/tool_data_table_conf.xml.cistrome

https://bitbucket.org/cistrome/cistrome-harvard/ · Unknown · 114 lines · 114 code · 0 blank · 0 comment · 0 complexity · 641f8c551e1a61412f17e045022541b2 MD5 · raw file

  1. <!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc-->
  2. <tables>
  3. <!-- Locations of all fasta files under genome directory -->
  4. <table name="all_fasta" comment_char="#">
  5. <columns>value, dbkey, name, path</columns>
  6. <file path="tool-data/all_fasta.loc" />
  7. </table>
  8. <!-- Locations of indexes in the BFAST mapper format -->
  9. <table name="bfast_indexes" comment_char="#">
  10. <columns>value, dbkey, formats, name, path</columns>
  11. <file path="tool-data/bfast_indexes.loc" />
  12. </table>
  13. <!-- Locations of nucleotide (mega)blast databases -->
  14. <table name="blastdb" comment_char="#">
  15. <columns>value, name, path</columns>
  16. <file path="tool-data/blastdb.loc" />
  17. </table>
  18. <!-- Locations of protein (mega)blast databases -->
  19. <table name="blastdb_p" comment_char="#">
  20. <columns>value, name, path</columns>
  21. <file path="tool-data/blastdb_p.loc" />
  22. </table>
  23. <!-- Locations of indexes in the Bowtie mapper format -->
  24. <table name="bowtie_indexes" comment_char="#">
  25. <columns>value, dbkey, name, path</columns>
  26. <file path="tool-data/bowtie_indices.loc" />
  27. </table>
  28. <!-- Locations of indexes in the Bowtie color mapper format -->
  29. <table name="bowtie_indexes_color" comment_char="#">
  30. <columns>value, dbkey, name, path</columns>
  31. <file path="tool-data/bowtie_indices_color.loc" />
  32. </table>
  33. <!-- Locations of indexes in the BWA mapper format -->
  34. <table name="bwa_indexes" comment_char="#">
  35. <columns>value, dbkey, name, path</columns>
  36. <file path="tool-data/bwa_index.loc" />
  37. </table>
  38. <!-- Locations of indexes in the BWA color mapper format -->
  39. <table name="bwa_indexes_color" comment_char="#">
  40. <columns>value, dbkey, name, path</columns>
  41. <file path="tool-data/bwa_index_color.loc" />
  42. </table>
  43. <!-- Locations of MAF files that have been indexed with bx-python -->
  44. <table name="indexed_maf_files">
  45. <columns>name, value, dbkey, species</columns>
  46. <file path="tool-data/maf_index.loc" />
  47. </table>
  48. <!-- Locations of fasta files appropriate for NGS simulation -->
  49. <table name="ngs_sim_fasta" comment_char="#">
  50. <columns>value, dbkey, name, path</columns>
  51. <file path="tool-data/ngs_sim_fasta.loc" />
  52. </table>
  53. <!-- Locations of 2bit sequence files for use in Lastz -->
  54. <table name="lastz_seqs" comment_char="#">
  55. <columns>value, name, path</columns>
  56. <file path="tool-data/lastz_seqs.loc" />
  57. </table>
  58. <!-- Locations of PerM base index files -->
  59. <table name="perm_base_indexes" comment_char="#">
  60. <columns>value, name, path</columns>
  61. <file path="tool-data/perm_base_index.loc" />
  62. </table>
  63. <!-- Locations of PerM color index files -->
  64. <table name="perm_color_indexes" comment_char="#">
  65. <columns>value, name, path</columns>
  66. <file path="tool-data/perm_color_index.loc" />
  67. </table>
  68. <!-- Location of Picard dict file and other files -->
  69. <table name="picard_indexes" comment_char="#">
  70. <columns>value, dbkey, name, path</columns>
  71. <file path="tool-data/picard_index.loc" />
  72. </table>
  73. <!-- Location of SRMA dict file and other files -->
  74. <table name="srma_indexes" comment_char="#">
  75. <columns>value, dbkey, name, path</columns>
  76. <file path="tool-data/picard_index.loc" />
  77. </table>
  78. <!-- Locations of indexes in the Bowtie mapper format for TopHat to use -->
  79. <table name="tophat_indexes" comment_char="#">
  80. <columns>value, dbkey, name, path</columns>
  81. <file path="tool-data/bowtie_indices.loc" />
  82. </table>
  83. <!-- Locations of indexes in the Bowtie color-space mapper format for TopHat to use -->
  84. <table name="tophat_indexes_color" comment_char="#">
  85. <columns>value, dbkey, name, path</columns>
  86. <file path="tool-data/bowtie_indices_color.loc" />
  87. </table>
  88. <!-- Locations of configurations in the CCAT peak/region caller format -->
  89. <table name="ccat_configurations" comment_char="#">
  90. <columns>value, name, path</columns>
  91. <file path="tool-data/ccat_configurations.loc" />
  92. </table>
  93. <!-- Location of Mosaik files -->
  94. <table name="mosaik_indexes" comment_char="#">
  95. <columns>value, dbkey, name, path</columns>
  96. <file path="tool-data/mosaik_index.loc" />
  97. </table>
  98. <!-- Location of Picard dict files valid for GATK -->
  99. <table name="gatk_picard_indexes" comment_char="#">
  100. <columns>value, dbkey, name, path</columns>
  101. <file path="tool-data/gatk_sorted_picard_index.loc" />
  102. </table>
  103. <!-- Available of GATK references -->
  104. <table name="gatk_annotations" comment_char="#">
  105. <columns>value, name, gatk_value, tools_valid_for</columns>
  106. <file path="tool-data/gatk_annotations.txt" />
  107. </table>
  108. <!-- added by Cistrome/Galaxy -->
  109. <!-- Location of names of gene universes supported by Cistrome expression array tools -->
  110. <table name="gene_universe" comment_char="#">
  111. <columns>value, name</columns>
  112. <file path="tool-data/gene_universe.txt" />
  113. </table>
  114. </tables>