# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Dan Blankenberg <dan@bx.psu.edu> # Date 1283375708 14400 # Node ID 695a12fec1e2195cf8ccdf80d6d5318a464c37e3 # Parent f205636ed466f490a081681e76b23196dbc80e7c Add a wig to bigWig converter tool. --- a/tool_conf.xml.sample +++ b/tool_conf.xml.sample @@ -88,6 +88,7 @@ <tool file="filters/wiggle_to_simple.xml" /><tool file="filters/sff_extractor.xml" /><tool file="filters/gtf2bedgraph.xml" /> + <tool file="filters/wig_to_bigwig.xml" /></section><section name="Extract Features" id="features"><tool file="filters/ucsc_gene_bed_to_exon_bed.xml" /> --- /dev/null +++ b/tools/filters/wig_to_bigwig.xml @@ -0,0 +1,54 @@ +<tool id="wig_to_bigWig" name="Wig to bigWig" version="1.0.0"> + <description>converter</description> + <command>grep -v "^track" $input1 | wigToBigWig stdin $chromInfo $out_file1 -blockSize=$blockSize -itemsPerSlot=$itemsPerSlot $clip $unc</command> + <requirements> + <requirement type="binary">wigToBigWig</requirement> + </requirements> + <inputs> + <param format="wig" name="input1" type="data" label="Convert"> + <validator type="unspecified_build" /> + </param> + <param name="blockSize" size="4" type="integer" value="256" label="Items to bundle in r-tree" help="Default is 256 (blockSize)" /> + <param name="itemsPerSlot" size="4" type="integer" value="1024" label="Data points bundled at lowest level" help="Default is 1024 (itemsPerSlot)" /> + <param name="clip" type="boolean" truevalue="-clip" falsevalue="" checked="False" label="Clip chromosome positions" help="Issue warning messages rather than dying if wig file contains items off end of chromosome. (clip)"/> + <param name="unc" type="boolean" truevalue="-unc" falsevalue="" checked="False" label="Do not use compression" help="(unc)"/> + </inputs> + <outputs> + <data format="bigwig" name="out_file1" /> + </outputs> + <tests> + <test> + <param name="input1" value="2.wig" dbkey="hg17" /> + <param name="blockSize" value="256" /> + <param name="itemsPerSlot" value="1024" /> + <param name="clip" value="False" /> + <param name="unc" value="False" /> + <output name="out_file1" file="2.bigwig"/> + </test> + </tests> + <help> +**Syntax** + +This tool converts wiggle data into bigWig 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 + +</help> +</tool> Binary file test-data/2.bigwig has changed