Mercurial > repos > xuebing > sharplabtool
view tools/filters/bed_to_bigbed.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="bed_to_bigBed" name="BED-to-bigBed" version="1.0.0"> <description>converter</description> <command>bedToBigBed $input1 $chromInfo $out_file1 #if $settings.settingsType == "full": -blockSize=${settings.blockSize} -itemsPerSlot=${settings.itemsPerSlot} ${settings.unc} #end if 2>&1 || echo "Error running bedToBigBed." >&2 </command> <requirements> <requirement type="package">ucsc_tools</requirement> </requirements> <inputs> <param format="bed" 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="512" label="Data points bundled at lowest level" help="Default is 512 (itemsPerSlot)" /> <param name="unc" type="boolean" truevalue="-unc" falsevalue="" checked="False" label="Do not use compression" help="(unc)"/> </when> </conditional> </inputs> <outputs> <data format="bigbed" name="out_file1" /> </outputs> <tests> <test> <param name="input1" value="7.bed" dbkey="hg17" /> <param name="settingsType" value="full" /> <param name="blockSize" value="256" /> <param name="itemsPerSlot" value="512" /> <param name="unc" value="False" /> <output name="out_file1" file="7.bigbed"/> </test> <test> <param name="input1" value="7.bed" dbkey="hg17" /> <param name="settingsType" value="preset" /> <output name="out_file1" file="7.bigbed"/> </test> </tests> <help> This tool converts a **sorted** BED file into a bigBed file. Currently, the bedFields option to specify the number of non-standard fields is not supported as an AutoSQL file must be provided, which is a format currently not supported by Galaxy. </help> </tool>