<tool id="spaln" name="Spaln: align cDNA or Protein to genome" version="@TOOL_VERSION@+galaxy0">
    <description>Maps and aligns a set of cDNA or protein sequences onto a whole genomic sequence.</description>
    <macros>
        <token name="@TOOL_VERSION@">2.3.2</token>
    </macros>
    <edam_topics>
        <edam_topic>topic_3512</edam_topic>
    </edam_topics>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">spaln</requirement>
    </requirements>
    <command detect_errors="aggressive"><![CDATA[
	    spaln -t\${GALAXY_SLOTS:-1} -O$format -o '$output1' '$genome' '$query'
    ]]></command>
    <inputs>
        <param type="data" name="genome" format="fasta" label="Genome sequence to search (FASTA format)" />
        <param type="data" name="query" format="fasta" label="Query sequence(s) (protein or cDNA)" />
	<param argument="-O" type="select" name="format" label="Output format">
	    <option value="0">GFF3 format genes</option>
	    <option value="2">GFF3 format matches</option>
	    <option value="3">BED format</option>
	    <option value="4">Tabular format exon information</option>
        </param>
    </inputs>
    <outputs>
        <data name="output1" format="tabular">
	    <change_format>
            <!-- these values correspond with the format options of the spaln command, not all of which are current supported -->
            <when input="format" value="0" format="gff3" />
            <when input="format" value="2" format="gff3" />
            <when input="format" value="3" format="bed12" />
            <when input="format" value="4" format="tabular" />
	    </change_format>
	    <!-- <actions> .. <conditional> .. <when> .. <action> current does not work in Galaxy,
		 something that https://github.com/galaxyproject/galaxy/pull/7197 is addressing, so this is
                 commented out till that is merged 
	    <actions>
	        <conditional name="format">
		    <when value="4">
                        <action type="metadata" name="column_names" default="rID,gID,%id,ExonL,MisMch,Unpair,ref_l,ref_r,tgt_l,tgt_r,eScore,IntrnL,iScore,Sig3/I,Sig5/T  # -  X P DiNuc" />
		    </when>
		</conditional>
	    </actions>
            -->
	</data>
    </outputs>
    <tests>
        <test>
            <param name="genome" ftype="fasta" value="genome.fasta" />
            <param name="query" ftype="fasta" value="query.fasta" />
            <param name="format" value="0"/>
	        <output name="output1" value="output1_gff_genes.gff3" />
        </test>
        <test>
            <param name="genome" ftype="fasta" value="genome.fasta" />
            <param name="query" ftype="fasta" value="query.fasta" />
            <param name="format" value="2"/>
	        <output name="output1" value="output1_gff_matches.gff3" />
        </test>
        <test>
            <param name="genome" ftype="fasta" value="genome.fasta" />
            <param name="query" ftype="fasta" value="query.fasta" />
            <param name="format" value="3"/>
	        <output name="output1" value="output1.bed12" />
        </test>
        <test>
            <param name="genome" ftype="fasta" value="genome.fasta" />
            <param name="query" ftype="fasta" value="query.fasta" />
            <param name="format" value="4"/>
	        <output name="output1" value="output1.tabular" />
        </test>
    </tests>
    <help><![CDATA[
        Spaln_ (space-efficient spliced alignment) is a stand-alone program that maps and aligns a set of cDNA or
        protein sequences onto a whole genomic sequence in a single job. 

        This Galaxy wrapper currently only supports the default (i.e. *-O3*) algorithm for Spaln with default parameters.

        .. _Spaln: http://www.genome.ist.i.kyoto-u.ac.jp/~aln_user/spaln/
    ]]></help>
    <citations>
        <citation type="doi">0.1093/nar/gkn105</citation>
    </citations>
</tool>