mirror of
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Syncrhonize wiggle_to_simple.xml tool test cases, fix newlines.
As pointed by Peter (http://dev.list.galaxyproject.org/Bug-Two-copies-of-wiggle-to-simple-xml-tt4662486.html). There are still two copies.
This commit is contained in:
John Chilton
@@ -1,88 +1,88 @@
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<tool id="wiggle2simple1" name="Wiggle-to-Interval">
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<description>converter</description>
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<command interpreter="python">wiggle_to_simple.py $input $out_file1 </command>
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<inputs>
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<param format="wig" name="input" type="data" label="Convert"/>
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</inputs>
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<outputs>
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<data format="interval" name="out_file1" />
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</outputs>
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<tests>
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<test>
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<param name="input" value="2.wig" />
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<output name="out_file1" file="2.interval"/>
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<tool id="wiggle2simple1" name="Wiggle-to-Interval">
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<description>converter</description>
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<command interpreter="python">wiggle_to_simple.py $input $out_file1 </command>
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<inputs>
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<param format="wig" name="input" type="data" label="Convert"/>
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</inputs>
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<outputs>
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<data format="interval" name="out_file1" />
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</outputs>
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<tests>
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<test>
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<param name="input" value="2.wig" />
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<output name="out_file1" file="2.interval"/>
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</test>
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<test>
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<param name="input" value="3.wig" />
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<output name="out_file1" file="3_wig.bed"/>
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</test>
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</tests>
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<help>
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**Syntax**
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This tool converts wiggle data into interval type.
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- **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.
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- **BED format** with no declaration line and four columns of data::
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chromA chromStartA chromEndA dataValueA
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chromB chromStartB chromEndB dataValueB
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- **variableStep** two column data; started by a declaration line and followed with chromosome positions and data values::
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variableStep chrom=chrN [span=windowSize]
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chromStartA dataValueA
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chromStartB dataValueB
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- **fixedStep** single column data; started by a declaration line and followed with data values::
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fixedStep chrom=chrN start=position step=stepInterval [span=windowSize]
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dataValue1
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dataValue2
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-----
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**Example**
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- input wiggle format file::
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#track type=wiggle_0 name="Bed Format" description="BED format"
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chr19 59302000 59302300 -1.0
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chr19 59302300 59302600 -0.75
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chr19 59302600 59302900 -0.50
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chr19 59302900 59303200 -0.25
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chr19 59303200 59303500 0.0
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#track type=wiggle_0 name="variableStep" description="variableStep format"
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variableStep chrom=chr19 span=150
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59304701 10.0
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59304901 12.5
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59305401 15.0
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59305601 17.5
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#track type=wiggle_0 name="fixedStep" description="fixed step" visibility=full
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fixedStep chrom=chr19 start=59307401 step=300 span=200
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1000
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900
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800
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700
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600
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- convert the above file to interval file::
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chr19 59302000 59302300 + -1.0
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chr19 59302300 59302600 + -0.75
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chr19 59302600 59302900 + -0.5
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chr19 59302900 59303200 + -0.25
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chr19 59303200 59303500 + 0.0
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chr19 59304701 59304851 + 10.0
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chr19 59304901 59305051 + 12.5
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chr19 59305401 59305551 + 15.0
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chr19 59305601 59305751 + 17.5
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chr19 59307701 59307901 + 1000.0
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chr19 59308001 59308201 + 900.0
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chr19 59308301 59308501 + 800.0
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chr19 59308601 59308801 + 700.0
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chr19 59308901 59309101 + 600.0
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</help>
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</tool>
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</test>
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</tests>
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<help>
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**Syntax**
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This tool converts wiggle data into interval type.
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- **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.
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- **BED format** with no declaration line and four columns of data::
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chromA chromStartA chromEndA dataValueA
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chromB chromStartB chromEndB dataValueB
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- **variableStep** two column data; started by a declaration line and followed with chromosome positions and data values::
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variableStep chrom=chrN [span=windowSize]
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chromStartA dataValueA
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chromStartB dataValueB
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- **fixedStep** single column data; started by a declaration line and followed with data values::
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fixedStep chrom=chrN start=position step=stepInterval [span=windowSize]
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dataValue1
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dataValue2
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-----
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**Example**
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- input wiggle format file::
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#track type=wiggle_0 name="Bed Format" description="BED format"
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chr19 59302000 59302300 -1.0
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chr19 59302300 59302600 -0.75
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chr19 59302600 59302900 -0.50
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chr19 59302900 59303200 -0.25
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chr19 59303200 59303500 0.0
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#track type=wiggle_0 name="variableStep" description="variableStep format"
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variableStep chrom=chr19 span=150
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59304701 10.0
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59304901 12.5
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59305401 15.0
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59305601 17.5
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#track type=wiggle_0 name="fixedStep" description="fixed step" visibility=full
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fixedStep chrom=chr19 start=59307401 step=300 span=200
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1000
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900
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800
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700
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600
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- convert the above file to interval file::
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chr19 59302000 59302300 + -1.0
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chr19 59302300 59302600 + -0.75
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chr19 59302600 59302900 + -0.5
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chr19 59302900 59303200 + -0.25
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chr19 59303200 59303500 + 0.0
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chr19 59304701 59304851 + 10.0
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chr19 59304901 59305051 + 12.5
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chr19 59305401 59305551 + 15.0
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chr19 59305601 59305751 + 17.5
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chr19 59307701 59307901 + 1000.0
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chr19 59308001 59308201 + 900.0
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chr19 59308301 59308501 + 800.0
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chr19 59308601 59308801 + 700.0
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chr19 59308901 59309101 + 600.0
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</help>
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</tool>
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@@ -1,84 +1,88 @@
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<tool id="wiggle2simple1" name="Wiggle-to-Interval">
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<description>converter</description>
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<command interpreter="python">wiggle_to_simple.py $input $out_file1 </command>
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<inputs>
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<param format="wig" name="input" type="data" label="Convert"/>
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</inputs>
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<outputs>
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<data format="interval" name="out_file1" />
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</outputs>
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<tests>
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<test>
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<param name="input" value="2.wig" />
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<output name="out_file1" file="2.interval"/>
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</test>
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</tests>
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<help>
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**Syntax**
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This tool converts wiggle data into interval type.
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|
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- **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.
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||||
|
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- **BED format** with no declaration line and four columns of data::
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chromA chromStartA chromEndA dataValueA
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chromB chromStartB chromEndB dataValueB
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- **variableStep** two column data; started by a declaration line and followed with chromosome positions and data values::
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variableStep chrom=chrN [span=windowSize]
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chromStartA dataValueA
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chromStartB dataValueB
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- **fixedStep** single column data; started by a declaration line and followed with data values::
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fixedStep chrom=chrN start=position step=stepInterval [span=windowSize]
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dataValue1
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dataValue2
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-----
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**Example**
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- input wiggle format file::
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#track type=wiggle_0 name="Bed Format" description="BED format"
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chr19 59302000 59302300 -1.0
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chr19 59302300 59302600 -0.75
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chr19 59302600 59302900 -0.50
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chr19 59302900 59303200 -0.25
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chr19 59303200 59303500 0.0
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#track type=wiggle_0 name="variableStep" description="variableStep format"
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variableStep chrom=chr19 span=150
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59304701 10.0
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59304901 12.5
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59305401 15.0
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59305601 17.5
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#track type=wiggle_0 name="fixedStep" description="fixed step" visibility=full
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fixedStep chrom=chr19 start=59307401 step=300 span=200
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1000
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900
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800
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700
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600
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|
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- convert the above file to interval file::
|
||||
|
||||
chr19 59302000 59302300 + -1.0
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||||
chr19 59302300 59302600 + -0.75
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chr19 59302600 59302900 + -0.5
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chr19 59302900 59303200 + -0.25
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chr19 59303200 59303500 + 0.0
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chr19 59304701 59304851 + 10.0
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chr19 59304901 59305051 + 12.5
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chr19 59305401 59305551 + 15.0
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chr19 59305601 59305751 + 17.5
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chr19 59307701 59307901 + 1000.0
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chr19 59308001 59308201 + 900.0
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chr19 59308301 59308501 + 800.0
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chr19 59308601 59308801 + 700.0
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chr19 59308901 59309101 + 600.0
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</help>
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</tool>
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<tool id="wiggle2simple1" name="Wiggle-to-Interval">
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<description>converter</description>
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<command interpreter="python">wiggle_to_simple.py $input $out_file1 </command>
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<inputs>
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<param format="wig" name="input" type="data" label="Convert"/>
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</inputs>
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<outputs>
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<data format="interval" name="out_file1" />
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</outputs>
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<tests>
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<test>
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<param name="input" value="2.wig" />
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<output name="out_file1" file="2.interval"/>
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</test>
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<test>
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<param name="input" value="3.wig" />
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<output name="out_file1" file="3_wig.bed"/>
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</test>
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</tests>
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<help>
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**Syntax**
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|
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This tool converts wiggle data into interval type.
|
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|
||||
- **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::
|
||||
|
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chromA chromStartA chromEndA dataValueA
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chromB chromStartB chromEndB dataValueB
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||||
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- **variableStep** two column data; started by a declaration line and followed with chromosome positions and data values::
|
||||
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variableStep chrom=chrN [span=windowSize]
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chromStartA dataValueA
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chromStartB dataValueB
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- **fixedStep** single column data; started by a declaration line and followed with data values::
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fixedStep chrom=chrN start=position step=stepInterval [span=windowSize]
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dataValue1
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dataValue2
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||||
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-----
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**Example**
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- input wiggle format file::
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#track type=wiggle_0 name="Bed Format" description="BED format"
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chr19 59302000 59302300 -1.0
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chr19 59302300 59302600 -0.75
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chr19 59302600 59302900 -0.50
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chr19 59302900 59303200 -0.25
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chr19 59303200 59303500 0.0
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#track type=wiggle_0 name="variableStep" description="variableStep format"
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variableStep chrom=chr19 span=150
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59304701 10.0
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59304901 12.5
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59305401 15.0
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59305601 17.5
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#track type=wiggle_0 name="fixedStep" description="fixed step" visibility=full
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fixedStep chrom=chr19 start=59307401 step=300 span=200
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1000
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900
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800
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700
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600
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- convert the above file to interval file::
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chr19 59302000 59302300 + -1.0
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chr19 59302300 59302600 + -0.75
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chr19 59302600 59302900 + -0.5
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chr19 59302900 59303200 + -0.25
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chr19 59303200 59303500 + 0.0
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chr19 59304701 59304851 + 10.0
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chr19 59304901 59305051 + 12.5
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chr19 59305401 59305551 + 15.0
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chr19 59305601 59305751 + 17.5
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chr19 59307701 59307901 + 1000.0
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chr19 59308001 59308201 + 900.0
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chr19 59308301 59308501 + 800.0
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chr19 59308601 59308801 + 700.0
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chr19 59308901 59309101 + 600.0
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</help>
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</tool>
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