comparison bamFingerprint.xml @ 29:60788be7b346 draft

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28:1e5fcb1555de

    <expand macro="stdio" />
    <macros>
        <import>deepTools_macros.xml</import>
    </macros>
    <command>
        #import tempfile
        #set $temp_dir = os.path.abspath(tempfile.mkdtemp())

        #set files=[]
        #set labels=[]

        @multiple_input_bams@

    bamFingerprint

        @THREADS@

            --outRawCounts '$outFileRawCounts' 
          #end if
      #else
        --plotFileFormat 'png'
      #end if


      #if $advancedOpt.showAdvancedOpt == "yes":
        
        #if str($advancedOpt.region.value) != '':
          --region '$advancedOpt.region'

    <outputs>
        <expand macro="output_image_file_format" />
        <data format="tabular" name="outFileRawCounts" label="${tool.name} on ${on_string}: bin counts">
            <filter>
            ((
                outputOpt['showOutputOpt'] == 'yes' and 
                outputOpt['saveRawCounts'] is True
            ))
            </filter>
        </data>
    </outputs>
    <help>

29:60788be7b346

    <expand macro="stdio" />
    <macros>
        <import>deepTools_macros.xml</import>
    </macros>
    <command>
        @multiple_input_bams@

    bamFingerprint

        @THREADS@

            --outRawCounts '$outFileRawCounts' 
          #end if
      #else
        --plotFileFormat 'png'
      #end if

      #if $advancedOpt.showAdvancedOpt == "yes":
        
        #if str($advancedOpt.region.value) != '':
          --region '$advancedOpt.region'

    <outputs>
        <expand macro="output_image_file_format" />
        <data format="tabular" name="outFileRawCounts" label="${tool.name} on ${on_string}: bin counts">
            <filter>
            ((
                output['showOutputSettings'] == 'yes' and 
                output['saveRawCounts'] is True
            ))
            </filter>
        </data>
    </outputs>
    <help>