<tool id="transtermhp" name="TransTermHP" version="@WRAPPER_VERSION@.1">
    <description>finds rho-independent transcription terminators in bacterial genomes</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="stdio"/>
    <command><![CDATA[
## fix for TRANSTERMHP not set on containers
TRANSTERMHP=\${TRANSTERMHP:-\$(dirname \$(command -v transterm))/../data/expterm.dat} &&
#if $reference_genome.source == 'history':
    ln -s '$reference_genome.genome_fasta' genomeref.fa &&
#end if

python '$__tool_directory__/transtermhp.py' \$TRANSTERMHP

#if $reference_genome.source == 'cached':
    '${reference_genome.fasta_indexes.fields.path}'
#elif $reference_genome.source == 'history':
    genomeref.fa
#end if

'$input_gff3'
> '$output'
    ]]></command>
    <inputs>
      <conditional name="reference_genome">
        <param name="source" type="select" label="Reference Genome">
              <option value="cached">Locally Cached</option>
              <option value="history">From History</option>
        </param>
        <when value="cached">
            <param name="fasta_indexes" type="select" label="Source FASTA Sequence">
                <options from_data_table="all_fasta"/>
                <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
            </param>
        </when>
        <when value="history">
            <param name="genome_fasta" type="data" format="fasta" label="Source FASTA Sequence"/>
        </when>
    </conditional>
    <param name="input_gff3" type="data" format="gff3" label="GFF3 formatted Gene Calls"/>

    <!-- Currently we do not support ANY of the command line options for
         TransTermHP due to the following statement:

            As mentioned above, if you change any of the basic scoring
            function and search parameters and are using the version 2.0
            confidence scheme (recommended) then you have to recompute
            the values in the expterm.dat file. If you have python
            installed this is easy (though perhaps time consuming).

            ref: http://manpages.ubuntu.com/manpages/precise/man1/transterm.1.html

        This is a TODO item that would be nice to get around to eventually
        (perhaps when a user demands it.)
        -->
    </inputs>
    <outputs>
        <data format="gff3" name="output"/>
    </outputs>
    <tests>
        <test>
            <param name="source" value="history" />
            <param name="genome_fasta" value="sequence.fasta" />
            <param name="input_gff3" value="sequence.gff3" />
            <output name="output" file="sequence.gff3.out" />
        </test>
    </tests>
    <help><![CDATA[
**What it does**

Finds rho-independent transcription terminators in bacterial genomes.
]]></help>
    <citations>
        <citation type="doi">doi:10.1186/gb-2007-8-2-r22</citation>
    </citations>
</tool>