Mercurial > repos > devteam > ncbi_blast_plus
diff tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml @ 6:a23b0627623c draft
Uploaded v0.0.15, clearer warning about searching against a FASTA file.
author | peterjc |
---|---|
date | Thu, 24 Jan 2013 12:40:41 -0500 |
parents | 393a7a35383c |
children | 1f546099212f |
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--- a/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml Fri Nov 09 06:53:55 2012 -0500 +++ b/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml Thu Jan 24 12:40:41 2013 -0500 @@ -1,4 +1,4 @@ -<tool id="ncbi_blastn_wrapper" name="NCBI BLAST+ blastn" version="0.0.14"> +<tool id="ncbi_blastn_wrapper" name="NCBI BLAST+ blastn" version="0.0.15"> <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> @@ -55,7 +55,7 @@ <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="Nucleotide BLAST database"> @@ -162,6 +162,15 @@ using the NCBI BLAST+ blastn command line tool. Algorithms include blastn, megablast, and discontiguous megablast. +.. class:: warningmark + +You can also search against a FASTA file of subject nucleotide +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**