/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

  1. <tool id="bed_to_bigBed" name="BED-to-bigBed" version="1.0.0">
  2. <description>converter</description>
  3. <command>bedToBigBed $input1 $chromInfo $out_file1
  4. #if $settings.settingsType == "full":
  5. -blockSize=${settings.blockSize} -itemsPerSlot=${settings.itemsPerSlot} ${settings.unc}
  6. #end if
  7. 2&gt;&amp;1 || echo "Error running bedToBigBed." >&amp;2
  8. </command>
  9. <requirements>
  10. <requirement type="package">ucsc_tools</requirement>
  11. </requirements>
  12. <inputs>
  13. <param format="bed" name="input1" type="data" label="Convert">
  14. <validator type="unspecified_build" />
  15. </param>
  16. <conditional name="settings">
  17. <param name="settingsType" type="select" label="Converter settings to use" help="Default settings should usually be used.">
  18. <option value="preset">Default</option>
  19. <option value="full">Full parameter list</option>
  20. </param>
  21. <when value="preset" />
  22. <when value="full">
  23. <param name="blockSize" size="4" type="integer" value="256" label="Items to bundle in r-tree" help="Default is 256 (blockSize)" />
  24. <param name="itemsPerSlot" size="4" type="integer" value="512" label="Data points bundled at lowest level" help="Default is 512 (itemsPerSlot)" />
  25. <param name="unc" type="boolean" truevalue="-unc" falsevalue="" checked="False" label="Do not use compression" help="(unc)"/>
  26. </when>
  27. </conditional>
  28. </inputs>
  29. <outputs>
  30. <data format="bigbed" name="out_file1" />
  31. </outputs>
  32. <tests>
  33. <test>
  34. <param name="input1" value="7.bed" dbkey="hg17" />
  35. <param name="settingsType" value="full" />
  36. <param name="blockSize" value="256" />
  37. <param name="itemsPerSlot" value="512" />
  38. <param name="unc" value="False" />
  39. <output name="out_file1" file="7.bigbed"/>
  40. </test>
  41. <test>
  42. <param name="input1" value="7.bed" dbkey="hg17" />
  43. <param name="settingsType" value="preset" />
  44. <output name="out_file1" file="7.bigbed"/>
  45. </test>
  46. </tests>
  47. <help>
  48. This tool converts a **sorted** BED file into a bigBed file.
  49. 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
  50. currently not supported by Galaxy.
  51. </help>
  52. </tool>