Mercurial > repos > xuebing > sharplabtool
view tools/filters/wig_to_bigwig.xml @ 0:9071e359b9a3
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author | xuebing |
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date | Fri, 09 Mar 2012 19:37:19 -0500 |
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<tool id="wig_to_bigWig" name="Wig-to-bigWig" version="1.1.0"> <description>converter</description> <command>grep -v "^track" $input1 | wigToBigWig stdin $chromInfo $out_file1 #if $settings.settingsType == "full": -blockSize=${settings.blockSize} -itemsPerSlot=${settings.itemsPerSlot} ${settings.clip} ${settings.unc} #else: -clip #end if 2>&1 || echo "Error running wigToBigWig." >&2</command> <requirements> <requirement type="package">ucsc_tools</requirement> </requirements> <inputs> <param format="wig" name="input1" type="data" label="Convert"> <validator type="unspecified_build" /> </param> <conditional name="settings"> <param name="settingsType" type="select" label="Converter settings to use" help="Default settings should usually be used."> <option value="preset">Default</option> <option value="full">Full parameter list</option> </param> <when value="preset" /> <when value="full"> <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="True" 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)"/> </when> </conditional> </inputs> <outputs> <data format="bigwig" name="out_file1" /> </outputs> <tests> <test> <param name="input1" value="2.wig" dbkey="hg17" /> <param name="settingsType" value="full" /> <param name="blockSize" value="256" /> <param name="itemsPerSlot" value="1024" /> <param name="clip" value="True" /> <param name="unc" value="False" /> <output name="out_file1" file="2.bigwig"/> </test> <test> <param name="input1" value="2.wig" dbkey="hg17" /> <param name="settingsType" value="preset" /> <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>