|
4
|
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 Bowtie2 mapper format -->
|
|
|
24 <table name="bowtie2_indexes" comment_char="#">
|
|
|
25 <columns>value, dbkey, name, path</columns>
|
|
|
26 <file path="tool-data/bowtie2_indices.loc" />
|
|
|
27 </table>
|
|
|
28 <!-- Locations of indexes in the BWA mapper format -->
|
|
|
29 <table name="bwa_indexes" comment_char="#">
|
|
|
30 <columns>value, dbkey, name, path</columns>
|
|
|
31 <file path="tool-data/bwa_index.loc" />
|
|
|
32 </table>
|
|
|
33 <!-- Locations of indexes in the BWA color-space mapper format -->
|
|
|
34 <table name="bwa_indexes_color" comment_char="#">
|
|
|
35 <columns>value, dbkey, name, path</columns>
|
|
|
36 <file path="tool-data/bwa_index_color.loc" />
|
|
|
37 </table>
|
|
|
38 <!-- Locations of MAF files that have been indexed with bx-python -->
|
|
|
39 <table name="indexed_maf_files">
|
|
|
40 <columns>name, value, dbkey, species</columns>
|
|
|
41 <file path="tool-data/maf_index.loc" />
|
|
|
42 </table>
|
|
|
43 <!-- Locations of fasta files appropriate for NGS simulation -->
|
|
|
44 <table name="ngs_sim_fasta" comment_char="#">
|
|
|
45 <columns>value, dbkey, name, path</columns>
|
|
|
46 <file path="tool-data/ngs_sim_fasta.loc" />
|
|
|
47 </table>
|
|
|
48 <!-- Locations of PerM base index files -->
|
|
|
49 <table name="perm_base_indexes" comment_char="#">
|
|
|
50 <columns>value, name, path</columns>
|
|
|
51 <file path="tool-data/perm_base_index.loc" />
|
|
|
52 </table>
|
|
|
53 <!-- Locations of PerM color-space index files -->
|
|
|
54 <table name="perm_color_indexes" comment_char="#">
|
|
|
55 <columns>value, name, path</columns>
|
|
|
56 <file path="tool-data/perm_color_index.loc" />
|
|
|
57 </table>
|
|
|
58 <!-- Location of Picard dict file and other files -->
|
|
|
59 <table name="picard_indexes" comment_char="#">
|
|
|
60 <columns>value, dbkey, name, path</columns>
|
|
|
61 <file path="tool-data/picard_index.loc" />
|
|
|
62 </table>
|
|
|
63 <!-- Location of Picard dict files valid for GATK -->
|
|
|
64 <table name="gatk_picard_indexes" comment_char="#">
|
|
|
65 <columns>value, dbkey, name, path</columns>
|
|
|
66 <file path="tool-data/gatk_sorted_picard_index.loc" />
|
|
|
67 </table>
|
|
|
68 <!-- Available of GATK references -->
|
|
|
69 <table name="gatk_annotations" comment_char="#">
|
|
|
70 <columns>value, name, gatk_value, tools_valid_for</columns>
|
|
|
71 <file path="tool-data/gatk_annotations.txt" />
|
|
|
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 indexes in the Bowtie2 mapper format for TopHat2 to use -->
|
|
|
89 <table name="tophat2_indexes" comment_char="#">
|
|
|
90 <columns>value, dbkey, name, path</columns>
|
|
|
91 <file path="tool-data/bowtie2_indices.loc" />
|
|
|
92 </table>
|
|
|
93 <!-- Locations of configurations in the CCAT peak/region caller format -->
|
|
|
94 <table name="ccat_configurations" comment_char="#">
|
|
|
95 <columns>value, name, path</columns>
|
|
|
96 <file path="tool-data/ccat_configurations.loc" />
|
|
|
97 </table>
|
|
|
98 <!-- Location of Mosaik files -->
|
|
|
99 <table name="mosaik_indexes" comment_char="#">
|
|
|
100 <columns>value, dbkey, name, path</columns>
|
|
|
101 <file path="tool-data/mosaik_index.loc" />
|
|
|
102 </table>
|
|
|
103 </tables>
|
