/tools/regVariation/getIndels_2way.xml

https://bitbucket.org/cistrome/cistrome-harvard/ · XML · 59 lines · 43 code · 16 blank · 0 comment · 0 complexity · ce380c755b2935b67cc3d852a3f501fe MD5 · raw file

  1. <tool id="getIndels_2way" name="Fetch Indels">
  2. <description> from pairwise alignments</description>
  3. <command interpreter="python">
  4. getIndels.py $input1 $out_file1
  5. </command>
  6. <inputs>
  7. <page>
  8. <param format="maf" name="input1" type="data" label="Select data"/>
  9. </page>
  10. </inputs>
  11. <outputs>
  12. <data format="tabular" name="out_file1" metadata_source="input1"/>
  13. </outputs>
  14. <requirements>
  15. <requirement type="python-module">numpy</requirement>
  16. </requirements>
  17. <tests>
  18. <test>
  19. <param name="input1" value="6.maf"/>
  20. <output name="out_file1" file="6_indels.tabular"/>
  21. </test>
  22. </tests>
  23. <help>
  24. .. class:: infomark
  25. **What it does**
  26. This tool estimates the number of indels for every alignment block of the MAF file.
  27. -----
  28. .. class:: warningmark
  29. **Note**
  30. Any block/s not containing exactly 2 species will be omitted.
  31. -----
  32. **Example**
  33. - For the following alignment block::
  34. a score=7233.0
  35. s hg18.chr1 100 35 + 247249719 AT--GACTGAGGACTTAGTTTAAGATGTTCCTACT
  36. s rheMac2.chr11 200 31 + 134511895 ATAAG-CGGACGACTTAGTTTAAGATGTTCC----
  37. - running this tool will return::
  38. #Block Source Seq1_Start Seq1_End Seq2_Start Seq2_End Indel_length
  39. 1 hg18.chr1 101 102 202 204 2
  40. 1 rheMac2.chr11 103 104 204 205 1
  41. 1 rheMac2.chr11 129 133 229 230 4
  42. </help>
  43. </tool>