diff tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml @ 6:a23b0627623c draft

Uploaded v0.0.15, clearer warning about searching against a FASTA file.

--- a/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml	Fri Nov 09 06:53:55 2012 -0500
+++ b/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml	Thu Jan 24 12:40:41 2013 -0500
@@ -1,4 +1,4 @@
-<tool id="ncbi_blastx_wrapper" name="NCBI BLAST+ blastx" version="0.0.14">
+<tool id="ncbi_blastx_wrapper" name="NCBI BLAST+ blastx" version="0.0.15">
     <description>Search protein database 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,histdb" merge_outputs="output1"></parallelism>
@@ -56,7 +56,7 @@
             <param name="db_opts_selector" type="select" label="Subject database/sequences">
               <option value="db" selected="True">BLAST Database</option>
               <option value="histdb">BLAST database from your history</option>
-              <option value="file">FASTA file from your history (pairwise e-values)</option>
+              <option value="file">FASTA file from your history (see warning note below)</option>
             </param>
             <when value="db">
                 <param name="database" type="select" label="Protein BLAST database">
@@ -215,6 +215,15 @@
 Search a *protein database* using a *translated nucleotide query*,
 using the NCBI BLAST+ blastx command line tool.
 
+.. class:: warningmark
+
+You can also search against a FASTA file of subject protein
+sequences. This is *not* advised because it is slower (only one
+CPU is used), but more importantly gives e-values for pairwise
+searches (very small e-values which will look overly signficiant).
+In most cases you should instead turn the other FASTA file into a
+database first using *makeblastdb* and search against that.
+
 -----
 
 **Output format**