Mercurial > repos > peterjc > blastxml_to_top_descr

--- a/blastxml_to_top_descr/README.rst	Tue Jul 30 08:07:28 2013 -0400
+++ b/blastxml_to_top_descr/README.rst	Wed Sep 18 06:07:53 2013 -0400
@@ -39,7 +39,7 @@
 You will also need to modify the tools_conf.xml file to tell Galaxy to offer
 the tool. e.g. next to the NCBI BLAST+ tools. Simply add the line::

-    <tool file="filters/seq_select_by_id.xml" />
+    <tool file="ncbi_blast_plus/blastxml_to_top_descr.xml" />

 To run the tool's tests, also add this line to tools_conf.xml.sample then::

@@ -63,6 +63,7 @@
         - Tweak dependency on blast_datatypes to also work on Test Tool Shed
         - Adopt standard MIT License.
 v0.0.8  - Development moved to GitHub, https://github.com/peterjc/galaxy_blast
+v0.0.9  - Updated citation information (Cock et al. 2013).
 ======= ======================================================================
--- a/blastxml_to_top_descr/blastxml_to_top_descr.xml	Tue Jul 30 08:07:28 2013 -0400
+++ b/blastxml_to_top_descr/blastxml_to_top_descr.xml	Wed Sep 18 06:07:53 2013 -0400
@@ -1,4 +1,4 @@
-<tool id="blastxml_to_top_descr" name="BLAST top hit descriptions" version="0.0.8">
+<tool id="blastxml_to_top_descr" name="BLAST top hit descriptions" version="0.0.9">
     <description>Make a table from BLAST XML</description>
     <version_command interpreter="python">blastxml_to_top_descr.py --version</version_command>
     <command interpreter="python">
@@ -26,7 +26,7 @@
         </test>
     </tests>
     <help>
-
+
 **What it does**

 NCBI BLAST+ (and the older NCBI 'legacy' BLAST) can output in a range of
@@ -49,7 +49,15 @@
 to spot some problems (e.g. bacterial contaimination could be very
 obvious).

-**Citation**
+**References**
+
+If you use this Galaxy tool in work leading to a scientific publication please
+cite:
+
+Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013).
+Galaxy tools and workflows for sequence analysis with applications
+in molecular plant pathology. PeerJ 1:e167
+http://dx.doi.org/10.7717/peerj.167

 This wrapper is available to install into other Galaxy Instances via the Galaxy
 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr
--- a/blastxml_to_top_descr/repository_dependencies.xml	Tue Jul 30 08:07:28 2013 -0400
+++ b/blastxml_to_top_descr/repository_dependencies.xml	Wed Sep 18 06:07:53 2013 -0400
@@ -1,5 +1,4 @@
 <?xml version="1.0"?>
-<repositories description="This requires the BLAST datatype definitions (e.g. the BLAST XML format).">
-<!-- Revision 4:f9a7783ed7b6 on the main (and test) tool shed is v0.0.14 which added BLAST databases -->
-<repository changeset_revision="f9a7783ed7b6" name="blast_datatypes" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" />
+<repositories description="Requires BLAST XML and database datatype definitions.">
+<repository changeset_revision="b3a3ba0c1d47" name="blast_datatypes" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" />
 </repositories>