view tools/visualization/build_ucsc_custom_track.xml @ 1:cdcb0ce84a1b

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<tool id="build_ucsc_custom_track_1" name="Build custom track">
  <description>for UCSC genome browser</description>    
  <command interpreter="python">
    build_ucsc_custom_track.py 
      "$out_file1"
      #for $t in $tracks
        "${t.input.file_name}"
        "${t.input.ext}"
        #if $t.input.ext == "interval"
          ${t.input.metadata.chromCol},${t.input.metadata.startCol},${t.input.metadata.endCol},${t.input.metadata.strandCol}
        #else
          "NA"
        #end if
        "${t.name}"
        "${t.description}"
        "${t.color}"
        "${t.visibility}"
      #end for
  </command>
  <inputs>
    <repeat name="tracks" title="Track">
      <param name="input" type="data" format="interval,wig" label="Dataset"/>
      <param name="name" type="text" size="15" value="User Track">
        <validator type="length" max="15"/>
      </param>
      <param name="description" type="text" value="User Supplied Track (from Galaxy)">
        <validator type="length" max="60"/>
      </param>
  		<param label="Color" name="color" type="select">
  			<option selected="yes" value="0-0-0">Black</option>
  			<option value="255-0-0">Red</option>
  			<option value="0-255-0">Green</option>
  			<option value="0-0-255">Blue</option>
  			<option value="255-0-255">Magenta</option>
  			<option value="0-255-255">Cyan</option>
  			<option value="255-215-0">Gold</option>
  			<option value="160-32-240">Purple</option>
  			<option value="255-140-0">Orange</option>
  			<option value="255-20-147">Pink</option>
  			<option value="92-51-23">Dark Chocolate</option>
  			<option value="85-107-47">Olive green</option>
  		</param>
  		<param label="Visibility" name="visibility" type="select">
  			<option selected="yes" value="1">Dense</option>
  			<option value="2">Full</option>
  			<option value="3">Pack</option>
  			<option value="4">Squish</option>
  			<option value="0">Hide</option>
  		</param>
    </repeat>
  </inputs>
	<outputs>
  	<data format="customtrack" name="out_file1" />
	</outputs>
    <tests>
        <!--TODO: add a 2nd test here that includes 2 tracks -->
        <test>
  		    <param name="input" value="customTrack1.bed" />
  		    <param name="name" value="User Track" />
  		    <param name="description" value="User Supplied Track (from Galaxy)" />
  		    <param name="color" value="0-0-0" />
  		    <param name="visibility" value="1" />
  		    <output name="out_file1" file="build_ucsc_custom_track_out1.customtrack" />
        </test>
	</tests>
<help>

.. class:: infomark

This tool allows you to build custom tracks using datasets in your history for the UCSC genome browser. You can view these custom tracks on the UCSC genome browser by clicking on **display at UCSC main/test** link in the history panel of the output dataset.

-----

.. class:: warningmark

Please note that this tool requires **all input datasets(tracks) to have the same genome build**. The tool throws an error when this requirement is not met. You may then have to choose a valid dataset or remove invalid tracks.

</help>

<code file="build_ucsc_custom_track_code.py" />
  
</tool>