comparison tools/ncbi_blast_plus/blastxml_to_tabular.xml @ 8:1f546099212f draft

Uploaded v0.0.17, default to extended 24 column tabular output (rather than standard 12 column output). This should avoid many cases of repeated BLAST jobs being run due to later needing the extra columns.

7:4ce66a5401d0

<tool id="blastxml_to_tabular" name="BLAST XML to tabular" version="0.0.8">
    <description>Convert BLAST XML output to tabular</description>
    <command interpreter="python">
      blastxml_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>
        </param>
    </inputs>
    <outputs>
        <data name="tabular_file" format="tabular" label="BLAST results as tabular" />
    </outputs>

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
------ --------- --------------------------------------------

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 22 column tabular
BLAST output.

====== ============= ===========================================
Column NCBI name     Description
------ ------------- -------------------------------------------
    13 sallseqid     All subject Seq-id(s), separated by a ';'

====== ============= ===========================================

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 idenity (column 3).

    </help>
</tool>

8:1f546099212f

<tool id="blastxml_to_tabular" name="BLAST XML to tabular" version="0.0.10">
    <description>Convert BLAST XML output to tabular</description>
    <command interpreter="python">
      blastxml_to_tabular.py $blastxml_file $tabular_file $out_format
    </command>
    <stdio>
        <!-- Anything other than zero is an error -->
        <exit_code range="1:" />
        <exit_code range=":-1" />
    </stdio>
    <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">Tabular (standard 12 columns)</option>
            <option value="ext" selected="True">Tabular (extended 24 columns)</option>
        </param>
    </inputs>
    <outputs>
        <data name="tabular_file" format="tabular" label="BLAST results as tabular" />
    </outputs>

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 can convert it into the
standard 12 column tabular equivalent:

====== ========= ============================================
Column NCBI name Description
------ --------- --------------------------------------------

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 22 column tabular
BLAST output. This tool now uses this extended 24 column output by default.

====== ============= ===========================================
Column NCBI name     Description
------ ------------- -------------------------------------------
    13 sallseqid     All subject Seq-id(s), separated by a ';'

====== ============= ===========================================

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>