view tools/maf/maf_limit_size.xml @ 1:cdcb0ce84a1b

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<tool id="maf_limit_size1" name="Filter MAF blocks" version="1.0.1">
  <description>by Size</description>
  <command interpreter="python">maf_limit_size.py $input1 $out_file1 $min_size $max_size</command>
  <inputs>
    <page>
        <param format="maf" name="input1" label="MAF File" type="data"/>
        <param name="min_size" label="Minimum Size" value="0" type="integer"/>
        <param name="max_size" label="Maximum Size" value="0" type="integer" help="A maximum size less than 1 indicates no limit"/>
    </page>
   </inputs>
  <outputs>
    <data format="maf" name="out_file1" />
  </outputs>
  <tests>
    <test>
      <param name="input1" value="3.maf" ftype="maf" />
      <param name="min_size" value="0"/>
      <param name="max_size" value="0"/>
      <output name="out_file1" file="maf_limit_size1_out.maf" />
    </test>
  </tests>
  <help>

**What it does**

This tool takes a MAF file and a size range and extracts the MAF blocks which fall within the specified range.

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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>