/tool_data_table_conf.xml.cistrome

  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>