<tool id="selectsequencesfrommsa" name="Select Sequences" version="1.0.5">
  <description>
    Tool to select representative sequences from a multiple sequence alignment.
  </description>
  <requirements>
    <requirement type="package" version="1.0.5">selectsequencesfrommsa</requirement>
  </requirements>
  <command detect_errors="aggressive"><![CDATA[
    SelectSequencesFromMSA
      -c '$input_clustal'
      $x
      -o `pwd`
      -n $n
      -i $i
      -m $m
      -f result.selected
      > warnings
    ]]>
  </command>
  <inputs>
    <param name="input_clustal" type="data" format="clustal" label="Input clustal alignment"/>
    <param argument="-n" type="integer" value="6" min="1" label="Number of sequences in the output alignment." help=""/>
    <param argument="-i" type="float" value="80" min="0.1" label="Optimize for this percentage of mean pairwise identity" help=""/>
    <param argument="-m" type="float" value="95" min="0.1" label="Sequences with a higher percentage of pairwise identity will be removed." help=""/>
    <param argument="-x" truevalue="-x" falsevalue="" checked="True" type="boolean" label="The first sequence (=reference sequence) is always present in the output alignment." help=""/>
  </inputs>
  <outputs>
    <data format="clustal" name="clustal" from_work_dir="result.selected" label="Clustal alignment of selected sequences"/>
  </outputs>
  <tests>
    <test>
      <param name="input_clustal" value="result.clustal"/>
      <output name="clustal" file="result.selected"/>
    </test>
  </tests>
  <help>
    
<![CDATA[
             
**What it does**

Tool to select representative sequences from a multiple sequence alignment in clustal format.
Useful before running RNAz, RNAcode, RNAalifold on alignments with many entries.

**Input**
Multiple sequence alignment in clustal format

**Options**
-n Number of sequences in the output alignment. (Default: 6)
-i Optimize for this percentage of mean pairwise identity (Default: 80)
-m Sequences with a higher percentage of pairwise identity will be removed (Default: 95)
-x The first sequence (=reference sequence) is always present in the output alignment per default. Default: True

**Output**
Clustal alignment with selected sequences

]]>

  </help>
  <citations>
    <citation type="doi">10.1093/nar/gkw558</citation>
  </citations>
</tool>