<?xml version="1.0"?>
<tool name="Codon Switch Tool" id="codon_switch" version="0.2.6">
  <description>for each sequence in a file</description>
  <requirements>
    <requirement type="package" version="2.7.15">python</requirement>
    <requirement type="package" version="1.72">biopython</requirement>
    <requirement type="package" version="0.23.4">pandas</requirement>
    <requirement type="package" version="1.15.3">numpy</requirement>
  </requirements>

  <command>
<![CDATA[
  python '$__tool_directory__/codon_switch.py' -i $input -l $input_type -p $patterns -g $genome -g $genome_type -c $codon_table -f $num_plasmids -m $row_len -d $demonstration -o $output
]]>
  </command>
  <inputs>
    <param name="input" format="genbank" type="data" label="Input plasmid"/>

    <param name="input_type" type="select" format="text">
			<label>Indicate the input file format.</label>
			<option value="genbank">genbank</option>
		</param>

    <param name="patterns" format="txt" type="data" label="Patterns file"/>

    <param name="genome" format="genbank" type="data" label="Input Genome"/>

    <param name="genome_type" type="select" format="text">
			<label>Indicate the input genome format.</label>
      <option value="fasta">fasta</option>
      <option value="genbank">genbank</option>
		</param>

    <param name="demonstration" type="select" format="text">
			<label>Demonstration</label>
      <option value="demonstration">yes</option>
      <option value="no_demonstration">no</option>
		</param>

    <param name="num_plasmids" type="select" format="text">
			<label>Indicate the number of best output plamids.</label>
      <option value=3>3</option>
      <option value=7>7</option>
		</param>

    <param name="row_len" type="select" format="text">
			<label>Indicate the length of the row in report file.</label>
      <option value=9>9</option>
      <option value=27>27</option>
		</param>

    <param name="codon_table" type="select" format="text">
			<label>Choose the proper codon table for your organism.</label>
        <option value="Alternative Flatworm Mitochondrial">"Alternative Flatworm Mitochondrial"</option>
        <option value="Alternative Yeast Nuclear">"Alternative Yeast Nuclear"</option>
        <option value="Archaeal">"Archaeal"</option>
        <option value="Ascidian Mitochondrial">"Ascidian Mitochondrial"</option>
        <option value="Bacterial">"Bacterial"</option>
        <option value="Blastocrithidia Nuclear">"Blastocrithidia Nuclear"</option>
        <option value="Blepharisma Macronuclear">"Blepharisma Macronuclear"</option>
        <option value="Candidate Division SR1">"Candidate Division SR1"</option>
        <option value="Chlorophycean Mitochondrial">"Chlorophycean Mitochondrial"</option>
        <option value="Ciliate Nuclear">"Ciliate Nuclear"</option>
        <option value="Coelenterate Mitochondrial">"Coelenterate Mitochondrial"</option>
        <option value="Condylostoma Nuclear">"Condylostoma Nuclear"</option>
        <option value="Dasycladacean Nuclear">"Dasycladacean Nuclear"</option>
        <option value="Echinoderm Mitochondrial">"Echinoderm Mitochondrial"</option>
        <option value="Euplotid Nuclear">"Euplotid Nuclear"</option>
        <option value="Flatworm Mitochondrial">"Flatworm Mitochondrial"</option>
        <option value="Gracilibacteria">"Gracilibacteria"</option>
        <option value="Hexamita Nuclear">"Hexamita Nuclear"</option>
        <option value="Invertebrate Mitochondrial">"Invertebrate Mitochondrial"</option>
        <option value="Karyorelict Nuclear">"Karyorelict Nuclear"</option>
        <option value="Mesodinium Nuclear">"Mesodinium Nuclear"</option>
        <option value="Mold Mitochondrial">"Mold Mitochondrial"</option>
        <option value="Mycoplasma">"Mycoplasma"</option>
        <option value="Pachysolen tannophilus Nuclear">"Pachysolen tannophilus Nuclear"</option>
        <option value="Peritrich Nuclear">"Peritrich Nuclear"</option>
        <option value="Plant Plastid">"Plant Plastid"</option>
        <option value="Protozoan Mitochondrial">"Protozoan Mitochondrial"</option>
        <option value="Pterobranchia Mitochondrial">"Pterobranchia Mitochondrial"</option>
        <option value="SGC0">"SGC0"</option>
        <option value="SGC1">"SGC1"</option>
        <option value="SGC2">"SGC2"</option>
        <option value="SGC3">"SGC3"</option>
        <option value="SGC4">"SGC4"</option>
        <option value="SGC5">"SGC5"</option>
        <option value="SGC8">"SGC8"</option>
        <option value="SGC9">"SGC9"</option>
        <option value="Scenedesmus obliquus Mitochondrial">"Scenedesmus obliquus Mitochondrial"</option>
        <option value="Spiroplasma">"Spiroplasma"</option>
        <option value="Standard">"Standard"</option>
        <option value="Thraustochytrium Mitochondrial">"Thraustochytrium Mitochondrial"</option>
        <option value="Trematode Mitochondrial">"Trematode Mitochondrial"</option>
        <option value="Vertebrate Mitochondrial">"Vertebrate Mitochondrial"</option>
        <option value="Yeast Mitochondrial">"Yeast Mitochondrial"</option>
		</param>
  </inputs>

  <outputs>
    <data format="tabular" name="output" />
  </outputs>

  <help>
This tool permits codon switch and transversion in targeted regions.
  </help>
</tool>