<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.

  </help>

</tool>