changeset 8:e23b621eb7bb draft

Uploaded v0.0.9, embed citation, updated README
author peterjc
date Thu, 26 Mar 2015 11:15:22 -0400
parents 0ac3ef59ea93
children 887adf823bc0
files blast2go/README.rst blast2go/blast2go.py blast2go/blast2go.xml blast2go/massage_xml_for_blast2go.py blast2go/repository_dependencies.xml blast2go/tool_dependencies.xml tools/blast2go/README.rst tools/blast2go/blast2go.py tools/blast2go/blast2go.xml tools/blast2go/massage_xml_for_blast2go.py tools/blast2go/repository_dependencies.xml tools/blast2go/tool_dependencies.xml
diffstat 12 files changed, 606 insertions(+), 588 deletions(-) [+]
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--- a/blast2go/README.rst	Mon Sep 23 05:53:37 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,208 +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 (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.
--- a/blast2go/blast2go.py	Mon Sep 23 05:53:37 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,134 +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.
-
-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"
--- a/blast2go/blast2go.xml	Mon Sep 23 05:53:37 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,118 +0,0 @@
-<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>
--- a/blast2go/massage_xml_for_blast2go.py	Mon Sep 23 05:53:37 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,92 +0,0 @@
-#!/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)
--- a/blast2go/repository_dependencies.xml	Mon Sep 23 05:53:37 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,4 +0,0 @@
-<?xml version="1.0"?>
-<repositories description="Requires BLAST XML and database datatype definitions.">
-    <repository changeset_revision="b3a3ba0c1d47" name="blast_datatypes" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" />
-</repositories>
--- a/blast2go/tool_dependencies.xml	Mon Sep 23 05:53:37 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,32 +0,0 @@
-<?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>
-
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/blast2go/README.rst	Thu Mar 26 11:15:22 2015 -0400
@@ -0,0 +1,220 @@
+Galaxy wrapper for Blast2GO for pipelines, b2g4pipe
+===================================================
+
+This wrapper is copyright 2011-2014 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, currently a free to use download available at:
+http://www.blast2go.com/data/blast2go/b2g4pipe_v2.5.zip
+
+Note that this has been superceded by a non-free "Blast2GO Command Line (CLI)":
+http://www.blast2go.com/blast2gocli/
+
+This wrapper is freely 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 last free 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 now 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. e.g.
+https://www.blast2go.com/b2gsupport/resources/35-localb2gdb
+
+
+
+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.
+v0.0.9  - Update README file now that BioBam are selling the latest version
+          of the Blast2GO command line tool. For now b2g4pipe v2.5 is still
+          available as a free download.
+        - Tool definition now embeds citation information.
+======= ======================================================================
+
+
+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 tools/blast2go/README.rst tools/blast2go/blast2go.xml tools/blast2go/blast2go.py tools/blast2go/massage_xml_for_blast2go.py tools/blast2go/repository_dependencies.xml tools/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
+    tools/blast2go/README.rst
+    tools/blast2go/blast2go.xml
+    tools/blast2go/blast2go.py
+    tools/blast2go/massage_xml_for_blast2go.py
+    tools/blast2go/repository_dependencies.xml
+    tools/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.
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/blast2go/blast2go.py	Thu Mar 26 11:15:22 2015 -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"
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/blast2go/blast2go.xml	Thu Mar 26 11:15:22 2015 -0400
@@ -0,0 +1,124 @@
+<tool id="blast2go" name="Blast2GO" version="0.0.9">
+    <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>
+    <citations>
+        <citation type="doi">10.7717/peerj.167</citation>
+        <citation type="doi">10.1093/nar/gkn176</citation>
+        <citation type="doi">10.1155/2008/619832</citation>
+        <citation type="doi">10.1093/bioinformatics/bti610</citation>
+    </citations>
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/blast2go/massage_xml_for_blast2go.py	Thu Mar 26 11:15:22 2015 -0400
@@ -0,0 +1,92 @@
+#!/usr/bin/env python
+"""Script for reformatting Blast XML to suit 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)
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/blast2go/repository_dependencies.xml	Thu Mar 26 11:15:22 2015 -0400
@@ -0,0 +1,4 @@
+<?xml version="1.0"?>
+<repositories description="Requires BLAST XML and database datatype definitions.">
+    <repository changeset_revision="5482a8cd0f36" name="blast_datatypes" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" />
+</repositories>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/blast2go/tool_dependencies.xml	Thu Mar 26 11:15:22 2015 -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>
+