Mercurial > repos > devteam > ncbi_blast_plus
diff tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml @ 8:1f546099212f draft
Uploaded v0.0.17, default to extended 24 column tabular output (rather than standard 12 column output). This should avoid many cases of repeated BLAST jobs being run due to later needing the extra columns.
author | peterjc |
---|---|
date | Tue, 19 Feb 2013 12:49:43 -0500 |
parents | a23b0627623c |
children | 9dabbfd73c8a |
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--- a/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml Fri Feb 08 05:51:26 2013 -0500 +++ b/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml Tue Feb 19 12:49:43 2013 -0500 @@ -1,4 +1,4 @@ -<tool id="ncbi_tblastn_wrapper" name="NCBI BLAST+ tblastn" version="0.0.15"> +<tool id="ncbi_tblastn_wrapper" name="NCBI BLAST+ tblastn" version="0.0.17"> <description>Search translated nucleotide database with protein 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> @@ -82,8 +82,8 @@ </conditional> <param name="evalue_cutoff" type="float" size="15" value="0.001" label="Set expectation value cutoff" /> <param name="out_format" type="select" label="Output format"> - <option value="6" selected="True">Tabular (standard 12 columns)</option> - <option value="ext">Tabular (extended 24 columns)</option> + <option value="6">Tabular (standard 12 columns)</option> + <option value="ext" selected="True">Tabular (extended 24 columns)</option> <option value="5">BLAST XML</option> <option value="0">Pairwise text</option> <option value="0 -html">Pairwise HTML</option> @@ -216,7 +216,7 @@ <output name="output1" file="tblastn_four_human_vs_rhodopsin.tabular" ftype="tabular" /> </test> <test> - <!-- Same as above, but parse deflines - on BLAST 2.2.25+ makes no difference --> + <!-- Same as above, but parse deflines - on BLAST 2.2.25+ - 2.2.27+ makes no difference --> <param name="query" value="four_human_proteins.fasta" ftype="fasta" /> <param name="db_opts_selector" value="file" /> <param name="subject" value="rhodopsin_nucs.fasta" ftype="fasta" /> @@ -299,7 +299,7 @@ included by selecting the extended tabular output. The extra columns are included *after* the standard 12 columns. This is so that you can write workflow filtering steps that accept either the 12 or 24 column tabular -BLAST output. +BLAST output. Galaxy now uses this extended 24 column output by default. ====== ============= =========================================== Column NCBI name Description