changeset 1:b07aa90c95e6 draft

Uploaded v0.0.2, corrects typo on tool ID, adds citation markup.

--- a/tools/mummer/README.rst	Mon Oct 27 12:56:55 2014 -0400
+++ b/tools/mummer/README.rst	Tue Oct 28 06:57:35 2014 -0400
@@ -1,11 +1,11 @@
-Galaxy wrapper for EffectiveT3 v1.0.1
-=====================================
+Galaxy wrapper for drawing dotplots using MUMmer 3
+==================================================
 
 This wrapper is copyright 2014 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 suite MUMmer v3.
+This is a dotplot tool wrapping functionality from the MUMmer v3 suite.
 
 S. Kurtz et al. (2004).
 Versatile and open software for comparing large genomes.
@@ -21,7 +21,8 @@
 This should be straightforward, Galaxy should automatically download and install
 the MUMmer files.
 
-It also needs gnuplot, and ps2pdf.
+It also needs the tools ``gnuplot`` and ``ps2pdf`` to be installed and on the
+system ``$PATH``.
 
 
 Manual Installation
@@ -46,7 +47,7 @@
 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 mummer_wrapper
+    $ ./run_tests.sh -id mummerplot_wrapper
 
 That's it.
 
@@ -57,7 +58,9 @@
 ======= ======================================================================
 Version Changes
 ------- ----------------------------------------------------------------------
-v0.0.1  - Initial public release
+v0.0.1  - Initial public release.
+v0.0.2  - Correct typo in Tool identifier.
+        - Include MUMmer citation in Galaxy XML markup.
 ======= ======================================================================
 
 

--- a/tools/mummer/mummer.xml	Mon Oct 27 12:56:55 2014 -0400
+++ b/tools/mummer/mummer.xml	Tue Oct 28 06:57:35 2014 -0400
@@ -1,5 +1,5 @@
-<tool id="mumer_wrapper" name="MUMmer" version="0.0.1">
-    <description>Draw dotplot with mummer/nucmer/promer/mummerplot</description>
+<tool id="mummerplot_wrapper" name="MUMmer dotplot" version="0.0.2">
+    <description>Combine mummer/nucmer/promer with mummerplot</description>
     <requirements>
             <requirement type="binary">ps2pdf</requirement>
             <requirement type="binary">nucmer</requirement>
@@ -43,8 +43,8 @@
     <help>
 **What it does**
 
-Takes two FASTA files (*species A* and *species B*), compairs them using one
-of the MUMmer 3 tools (``mummer``, ``nucmer``, or ``promer``), comparing both
+Takes two FASTA files (*species A* and *species B*), compares them using one
+of the MUMmer 3 tools (``mummer``, ``nucmer``, or ``promer``), checking both
 strands, and then draws a dotplot using ``mummerplot``.
 
 The full MUMmer suite is more flexible and capable than this limited wrapper.
@@ -65,4 +65,7 @@
 This wrapper is available to install into other Galaxy Instances via the Galaxy
 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/mummer
     </help>
+    <citations>
+        <citation type="doi">10.1186/gb-2004-5-2-r12</citation>
+    </citations>
 </tool>