--- a/tools/protein_analysis/README.rst	Wed Sep 18 06:16:58 2013 -0400
+++ b/tools/protein_analysis/README.rst	Fri Nov 21 08:19:09 2014 -0500
@@ -41,23 +41,23 @@
 
 First install those command line tools you wish to use the wrappers for:
 
-1. Install the command line version of SignalP 3.0 and ensure "signalp" is
+1. Install the command line version of SignalP 3.0 and ensure ``signalp`` is
    on the PATH, see: http://www.cbs.dtu.dk/services/SignalP/
 
-2. Install the command line version of TMHMM 2.0 and ensure "tmhmm" is on
+2. Install the command line version of TMHMM 2.0 and ensure ``tmhmm`` is on
    the PATH, see: http://www.cbs.dtu.dk/services/TMHMM/
 
-3. Install the command line version of Promoter 2.0 and ensure "promoter" is
+3. Install the command line version of Promoter 2.0 and ensure ``promoter`` is
    on the PATH, see: http://www.cbs.dtu.dk/services/Promoter
 
-4. Install the WoLF PSORT v0.2 package, and ensure "runWolfPsortSummary"
+4. Install the WoLF PSORT v0.2 package, and ensure ``runWolfPsortSummary``
    is on the PATH (we use an extra wrapper script to change to the WoLF PSORT
    directory, run runWolfPsortSummary, and then change back to the original
    directory), see: http://wolfpsort.org/WoLFPSORT_package/version0.2/
 
 5. Install hmmsearch from HMMER 2.3.2 (the last stable release of HMMER 2)
-   but put it on the path under the name hmmsearch2 (allowing it to co-exist
-   with HMMER 3), or edit rlxr_motif.py accordingly.
+   but put it on the path under the name ``hmmsearch2`` (allowing it to
+   co-exist with HMMER 3), or edit ``rlxr_motif.py`` accordingly.
 
 Verify each of the tools is installed and working from the command line
 (when logged in as the Galaxy user if appropriate).
@@ -66,37 +66,36 @@
 Manual Installation
 ===================
 
-1. Create a folder tools/protein_analysis under your Galaxy installation.
+1. Create a folder ``tools/protein_analysis`` under your Galaxy installation.
    This folder name is not critical, and can be changed if desired - you
-   must update the paths used in tool_conf.xml to match.
+   must update the paths used in ``tool_conf.xml`` to match.
 
 2. Copy/move the following files (from this archive) there:
 
-   * tmhmm2.xml (Galaxy tool definition)
-   * tmhmm2.py (Python wrapper script)
+   * ``tmhmm2.xml`` (Galaxy tool definition)
+   * ``tmhmm2.py`` (Python wrapper script)
 
-   * signalp3.xml (Galaxy tool definition)
-   * signalp3.py (Python wrapper script)
+   * ``signalp3.xml`` (Galaxy tool definition)
+   * ``signalp3.py`` (Python wrapper script)
 
-   * promoter2.xml (Galaxy tool definition)
-   * promoter2.py (Python wrapper script)
+   * ``promoter2.xml`` (Galaxy tool definition)
+   * ``promoter2.py`` (Python wrapper script)
 
-   * psortb.xml (Galaxy tool definition)
-   * psortb.py (Python wrapper script)
+   * ``psortb.xml`` (Galaxy tool definition)
+   * ``psortb.py`` (Python wrapper script)
 
-   * wolf_psort.xml (Galaxy tool definition)
-   * wolf_psort.py (Python wrapper script)
+   * ``wolf_psort.xml`` (Galaxy tool definition)
+   * ``wolf_psort.py`` (Python wrapper script)
 
-   * rxlr_motifs.xml (Galaxy tool definition)
-   * rxlr_motifs.py (Python script)
+   * ``rxlr_motifs.xml`` (Galaxy tool definition)
+   * ``rxlr_motifs.py`` (Python script)
 
-   * seq_analysis_utils.py (shared Python code)
-   * LICENCE
-   * README.rst (this file)
+   * ``seq_analysis_utils.py`` (shared Python code)
+   * ``LICENCE``
+   * ``README.rst`` (this file)
 
-3. Edit your Galaxy conjuration file tool_conf.xml (to use the tools) AND
-   also tool_conf.xml.sample (to run the tests) to include the new tools
-   by adding::
+3. Edit your Galaxy conjuration file ``tool_conf.xml`` to include the
+   new tools by adding::
 
     <section name="Protein sequence analysis" id="protein_analysis">
       <tool file="protein_analysis/tmhmm2.xml" />
@@ -111,22 +110,24 @@
 
    Leave out the lines for any tools you do not wish to use in Galaxy.
 
-4. Copy/move the test-data files (from this archive) to Galaxy's
-   subfolder test-data.
+4. Copy/move the ``test-data/*`` files (from this archive) to Galaxy's
+   subfolder ``test-data/``.
 
 5. Run the Galaxy functional tests for these new wrappers with::
 
-    ./run_functional_tests.sh -id tmhmm2
-    ./run_functional_tests.sh -id signalp3
-    ./run_functional_tests.sh -id Psortb
-    ./run_functional_tests.sh -id rxlr_motifs
+    $ ./run_tests.sh -id tmhmm2
+    $ ./run_tests.sh -id signalp3
+    $ ./run_tests.sh -id Psortb
+    $ ./run_tests.sh -id rxlr_motifs
 
-   Alternatively, this should work (assuming you left the name and id as shown in
-   the XML file tool_conf.xml.sample)::
+   Alternatively, this should work (assuming you left the seciont name and id
+   as shown above in your XML file ``tool_conf.xml``)::
 
-    ./run_functional_tests.sh -sid Protein_sequence_analysis-protein_analysis
+    $ ./run_tests.sh -sid Protein_sequence_analysis-protein_analysis
 
-   To check the section ID expected, use ./run_functional_tests.sh -list
+   To check the section ID expected, use:
+
+    $ ./run_tests.sh -list
 
 6. Restart Galaxy and check the new tools are shown and work.
 
@@ -139,7 +140,7 @@
 ------- ----------------------------------------------------------------------
 v0.0.1  - Initial release
 v0.0.2  - Corrected some typos in the help text
-        - Renamed test output file to use Galaxy convention of *.tabular
+        - Renamed test output file to use Galaxy convention of ``*.tabular``
 v0.0.3  - Check for tmhmm2 silent failures (no output)
         - Additional unit tests
 v0.0.4  - Ignore comment lines in tmhmm2 output.
@@ -150,11 +151,11 @@
 v0.0.8  - Added WoLF PSORT wrapper to the suite.
 v0.0.9  - Added our RXLR motifs tool to the suite.
 v0.1.0  - Added Promoter 2.0 wrapper (similar to SignalP & TMHMM wrappers)
-        - Support Galaxy's <parallelism> tag for SignalP, TMHMM & Promoter
+        - Support Galaxy's ``<parallelism>`` tag for SignalP, TMHMM & Promoter
 v0.1.1  - Fixed an error in the header of the tabular output from Promoter
 v0.1.2  - Use the new <stdio> settings in the XML wrappers to catch errors
-        - Use SGE style $NSLOTS for thread count (otherwise default to 4)
-v0.1.3  - Added missing file whisson_et_al_rxlr_eer_cropped.hmm to Tool Shed
+        - Use SGE style ``$NSLOTS`` for thread count (otherwise default to 4)
+v0.1.3  - Added missing file ``whisson_et_al_rxlr_eer_cropped.hmm`` to Tool Shed
 v0.2.0  - Added PSORTb wrapper to the suite, based on earlier work
           contributed by Konrad Paszkiewicz.
 v0.2.1  - Use a script to create the Tool Shed tar-ball (removed some stray
@@ -170,13 +171,16 @@
         - Adopted standard MIT licence.
         - Use reStructuredText for this README file.
         - Development moved to GitHub, https://github.com/peterjc/pico_galaxy
+v0.2.6  - Use the new ``$GALAXY_SLOTS`` environment variable for thread count.
+        - Updated the ``suite_config.xml`` file (overdue).
+        - Tool definition now embeds citation information.
 ======= ======================================================================
 
 
 Developers
 ==========
 
-This script and other tools are being developed on the following hg branches:
+This script and other tools were initially developed on the following hg branches:
 http://bitbucket.org/peterjc/galaxy-central/src/seq_analysis
 http://bitbucket.org/peterjc/galaxy-central/src/tools