<tool id="ucsc_axtomaf" name="axtToMaf" version="@TOOL_VERSION@+galaxy1" profile="21.05" license="MIT">
    <description>
        Convert dataset from axt to MAF format
    </description>
    <macros>
        <token name="@TOOL_VERSION@">469</token>
        <xml name="sanitize_query">
            <sanitizer>
                <valid initial="string.printable">
                    <remove value=" "/>
                    <remove value="&apos;" />
                </valid>
                <mapping initial="none">
                    <add source=" " target=""/>
                    <add source="&apos;" target="&apos;&quot;&apos;&quot;&apos;"/>
                </mapping>
            </sanitizer>
        </xml>
    </macros>
    <xrefs>
        <xref type="bio.tools">UCSC_Genome_Browser_Utilities</xref>
    </xrefs>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">ucsc-axttomaf</requirement>
    </requirements>
    <version_command><![CDATA[ echo "@TOOL_VERSION@" ]]></version_command>
    <command detect_errors="exit_code"><![CDATA[
    axtToMaf
        '$in_axt'
        #if str( $target_reference_index_source.target_reference_index_source_selector ) == "history":
            '${target_reference_index_source.in_tar_ref_index}'
        #else:
            '$target_reference_index_source.tar_ref_index_file.fields.path'
        #end if
        #if str( $query_reference_index_source.query_reference_index_source_selector ) == "history":
            '${query_reference_index_source.in_que_ref_index}'
        #else:
            '$query_reference_index_source.que_ref_index_file.fields.path'
        #end if
        #if str($t_prefix)
            -tPrefix='$t_prefix'
        #end if
        #if str($q_prefix)
            -qPrefix='$q_prefix'
        #end if
        $score
        $scoreZero
        '$out'
    ]]></command>
    <inputs>
        <param name="in_axt" format="axt" type="data" label="axt file" />

        <conditional name="target_reference_index_source">
            <param name="target_reference_index_source_selector" type="select" label="Choose the source for the target reference genome index">
                <option value="cached">Built-in</option>
                <option value="history">My history</option>
            </param>
            <when value="cached">
                <param name="tar_ref_index_file" type="select" label="Using reference genome index">
                  <options from_data_table="fasta_indexes" />
                </param>
            </when>
            <when value="history">
                <param name="in_tar_ref_index" format="tabular" type="data" label="Dataset with chrom sizes for target sequence. Typically a '.fai' file." />
            </when>
        </conditional>

        <conditional name="query_reference_index_source">
            <param name="query_reference_index_source_selector" type="select" label="Choose the source for the target reference genome index">
                <option value="cached">Built-in</option>
                <option value="history">My history</option>
            </param>
            <when value="cached">
                <param name="que_ref_index_file" type="select" label="Using reference genome index">
                  <options from_data_table="fasta_indexes" />
                </param>
            </when>
            <when value="history">
                <param name="in_que_ref_index" format="tabular" type="data" label="Dataset with chrom sizes for query sequence. Typically a '.fai' file." />
            </when>
        </conditional>

        <param name="t_prefix" type="text" optional="true" label="add this to start of TARGET sequence name in maf" help="Typically organism name and a dot (hg38.) is used">
            <expand macro="sanitize_query"/>
        </param>
        <param name="q_prefix" type="text" optional="true" label="add this to start of QUERY sequence name in maf" help="Typically organism name and a dot (mm10.) is used">
            <expand macro="sanitize_query"/>
        </param>
        <param argument="-score" type="boolean" truevalue="-score" falsevalue="" label="Recalculate score" />
        <param argument="-scoreZero" type="boolean" truevalue="-scoreZero" falsevalue="" label="Recalculate score if zero" />
    </inputs>
    <outputs>
        <data name="out" format="maf" />
    </outputs>
    <tests>
        <test>
            <param name="in_axt" value="1.axt"/>
            <conditional name="target_reference_index_source">
                <param name="target_reference_index_source_selector" value="history" />
                <param name="in_tar_ref_index" value="hg38.fasta.fai"/>
            </conditional>
            <conditional name="query_reference_index_source">
                <param name="query_reference_index_source_selector" value="history" />
                <param name="in_que_ref_index" value="mm39.fasta.fai"/>
            </conditional>
            <output name="out" file="1.maf"/>
        </test>
        <test>
            <param name="in_axt" value="2.axt"/>
            <conditional name="target_reference_index_source">
                <param name="target_reference_index_source_selector" value="history" />
                <param name="in_tar_ref_index" value="hg38.noprefix.fasta.fai"/>
            </conditional>
            <conditional name="query_reference_index_source">
                <param name="query_reference_index_source_selector" value="history" />
                <param name="in_que_ref_index" value="mm39.noprefix.fasta.fai"/>
            </conditional>
            <param name="t_prefix" value="hg38." />
            <param name="q_prefix" value="mm39." />
            <output name="out" file="1.maf"/>
        </test>
        <test>
            <param name="in_axt" value="1.axt"/>
            <conditional name="target_reference_index_source">
                <param name="target_reference_index_source_selector" value="cached" />
                <param name="tar_ref_index_file" value="hg38"/>
            </conditional>
            <conditional name="query_reference_index_source">
                <param name="query_reference_index_source_selector" value="cached" />
                <param name="que_ref_index_file" value="mm39"/>
            </conditional>
            <output name="out" file="1.maf"/>
        </test>
    </tests>
    <help><![CDATA[
**What it does**

`axtToMaf`_ is a tool to convert dataset from `axt format`_ to `MAF format`_.

For implementation details see axtToMaf's `source code`_.

.. _axtToMaf: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/FOOTER.txt
.. _axt format: https://genome.ucsc.edu/goldenPath/help/axt.html
.. _MAF format: https://genome.ucsc.edu/FAQ/FAQformat.html#format5
.. _source code: https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/mouseStuff/axtToMaf/axtToMaf.c
    ]]>    </help>
    <citations>
        <citation type="doi">10.1093/bib/bbs038</citation>
    </citations>
</tool>