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galaxy-central (ngs) / tools / maf / interval2maf_pairwise.xml

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<tool id="Interval2Maf_pairwise1" name="Extract Pairwise MAF blocks" version="1.0.1">
  <description>given a set of genomic intervals</description>
  <command interpreter="python">interval2maf.py --dbkey=${input1.dbkey} --chromCol=${input1.metadata.chromCol} --startCol=${input1.metadata.startCol} --endCol=${input1.metadata.endCol} --strandCol=${input1.metadata.strandCol} --mafType=$mafType --interval_file=$input1 --output_file=$out_file1 --indexLocation=${GALAXY_DATA_INDEX_DIR}/maf_pairwise.loc</command>
  <inputs>
    <param name="input1" type="data" format="interval" label="Interval File">
      <validator type="unspecified_build" />
    </param>
    <param name="mafType" type="select" label="Choose MAF source">
      <options from_file="maf_pairwise.loc">
        <column name="name" index="0"/>
        <column name="value" index="1"/>
        <column name="dbkey" index="2"/>
        <column name="species" index="3"/>
        <filter type="data_meta" ref="input1" key="dbkey" column="2" multiple="True" separator=","/>
        <validator type="no_options" message="No alignments are available for the build associated with the selected interval file"/>
      </options>
    </param> 
   </inputs>
  <outputs>
    <data format="maf" name="out_file1" />
  </outputs>
  <tests>
    <test>
      <param name="input1" value="8.bed" dbkey="hg17" format="bed"/>
      <param name="mafType" value="PAIRWISE_hg17_fr1"/>
      <output name="out_file1" file="Interval2Maf_pairwise_out.maf"/>
    </test>
  </tests>
  <help>
**What it does**

This tool takes genomic coordinates, superimposes them on pairwise alignments (in MAF format) stored on the Galaxy site, and excises alignment blocks corresponding to each set of coordinates. Alignment blocks that extend past START and/or END positions of an interval are trimmed. Note that a single genomic interval may correspond to two or more alignment blocks. 

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**Example** 

Here a single interval is superimposed on three MAF blocks. Blocks 1 and 3 are trimmed because they extend beyond boundaries of the interval:

.. image:: ./static/images/maf_icons/interval2maf.png

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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>