Mercurial > repos > peterjc > blast_rbh

changeset 21:b41f8c43705e draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
v0.1.7 - Updated citation & misc internal changes
author peterjc
date Fri, 04 Sep 2015 07:05:56 -0400
parents e8f8c580bcca
children 75ab3e2cfa0e
files tools/blast_rbh/README.rst tools/blast_rbh/blast_rbh.xml
diffstat 2 files changed, 11 insertions(+), 10 deletions(-) [+]
line wrap: on
line diff
--- a/tools/blast_rbh/README.rst	Fri May 15 05:47:40 2015 -0400
+++ b/tools/blast_rbh/README.rst	Fri Sep 04 07:05:56 2015 -0400
@@ -19,16 +19,17 @@
 Citation
 ========
 
-Please cite the following paper (currently available as a preprint):
+Please cite the following paper:
 
 NCBI BLAST+ integrated into Galaxy.
 P.J.A. Cock, J.M. Chilton, B. Gruening, J.E. Johnson, N. Soranzo
-bioRxiv DOI: http://dx.doi.org/10.1101/014043 (preprint)
+*GigaScience* 2015, 4:39
+DOI: http://dx.doi.org/10.1186/s13742-015-0080-7
 
 You should also cite the NCBI BLAST+ tools:
 
 BLAST+: architecture and applications.
-C. Camacho et al. BMC Bioinformatics 2009, 10:421.
+C. Camacho et al. *BMC Bioinformatics* 2009, 10:421.
 DOI: http://dx.doi.org/10.1186/1471-2105-10-421
 
 
@@ -82,6 +83,7 @@
         - Added "NCBI BLAST+ integrated into Galaxy" preprint citation.
 v0.1.7  - Reorder XML elements (internal change only).
         - Planemo for Tool Shed upload (``.shed.yml``, internal change only).
+        - Updated citation information with GigaScience paper.
 ======= ======================================================================
 
 
@@ -95,12 +97,12 @@
 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)::
 
-    $ planemo shed_upload --shed_target testtoolshed --check_diff ~/repositories/galaxy_blast/tools/blast_rbh/
+    $ planemo shed_update --shed_target testtoolshed --check_diff ~/repositories/galaxy_blast/tools/blast_rbh/
     ...
 
 or::
 
-    $ planemo shed_upload --shed_target toolshed --check_diff ~/repositories/galaxy_blast/tools/blast_rbh/
+    $ planemo shed_update --shed_target toolshed --check_diff ~/repositories/galaxy_blast/tools/blast_rbh/
     ...
 
 To just build and check the tar ball, use::
--- a/tools/blast_rbh/blast_rbh.xml	Fri May 15 05:47:40 2015 -0400
+++ b/tools/blast_rbh/blast_rbh.xml	Fri Sep 04 07:05:56 2015 -0400
@@ -238,12 +238,12 @@
 
 P.J.A. Cock, J.M. Chilton, B. Gruening, J.E. Johnson, N. Soranzo (2015).
 NCBI BLAST+ integrated into Galaxy.
-bioRxiv prepint.
-http://dx.doi.org/10.1101/014043
+*GigaScience* 4:39
+http://dx.doi.org/10.1186/s13742-015-0080-7
 
 Christiam Camacho et al. (2009).
 BLAST+: architecture and applications.
-BMC Bioinformatics. 15;10:421.
+*BMC Bioinformatics* 15;10:421.
 http://dx.doi.org/10.1186/1471-2105-10-421
 
 This wrapper is available to install into other Galaxy Instances via the Galaxy
@@ -251,7 +251,6 @@
     </help>
     <citations>
         <citation type="doi">10.1186/1471-2105-10-421</citation>
-        <citation type="doi">10.1101/014043</citation>
-        <!-- TODO - Update once "NCBI BLAST+ integrated into Galaxy" formally published -->
+        <citation type="doi">10.1186/s13742-015-0080-7</citation>
     </citations>
 </tool>