[2] | 1 | <tool id="blastxml_to_tabular" name="BLAST XML to tabular" version="0.0.1"> |
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| 2 | <description>Convert BLAST XML output to tabular</description> |
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| 3 | <command interpreter="python"> |
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| 4 | blastxml_to_tabular.py $blastxml_file $tabular_file |
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| 5 | </command> |
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| 6 | <inputs> |
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| 7 | <param name="blastxml_file" type="data" format="blastxml" label="BLAST results as XML"/> |
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| 8 | </inputs> |
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| 9 | <outputs> |
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| 10 | <data name="tabular_file" format="tabular" label="BLAST results as tabular" /> |
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| 11 | </outputs> |
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| 12 | <requirements> |
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| 13 | </requirements> |
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| 14 | <tests> |
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| 15 | </tests> |
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| 16 | <help> |
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| 17 | |
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| 18 | **What it does** |
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| 19 | |
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| 20 | NCBI BLAST+ (and the older NCBI 'legacy' BLAST) can output in a range of formats including |
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| 21 | tabular and a more detailed XML format. A complex workflow may need both the XML and the |
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| 22 | tabular output. |
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| 23 | |
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| 24 | This tool takes the BLAST XML output and converts it into the 12 column tabular equivalent: |
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| 25 | |
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| 26 | 1. Id of your sequence |
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| 27 | 2. GI of the database hit |
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| 28 | 3. % identity |
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| 29 | 4. Alignment length |
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| 30 | 5. # mismatches |
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| 31 | 6. # gaps |
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| 32 | 7. Start position in your sequence |
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| 33 | 8. End position in your sequence |
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| 34 | 9. Start position in database hit |
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| 35 | 10. End position in database hit |
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| 36 | 11. E-value |
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| 37 | 12. Bit score |
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| 38 | |
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| 39 | |
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| 40 | </help> |
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| 41 | </tool> |
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