/tools/stats/wiggle_to_simple.xml

<tool id="wiggle2simple1" name="Wiggle-to-Interval">

  <description>converter</description>

  <command interpreter="python">wiggle_to_simple.py $input $out_file1 </command>

  <inputs>

    <param format="wig" name="input" type="data" label="Convert"/>

  </inputs>

  <outputs>

    <data format="interval" name="out_file1" />

  </outputs>

  <tests>

    <test>

      <param name="input" value="2.wig" />

      <output name="out_file1" file="2.interval"/>

    </test>

  </tests>

  <help>

**Syntax**



This tool converts wiggle data into interval type.



- **Wiggle format**: The .wig format is line-oriented. Wiggle data is preceded by a UCSC track definition line.  Following the track definition line is the track data, which can be entered in three different formats described below.



  - **BED format** with no declaration line and four columns of data::



      chromA  chromStartA  chromEndA  dataValueA

      chromB  chromStartB  chromEndB  dataValueB



  - **variableStep** two column data; started by a declaration line and followed with chromosome positions and data values::



      variableStep  chrom=chrN  [span=windowSize]

      chromStartA  dataValueA

      chromStartB  dataValueB



  - **fixedStep** single column data; started by a declaration line and followed with data values::



      fixedStep  chrom=chrN  start=position  step=stepInterval  [span=windowSize]

      dataValue1

      dataValue2



-----



**Example**



- input wiggle format file::



    #track type=wiggle_0 name="Bed Format" description="BED format"

    chr19 59302000 59302300 -1.0

    chr19 59302300 59302600 -0.75

    chr19 59302600 59302900 -0.50

    chr19 59302900 59303200 -0.25

    chr19 59303200 59303500 0.0

    #track type=wiggle_0 name="variableStep" description="variableStep format"

    variableStep chrom=chr19 span=150

    59304701 10.0

    59304901 12.5

    59305401 15.0

    59305601 17.5

    #track type=wiggle_0 name="fixedStep" description="fixed step" visibility=full

    fixedStep chrom=chr19 start=59307401 step=300 span=200

    1000

    900

    800

    700

    600



- convert the above file to interval file::



    chr19	59302000	59302300	+	-1.0

    chr19	59302300	59302600	+	-0.75

    chr19	59302600	59302900	+	-0.5

    chr19	59302900	59303200	+	-0.25

    chr19	59303200	59303500	+	0.0

    chr19	59304701	59304851	+	10.0

    chr19	59304901	59305051	+	12.5

    chr19	59305401	59305551	+	15.0

    chr19	59305601	59305751	+	17.5

    chr19	59307701	59307901	+	1000.0

    chr19	59308001	59308201	+	900.0

    chr19	59308301	59308501	+	800.0

    chr19	59308601	59308801	+	700.0

    chr19	59308901	59309101	+	600.0



</help>

</tool>