<tool id="blast_xml_to_tabular" name="BLAST XML to tabular" version="1.1.0">
    <description>Convert BLAST XML output to tabular</description>
    <command detect_errors="exit_code">
        <![CDATA[  
          '$__tool_directory__/blast_xml_to_tabular.py'
            '${blastxml_file}'
            '${tabular_file}'
            '${out_format}'
        ]]>
    </command>
    <inputs>
        <param name="blastxml_file" type="data" format="blastxml" label="BLAST results as XML"/> 
        <param name="out_format" type="select" label="Output format">
            <option value="std" selected="True">Tabular (standard 12 columns)</option>
            <option value="ext">Tabular (extended 24 columns)</option>
            <option value="ext+">Tabular (extended 26 columns)</option>
        </param>
    </inputs>
    <outputs>
        <data name="tabular_file" format="tabular" label="BLAST results: data $blastxml_file.hid as tabular" />
    </outputs>
    <help>

.. class:: infomark

**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 - but running BLAST twice is
slow and wasteful.

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

====== ========= ============================================
Column NCBI name Description
------ --------- --------------------------------------------
     1 qseqid    Query Seq-id (ID of your sequence)
     2 sseqid    Subject Seq-id (ID of the database hit)
     3 pident    Percentage of identical matches
     4 length    Alignment length
     5 mismatch  Number of mismatches
     6 gapopen   Number of gap openings
     7 qstart    Start of alignment in query
     8 qend      End of alignment in query
     9 sstart    Start of alignment in subject (database hit)
    10 send      End of alignment in subject (database hit)
    11 evalue    Expectation value (E-value)
    12 bitscore  Bit score
====== ========= ============================================

The BLAST+ tools can optionally output additional columns of information,
but this takes longer to calculate. Most (but not all) of these columns are
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.

====== ============= ===========================================
Column NCBI name     Description
------ ------------- -------------------------------------------
    13 sallseqid     All subject Seq-id(s), separated by a ';'
    14 score         Raw score
    15 nident        Number of identical matches
    16 positive      Number of positive-scoring matches
    17 gaps          Total number of gaps
    18 ppos          Percentage of positive-scoring matches
    19 qframe        Query frame
    20 sframe        Subject frame
    21 qseq          Aligned part of query sequence
    22 sseq          Aligned part of subject sequence
    23 qlen          Query sequence length
    24 slen          Subject sequence length
====== ============= ===========================================

Very slight modifications were made to the "BLAST XML to tabular" tool that
ships with Galaxy to output two more column columns:

====== ============= ===========================================
Column NCBI name     Description
------ ------------- -------------------------------------------
    25 pcov          Percentage coverage
    26 sallseqdescr  All subject Seq-descr(s), separated by a ','
====== ============= ===========================================

----

.. class:: infomark

This is a slightly modified version of a tool that ships with Galaxy.
If the 12 or 24 columns formats are desired, use the original tool.

.. class:: warningmark

Beware that the XML file (and thus the conversion) and the tabular output
direct from BLAST+ may differ in the presence of XXXX masking on regions
low complexity (columns 21 and 22), and thus also calculated figures like
the percentage identity (column 3).

    </help>
</tool>