view bedExtendRanges.xml @ 8:ad32956798e3 draft

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<tool id="bedExtendRanges" name="bedExtendRanges">
    <description> Extend length of entries in bed 6+. </description>
    <requirements>
        <requirement type="package" version="1.0">bedExtendRanges</requirement>
    </requirements>
    <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>

    <tests>
	<test>
	    <param name="input" value="2.bed" />
	    <param name="genome" value="hg19" />
	    <param name="length" value="5000" />
	    <output name="output" file="4.bed" />
	</test>
    </tests>

    <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.

.. _bedExtendRanges: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedExtendRanges

**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>