Mercurial > repos > timpalpant > java_genomics_toolkit

comparison tool_data_table_conf.xml.sample @ 14:f58706d4d421 draft

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author timpalpant
date Sat, 19 May 2012 10:40:16 -0400
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13:eb53be9a09f4 14:f58706d4d421
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 Bowtie2 mapper format -->
29 <table name="bowtie2_indexes" comment_char="#">
30 <columns>value, dbkey, name, path</columns>
31 <file path="tool-data/bowtie2_indices.loc" />
32 </table>
33 <!-- Locations of indexes in the Bowtie color-space mapper format -->
34 <table name="bowtie_indexes_color" comment_char="#">
35 <columns>value, dbkey, name, path</columns>
36 <file path="tool-data/bowtie_indices_color.loc" />
37 </table>
38 <!-- Locations of indexes in the BWA mapper format -->
39 <table name="bwa_indexes" comment_char="#">
40 <columns>value, dbkey, name, path</columns>
41 <file path="tool-data/bwa_index.loc" />
42 </table>
43 <!-- Locations of indexes in the BWA color-space mapper format -->
44 <table name="bwa_indexes_color" comment_char="#">
45 <columns>value, dbkey, name, path</columns>
46 <file path="tool-data/bwa_index_color.loc" />
47 </table>
48 <!-- Locations of MAF files that have been indexed with bx-python -->
49 <table name="indexed_maf_files">
50 <columns>name, value, dbkey, species</columns>
51 <file path="tool-data/maf_index.loc" />
52 </table>
53 <!-- Locations of fasta files appropriate for NGS simulation -->
54 <table name="ngs_sim_fasta" comment_char="#">
55 <columns>value, dbkey, name, path</columns>
56 <file path="tool-data/ngs_sim_fasta.loc" />
57 </table>
58 <!-- Locations of 2bit sequence files for use in Lastz -->
59 <table name="lastz_seqs" comment_char="#">
60 <columns>value, name, path</columns>
61 <file path="tool-data/lastz_seqs.loc" />
62 </table>
63 <!-- Locations of PerM base index files -->
64 <table name="perm_base_indexes" comment_char="#">
65 <columns>value, name, path</columns>
66 <file path="tool-data/perm_base_index.loc" />
67 </table>
68 <!-- Locations of PerM color-space index files -->
69 <table name="perm_color_indexes" comment_char="#">
70 <columns>value, name, path</columns>
71 <file path="tool-data/perm_color_index.loc" />
72 </table>
73 <!-- Location of SAMTools indexes and other files -->
74 <table name="sam_fa_indexes" comment_char="#">
75 <columns>line_type, value, path</columns>
76 <file path="tool-data/sam_fa_indices.loc" />
77 </table>
78 <!-- Location of Picard dict file and other files -->
79 <table name="picard_indexes" comment_char="#">
80 <columns>value, dbkey, name, path</columns>
81 <file path="tool-data/picard_index.loc" />
82 </table>
83 <!-- Location of Picard dict files valid for GATK -->
84 <table name="gatk_picard_indexes" comment_char="#">
85 <columns>value, dbkey, name, path</columns>
86 <file path="tool-data/gatk_sorted_picard_index.loc" />
87 </table>
88 <!-- Available of GATK references -->
89 <table name="gatk_annotations" comment_char="#">
90 <columns>value, name, gatk_value, tools_valid_for</columns>
91 <file path="tool-data/gatk_annotations.txt" />
92 </table>
93 <!-- Location of SRMA dict file and other files -->
94 <table name="srma_indexes" comment_char="#">
95 <columns>value, dbkey, name, path</columns>
96 <file path="tool-data/picard_index.loc" />
97 </table>
98 <!-- Locations of indexes in the Bowtie mapper format for TopHat to use -->
99 <table name="tophat_indexes" comment_char="#">
100 <columns>value, dbkey, name, path</columns>
101 <file path="tool-data/bowtie_indices.loc" />
102 </table>
103 <!-- Locations of indexes in the Bowtie color-space mapper format for TopHat to use -->
104 <table name="tophat_indexes_color" comment_char="#">
105 <columns>value, dbkey, name, path</columns>
106 <file path="tool-data/bowtie_indices_color.loc" />
107 </table>
108 <!-- Locations of configurations in the CCAT peak/region caller format -->
109 <table name="ccat_configurations" comment_char="#">
110 <columns>value, name, path</columns>
111 <file path="tool-data/ccat_configurations.loc" />
112 </table>
113 <!-- Location of Mosaik files -->
114 <table name="mosaik_indexes" comment_char="#">
115 <columns>value, dbkey, name, path</columns>
116 <file path="tool-data/mosaik_index.loc" />
117 </table>
118 </tables>