<tool id="liftOver2" name="[Galaxy]Convert genome coordinates" version="1.0.2">

  <description> between assemblies and genomes</description>

  <command interpreter="python">bedLiftover_wrapper.py $input "$out_file1" "$out_file2" $dbkey $to_dbkey $minMatch</command>

  <inputs>

    <param format="interval" name="input" type="data" label="Convert coordinates of">

      <validator type="unspecified_build" />
      <validator type="dataset_metadata_in_file" filename="liftOver.loc" metadata_name="dbkey" metadata_column="0" message="Liftover mappings are currently not available for the specified build." />

    </param>
    <param name="to_dbkey" type="select" label="To">

      <options from_file="liftOver.loc">

        <column name="name" index="1"/>

        <column name="value" index="2"/>

        <column name="dbkey" index="0"/>

        <filter type="data_meta" ref="input" key="dbkey" column="0" />

      </options>
    </param> 
    <param name="minMatch" size="10" type="float" value="0.95" label="Minimum ratio of bases that must remap" />
  </inputs>

  <outputs>

    <data format="input" name="out_file1" />

    <data format="input" name="out_file2" />

  </outputs>

  <requirements>

    <requirement type="binary">liftOver</requirement>

  </requirements>

  <tests>

    <test>

      <param name="input" value="5.bed" dbkey="hg18" ftype="bed" />

      <param name="to_dbkey" value="panTro2" />

      <param name="minMatch" value="0.95" />

      <output name="out_file1" file="5_liftover_mapped.bed"/>

      <output name="out_file2" file="5_liftover_unmapped.bed"/>

    </test>

  </tests>

  <help>

.. class:: warningmark



Make sure that the genome build of the input dataset is specified (click the pencil icon in the history item to set it if necessary).



.. class:: warningmark



This tool will only work on interval datasets with chromosome in column 1,
start co-ordinate in column 2 and end co-ordinate in column 3. BED comments
and track and browser lines will be ignored, but if other non-interval lines
are present the tool will return empty output datasets.



-----



.. class:: infomark



**What it does**



This tool converts coordinates and annotations between assemblies and genomes. It produces 2 files, one containing all the mapped coordinates and the other containing the unmapped coordinates, if any. 



-----



**Example**



Converting the following hg16 intervals to hg18 intervals::



    chrX  85170   112199  AK002185  0  +

    chrX  110458  112199  AK097346  0  +

    chrX  112203  121212  AK074528  0  -



will produce the following hg18 intervals::



    chrX  132991  160020  AK002185  0  +

    chrX  158279  160020  AK097346  0  +

    chrX  160024  169033  AK074528  0  -



  </help>

  <code file="liftOver_wrapper_code.py" />

</tool>