/tools/hyphy/hyphy_nj_tree_wrapper.xml

https://bitbucket.org/cistrome/cistrome-harvard/ · XML · 46 lines · 34 code · 5 blank · 7 comment · 0 complexity · 71b6b7809637f4fdbbea69688e655fd2 MD5 · raw file

  1. <?xml version="1.1.1"?>
  2. <tool name="Neighbor Joining Tree" id="hyphy_nj_tree_wrapper1">
  3. <description>Builder</description>
  4. <command interpreter="python">hyphy_nj_tree_wrapper.py $input1 $out_file1 $out_file2 $distance_metric ${GALAXY_DATA_INDEX_DIR}</command>
  5. <inputs>
  6. <page>
  7. <param format="fasta" name="input1" type="data" label="Fasta file"/>
  8. <param name="distance_metric" type="select" label="Distance Model">
  9. <option value="TN93">Tamura-Nei (93)</option>
  10. <!-- <option value="TN93_RV">Tamura-Nei (93) distance and rate variation (unequal character frequencies, A->G, C->T and transversional bias corrections, gamma distributed rate variation from site to site)</option> -->
  11. <!-- <option value="TN84">Tajima-Nei (84) distance (unequal character frequencies)</option> -->
  12. <!-- <option value="K2P_RV">Kimura 2 parameter and rate variation (equal character frequencies, transition/trasversion bias correction, gamma distributed rate variation from site to site)</option> -->
  13. <option value="K2P">Kimura 2 parameter</option>
  14. <option value="JC69">Jukes-Cantor</option>
  15. <!-- <option value="T3P">Tamura 3-parameter (correction for GC content bias and transition/trasversion bias)</option> -->
  16. <!-- <option value="p_Distance">Number of observed substitutions per site</option> -->
  17. <!-- <option value="Unaligned_LZ">Distance measure for unaligned sequences based on Lempel Ziv measure of information content</option> -->
  18. <!-- <option value="Unaligned_LZ_FR">Distance measure for unaligned sequences based on Lempel Ziv measure of information content using the best choice forward and reverse string orientations</option> -->
  19. </param>
  20. </page>
  21. </inputs>
  22. <outputs>
  23. <data name="out_file1" format="tabular" />
  24. <data name="out_file2" format="pdf" />
  25. </outputs>
  26. <requirements>
  27. <requirement type="binary">ps2pdf</requirement>
  28. </requirements>
  29. <tests>
  30. <test>
  31. <param name="input1" value="nj_tree_inp.fasta"/>
  32. <param name="distance_metric" value="TN93"/>
  33. <output name="out_file1" file="nj_tree_newick_out.tabular"/>
  34. <output name="out_file2" file="nj_tree_pdf_out.pdf"/>
  35. </test>
  36. </tests>
  37. <help>
  38. This tool takes a single or multiple FASTA alignment file and builds Neighbor Joining Trees using HYPHY_, a maximum likelihood analyses package.
  39. .. _HYPHY: http://www.hyphy.org
  40. </help>
  41. </tool>