annotate tools/filters/bed_to_bigbed.xml @ 1:cdcb0ce84a1b

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<tool id="bed_to_bigBed" name="BED-to-bigBed" version="1.0.0">
  <description>converter</description>
  <command>bedToBigBed $input1 $chromInfo $out_file1 
    #if $settings.settingsType == "full":
      -blockSize=${settings.blockSize} -itemsPerSlot=${settings.itemsPerSlot} ${settings.unc}
    #end if
    2&gt;&amp;1 || echo "Error running bedToBigBed." >&amp;2
  </command>
  <requirements>
    <requirement type="package">ucsc_tools</requirement>
  </requirements>
  <inputs>
    <param format="bed" name="input1" type="data" label="Convert">
      <validator type="unspecified_build" />
    </param>
    <conditional name="settings">
      <param name="settingsType" type="select" label="Converter settings to use" help="Default settings should usually be used.">
        <option value="preset">Default</option>
        <option value="full">Full parameter list</option>
      </param>
      <when value="preset" />
      <when value="full">
        <param name="blockSize" size="4" type="integer" value="256" label="Items to bundle in r-tree" help="Default is 256 (blockSize)" />
        <param name="itemsPerSlot" size="4" type="integer" value="512" label="Data points bundled at lowest level" help="Default is 512 (itemsPerSlot)" />
        <param name="unc" type="boolean" truevalue="-unc" falsevalue="" checked="False" label="Do not use compression" help="(unc)"/>
      </when>
    </conditional>
  </inputs>
  <outputs>
    <data format="bigbed" name="out_file1" />
  </outputs>
  <tests>
    <test>
      <param name="input1" value="7.bed" dbkey="hg17" />
      <param name="settingsType" value="full" />
      <param name="blockSize" value="256" />
      <param name="itemsPerSlot" value="512" />
      <param name="unc" value="False" />
      <output name="out_file1" file="7.bigbed"/>
    </test>
    <test>
      <param name="input1" value="7.bed" dbkey="hg17" />
      <param name="settingsType" value="preset" />
      <output name="out_file1" file="7.bigbed"/>
    </test>
  </tests>
  <help>

This tool converts a **sorted** BED file into a bigBed file.

Currently, the bedFields option to specify the number of non-standard fields is not supported as an AutoSQL file must be provided, which is a format
currently not supported by Galaxy.

</help>
</tool>