<tool id="maf_by_block_number1" name="Extract MAF by block number" version="1.0.1">
  <description>given a set of block numbers and a MAF file</description>
  <command interpreter="python">maf_by_block_number.py $input1 $input2 $out_file1 $block_col $species</command>
  <inputs>
    <param format="txt" name="input1" type="data" label="Block Numbers"/>
    <param format="maf" name="input2" label="MAF File" type="data"/>
    <param name="block_col" type="data_column" label="Column containing Block number" data_ref="input1" accept_default="True" />
    <param name="species" type="select" display="checkboxes" multiple="true" label="Choose species" help="Select species to be included in the final alignment">
      <options>
        <filter type="data_meta" ref="input2" key="species" />
      </options>
    </param>
   </inputs>
  <outputs>
    <data format="maf" name="out_file1" />
  </outputs>
  <tests>
    <test>
      <param name="input1" value="maf_by_block_numbers.dat"/>
      <param name="input2" value="3.maf"/>
      <param name="block_col" value="1"/>
      <param name="species" value="hg17,panTro1,mm5,rn3,canFam1"/>
      <output name="out_file1" file="maf_by_block_number_out.dat" />
    </test>
  </tests>
  <help>

**What it does**

This tool takes a list of block numbers, one per line, and extracts the corresponding MAF blocks from the provided file. Block numbers start at 0.

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**Citation**

If you use this tool, please cite `Blankenberg D, Taylor J, Nekrutenko A; The Galaxy Team. Making whole genome multiple alignments usable for biologists. Bioinformatics. 2011 Sep 1;27(17):2426-2428. &lt;http://www.ncbi.nlm.nih.gov/pubmed/21775304&gt;`_


  </help>
</tool>