annotate tools/filters/wc_gnu.xml @ 1:cdcb0ce84a1b

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<tool id="wc_gnu" name="Line/Word/Character count">
    <description>of a dataset</description>
    <command>
        #set $word_to_arg = { 'characters':'m', 'words':'w', 'lines':'l' }
        #set $arg_order = [ 'lines', 'words', 'characters' ]
        #if not isinstance( $options.value, list ):
            #set $args = [ $options.value ]
        #else:
            #set $args = $options.value
        #end if
        #if $include_header.value:
            echo "#${ "\t".join( [ i for i in $arg_order if i in $args ] ) }" &gt; $out_file1
            &amp;&amp;
        #end if
        wc
        #for $option in $args:
           -${ word_to_arg[ str(option) ] }
        #end for
        $input1 | awk '{ print ${ '"\\t"'.join( [ "$%i" % ( i+1 ) for i in range( len( $args ) ) ] ) } }'
        &gt;&gt; $out_file1
    </command>
    <inputs>
        <param format="txt" name="input1" type="data" label="Text file"/>
        <param name="options" type="select" multiple="True" display="checkboxes" label="Desired values">
            <!-- <option value="bytes" selected="True">Byte count</option> -->
            <option value="lines" selected="True">Line count</option>
            <option value="words" selected="True">Word count</option>
            <option value="characters" selected="True">Character count</option>
            <validator type="no_options" message="You must pick at least one attribute to count." />
        </param>
        <param name="include_header" type="boolean" label="Include Output header" checked="True"/>
    </inputs>
    <outputs>
        <data format="tabular" name="out_file1"/>
    </outputs>
    <tests>
        <test>
          <param name="input1" value="1.bed"/>
          <param name="options" value="lines,words,characters"/>
          <param name="include_header" value="True"/>
          <output name="out_file1" file="wc_gnu_out_1.tabular"/>
        </test>
        <test>
          <param name="input1" value="1.bed"/>
          <param name="options" value="lines,words,characters"/>
          <param name="include_header" value="False"/>
          <output name="out_file1" file="wc_gnu_out_2.tabular"/>
        </test>
    </tests>
    <help>

**What it does**

This tool outputs counts of specified attributes (lines, words, characters) of a dataset. 

-----

**Example Output**

::

  #lines  words  characters
  7499	  41376	 624971

    </help>
</tool>