view bed_to_bigwig.xml @ 3:4e9e1625dae3 default tip

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<tool id="bed_to_bigwig" name="bed_to_bigwig">
  <description>make bigwig from BED or BAM</description>
  <command interpreter="sh"> bed_to_bigwig.sh $input $outfile 
    #if $inputa_format.bedorbam == "bed":
    bed
    #else:
    bam
    #end if
    $sorted $genome none $split >$log 2> $log </command>
  <inputs>
      <conditional name="inputa_format">
    	<param name="bedorbam" type="select" label="Select input format" >
		<option value="bed" selected="true">BED</option>
		<option value="bam"> BAM</option>
	    </param>
	    <when value="bed">
		    <param name="input" type="data" format="bed" label="Input file"/>
	    </when>
	    <when value="bam">
		    <param name="input" type="data" format="bam" label="Input file"/>
	    </when>
    </conditional>
           <param name="genome" type="select" label="Select chromsome size file" >
                <options from_file="chrsize.loc">
                    <column name="name" index="0"/>
                    <column name="value" index="1"/>
                </options>
            </param>

    <param name="sorted" label="Check if the input is sorted" type="boolean" truevalue="sorted" falsevalue="none" checked="False"/>
    <param name="split" label="Split junctions" help="Treat 'split' BAM or BED12 entries as distinct BED intervals." type="boolean" truevalue="-split" falsevalue="" checked="False"/>
  </inputs>
  <outputs>
    <data format="txt" name="log" label="makebigwig LOG" />
        <data format="bigwig" name="outfile" />

  </outputs>
</tool>