root/galaxy-central/tools/maf/maf_limit_to_species.xml

<tool id="MAF_Limit_To_Species1" name="Filter MAF blocks">
  <description>by Species</description>
  <command interpreter="python">maf_limit_to_species.py $species $input1 $out_file1 $allow_partial $min_species</command>
  <inputs>
    <param name="input1" type="data" format="maf" label="MAF file"/>
    <param name="allow_partial" type="select" label="Exclude blocks which have missing species" >
      <option value="1">No</option>
      <option value="0">Yes</option>
    </param>
    <param name="min_species" type="select" label="Exclude blocks which have only one species" >
      <option value="1">Yes</option>
      <option value="0">No</option>
    </param>
    <param name="species" type="select" label="Species to keep" display="checkboxes" multiple="true">
      <options>
        <filter type="data_meta" ref="input1" key="species" />
      </options>
    </param>
  </inputs>
  <outputs>
    <data format="maf" name="out_file1" />
  </outputs>
  <tests>
    <test>
      <param name="input1" value="4.maf"/>
      <param name="species" value="bosTau2,canFam2,hg17,panTro1,rheMac2,rn3"/>
      <param name="allow_partial" value="0"/>
      <param name="min_species" value="0"/>
      <output name="out_file1" file="cf_maf_limit_to_species.dat"/>
    </test>
  </tests>
  <help>

**What It Does**

This tool allows the user to remove any undesired species from a MAF file. Columns which contain only gaps are removed. The options for this tool are:

 * **Exclude blocks which have missing species** - suppose you want to restrict an 8-way alignment to human, mouse, and rat.  The tool will first remove all other species. Next, if this option is set to **YES** the tool WILL NOT return MAF blocks, which do not include human, mouse, or rat. This means that all alignment blocks returned by the tool will have exactly three sequences in this example.

 * **Exclude blocks with have only one species** - if this option is set to **YES** all single sequence alignment blocks WILL NOT be returned.

  </help>
</tool>