diff tools/ncbi_blast_plus/ncbi_blastn_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_blastn_wrapper.xml	Thu Apr 25 09:38:37 2013 -0400
+++ b/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml	Mon Sep 23 06:14:13 2013 -0400
@@ -1,4 +1,4 @@
-<tool id="ncbi_blastn_wrapper" name="NCBI BLAST+ blastn" version="0.0.19">
+<tool id="ncbi_blastn_wrapper" name="NCBI BLAST+ blastn" version="0.0.20">
     <description>Search nucleotide database with 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,histdb" merge_outputs="output1"></parallelism>
@@ -37,6 +37,9 @@
 #if (str($adv_opts.max_hits) and int(str($adv_opts.max_hits)) > 0):
 -max_target_seqs $adv_opts.max_hits
 #end if
+#if (str($adv_opts.identity_cutoff) and float(str($adv_opts.identity_cutoff)) > 0 ):
+-perc_identity $adv_opts.identity_cutoff
+#end if
 #if (str($adv_opts.word_size) and int(str($adv_opts.word_size)) > 0):
 -word_size $adv_opts.word_size
 #end if
@@ -126,6 +129,7 @@
                 <param name="max_hits" type="integer" value="0" label="Maximum hits to show" help="Use zero for default limits">
                     <validator type="in_range" min="0" />
                 </param>
+                <param name="identity_cutoff" type="float" min="0" max="100" value="0" label="Percent identity cutoff (-perc_identity)" help="Use zero for no cutoff" />
                 <!-- I'd like word_size to be optional, with minimum 4 for blastn -->
                 <param name="word_size" type="integer" value="0" label="Word size for wordfinder algorithm" help="Use zero for default, otherwise minimum 4.">
                     <validator type="in_range" min="0" />
@@ -148,6 +152,18 @@
             </change_format>
         </data>
     </outputs>
+    <tests>
+        <test>
+            <param name="query" value="rhodopsin_nucs.fasta" ftype="fasta" />
+            <param name="db_opts_selector" value="file" />
+            <param name="subject" value="three_human_mRNA.fasta" ftype="fasta" />
+            <param name="database" value="" />
+            <param name="evalue_cutoff" value="1e-40" />
+            <param name="out_format" value="6" />
+            <param name="adv_opts_selector" value="basic" />
+            <output name="output1" file="blastn_rhodopsin_vs_three_human.tabular" ftype="tabular" />
+        </test>
+    </tests>
     <help>
     
 .. class:: warningmark
@@ -233,7 +249,20 @@
 
 **References**
 
-Zhang et al. A Greedy Algorithm for Aligning DNA Sequences. 2000. JCB: 203-214.
+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>