comparison tools/ncbi_blast_plus/blastxml_to_tabular.xml @ 11:4c4a0da938ff draft

Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25. Supports $GALAXY_SLOTS. Includes more tests and heavy use of macros.

10:70e7dcbf6573

<tool id="blastxml_to_tabular" name="BLAST XML to tabular" version="0.0.11">
    <description>Convert BLAST XML output to tabular</description>
    <version_command interpreter="python">blastxml_to_tabular.py --version</version_command>
    <command interpreter="python">
      blastxml_to_tabular.py $blastxml_file $tabular_file $out_format
    </command>

            <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>
    <requirements>
    </requirements>
    <tests>
        <test>

            <param name="blastxml_file" value="blastp_human_vs_pdb_seg_no.xml" ftype="blastxml" />
            <param name="out_format" value="ext" />
            <!-- Note this has some white space differences from the actual blastp output -->
            <output name="tabular_file" file="blastp_human_vs_pdb_seg_no_converted_ext.tabular" ftype="tabular" />
        </test>
    </tests>
    <help>
    
**What it does**

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 ';'
    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

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

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

11:4c4a0da938ff

<tool id="blastxml_to_tabular" name="BLAST XML to tabular" version="0.0.22">
    <description>Convert BLAST XML output to tabular</description>
    <version_command interpreter="python">blastxml_to_tabular.py --version</version_command>
    <command interpreter="python">
      blastxml_to_tabular.py $blastxml_file $tabular_file $out_format
    </command>

            <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="$blastxml_file.display_name (as tabular)" />
    </outputs>
    <requirements>
    </requirements>
    <tests>
        <test>

            <param name="blastxml_file" value="blastp_human_vs_pdb_seg_no.xml" ftype="blastxml" />
            <param name="out_format" value="ext" />
            <!-- Note this has some white space differences from the actual blastp output -->
            <output name="tabular_file" file="blastp_human_vs_pdb_seg_no_converted_ext.tabular" ftype="tabular" />
        </test>
        <test>
            <param name="blastxml_file" value="blastn_arabidopsis.xml" ftype="blastxml" />
            <param name="out_format" value="std" />
            <output name="tabular_file" file="blastn_arabidopsis.standard.tabular" ftype="tabular" />
        </test>
        <test>
            <param name="blastxml_file" value="blastn_arabidopsis.xml" ftype="blastxml" />
            <param name="out_format" value="ext" />
            <output name="tabular_file" file="blastn_arabidopsis.extended.tabular" ftype="tabular" />
        </test>
    </tests>
    <help>
    
**What it does**

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 25 column tabular
BLAST output. This tool now uses this extended 25 column output by default.

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

    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
    25 salltitles    All subject title(s), separated by '<>'
====== ============= ===========================================

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