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<tool id="blastXmlToPsl" name="blastXmlToPsl" version="1.1">
    <requirements>
    </requirements>
    <stdio>
        <exit_code range="1:" />
    </stdio>
    <command><![CDATA[
        $__tool_directory__/blastXmlToPsl $input $output
        #if $convertToNucCoords == "true"
          -convertToNucCoords
        #end if
    ]]></command>
    <inputs>
        <param type="data" name="input" format="xml" />
        <param type="boolean" name="convertToNucCoords" checked="true" label="-convertToNucCoords" help="Only support for TBLASTN restuls. Convert protein to nucleic alignments to nucleic
   to nucleic coordinates"/>
    </inputs>
    <outputs>
        <data format="psl" name="output" />
    </outputs>
    <tests>
        <test>
            <param name="input" value="tblastn_Dbia3_ci.xml" />
            <param name="convertToNucCoords" value="true" />
            <output name="output" value="tblastn_Dbia3_ci.psl" />
        </test>
        <test>
            <param name="input" value="blastn_mRNA_seq.xml" />
            <param name="convertToNucCoords" value="false" />
            <output name="output" value="blastn_mRNA_seq.psl" />
        </test>
    </tests>
    <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>
    <citations>
        <citation type="bibtex">
            @article{Kent01062002,
            author = {Kent, W. James and Sugnet, Charles W. and Furey, Terrence S. and Roskin, Krishna M. and Pringle, Tom H. and Zahler, Alan M. and Haussler,  and David},
            title = {The Human Genome Browser at UCSC},
            volume = {12},
            number = {6},
            pages = {996-1006},
            year = {2002},
            doi = {10.1101/gr.229102},
            URL = {http://genome.cshlp.org/content/12/6/996.abstract},
            eprint = {http://genome.cshlp.org/content/12/6/996.full.pdf+html},
            journal = {Genome Research}
            }
        </citation>
    </citations>
</tool>