diff tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml @ 10:70e7dcbf6573 draft

Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.

--- a/tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml	Thu Apr 25 09:38:37 2013 -0400
+++ b/tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml	Mon Sep 23 06:14:13 2013 -0400
@@ -1,4 +1,4 @@
-<tool id="ncbi_rpstblastn_wrapper" name="NCBI BLAST+ rpstblastn" version="0.0.3">
+<tool id="ncbi_rpstblastn_wrapper" name="NCBI BLAST+ rpstblastn" version="0.0.4">
     <description>Search protein domain database (PSSMs) with translated nucleotide query sequence(s)</description>
     <!-- If job splitting is enabled, break up the query file into parts -->
     <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="1000" shared_inputs="subject" merge_outputs="output1"></parallelism>
@@ -19,13 +19,13 @@
 #end if
 -evalue $evalue_cutoff
 -out "$output1"
-##Set the extended list here so if/when we add things, saved workflows are not affected
+## Set the extended list here so if/when we add things, saved workflows are not affected
 #if str($out_format)=="ext":
     -outfmt "6 std sallseqid score nident positive gaps ppos qframe sframe qseq sseq qlen slen"
 #else:
     -outfmt $out_format
 #end if
-##Seems rpstblastn does not currently support multiple threads :(
+## rpstblastn does not support multiple threads up to release 2.2.27+. Added in BLAST 2.2.28+.
 ##-num_threads 8
 #if $adv_opts.adv_opts_selector=="advanced":
 $adv_opts.filter_query
@@ -231,7 +231,20 @@
 
 **References**
 
-Marchler-Bauer A, Bryant SH. CD-Search: protein domain annotations on the fly. Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W327-31.
+If you use this Galaxy tool in work leading to a scientific publication please
+cite the following papers:
+
+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
 
+Christiam Camacho et al. (2009).
+BLAST+: architecture and applications.
+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
+Tool Shed at http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus
     </help>
 </tool>