1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/0b5cb60e4810/ changeset: 0b5cb60e4810 user: anton date: 2012-04-26 16:44:26 summary: Modified metagenomic mapper to use BLAST+ blastn in megablast mode affected #: 2 files diff -r 127709d69d2c08bbceb3aa811c42696aec26ad10 -r 0b5cb60e48104bd1df937bd6c7051abfda7190ff tools/metag_tools/megablast_wrapper.py --- a/tools/metag_tools/megablast_wrapper.py +++ b/tools/metag_tools/megablast_wrapper.py @@ -56,7 +56,7 @@ stop_err( 'Cannot locate the target database directory. Please check your location file.' ) # arguments for megablast - megablast_command = "megablast -d %s -i %s -o %s -m 8 -a 8 -W %s -p %s -e %s -F %s > /dev/null" \ + megablast_command = "blastn -task megablast -db %s -query %s -out %s -outfmt '6 qseqid sgi slen ppos length mismatch gaps qstart qend sstart send evalue bitscore' -num_threads 2 -word_size %s -perc_identity %s -evalue %s -dust %s > /dev/null" \ % ( options.db_build, query_filename, mega_temp_output, mega_word_size, mega_iden_cutoff, mega_evalue_cutoff, options.filter_query ) print megablast_command @@ -96,11 +96,9 @@ line = line.rstrip( '\r\n' ) fields = line.split() try: - # get gi and length of that gi seq - gi, gi_len = fields[1].split( '_' ) # convert the last column (causing problem in filter tool) to float fields[-1] = float( fields[-1] ) - new_line = "%s\t%s\t%s\t%s\t%0.1f" % ( fields[0], gi, gi_len, '\t'.join( fields[2:-1] ), fields[-1] ) + new_line = "%s\t%0.1f" % ( '\t'.join( fields[:-1] ), fields[-1] ) except: new_line = line invalid_lines += 1 diff -r 127709d69d2c08bbceb3aa811c42696aec26ad10 -r 0b5cb60e48104bd1df937bd6c7051abfda7190ff tools/metag_tools/megablast_wrapper.xml --- a/tools/metag_tools/megablast_wrapper.xml +++ b/tools/metag_tools/megablast_wrapper.xml @@ -1,4 +1,4 @@ -<tool id="megablast_wrapper" name="Megablast" version="1.1.0"> +<tool id="megablast_wrapper" name="Megablast" version="1.2.0"><description> compare short reads against htgs, nt, and wgs databases</description><command interpreter="python"> megablast_wrapper.py @@ -16,15 +16,15 @@ <param name="source_select" type="select" display="radio" label="against target database"><options from_data_table="blastdb" /></param> - <param name="word_size" type="select" label="using word size" help="Size of best perfect match (-W)"> + <param name="word_size" type="select" label="using word size" help="Size of best perfect match (-word_size)"><option value="28">28</option><option value="16">16</option></param> - <param name="iden_cutoff" type="float" size="15" value="90.0" label="report hits above this identity (-p)" help="no cutoff if 0" /> - <param name="evalue_cutoff" type="float" size="15" value="0.001" label="set expectation value cutoff (-e)" /> - <param name="filter_query" type="select" label="Filter out low complexity regions? (-F)"> - <option value="T">Yes</option> - <option value="F">No</option> + <param name="iden_cutoff" type="float" size="15" value="90.0" label="report hits above this identity (-perc_identity)" help="no cutoff if 0" /> + <param name="evalue_cutoff" type="float" size="15" value="0.001" label="set expectation value cutoff (-evalue)" /> + <param name="filter_query" type="select" label="Filter out low complexity regions? (-dust)"> + <option value="yes">Yes</option> + <option value="no">No</option></param></inputs><outputs> @@ -41,7 +41,7 @@ <param name="word_size" value="28" /><param name="iden_cutoff" value="99.0" /><param name="evalue_cutoff" value="10.0" /> - <param name="filter_query" value="T" /> + <param name="filter_query" value="yes" /><output name="output1" file="megablast_wrapper_test1.out"/></test></tests> @@ -55,7 +55,7 @@ **What it does** -This tool runs **megablast** (for information about megablast, please see the reference below) a high performance nucleotide local aligner developed by Webb Miller and colleagues. +This tool runs **megablast** function of BLAST+ blastn tool - a high performance nucleotide local aligner developed by Webb Miller and colleagues. ----- Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.