<tool id="blastxml_to_tabular_selectable" name="BLAST XML to selected tabular columns" version="0.0.9">
    <description>Convert BLAST XML output to tabular</description>
    <command interpreter="python">
      blastxml_to_tabular_selectable.py -o $tabular_file 
      #if $output.out_format == 'cols' and $output.columns:
        -c '$output.columns'
      #else
        -c '$output.out_format' 
      #end if
      $qdef
      $allqueries
      #if $unmatched:
        -u $unmatched_file
      #end if
      #if $maxhits.__str__ != '':
        --maxhits $maxhits
      #end if
      #if $maxhsps.__str__ != '':
        --maxhsps $maxhsps
      #end if
      #for i in $blastxml_file#${i} #end for#
      ## $blastxml_file 
    </command>
    <inputs>
        <param name="blastxml_file" type="data" format="blastxml" multiple="true" label="BLAST results as XML"/> 
        <param name="qdef" type="boolean" truevalue="-d" falsevalue="" checked="False" label="Use Iteration_query-def value for qseqid"/>
        <param name="allqueries" type="boolean" truevalue="-a" falsevalue="" checked="False" label="Output all queries including those with no hits"/>
        <param name="unmatched" type="boolean" truevalue="-u" falsevalue="" checked="False" label="Output a list with queries having no hits"/>
        <param name="maxhits" type="integer" value="1" optional="true" label="Maximum number of Hits to display for a query">
          <validator type="in_range" min="1" />
        </param>
        <param name="maxhsps" type="integer" value="1" optional="true" label="Maximum number of HSPs to display for a Hit">
          <validator type="in_range" min="1" />
        </param>
      
        <conditional name="output">
          <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="cols">Tabular (select columns to output)</option>
          </param>
          <when value="std"/>
          <when value="ext"/>
          <when value="cols">
            <param name="columns" type="select" multiple="true" display="checkboxes" label="Output columns">
              <option value="qseqid"> 1 qseqid     Query Seq-id (ID of your sequence)</option>
              <option value="sseqid"> 2 sseqid     Subject Seq-id (ID of the database hit)</option>
              <option value="pident"> 3 pident     Percentage of identical matches</option>
              <option value="length"> 4 length     Alignment length</option>
              <option value="mismatch"> 5 mismatch   Number of mismatches</option>
              <option value="gapopen"> 6 gapopen    Number of gap openings</option>
              <option value="qstart"> 7 qstart     Start of alignment in query</option>
              <option value="qend"> 8 qend       End of alignment in query</option>
              <option value="sstart"> 9 sstart     Start of alignment in subject (database hit)</option>
              <option value="send">10 send       End of alignment in subject (database hit)</option>
              <option value="evalue">11 evalue     Expectation value (E-value)</option>
              <option value="bitscore">12 bitscore   Bit score</option>
              <option value="sallseqid">13 sallseqid  All subject Seq-id(s), separated by a ';'</option>
              <option value="score">14 score      Raw score</option>
              <option value="nident">15 nident     Number of identical matches</option>
              <option value="positive">16 positive   Number of positive-scoring matches</option>
              <option value="gaps">17 gaps       Total number of gaps</option>
              <option value="ppos">18 ppos       Percentage of positive-scoring matches</option>
              <option value="qframe">19 qframe     Query frame</option>
              <option value="sframe">20 sframe     Subject frame</option>
              <option value="qseq">21 qseq       Aligned part of query sequence</option>
              <option value="sseq">22 sseq       Aligned part of subject sequence</option>
              <option value="qlen">23 qlen       Query sequence length</option>
              <option value="slen">24 slen       Subject sequence length</option>
              <option value="salltitles">25 salltitles = All subject title(s), separated by a '&lt;&gt;'</option>
            </param>
          </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="tabular_file" format="tabular" label="BLAST results as tabular for ${on_string}" />
        <data name="unmatched_file" format="tabular" label="Query sequences with no hits for ${on_string}">
          <filter>unmatched == True</filter>
        </data>
    </outputs>
    <requirements>
    </requirements>
    <tests>
        <test>
            <param name="blastxml_file" value="blastp_rhodopsin_proteins.xml" ftype="blastxml" />
            <param name="out_format" value="std" />
            <output name="tabular_file" file="blastp_rhodopsin_proteins_std.tabular" ftype="tabular" />
        </test>
        <test>
            <param name="blastxml_file" value="blastp_rhodopsin_proteins.xml" ftype="blastxml" />
            <param name="out_format" value="ext" />
            <output name="tabular_file" file="blastp_rhodopsin_proteins_ext.tabular" ftype="tabular" />
        </test>
        <test>
            <param name="blastxml_file" value="blastp_rhodopsin_proteins.xml" ftype="blastxml" />
            <param name="out_format" value="cols" />
            <param name="columns" value="qseqid,sseqid,length,bitscore" />
            <output name="tabular_file" file="blastp_rhodopsin_proteins_selcol.tabular" ftype="tabular" />
        </test>
        <test>
            <param name="blastxml_file" value="blastp_rhodopsin_proteins.xml" ftype="blastxml" />
            <param name="out_format" value="ext" />
            <param name="maxhits" value="10" />
            <param name="maxhsps" value="10" />
            <output name="tabular_file" file="blastp_rhodopsin_proteins_ext_allhits.tabular" ftype="tabular" />
        </test>
        <test>
            <param name="blastxml_file" value="blastp_rhodopsin_proteins.xml" ftype="blastxml" />
            <param name="out_format" value="ext" />
            <param name="maxhits" value="1" />
            <param name="maxhsps" value="1" />
            <param name="unmatched" value="True" />
            <param name="allqueries" value="True" />
            <output name="tabular_file" file="blastp_rhodopsin_proteins_ext_allqueries.tabular" ftype="tabular" />
            <output name="unmatched_file" file="unmatched_queries.tabular" ftype="tabular" />
        </test>
    </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 - 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 22 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
    25 salltitles    All subject title(s), separated by a '&lt;&gt;'
====== ============= ===========================================

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>