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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-->
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2 <tables>
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3 <!-- Locations of all fasta files under genome directory -->
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4 <table name="all_fasta" comment_char="#" allow_duplicate_entries="False">
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5 <columns>value, dbkey, name, path</columns>
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6 <file path="tool-data/all_fasta.loc" />
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7 </table>
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8 <!-- Locations of indexes in the BFAST mapper format -->
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9 <table name="bfast_indexes" comment_char="#" allow_duplicate_entries="False">
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10 <columns>value, dbkey, formats, name, path</columns>
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11 <file path="tool-data/bfast_indexes.loc" />
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12 </table>
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13 <!-- Locations of nucleotide BLAST databases -->
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14 <table name="blastdb" comment_char="#" allow_duplicate_entries="False">
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15 <columns>value, name, path</columns>
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16 <file path="tool-data/blastdb.loc" />
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17 </table>
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18 <!-- Locations of protein BLAST databases -->
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19 <table name="blastdb_p" comment_char="#" allow_duplicate_entries="False">
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20 <columns>value, name, path</columns>
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21 <file path="tool-data/blastdb_p.loc" />
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22 </table>
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23 <!-- Locations of protein domain BLAST databases -->
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24 <table name="blastdb_d" comment_char="#" allow_duplicate_entries="False">
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25 <columns>value, name, path</columns>
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26 <file path="tool-data/blastdb_d.loc" />
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27 </table>
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28 <!-- Locations of indexes in the BWA mapper format -->
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29 <table name="bwa_indexes" comment_char="#" allow_duplicate_entries="False">
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30 <columns>value, dbkey, name, path</columns>
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31 <file path="tool-data/bwa_index.loc" />
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32 </table>
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33 <!-- Locations of indexes in the BWA color-space mapper format -->
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34 <table name="bwa_indexes_color" comment_char="#" allow_duplicate_entries="False">
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35 <columns>value, dbkey, name, path</columns>
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36 <file path="tool-data/bwa_index_color.loc" />
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37 </table>
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38 <!-- Locations of MAF files that have been indexed with bx-python -->
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39 <table name="indexed_maf_files">
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40 <columns>name, value, dbkey, species</columns>
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41 <file path="tool-data/maf_index.loc" />
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42 </table>
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43 <!-- Locations of fasta files appropriate for NGS simulation -->
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44 <table name="ngs_sim_fasta" comment_char="#" allow_duplicate_entries="False">
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45 <columns>value, dbkey, name, path</columns>
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46 <file path="tool-data/ngs_sim_fasta.loc" />
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47 </table>
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48 <!-- Locations of PerM base index files -->
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49 <table name="perm_base_indexes" comment_char="#" allow_duplicate_entries="False">
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50 <columns>value, name, path</columns>
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51 <file path="tool-data/perm_base_index.loc" />
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52 </table>
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53 <!-- Locations of PerM color-space index files -->
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54 <table name="perm_color_indexes" comment_char="#" allow_duplicate_entries="False">
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55 <columns>value, name, path</columns>
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56 <file path="tool-data/perm_color_index.loc" />
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57 </table>
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58 <!-- Location of Picard dict file and other files -->
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59 <table name="picard_indexes" comment_char="#" allow_duplicate_entries="False">
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60 <columns>value, dbkey, name, path</columns>
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61 <file path="tool-data/picard_index.loc" />
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62 </table>
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63 <!-- Location of SRMA dict file and other files -->
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64 <table name="srma_indexes" comment_char="#" allow_duplicate_entries="False">
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65 <columns>value, dbkey, name, path</columns>
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66 <file path="tool-data/picard_index.loc" />
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67 </table>
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68 <!-- Location of Mosaik files -->
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69 <table name="mosaik_indexes" comment_char="#" allow_duplicate_entries="False">
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70 <columns>value, dbkey, name, path</columns>
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71 <file path="tool-data/mosaik_index.loc" />
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72 </table>
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73 <!-- Locations of indexes in the 2bit format -->
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74 <table name="twobit" comment_char="#" allow_duplicate_entries="False">
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75 <columns>value, path</columns>
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76 <file path="tool-data/twobit.loc" />
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77 </table>
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78 <!-- Available IGV builds, loaded from URL -->
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79 <table name="igv_broad_genomes" comment_char="#" allow_duplicate_entries="False">
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80 <columns>name, url, value</columns>
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81 <file url="http://igv.broadinstitute.org/genomes/genomes.txt" />
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82 </table>
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83 <!-- Available liftOver chain file -->
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84 <table name="liftOver" comment_char="#" allow_duplicate_entries="False">
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85 <columns>dbkey, name, value</columns>
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86 <file path="tool-data/liftOver.loc" />
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87 </table>
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88 <!-- iobio bam servers -->
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89 <table name="bam_iobio" comment_char="#" allow_duplicate_entries="False">
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90 <columns>value, name, url</columns>
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91 <file path="tool-data/bam_iobio.loc" />
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92 </table>
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93 <!-- iobio vcf servers -->
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94 <table name="vcf_iobio" comment_char="#" allow_duplicate_entries="False">
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95 <columns>value, name, url</columns>
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96 <file path="tool-data/vcf_iobio.loc" />
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97 </table>
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98 <!-- simple biom servers -->
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99 <table name="biom_simple_display" comment_char="#" allow_duplicate_entries="False">
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100 <columns>value, name, url</columns>
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101 <file path="tool-data/biom_simple_display.loc" />
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102 </table>
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103 <!-- simple intermine servers -->
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104 <table name="intermine_simple_display" comment_char="#" allow_duplicate_entries="False">
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105 <columns>value, name, url</columns>
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106 <file path="tool-data/intermine_simple_display.loc" />
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107 </table>
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108 <!-- Locations of 2bit sequence files for use in Lastz -->
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109 <table name="n_spiecies" comment_char="#">
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110 <columns>value, name, path</columns>
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111 <file path="tool-data/n_spiecies.loc" />
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112 </table>
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113 <!-- Locations of 2bit sequence files for use in Lastz -->
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114 <table name="mirbase" comment_char="#">
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115 <columns>value, name, dbkey, path</columns>
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116 <file path="tool-data/mirbase.loc" />
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117 </table>
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118 <!-- Locations of 2bit sequence files for use in Lastz -->
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119 <table name="mirgene" comment_char="#">
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120 <columns>value, name</columns>
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121 <file path="tool-data/mirgene.loc" />
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122 </table>
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123 <table name="Mirbase_v22" comment_char="#">
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124 <columns>value, name, id</columns>
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125 <file path="tool-data/Mirbase_v22.loc" />
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126 </table>
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127 </tables>
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128
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