<tool id="EMBOSS: msbar55" name="msbar" version="@VERSION@.1">
  <description>Mutate sequence beyond all recognition</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements" />
  <code file="emboss_format_corrector.py" />
  <command>msbar -sequence '$input1' -outseq '$out_file1' -count $count -point $point -block $block -codon $codon -inframe $inframe -minimum $minimum -maximum $maximum -osformat2 $out_format1
  -auto</command>
  <inputs>
    <param name="input1" type="data" format="fasta" label="Sequence 1" />
    <param name="count" type="integer" value="1" label="Number of times to perform the mutation operations" />
    <param name="point" type="select" label="Types of point mutations to perform">
      <option value="0">None</option>
      <option value="1">Any of the following</option>
      <option value="2">Insertions</option>
      <option value="3">Deletions</option>
      <option value="4">Changes</option>
      <option value="5">Duplications</option>
      <option value="6">Moves</option>
    </param>
    <param name="block" type="select" label="Types of block mutations to perform">
      <option value="0">None</option>
      <option value="1">Any of the following</option>
      <option value="2">Insertions</option>
      <option value="3">Deletions</option>
      <option value="4">Changes</option>
      <option value="5">Duplications</option>
      <option value="6">Moves</option>
    </param>
    <param name="codon" type="select" label="Types of codon mutations to perform" help="These are only done if the sequence is nucleic">
      <option value="0">None</option>
      <option value="1">Any of the following</option>
      <option value="2">Insertions</option>
      <option value="3">Deletions</option>
      <option value="4">Changes</option>
      <option value="5">Duplications</option>
      <option value="6">Moves</option>
    </param>
    <param name="inframe" type="select" label="Do 'codon' and 'block' operations in frame">
      <option value="no">No</option>
      <option value="yes">Yes</option>
    </param>
    <param name="minimum" type="integer" value="1" label="Minimum size for a block mutation" />
    <param name="maximum" type="integer" value="10" label="Maximum size for a block mutation" />
    <param name="out_format1" type="select" label="Output sequence file format">
      <option value="fasta">FASTA (m)</option>
      <option value="acedb">ACeDB (m)</option>
      <option value="asn1">ASN.1 (m)</option>
      <option value="clustal">Clustal (m)</option>
      <option value="codata">CODATA (m)</option>
      <option value="embl">EMBL (m)</option>
      <option value="fitch">Fitch (m)</option>
      <option value="gcg">Wisconsin Package GCG 9.x and 10.x (s)</option>
      <option value="genbank">GENBANK (m)</option>
      <option value="gff">GFF (m)</option>
      <option value="hennig86">Hennig86 (m)</option>
      <option value="ig">Intelligenetics (m)</option>
      <option value="jackknifer">Jackknifer (m)</option>
      <option value="jackknifernon">Jackknifernon (m)</option>
      <option value="mega">Mega (m)</option>
      <option value="meganon">Meganon (m)</option>
      <option value="msf">Wisconsin Package GCG's MSF (m)</option>
      <option value="pir">NBRF (PIR) (m)</option>
      <option value="ncbi">NCBI style FASTA (m)</option>
      <option value="nexus">Nexus/PAUP (m)</option>
      <option value="nexusnon">Nexusnon/PAUPnon (m)</option>
      <option value="phylip">PHYLIP interleaved (m)</option>
      <option value="phylipnon">PHYLIP non-interleaved (m)</option>
      <option value="selex">SELEX (m)</option>
      <option value="staden">Staden (s)</option>
      <option value="strider">DNA strider (m)</option>
      <option value="swiss">SwisProt entry (m)</option>
      <option value="text">Plain sequence (s)</option>
      <option value="treecon">Treecon (m)</option>
    </param>
  </inputs>
  <outputs>
    <data name="out_file1" format="fasta" />
  </outputs>
  <tests>
    <test>
      <param name="input1" value="2.fasta"/>
      <param name="count" value="1"/>
      <param name="point" value="0"/>
      <param name="block" value="0"/>
      <param name="codon" value="0"/>
      <param name="inframe" value="no"/>
      <param name="minimum" value="1"/>
      <param name="maximum" value="10"/>
      <param name="out_format1" value="fasta"/>
      <output name="out_file1" file="emboss_msbar_out.fasta"/>
    </test>
  </tests>
  <help>
.. class:: warningmark

The input dataset needs to be sequences.

-----

    You can view the original documentation here_.

    .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/msbar.html
  </help>
  <expand macro="citations" />
</tool>