.g. Database in Spain (August 2012)
-(3) Properties filename for the setup, e.g. /opt/b2g4pipe/Spain_2012_August.properties
-
-Avoid including "Blast2GO" in the description (column 2) as this text will be
-included in the automatically assigned output dataset name. The blast2go.loc
-file allows you to customise the database setup. If for example you have a local
-Blast2GO server running (which we recommend for speed), and you want this to be
-the default setting, include it as the first line in your blast2go.loc file.
-
-Consult the Blast2GO documentation for details about the property files and
-setting up a local MySQL Blast2GO database.
-
-
-History
-=======
-
-v0.0.1 - Initial public release
-v0.0.2 - Documentation clarifications, e.g. concatenated BLAST XML is allowed.
-       - Fixed error handler in wrapper script (for when b2g4pipe fails).
-       - Reformats the XML to use old NCBI-style concatenated BLAST XML since
-         b2g4pipe crashes with heap space error on with large files using
-         current NCBI output.
-v0.0.3 - Include sample loc file, tool-data/blast2go.loc.sample
-v0.0.4 - Include repository_dependencies.xml file for 'blastxml' format
-         (previously included in the core Galaxy installation)
-v0.0.5 - Quote arguments in case of spaces in filenames (internal change)
-       - Last release supporting b2g4pipe v2.3.5
-v0.0.6 - Support for b2g4pipe v2.5 instead of v2.3.5
-          - Now invoked with a class path and es.blast2go.prog.B2GAnnotPipe
-            rather then simply calling the jar file
-          - Now uses the switch -annot instead of -a (this change breaks
-            support for b2g4pipe v2.3.5 unfortunately)
-       - Catch a few error messages and treat them explicitly as errors.
-
-
-Developers
-==========
-
-This script and related tools are being developed on the following hg branch:
-http://bitbucket.org/peterjc/galaxy-central/src/tools
-
-For making the "Galaxy Tool Shed" http://community.g2.bx.psu.edu/ tarball I use
-the following command from the Galaxy root folder:
-
-$ tar -czf blast2go.tar.gz tools/blast2go/blast2go.xml tools/blast2go/blast2go.py tools/blast2go/blast2go.txt tools/blast2go/repository_dependencies.xml tool-data/blast2go.loc.sample
-
-Check this worked:
-
-$ tar -tzf blast2go.tar.gz
-tools/blast2go/blast2go.xml
-tools/blast2go/blast2go.py
-tools/blast2go/blast2go.txt
-tools/blast2go/repository_dependencies.xml
-tool-data/blast2go.loc.sample
-
-
-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.
-
-NOTE: This is the licence for the Galaxy Wrapper only. Blast2GO and
-associated data files are available and licenced separately.
diff -r e4419efbefad -r 872cf247c899 tools/blast2go/blast2go.xml
--- a/tools/blast2go/blast2go.xml	Fri Feb 22 08:47:27 2013 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,95 +0,0 @@
-<tool id="blast2go" name="Blast2GO" version="0.0.6">
-    <description>Maps BLAST results to GO annotation terms</description>
-    <command interpreter="python">
-        blast2go.py "${xml}" "${prop.fields.path}" "${tab}"
-    </command>
-    <stdio>
-        <!-- Wrapper ensures anything other than zero is an error -->
-        <exit_code range="1:" />
-        <exit_code range=":-1" />
-    </stdio>
-    <inputs>
-        <param name="xml" type="data" format="blastxml" label="BLAST XML results" description="You must have run BLAST against a protein database such as the NCBI non-redundant (NR) database. Use BLASTX for nucleotide queries, BLASTP for protein queries." /> 
-        <param name="prop" type="select" label="Blast2GO settings" description="One or more configurations can be setup, such as using the Blast2GO team's server in Spain, or a local database.">
-             <options from_file="blast2go.loc">
-                 <column name="value" index="0"/>
-                 <column name="name" index="1"/>
-                 <column name="path" index="2"/>
-             </options>
-        </param>
-    </inputs>
-    <outputs>
-        <data name="tab" format="tabular" label="Blast2GO ${prop.fields.name}" />
-    </outputs>
-    <requirements>
-    </requirements>
-    <tests>
-    </tests>
-    <help>
-.. class:: warningmark
-
-**Note**. Blast2GO may take a substantial amount of time, especially if
-running against the public server in Spain. For large input datasets it
-is advisable to allow overnight processing, or consider subdividing.
-
------
-
-**What it does**
-
-This runs b2g4Pipe, the command line (no GUI) version of Blast2GO designed
-for use in pipelines.
-
-It takes as input BLAST XML results against a protein database, typically
-the NCBI non-redundant (NR) database. This tool will accept concatenated
-BLAST XML files (although they are technically invalid XML), which is very
-useful if you have sub-divided your protein FASTA files and run BLAST on
-them in batches.
-
-The BLAST matches are used to assign Gene Ontology (GO) annotation terms
-to each query sequence.
-
-The output from this tool is a tabular file containing three columns, with
-the order taken from query order in the original BLAST XML file:
-
-====== ====================================
-Column Description
------- ------------------------------------
-     1 ID and description of query sequence
-     2 GO term
-     3 GO description
-====== ====================================
-
-Note that if no GO terms are assigned to a sequence (e.g. if it had no
-BLAST matches), then it will not be present in the output file.
-
-
-**Advanced Settings**
-
-Blast2GO has a properties setting file which includes which database
-server to connect to (e.g. the public server in Valencia, Spain, or a
-local server), as well as more advanced options such as thresholds and
-evidence code weights. To change these settings, your Galaxy administrator
-must create a new properties file, and add it to the drop down menu above.
-
-
-**References**
-
-S. Götz et al.
-High-throughput functional annotation and data mining with the Blast2GO suite.
-Nucleic Acids Res. 36(10):3420–3435, 2008.
-http://dx.doi.org/10.1093/nar/gkn176
-
-A. Conesa and S. Götz.
-Blast2GO: A Comprehensive Suite for Functional Analysis in Plant Genomics.
-Int. J. Plant Genomics. 619832, 2008.
-http://dx.doi.org/10.1155/2008/619832
-
-A. Conesa et al.
-Blast2GO: A universal tool for annotation, visualization and analysis in functional genomics research.
-Bioinformatics 21:3674-3676, 2005.
-http://dx.doi.org/10.1093/bioinformatics/bti610
-
-http://www.blast2go.org/
-
-    </help>
-</tool>
diff -r e4419efbefad -r 872cf247c899 tools/blast2go/repository_dependencies.xml
--- a/tools/blast2go/repository_dependencies.xml	Fri Feb 22 08:47:27 2013 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,5 +0,0 @@
-<?xml version="1.0"?>
-<repositories description="This requires the BLAST datatype definitions (e.g. the BLAST XML format).">
-<!-- Revision 4:f9a7783ed7b6 on the main tool shed is v0.0.14 which added BLAST databases -->
-<repository toolshed="http://toolshed.g2.bx.psu.edu" name="blast_datatypes" owner="devteam" changeset_revision="f9a7783ed7b6" />
-</repositories>