/tools/filters/CreateInterval.xml

https://bitbucket.org/h_morita_dbcls/galaxy-central · XML · 56 lines · 44 code · 12 blank · 0 comment · 0 complexity · f069df1b031eca3b8e85e63e6eccfa7c MD5 · raw file

  1. <tool id="createInterval" name="Create single interval">
  2. <description>as a new query</description>
  3. <command interpreter="perl">CreateInterval.pl $chrom $start $end "$name" $strand $out_file1</command>
  4. <inputs>
  5. <param name="chrom" size="20" type="text" value="chr7" label="Chromosome"/>
  6. <param name="start" size="20" type="integer" value="100" label="Start position"/>
  7. <param name="end" size="20" type="integer" value="1000" label="End position"/>
  8. <param name="name" size="20" type="text" value="myInterval" label="Name"/>
  9. <param name="strand" type="select" label="Strand" help="If your interval is strandless set strand to plus" >
  10. <option value="plus">plus</option>
  11. <option value="minus">minus</option>
  12. </param>
  13. </inputs>
  14. <outputs>
  15. <data format="bed" name="out_file1" />
  16. </outputs>
  17. <tests>
  18. <test>
  19. <param name="chrom" value="chr7"/>
  20. <param name="start" value="100"/>
  21. <param name="end" value="1000"/>
  22. <param name="name" value="myinterval"/>
  23. <param name="strand" value="plus"/>
  24. <output name="out_file1" file="eq-createinterval.dat"/>
  25. </test>
  26. </tests>
  27. <help>
  28. .. class:: warningmark
  29. **TIP**. Once your interval appears in history, you must tell Galaxy which genome it belongs to by clicking pencil icon or the "?" link in the history item.
  30. -----
  31. **What it does**
  32. This tool allows you to create a single genomic interval. The resulting history item will be in the BED format.
  33. -----
  34. **Example**
  35. Typing the following values in the form::
  36. Chromosome: chrX
  37. Start position: 151087187
  38. End position: 151370486
  39. Name: NM_000808
  40. Strand: minus
  41. will create a single interval::
  42. chrX 151087187 151370486 NM_000808 0 -
  43. </help>
  44. </tool>