view bedClip.xml @ 8:ad32956798e3 draft

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<tool id="bedClip" name="bedClip">
    <description> Remove lines from bed file that refer to off-chromosome places.</description>
    <requirements>
        <requirement type="package" version="1.0">fetchChromSizes</requirement>
        <requirement type="package" version="1.0">bedClip</requirement>
    </requirements>
    <command interpreter="bash"> 
	## Set genome assembly 

	#set $Genome = str( $genome_cond.genome )
	#if str( $genome_cond ) == 'OTHER':
		#set $Genome = str( $genome_cond.genome_other )
	#end if
	
	bedClip.sh $input $Genome $output
    </command>
    <inputs>
        <param name="input" type="data" format="bed" label="Input"/>
        <conditional name="genome_cond">
	    <param name="genome" type="select" label="Genome Assembly">
        	<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>

    </inputs>
  
    <outputs>
        <data format="input" name="output"/> 
    </outputs>
    
    <tests>
        <test>
            <param name="input" value="3.bed" />
            <param name="genome" value="hg19" />
            <output name="output" file="1.bed" />
        </test>
    </tests>

    <help>
**What it does**
bedClip - Remove lines from bed file that refer to off-chromosome places.

**Usage**

  bedClip input.bed chrom.sizes output.bed

    </help>
</tool>