commit/galaxy-central: jmchilton: Syncrhonize wiggle_to_simple.xml tool test cases, fix newlines.
1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b9e7d751cfb5/ Changeset: b9e7d751cfb5 User: jmchilton Date: 2013-11-07 18:56:48 Summary: 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-tt4...). There are still two copies. Affected #: 2 files diff -r 06e1572df7253f4cff8b643e88ea36157ad7d4e0 -r b9e7d751cfb5a263d778786efa4e4b4e965b3992 tools/filters/wiggle_to_simple.xml --- a/tools/filters/wiggle_to_simple.xml +++ b/tools/filters/wiggle_to_simple.xml @@ -1,88 +1,88 @@ -<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"/> +<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> + </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> diff -r 06e1572df7253f4cff8b643e88ea36157ad7d4e0 -r b9e7d751cfb5a263d778786efa4e4b4e965b3992 tools/stats/wiggle_to_simple.xml --- a/tools/stats/wiggle_to_simple.xml +++ b/tools/stats/wiggle_to_simple.xml @@ -1,84 +1,88 @@ -<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> +<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> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.
participants (1)
-
commits-noreply＠bitbucket.org