comparison tools/filters/wiggle_to_simple.xml @ 0:9071e359b9a3

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0:9071e359b9a3

<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>
    <test>
      <param name="input" value="3.wig" />
      <output name="out_file1" file="3_wig.bed"/>
    </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>