<tool id="liftOver1" name="Convert genome coordinates" version="1.0.3">
  <description> between assemblies and genomes</description>
  <command interpreter="python">
  liftOver_wrapper.py 
  $input 
  "$out_file1" 
  "$out_file2" 
  $dbkey 
  $to_dbkey 
  #if isinstance( $input.datatype, $__app__.datatypes_registry.get_datatype_by_extension('gff').__class__) or isinstance( $input.datatype, $__app__.datatypes_registry.get_datatype_by_extension('gtf').__class__):
        "gff"
  #else:
        "interval"
  #end if
  $minMatch ${multiple.choice} ${multiple.minChainT} ${multiple.minChainQ} ${multiple.minSizeQ}
  </command>
  <inputs>
    <param format="interval,gff,gtf" name="input" type="data" label="Convert coordinates of">
      <validator type="unspecified_build" />
      <validator type="dataset_metadata_in_file" filename="liftOver.loc" metadata_name="dbkey" metadata_column="0" message="Liftover mappings are currently not available for the specified build." />
    </param>
    <param name="to_dbkey" type="select" label="To">
      <options from_file="liftOver.loc">
        <column name="name" index="1"/>
        <column name="value" index="2"/>
        <column name="dbkey" index="0"/>
        <filter type="data_meta" ref="input" key="dbkey" column="0" />
      </options>
    </param> 
    <param name="minMatch" size="10" type="float" value="0.95" label="Minimum ratio of bases that must remap" help="Recommended values: same species = 0.95, different species = 0.10" />
    <conditional name="multiple">
	    <param name="choice" type="select" label="Allow multiple output regions?" help="Recommended values: same species = No, different species = Yes">
	    	<option value="0" selected="true">No</option>
	    	<option value="1">Yes</option>
		</param>
		<when value="0">
		    <param name="minSizeQ" type="hidden" value="0" />
    		<param name="minChainQ" type="hidden" value="0" />
    		<param name="minChainT" type="hidden" value="0" />
    	</when>
    	<when value="1">
    	    <param name="minSizeQ" size="10" type="integer" value="0" label="Minimum matching region size in query" help="Recommended value: set to >= 300 bases for complete transcripts"/>
    		<param name="minChainQ" size="10" type="integer" value="500" label="Minimum chain size in query"/>
    		<param name="minChainT" size="10" type="integer" value="500" label="Minimum chain size in target"/>
    	</when>
	</conditional>
  </inputs>
  <outputs>
    <data format="input" name="out_file1" label="${tool.name} on ${on_string} [ MAPPED COORDINATES ]">
      <actions>
        <action type="metadata" name="dbkey">
          <option type="from_file" name="liftOver.loc" column="1" offset="0">
            <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
            <filter type="param_value" ref="to_dbkey" column="2"/>
          </option>
        </action>
      </actions>
    </data>
    <data format="input" name="out_file2" label="${tool.name} on ${on_string} [ UNMAPPED COORDINATES ]" />
  </outputs>
  <requirements>
    <requirement type="package">ucsc_tools</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" />
      <param name="choice" value="0" />
      <output name="out_file1" file="5_liftover_mapped.bed"/>
      <output name="out_file2" file="5_liftover_unmapped.bed"/>
    </test>
    <test>
      <param name="input" value="5.bed" dbkey="hg18" ftype="bed" />
      <param name="to_dbkey" value="panTro2" />
      <param name="minMatch" value="0.10" />
      <param name="choice" value="1" />
      <param name="minSizeQ" value="0" />
      <param name="minChainQ" value="500" />
      <param name="minChainT" value="500" />
      <output name="out_file1" file="5_mult_liftover_mapped.bed"/>
      <output name="out_file2" file="5_mult_liftover_unmapped.bed"/>
    </test>
    <test>
      <param name="input" value="cuffcompare_in1.gtf" dbkey="hg18" ftype="gtf" />
      <param name="to_dbkey" value="panTro2" />
      <param name="minMatch" value="0.95" />
      <param name="choice" value="0" />
      <output name="out_file1" file="cuffcompare_in1_liftover_mapped.bed"/>
      <output name="out_file2" file="cuffcompare_in1_liftover_unmapped.bed"/>
    </test>
    <test>
      <param name="input" value="cuffcompare_in1.gtf" dbkey="hg18" ftype="gtf" />
      <param name="to_dbkey" value="panTro2" />
      <param name="minMatch" value="0.10" />
      <param name="choice" value="1" />
      <param name="minSizeQ" value="0" />
      <param name="minChainQ" value="500" />
      <param name="minChainT" value="500" />
      <output name="out_file1" file="cuffcompare_in1_mult_liftover_mapped.bed"/>
      <output name="out_file2" file="cuffcompare_in1_mult_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 can work with interval, GFF, and GTF datasets. It requires the interval datasets to have 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 is based on the LiftOver utility and Chain track from `the UC Santa Cruz Genome Browser`__.

It 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. 

 .. __: http://genome.ucsc.edu/

-----

**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>
</tool>