/tools/filters/bed_to_bigbed.xml
https://bitbucket.org/cistrome/cistrome-harvard/ · XML · 55 lines · 52 code · 3 blank · 0 comment · 0 complexity · 6598cddad457cdade66754607293ead6 MD5 · raw file
- <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>