Mercurial > repos > peterjc > blast2go

--- a/tools/blast2go/README.rst	Thu Jul 31 05:40:57 2014 -0400
+++ b/tools/blast2go/README.rst	Fri May 15 06:01:16 2015 -0400
@@ -1,7 +1,7 @@
 Galaxy wrapper for Blast2GO for pipelines, b2g4pipe
 ===================================================

-This wrapper is copyright 2011-2014 by Peter Cock, The James Hutton Institute
+This wrapper is copyright 2011-2015 by Peter Cock, The James Hutton Institute
 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
 See the licence text below (MIT licence).

@@ -16,8 +16,10 @@
 http://toolshed.g2.bx.psu.edu/view/peterjc/blast2go


-References
-==========
+Citation
+========
+
+Please cite the following papers:

 Peter Cock, Bjoern Gruening, Konrad Paszkiewicz and Leighton Pritchard (2013).
 Galaxy tools and workflows for sequence analysis with applications
@@ -46,8 +48,8 @@
 ======================

 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
+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).

@@ -62,30 +64,30 @@

 * http://www.blast2go.com/data/blast2go/b2g4pipe_v2.5.zip

-You can change the path by setting the B2G4PIPE environement variable to
+You can change the path by setting the ``$B2G4PIPE`` environment 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
+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:
+``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)
+- ``blast2go.xml`` (the Galaxy tool definition)
+- ``blast2go.py`` (the Python wrapper script)
+- ``massage_xml_for_blast2go.py`` (Python BLAST 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
+``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::
+If you wish to run the unit tests, also move/copy the ``test-data/`` files
+under Galaxy's ``test-data/`` folder. Then::

-    $ ./run_functional_tests.sh -id blast2go
+    $ ./run_tests.sh -id blast2go


 Configuration
@@ -162,6 +164,8 @@
           of the Blast2GO command line tool. For now b2g4pipe v2.5 is still
           available as a free download.
         - Tool definition now embeds citation information.
+v0.0.10 - Reorder XML elements (internal change only).
+        - Planemo for Tool Shed upload (``.shed.yml``, internal change only).
 ======= ======================================================================


@@ -175,23 +179,33 @@
 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::
+For pushing a release to the test or main "Galaxy Tool Shed", use the following
+Planemo commands (which requires you have set your Tool Shed access details in
+``~/.planemo.yml`` and that you have access rights on the Tool Shed)::

-    $ 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
+    $ planemo shed_upload --shed_target testtoolshed --check_diff ~/repositories/galaxy_blast/tools/blast2go/
+    ...
+
+or::
+
+    $ planemo shed_upload --shed_target toolshed --check_diff ~/repositories/galaxy_blast/tools/blast2go/
+    ...

-Check this worked::
+To just build and check the tar ball, use::

-    $ tar -tzf blast2go.tar.gz
+    $ planemo shed_upload --tar_only  ~/repositories/galaxy_blast/tools/blast2go/
+    ...
+    $ tar -tzf shed_upload.tar.gz
+    test-data/blastp_sample.blast2go.tabular
+    test-data/blastp_sample.xml
+    tool-data/blast2go.loc.sample
     tools/blast2go/README.rst
+    tools/blast2go/blast2go.py
     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)
--- a/tools/blast2go/blast2go.xml	Thu Jul 31 05:40:57 2014 -0400
+++ b/tools/blast2go/blast2go.xml	Fri May 15 06:01:16 2015 -0400
@@ -1,16 +1,16 @@
-<tool id="blast2go" name="Blast2GO" version="0.0.9">
+<tool id="blast2go" name="Blast2GO" version="0.0.10">
     <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}" "${tab}"
-    </command>
     <stdio>
         <!-- Wrapper ensures anything other than zero is an error -->
         <exit_code range="1:" />
         <exit_code range=":-1" />
     </stdio>
+    <command interpreter="python">
+        blast2go.py "${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.">
--- a/tools/blast2go/massage_xml_for_blast2go.py	Thu Jul 31 05:40:57 2014 -0400
+++ b/tools/blast2go/massage_xml_for_blast2go.py	Fri May 15 06:01:16 2015 -0400
@@ -21,7 +21,6 @@
 """
 import sys
 import os
-import subprocess

 def stop_err(msg, error_level=1):
     """Print error message to stdout and quit with given error level."""
@@ -52,9 +51,9 @@
         header += line

     if "<BlastOutput_program>blastx</BlastOutput_program>" in header:
-        print "BLASTX output identified"
+        print("BLASTX output identified")
     elif "<BlastOutput_program>blastp</BlastOutput_program>" in header:
-        print "BLASTP output identified"
+        print("BLASTP output identified")
     else:
         in_handle.close()
         stop_err("Expect BLASTP or BLASTX output")
@@ -76,7 +75,7 @@

     out_handle.close()
     in_handle.close()
-    print "Input has %i queries" % count
+    print("Input has %i queries" % count)


 if __name__ == "__main__":
--- a/tools/blast2go/repository_dependencies.xml	Thu Jul 31 05:40:57 2014 -0400
+++ b/tools/blast2go/repository_dependencies.xml	Fri May 15 06:01:16 2015 -0400
@@ -1,4 +1,4 @@
 <?xml version="1.0"?>
 <repositories description="Requires BLAST XML and database datatype definitions.">
-    <repository changeset_revision="939a600f45e9" name="blast_datatypes" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    <repository changeset_revision="da92fef90117" name="blast_datatypes" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" />
 </repositories>