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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"

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@MITOS_NAME@ does a de-novo annotation of a given metazoan mitochondrial sequence.

**Inputs**

- A fasta formatted sequence

  - @MITOS_NAME@ processes only FASTA files containing a single sequence. If you have a FASTA file with multiple sequences you may use the tool *Split Fasta files into a collection". The resulting collection can then used as input to @MITOS_NAME@.
  
- The correct genetic code needs to be selected

- Reference data needs to be selected (can be provided by an administrator using the MITOS data manager)

**Outputs**

By default the annotation in BED format. Several other outputs can be enabled:

- The annotation can be given as well in GFF, SEQ, or mito (a custom tabular format)

- zipped raw data (all files computed during the run, e.g. BLAST and cmsearch outputs)

- protein and ncRNA prediction plots visualize the predicted genes and their qualities

- ncRNA structure plots (secondary structures of the predicted ncRNAs)

See http://mitos.bioinf.uni-leipzig.de/help.py

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