<tool id="blastXmlToPsl" name="blastXmlToPsl" version="0.1.0">
    <requirements>
    </requirements>
    <stdio>
        <exit_code range="1:" />
    </stdio>
    <command><![CDATA[
        $__tool_directory__/blastXmlToPsl -convertToNucCoords $input $output
    ]]></command>
    <inputs>
        <param type="data" name="input" format="xml" />
    </inputs>
    <outputs>
        <data format="psl" name="output" />
    </outputs>
    <help><![CDATA[
blastXmlToPsl - convert blast XML output to PSLs

usage:
   blastXmlToPsl [options] blastXml psl

options:
  -scores=file - Write score information to this file.  Format is:
    strands qName qStart qEnd tName tStart tEnd bitscore eVal qDef tDef

  -verbose=n - n >= 3 prints each line of file after parsing.
    n >= 4 dumps the result of each query

  -eVal=n n is e-value threshold to filter results. Format can be either
    an integer, double or 1e-10. Default is no filter.

  -pslx - create PSLX output (includes sequences for blocks)

  -convertToNucCoords - convert protein to nucleic alignments to nucleic
    to nucleic coordinates

  -qName=src - define element used to obtain the qName.  The following
    values are support:
     - query-ID - use contents of the <Iteration_query-ID> element if it
       exists, otherwise use <BlastOutput_query-ID>
     - query-def0 - use the first white-space separated word of the
       <Iteration_query-def> element if it exists, otherwise the first word
       of <BlastOutput_query-def>.

    Default is query-def0.

  -tName=src - define element used to obtain the tName.  The following
   values are support:
     - Hit_id - use contents of the <Hit-id> element.
     - Hit_def0 - use the first white-space separated word of the
       <Hit_def> element.
     - Hit_accession - contents of the <Hit_accession> element.

    Default is Hit-def0.

  -forcePsiBlast - treat as output of PSI-BLAST. blast-2.2.16 and maybe
   others indentify psiblast as blastp.

Output only results of last round from PSI BLAST
    ]]></help>
</tool>