/tools/extract/phastOdds/phastOdds_tool.xml

https://bitbucket.org/cistrome/cistrome-harvard/ · XML · 67 lines · 53 code · 14 blank · 0 comment · 0 complexity · 296eda54b0eb46e7e978b8a1a1f5a869 MD5 · raw file

  1. <tool id="phastOdds_for_intervals" name="Compute phastOdds score" version="1.0.0">
  2. <description>for each interval</description>
  3. <command interpreter="python">get_scores_galaxy.py $per_col ${score_file}.h5 ${score_file}.mapping.bed $input $output ${input.metadata.chromCol} ${input.metadata.startCol} ${input.metadata.endCol}</command>
  4. <inputs>
  5. <param format="interval" name="input" type="data" label="Interval file">
  6. <validator type="unspecified_build" message="Unspecified build, this tool works with data from genome builds hg17. Click the pencil icon in your history item to set the genome build."/>
  7. <validator type="dataset_metadata_in_file" filename="phastOdds.loc" metadata_name="dbkey" metadata_column="0" message="Sequences are currently unavailable for the specified build." />
  8. </param>
  9. <param name="score_file" type="select" label="Available datasets">
  10. <options from_file="phastOdds.loc">
  11. <column name="name" index="1"/>
  12. <column name="value" index="2"/>
  13. <column name="dbkey" index="0"/>
  14. <filter type="data_meta" ref="input" key="dbkey" column="0" />
  15. </options>
  16. </param>
  17. <param name="per_col" type="boolean" label="Standardize" help="Standardizes the score to be per alignment column" checked="yes" truevalue="-p" falsevalue=""/>
  18. </inputs>
  19. <outputs>
  20. <data format="interval" name="output" metadata_source="input"/>
  21. </outputs>
  22. <requirements>
  23. <requirement type="python-module">numpy</requirement>
  24. <requirement type="python-module">tables</requirement>
  25. </requirements>
  26. <tests>
  27. <test>
  28. <param name="input" value="4.bed" dbkey="hg17" ftype="bed"/>
  29. <param name="score_file" value="/galaxy/data/phastOdds_precomputed/encode_SEP-2005_tba.v2_phastOdds" />
  30. <param name="per_col" value="true" />
  31. <output name="output" file="phastOdds_tool_out.interval" />
  32. </test>
  33. </tests>
  34. <help>
  35. .. class:: warningmark
  36. This tool currently only works with interval data from genome build hg17.
  37. .. class:: warningmark
  38. This tool assumes that the input dataset is in interval format and contains at least a chrom column, a start column and an end column. These 3 columns can be dispersed throughout any number of other data columns.
  39. -----
  40. **Syntax**
  41. Append a column to each line of an interval file containing the phastOdds score for that interval.
  42. -----
  43. **Example**
  44. If your original data has the following format:
  45. +-----+-----+---+
  46. |chrom|start|end|
  47. +-----+-----+---+
  48. and you choose to compute phastOdds scores, your output will look like this:
  49. +-----+-----+---+-----+
  50. |chrom|start|end|score|
  51. +-----+-----+---+-----+
  52. </help>
  53. </tool>