Mercurial > repos > jjohnson > ensembl_variant_report

comparison tool_data_table_conf.xml.sample @ 1:a43d6ae3eb85 draft

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planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
author jjohnson
date Fri, 06 Jan 2017 16:26:21 -0500
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children 908c68e3c73f
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0:c3a9e63e8c51 1:a43d6ae3eb85
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="#" allow_duplicate_entries="False">
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="#" allow_duplicate_entries="False">
10 <columns>value, dbkey, formats, name, path</columns>
11 <file path="tool-data/bfast_indexes.loc" />
12 </table>
13 <!-- Locations of nucleotide BLAST databases -->
14 <table name="blastdb" comment_char="#" allow_duplicate_entries="False">
15 <columns>value, name, path</columns>
16 <file path="tool-data/blastdb.loc" />
17 </table>
18 <!-- Locations of protein BLAST databases -->
19 <table name="blastdb_p" comment_char="#" allow_duplicate_entries="False">
20 <columns>value, name, path</columns>
21 <file path="tool-data/blastdb_p.loc" />
22 </table>
23 <!-- Locations of protein domain BLAST databases -->
24 <table name="blastdb_d" comment_char="#" allow_duplicate_entries="False">
25 <columns>value, name, path</columns>
26 <file path="tool-data/blastdb_d.loc" />
27 </table>
28 <!-- Locations of indexes in the BWA mapper format -->
29 <table name="bwa_indexes" comment_char="#" allow_duplicate_entries="False">
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="#" allow_duplicate_entries="False">
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="#" allow_duplicate_entries="False">
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="#" allow_duplicate_entries="False">
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="#" allow_duplicate_entries="False">
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="#" allow_duplicate_entries="False">
60 <columns>value, dbkey, name, path</columns>
61 <file path="tool-data/picard_index.loc" />
62 </table>
63 <!-- Location of SRMA dict file and other files -->
64 <table name="srma_indexes" comment_char="#" allow_duplicate_entries="False">
65 <columns>value, dbkey, name, path</columns>
66 <file path="tool-data/picard_index.loc" />
67 </table>
68 <!-- Location of Mosaik files -->
69 <table name="mosaik_indexes" comment_char="#" allow_duplicate_entries="False">
70 <columns>value, dbkey, name, path</columns>
71 <file path="tool-data/mosaik_index.loc" />
72 </table>
73 <!-- Locations of indexes in the 2bit format -->
74 <table name="twobit" comment_char="#" allow_duplicate_entries="False">
75 <columns>value, path</columns>
76 <file path="tool-data/twobit.loc" />
77 </table>
78 <!-- Available IGV builds, loaded from URL -->
79 <table name="igv_broad_genomes" comment_char="#" allow_duplicate_entries="False">
80 <columns>name, url, value</columns>
81 <file url="http://igv.broadinstitute.org/genomes/genomes.txt" />
82 </table>
83 <!-- Available liftOver chain file -->
84 <table name="liftOver" comment_char="#" allow_duplicate_entries="False">
85 <columns>dbkey, name, value</columns>
86 <file path="tool-data/liftOver.loc" />
87 </table>
88 <!-- iobio bam servers -->
89 <table name="bam_iobio" comment_char="#" allow_duplicate_entries="False">
90 <columns>value, name, url</columns>
91 <file path="tool-data/bam_iobio.loc" />
92 </table>
93 <!-- iobio vcf servers -->
94 <table name="vcf_iobio" comment_char="#" allow_duplicate_entries="False">
95 <columns>value, name, url</columns>
96 <file path="tool-data/vcf_iobio.loc" />
97 </table>
98 <!-- simple biom servers -->
99 <table name="biom_simple_display" comment_char="#" allow_duplicate_entries="False">
100 <columns>value, name, url</columns>
101 <file path="tool-data/biom_simple_display.loc" />
102 </table>
103 </tables>