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planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/mitos commit a7354d02377105590891f7337f472dc2a2f224a4

<tool id="mitos" name="MITOS" version="1.0.1">	
  <description>de-novo annotation of metazoan mitochondrial genomes</description>
  <!--Gene structure, regions which make an RNA product and features such as promoters, coding regions, gene fusion, splice sites etc.-->
  <edam_topics>
      <edam_topic>topic_0114</edam_topic>
  </edam_topics>
  <!--Annotate a genome sequence with terms from a controlled vocabulary-->
  <edam_operations>
      <edam_operation>operation_0362</edam_operation>
  </edam_operations>
  <requirements>
    <requirement type="package" version="1.0.1">mitos</requirement>
    <requirement type="package">zip</requirement>
  </requirements>
  <version_command>python usage: %prog [options] --version</version_command>
  <command detect_errors="aggressive"><![CDATA[
mkdir outdir && 

runmitos.py 
--input '$input'
--code $code
--outdir outdir
--refdir /home/maze/workspace/mtdb/data/
#if not "prot" in $advanced.featuretypes
--noprot
#end if
#if not "trna" in $advanced.featuretypes
--notrna
#end if
#if not "rrna" in $advanced.featuretypes
--norrna
#end if
--finovl $advanced.finovl
--evalue $advanced_prot.evalue
--cutoff $advanced_prot.cutoff
#set maxovl=float($advanced_prot.maxovl)/100.0
--maxovl $maxovl
--clipfac $advanced_prot.clipfac
#set fragovl=float($advanced_prot.fragovl)/100.0
--fragovl $fragovl
--fragfac $advanced_prot.fragfac
--ststrange $advanced_prot.ststrange

#if "zip" in $outputs:
    zip -9 -y -r output.zip output/"
#end if

]]></command>
  <inputs>
    <param argument="--input" label="Sequences" optional="false" type="data" format="fasta"/>
    <param argument="--code" label="Genetic code" name="code" type="select">
      <option value="2">Vertebrate</option>
      <option value="4">Mold, Protozoan, Coelenteral</option>
      <option value="5">Invertebrate</option>
      <option value="9">Echinoderm, Flatworm</option>
      <option value="13">Ascidian</option>
      <option value="14">Alternative Flatworm</option>
    </param>
    <section name="advanced" title="Advanced options">
      <param name="featuretypes" label="Feature types" help="Feature types that should be predicted by MITOS" type="select" multiple="true">
        <option value="prot" selected="true">Proteins</option>
        <option value="trna" selected="true">tRNAs</option>
        <option value="rrna" selected="true">rRNAs</option>
      </param>
      <param argument="--finovl" label="Final overlap (nt)" help="Maximum number of nucleotides by which genes of different types may overlap" type="integer" value="35" min="0"/>
    </section>
    <section name="advanced_prot" title="Advanced options for protein coding gene prediction">
      <param argument="--evalue" label="BLAST E-value Exponent" help="Negation of the exponent of the E-value threshold used by BLAST, i.e. a value X gives an E-value of 10^(-X)" type="float" value="2" min="0"/>
      <param argument="--cutoff" label="Quality cutoff" help="Minimum allowed quality in % of the maximum quality value per reading frame" type="integer" value="50" min="0" max="100"/>
      <param argument="--maxovl" label="Maximum overlap" help="Maximum allowed overlap of proteins in percent of the smaller feature " type="integer" value="20" min="0" max="100"/>
      <param argument="--clipfac" label="Clipping factor" help="Clip overlapping proteins with the same name that differ by less than the specified factor" type="float" value="10" min="0"/>
      <param argument="--fragovl" label="Fragment overlap" help="Maximum allowed overlap of proteins in the query (in percent of the shorter query range) for two hits to be counted as fragments of the same gene" type="integer" value="20" min="0" max="100"/>
      <param argument="--fragfac" label="Fragment quality factor" help="Maximum factor by which fragments of the same protein may differ in their quality" type="float" value="10"/>
      <param argument="--ststrange" label="Start/stop range" help="Number of aminoacids searched for start and stop codon of proteins" type="integer" value="6"/>
    </section>
    <param name="outputs" type="select" multiple="true" label="Additional outputs">
	    <option value="mito">mito</mito>
	    <option value="seq">SEQ</mito>
	    <option value="raw">zipped raw results</mito>
	    </param>
  </inputs>
  <outputs>
    <data name="bedout" format="bed" from_work_dir="outdir/result.bed"/>
    <data name="seqout" format="txt" from_work_dir="outdir/result.seq">
	    <filter>"seq" in outputs</filter>
    </data>
    <data name="mitoout" format="tabular" from_work_dir="outdir/result">
	    <filter>"mito" in outputs</filter>
    </data>
    <data name="rawout" format="zip" from_work_dir="outdir.zip">
	    <filter>"raw" in outputs</filter>
    </data>
  </outputs>
  <help><![CDATA[
TODO: Write help
  ]]></help>
  <citations>
    <citation type="doi">10.1016/j.ympev.2012.08.023</citation>
  </citations>
</tool>