view bedExtendRanges.xml @ 4:5b5460b79488 draft

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<tool id="bedExtendRanges" name="bedExtendRanges">
  <description> Extend length of entries in bed 6+. </description>
  <command> 
	## Set genome assembly 

	#set $Genome = str( $genome_cond.genome )
	#if str( $genome_cond ) == 'OTHER':
		#set $Genome = str( $genome_cond.genome_other )
	#end if
	
	bedExtendRanges -user=genome -host=genome-mysql.cse.ucsc.edu $Genome $length $input 2> /dev/null > $output
  </command>
  <inputs>
    <param name="input" type="data" format="bed" label="Input"/>
    <conditional name="genome_cond">
      <param name="genome" type="select" label="Genome Assembly (-g)">
        <option value="hg19">Human (Homo sapiens): hg19</option>
        <option value="hg18">Human (Homo sapiens): hg18</option>
        <option value="mm10">Mouse (Mus musculus): mm10</option>
        <option value="mm9">Mouse (Mus musculus): mm9</option>
        <option value="ce10">C. elegans: ce10</option>
        <option value="ce6">C. elegans: ce6</option>
        <option value="dm3">D. melanogaster: dm3</option>
        <option value="OTHER">Other</option>
      </param>
      <when value="OTHER">
        <param name="genome_other" type="text" label="Other genome assemly"/>
      </when>
      <when value="hg19" type="text" />
      <when value="hg18" type="text" />
      <when value="mm10" type="text" />
      <when value="mm9" type="text" />
      <when value="ce10" type="text" />
      <when value="ce6" type="text" />
      <when value="dm3" type="text" />
    </conditional>
    <param name="length" type="integer" value="0" label="Length extension (base-pairs)" />

  </inputs>
  
  <outputs>
    <data format="input" name="output"/> 
  </outputs>
  <help>

**What it does**

bedExtendRanges - extend length of entries in bed 6+ data to be at least the given length,
taking strand directionality into account.

**Usage**

   bedExtendRanges database length files(s)

**Example**

  * bedExtendRanges -user=genome -host=genome-mysql.cse.ucsc.edu hg18 250 stdin

  will transform:
    chr1 500 525 . 100 +
    chr1 1000 1025 . 100 -
  to:
    chr1 500 750 . 100 +
    chr1 775 1025 . 100 -

  </help>
</tool>