--- a/blast2go-7b53cc52e7ed/.hg_archival.txt	Tue Jul 19 13:54:17 2011 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,5 +0,0 @@
-repo: 4bfd64cf18ab5d0fe74e14afdb6634d8a5f9abb2
-node: 7b53cc52e7eda18a49312bfab66a962d4b6ada71
-branch: default
-latesttag: null
-latesttagdistance: 2

--- a/blast2go-7b53cc52e7ed/tools/ncbi_blast_plus/blast2go.py	Tue Jul 19 13:54:17 2011 -0400
+++ /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 v2.3.5 cannot cope with current style large BLAST XML
-files (e.g. from BLAST 2.2.25+), so we have to 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/blast2go-7b53cc52e7ed/tools/ncbi_blast_plus/blast2go.txt	Tue Jul 19 13:54:17 2011 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,127 +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
-============
-
-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/b2g4pip/blast2go.jar
-
-To install the wrapper 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)
-
-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. Create the file tool-data/blast2go.loc under the Galaxy
-folder. 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 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.
-
-
-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
-
-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
-
-
-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/blast2go-7b53cc52e7ed/tools/ncbi_blast_plus/blast2go.xml	Tue Jul 19 13:54:17 2011 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,90 +0,0 @@
-<tool id="blast2go" name="Blast2GO" version="0.0.2">
-    <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>