changeset 5:e4419efbefad draft

Uploaded v0.0.6 of wrapper, which now supports b2g4pipe v2.5 (and no longer works with b2g4pipe v2.3.5). See manual install instructions!

--- a/tool-data/blast2go.loc.sample	Wed Feb 20 13:33:47 2013 -0500
+++ b/tool-data/blast2go.loc.sample	Fri Feb 22 08:47:27 2013 -0500
@@ -11,6 +11,14 @@
 # public database they host in Spain. We also strongly recommend
 # configuring a local Blast2GO database.
 #
-Local_2011_May	Local database (May 2011)	/opt/b2g4pipe/Local_2011_May.properties
-Spain_2010_May	Database in Spain (May 2010)	/opt/b2g4pipe/Spain_2010_May.properties
-Spain_2011_June	Database in Spain (June 2011)	/opt/b2g4pipe/Spain_2011_June.properties
+# The property filenames can be fullied 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
+# 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
+Spain_2011_June	Database in Spain (June 2011)	Spain_2011_June.properties
+Spain_2012_August	Database in Spain (August 2012)	Spain_2012_August.properties

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/blast2go/blast2go.py	Fri Feb 22 08:47:27 2013 -0500
@@ -0,0 +1,173 @@
+#!/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"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/blast2go/blast2go.txt	Fri Feb 22 08:47:27 2013 -0500
@@ -0,0 +1,153 @@
+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.

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/blast2go/blast2go.xml	Fri Feb 22 08:47:27 2013 -0500
@@ -0,0 +1,95 @@
+<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>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/blast2go/repository_dependencies.xml	Fri Feb 22 08:47:27 2013 -0500
@@ -0,0 +1,5 @@
+<?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>

--- a/tools/ncbi_blast_plus/blast2go.py	Wed Feb 20 13:33:47 2013 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,147 +0,0 @@
-#!/usr/bin/env python
-"""Galaxy wrapper for Blast2GO for pipelines, b2g4pipe v2.3.5.
-
-This script takes exactly three command line arguments:
- * Input BLAST XML filename
- * Blast2GO properties filename (settings file)
- * Output tabular 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.
-
-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"
-
-
-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(xml_file):
-   stop_err("Input BLAST XML file not found: %s" % xml_file)
-
-if not os.path.isfile(prop_file):
-   stop_err("Blast2GO configuration file not found: %s" % prop_file)
-
-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
-    if return_code:
-        cmd_str = " ".join(cmd)
-        if stderr and stdout:
-            stop_err("Return code %i from command:\n%s\n\n%s\n\n%s" % (return_code, cmd_str, stdout, stderr))
-        else:
-            stop_err("Return code %i from command:\n%s\n%s" % (return_code, cmd_str, stderr))
-    #For early diagnostics,
-    else:
-       print stdout
-       print stderr
-
-if not os.path.isfile(blast2go_jar):
-   stop_err("Blast2GO JAR file not found: %s" % blast2go_jar)
-
-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", "-jar", blast2go_jar,
-       "-in", tmp_xml_file,
-       "-prop", prop_file,
-       "-out", tabular_file, #Used as base name for output files
-       "-a", # Generate *.annot tabular file
-       #"-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/tools/ncbi_blast_plus/blast2go.txt	Wed Feb 20 13:33:47 2013 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,143 +0,0 @@
-Galaxy wrapper for Blast2GO for pipelines, b2g4pipe
-===================================================
-
-This wrapper is copyright 2011 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 v2.3.5,
-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).
-
-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/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 the tools/ncbi_blast_blast 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="ncbi_blast_plus/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 v2.3.5 is out of date, with the
-latest server IP address and database name given on the Blast2GO website.
-These files can be anywhere accessable to the Galaxy Unix user, we put them
-under /opt/b2g4pipe 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_2010_May
-(2) Description for the setup, e.g. Database in Spain (May 2010)
-(3) Properties filename for the setup, e.g. /opt/b2g4pipe/Spain_2010_May.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)
-
-
-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/ncbi_blast_plus/blast2go.xml tools/ncbi_blast_plus/blast2go.py tools/ncbi_blast_plus/blast2go.txt tools/ncbi_blast_plus/repository_dependencies.xml tool-data/blast2go.loc.sample
-
-Check this worked:
-
-$ tar -tzf blast2go.tar.gz
-tools/ncbi_blast_plus/blast2go.xml
-tools/ncbi_blast_plus/blast2go.py
-tools/ncbi_blast_plus/blast2go.txt
-tools/ncbi_blast_plus/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.

--- a/tools/ncbi_blast_plus/blast2go.xml	Wed Feb 20 13:33:47 2013 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,90 +0,0 @@
-<tool id="blast2go" name="Blast2GO" version="0.0.5">
-    <description>Maps BLAST results to GO annotation terms</description>
-    <command interpreter="python">
-        blast2go.py "${xml}" "${prop.fields.path}" "${tab}"
-    </command>
-    <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>

--- a/tools/ncbi_blast_plus/repository_dependencies.xml	Wed Feb 20 13:33:47 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>