root/galaxy-central/tools/ncbi_blast_plus/blastxml_to_tabular.xml @ 2

<tool id="blastxml_to_tabular" name="BLAST XML to tabular" version="0.0.1">
    <description>Convert BLAST XML output to tabular</description>
    <command interpreter="python">
      blastxml_to_tabular.py $blastxml_file $tabular_file
    </command>
    <inputs>
        <param name="blastxml_file" type="data" format="blastxml" label="BLAST results as XML"/> 
    </inputs>
    <outputs>
        <data name="tabular_file" format="tabular" label="BLAST results as tabular" />
    </outputs>
    <requirements>
    </requirements>
    <tests>
    </tests>
    <help>
    
**What it does**

NCBI BLAST+ (and the older NCBI 'legacy' BLAST) can output in a range of formats including
tabular and a more detailed XML format. A complex workflow may need both the XML and the
tabular output.

This tool takes the BLAST XML output and converts it into the 12 column tabular equivalent:

1. Id of your sequence 
2. GI of the database hit 
3. % identity
4. Alignment length
5. # mismatches
6. # gaps
7. Start position in your sequence
8. End position in your sequence
9. Start position in database hit
10. End position in database hit
11. E-value
12. Bit score


    </help>
</tool>