<tool id="MAF_Reverse_Complement_1" name="Reverse Complement" version="1.0.1">

  <description>a MAF file</description>

  <command interpreter="python">maf_reverse_complement.py $input1 $out_file1 $species</command>

  <inputs>

    <page>

        <param format="maf" name="input1" label="Alignment File" type="data"/>

        <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="input1" key="species" />

          </options>

        </param>

    </page>

   </inputs>

  <outputs>

    <data format="maf" name="out_file1" metadata_source="input1"/>

  </outputs>

  <tests>

    <test>

      <param name="input1" value="3.maf" dbkey="hg17" format="maf"/>

      <param name="species" value="hg17,panTro1,mm5,rn3,canFam1"/>

      <output name="out_file1" file="maf_reverse_complement_out.dat"/>

    </test>

  </tests>

  <help>

**What it does**



This tool takes a MAF file and creates a new MAF file, where each block has been reversed complemented.



**Example**

  

This MAF Block::



  a score=8157.000000

  s hg17.chr7    127471526 58 + 158628139 AATTTGTGGTTTATTCATTTTTCATTATTTTGTTTAAGGAGGTCTATAGTGGAAGAGG

  s panTro1.chr6 129885407 58 + 161576975 AATTTGTGGTTTATTCGTTTTTCATTATTTTGTTTAAGGAGGTCTATAGTGGAAGAGG

  s mm5.chr6      28904928 54 + 149721531 AA----CGTTTCATTGATTGCTCATCATTTAAAAAAAGAAATTCCTCAGTGGAAGAGG



becomes::



  a score=8157.000000

  s hg17.chr7     31156555 58 - 158628139 CCTCTTCCACTATAGACCTCCTTAAACAAAATAATGAAAAATGAATAAACCACAAATT

  s panTro1.chr6  31691510 58 - 161576975 CCTCTTCCACTATAGACCTCCTTAAACAAAATAATGAAAAACGAATAAACCACAAATT

  s mm5.chr6     120816549 54 - 149721531 CCTCTTCCACTGAGGAATTTCTTTTTTTAAATGATGAGCAATCAATGAAACG----TT

  </help>

</tool>