<tool id="glimmer_build_icm" name="Glimmer ICM builder" version="@WRAPPER_VERSION@">
    <description></description>
    <expand macro="bio_tools"/>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command><![CDATA[
        build-icm
            --depth $depth
            $no_stops
            --period $period
            --width $width

            #if $stop_codon_opts.stop_codon_opts_selector == "gb":
                --trans_table '${stop_codon_opts.genbank_gencode}'
            #else:
                --stop_codons '${stop_codon_opts.stop_codons}'
            #end if

            '$outfile' < '$infile' 2>&1;
]]></command>
    <inputs>
        <param name="infile" type="data" format="fasta" label="Trainings Dataset" help="A set of known genes in FASTA format." />
        <param name="depth" type="integer" value="7" label="Set the depth of the ICM" help="The depth is the maximum number of positions in the context window that will be used to determine the probability of the predicted position." />
        <param name="period" type="integer" value="3" label="Set the period of the ICM" help="The period is the number of different submodels for different positions in the text in a cyclic pattern. E.g., if the period is 3, the first submodel will determine positions 1, 4, 7, ..." />
        <param name="width" type="integer" value="12" label="Set the width of the ICM" help="The width includes the predicted position." />
        <param name="no_stops" type="boolean" truevalue="--no_stops" falsevalue="" checked="false" label="Do not use any input strings with in-frame stop codons" />

        <conditional name="stop_codon_opts">
            <param name="stop_codon_opts_selector" type="select" label="Specify start codons as">
              <option value="gb" selected="True">Genbank translation table entry</option>
              <option value="free_form">Comma-separated list</option>
            </param>
            <when value="gb">
                <param name="genbank_gencode" type="select" label="Use Genbank translation table to specify stop codons">
                    <option value="1" selected="True">1. Standard</option>
                    <option value="2">2. Vertebrate Mitochondrial</option>
                    <option value="3">3. Yeast Mitochondrial</option>
                    <option value="4">4. Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option>
                    <option value="5">5. Invertebrate Mitochondrial</option>
                    <option value="6">6. Ciliate, Dasycladacean and Hexamita Nuclear Code</option>
                    <option value="9">9. Echinoderm Mitochondrial</option>
                    <option value="10">10. Euplotid Nuclear</option>
                    <option value="11">11. Bacteria and Archaea</option>
                    <option value="12">12. Alternative Yeast Nuclear</option>
                    <option value="13">13. Ascidian Mitochondrial</option>
                    <option value="14">14. Flatworm Mitochondrial</option>
                    <option value="15">15. Blepharisma Macronuclear</option>
                    <option value="16">16. Chlorophycean Mitochondrial</option>
                    <option value="21">21. Trematode Mitochondrial</option>
                    <option value="22">22. Scenedesmus obliquus mitochondrial</option>
                    <option value="23">23. Thraustochytrium Mitochondrial</option>
                    <option value="24">24. Pterobranchia mitochondrial</option>
                </param>
            </when>
            <when value="free_form">
                <param name="stop_codons" type="text" value="tag,tga,taa" label="Specify stop codons as a comma-separated list" />
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data format="data" name="outfile" />
    </outputs>
    <tests>
        <test>
            <param name="infile" value='streptomyces_Tu6071_plasmid_genes.fasta' />
            <param name="depth" value="7" />
            <param name="period" value="3" />
            <param name="width" value="12" />
            <param name="no_stops" value="" />
            <param name="genbank_gencode" value="11" />
            <!-- compare files sizes, because the output is a binary -->
            <output name="outfile" file='streptomyces_Tu6071_plasmid_genes.icm' compare="sim_size" delta="1000" ftype="data" />
        </test>
    </tests>

    <help>
<![CDATA[

**What it does**

This program constructs an interpolated context model (ICM) from an input set of sequences.

This model can be used by Glimmer3 to predict genes.

**TIP** To extract CDS from a GenBank file use the tool *Extract ORF from a GenBank file*.

-----

**Example**

*Input*::

	- Genome Sequence

		>CELF22B7  C.aenorhabditis elegans (Bristol N2) cosmid F22B7
		GATCCTTGTAGATTTTGAATTTGAAGTTTTTTCTCATTCCAAAACTCTGT
		GATCTGAAATAAAATGTCTCAAAAAAATAGAAGAAAACATTGCTTTATAT
		TTATCAGTTATGGTTTTCAAAATTTTCTGACATACCGTTTTGCTTCTTTT
		TTTCTCATCTTCTTCAAATATCAATTGTGATAATCTGACTCCTAACAATC
		GAATTTCTTTTCCTTTTTCTTTTTCCAACAACTCCAGTGAGAACTTTTGA
		ATATCTTCAAGTGACTTCACCACATCAGAAGGTGTCAACGATCTTGTGAG
		AACATCGAATGAAGATAATTTTAATTTTAGAGTTACAGTTTTTCCTCCGA
		CAATTCCTGATTTACGAACATCTTCTTCAAGCATTCTACAGATTTCTTGA
		TGCTCTTCTAGGAGGATGTTGAAATCCGAAGTTGGAGAAAAAGTTCTCTC
		AACTGAAATGCTTTTTCTTCGTGGATCCGATTCAGATGGACGACCTGGCA
		GTCCGAGAGCCGTTCGAAGGAAAGATTCTTGTGAGAGAGGCGTGAAACAC
		AAAGGGTATAGGTTCTTCTTCAGATTCATATCACCAACAGTTTGAATATC
		CATTGCTTTCAGTTGAGCTTCGCATACACGACCAATTCCTCCAACCTAAA
		AAATTATCTAGGTAAAACTAGAAGGTTATGCTTTAATAGTCTCACCTTAC
		GAATCGGTAAATCCTTCAAAAACTCCATAATCGCGTTTTTATCATTTTCT
		.....

*Output*::
	interpolated context model (ICM)



]]>
    </help>
    <expand macro="citation" />
</tool>