details: http://www.bx.psu.edu/hg/galaxy/rev/bc540363324d changeset: 2368:bc540363324d user: Anton Nekrutenko <anton@bx.psu.edu> date: Fri Apr 24 15:06:51 2009 -0400 description: Added column info to MB wrapper 2 file(s) affected in this change: static/welcome.html tools/metag_tools/megablast_wrapper.xml diffs (76 lines): diff -r a1e84abd301a -r bc540363324d static/welcome.html --- a/static/welcome.html Fri Apr 24 13:42:38 2009 -0400 +++ b/static/welcome.html Fri Apr 24 15:06:51 2009 -0400 @@ -14,6 +14,7 @@ .current-quickie { width: 100%; background: black; + borderRadius:10; } .quickie .head { font-size: 200%; diff -r a1e84abd301a -r bc540363324d tools/metag_tools/megablast_wrapper.xml --- a/tools/metag_tools/megablast_wrapper.xml Fri Apr 24 13:42:38 2009 -0400 +++ b/tools/metag_tools/megablast_wrapper.xml Fri Apr 24 15:06:51 2009 -0400 @@ -2,20 +2,20 @@ <description> compare short reads against nt and wgs databases</description> <command interpreter="python">megablast_wrapper.py $source_select $input_query $output1 $word_size $iden_cutoff $evalue_cutoff $filter_query ${GALAXY_DATA_INDEX_DIR}</command> <inputs> - <param name="source_select" type="select" display="radio" label="Choose target database"> + <param name="input_query" type="data" format="fasta" label="Compare these sequences"/> + <param name="source_select" type="select" display="radio" label="against target database"> <options from_file="blastdb.loc"> <column name="name" index="0"/> <column name="value" index="0"/> </options> </param> - <param name="input_query" type="data" format="fasta" label="Sequence file"/> - <param name="word_size" type="select" label="Word size (-W)" help="Size of best perfect match"> + <param name="word_size" type="select" label="using word size" help="Size of best perfect match"> <option value="28">28</option> <option value="16">16</option> </param> - <param name="iden_cutoff" type="float" size="15" value="90.0" label="Identity percentage cut-off (-p)" help="no cutoff if 0" /> - <param name="evalue_cutoff" type="float" size="15" value="0.001" label="Expectation value (-e)" /> - <param name="filter_query" type="select" label="Filter query sequence (-F)"> + <param name="iden_cutoff" type="float" size="15" value="90.0" label="report hits above this identity" help="no cutoff if 0" /> + <param name="evalue_cutoff" type="float" size="15" value="0.001" label="set expectation value cutoff" /> + <param name="filter_query" type="select" label="Filter out low complexity regions?"> <option value="T">Yes</option> <option value="F">No</option> </param> @@ -49,18 +49,27 @@ 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. - ----- -**Parameters** +**Output format** -- *Word size* (**-W**) : the minimal length of an exact match -- *Identity percentage cut-off* (**-p**) : the minimal identity for an alignment -- *Expectation value* (**-e**) : the maximal expectation value for an alignment -- *Filter query sequence* (**-F**) : mask low-complexity regions in the query sequence +Output of this tool contains 13 columns delimited by Tabs: +1. Id of your sequence +2. GI of the database hit +3. Length of the database hit +4. % identity +5. Alignment length +6. # mismatches +7. # gaps +8. Start position in your sequence +9. End position in your sequence +10. Start position in database hit +11. End position in database hit +12. E-value +13. Bit score ------ +------- **Reference**