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<tool id="snap" name="Semi-HMM-based Nucleic Acid Parser (SNAP)" version="1.0">
    <requirements>
        <requirement type="package" version="1.0">snap</requirement>
    </requirements>
    <stdio>
        <exit_code range="1:" />
    </stdio>
    <command><![CDATA[
        snap
        #if $settings.advanced == "advanced"
        $settings.lcmask
            #if $settings.strand == "true"
                $settings.strand.onestrand
            #end if
        #end if
        #if $proteins == "-aa":
        $proteins "$output2"
        #end if
        #if $transcripts == "-tx":
        $transcripts "$output3"
        #end if
        -gff
        -quiet
        $organism
        $input1
        | python $__tool_directory__/gff2Togff3.py --output $output1
    ]]></command>
    <inputs>
        <param type="data" name="input1" format="fasta" />
        <param name="organism" label="Model Organism" type="select" multiple="false" format="text" help="Choose a specialised trainingset.">
            <option value="A.gambiae.hmm">A.gambiae</option>
            <option value="A.mellifera.hmm">A.mellifera</option>
            <option value="A.thaliana.hmm">Arabidopsis thaliana</option>
            <option value="Acanium.hmm">Acanium</option>
            <option value="At.hmm">Thale</option>
            <option value="B.malayi.hmm">Brugia</option>
            <option value="B.mori.hmm">B.mori</option>
            <option value="C.elegans.hmm">C.elegans</option>
            <option value="C.intestinalis.hmm">Ciona</option>
            <option value="Ce.hmm">Ce</option>
            <option value="D.melanogaster.hmm">Drosophila melanogaster</option>
            <option value="Dm.hmm">Dm</option>
            <option value="ixodesA.hmm">ixodesA</option>
            <option value="ixodesB.hmm">ixodesB</option>
            <option value="mam39-ro.hmm">mam39-ro</option>
            <option value="mam39.hmm">mam39</option>
            <option value="mam46-ro.hmm">mam46-ro</option>
            <option value="mam46.hmm">mam46</option>
            <option value="mam54-ro.hmm">mam54-ro</option>
            <option value="mam54.hmm">mam54</option>
            <option value="mamiso.hmm">mamiso</option>
            <option value="minimal.hmm">minimal</option>
            <option value="Nasonia.hmm">Nasonia</option>
            <option value="nGASP.hmm">nGASP</option>
            <option value="nGASPr.hmm">nGASPr</option>
            <option value="O.sativa.hmm">O.sativa</option>
            <option value="Os.hmm">Os</option>
        </param>
        <param name="proteins" type="select" label="Create FASTA file of proteins">
            <option value="">No</option>
            <option value="-aa">Yes</option>
        </param>
        <param name="transcripts" type="select" label="Create FASTA file of transcripts">
            <option value="">No</option>
            <option value="-tx">Yes</option>
        </param>
        <conditional name="settings">
            <param name="advanced" type="select" label="Specify advanced parameters">
                <option value="simple" selected="true">No, use program defaults.</option>
                <option value="advanced">Yes, see full parameter list.</option>
            </param>
            <when value="simple">
            </when>
            <when value="advanced">
                <param name="lcmask" type="boolean" label="treat lowercase as N" truevalue="-lcmask" falsevalue="" />
                <conditional name="strand">
                    <param name="strand" type="boolean" label="predict on one strand only" />
                    <when value="true">
                    <param name="onestrand" type="select" label="Specify which strand to predict">
                        <option value="-plus">predict on plus strand only.</option>
                        <option value="-minus">predict on minus strand only.</option>
                    </param>
                    </when>
                    <when value="false">
                    </when>
                </conditional>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="output1" format="gff3" label="${tool.name} on ${on_string}: GTF/GFF3">
        </data>
        <data name="output2" format="fasta" label="${tool.name} on ${on_string}: Protein sequence">
            <filter>proteins == "-aa"</filter>
        </data>
        <data name="output3" format="fasta" label="${tool.name} on ${on_string}: Coding sequence">
            <filter>transcripts == "-tx"</filter>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="input1" value="thale.dna.gz"/>
            <param name="organism" value="At.hmm" />
            <output name="output1" file="thale.gff3"/>
        </test>
    </tests>
    <help><![CDATA[
        The general form of the snap command line is:

    snap <HMM file> <FASTA file> [options]

HMM file:

    The most convenient way to specify the HMM file is by name. This requires
    that the ZOE environment variable is set. In this case, snap will look
    for the HMM file in $ZOE/HMM. You may also specify the HMM file by an
    explicit path. The following are equivalent if $ZOE is in /usr/local:

        snap C.elegans.hmm ...
        snap /usr/local/Zoe/HMM/C.elegans.hmm ...
        snap worm ...  # there are a few convenient aliases in $ZOE/HMM

FASTA file:

    If you have several sequences to analyze, it is more efficient to run
    snap on a concatenated FASTA file rather than separate runs on single
    sequence files. The seqeuence may be in a compressed format

    If sequences have been masked with lowercase letters, use -lcmask to
    prevent exons from appearing in masked DNA.

Output:

    Annotation is reported to stdout in a non-standard format (ZFF). You can
    change to GFF or ACEDB with the -gff or -ace options. Proteins and
    transcripts are reported to FASTA files with the -aa and -tx options.

External definitions:

    SNAP allows you to adjust the score of any sequence model at any point
    in a sequence. This behavior is invoked by giving a ZFF file to SNAP:

        snap <hmm> <sequence> -xdef <ZFF file>

    Each feature description uses the 'group' field to issue a command:

        SET     set the score
        ADJ     adjust the score up or down
        OK      set non-cannonical scores

     >FOO
     Acceptor 120 120 + +50 . . . SET  (sets an Acceptor to 50)
     Donor    212 212 + -20 . . . ADJ  (lowers a Donor by -20)
     Inter    338 579 +  -2 . . . ADJ  (lowers Inter by -2 in a range)
     Coding   440 512 -  +3 . . . ADJ  (raises Coding by +3 in a range)
     Donor    625 638 +  -5 . . . OK   (sets range of odd Donors to -5)

If the output has scrolled off your screen, try 'snap -help | more'

    ]]></help>
    <citations>
        <citation type="bibtex">
@misc{renameTODO,
  author = {LastTODO, FirstTODO},
  year = {TODO},
  title = {TODO},
  url = {http://korflab.ucdavis.edu/Software/snap-2013-11-29.tar.gz},
}</citation>
    </citations>
</tool>