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<tables>
<!-- Locations of MAF files that have been indexed with bx-python -->
<table name="indexed_maf_files">
<columns>name, value, dbkey, species</columns>
<file path="tool-data/maf_index.loc" />
</table>
<!-- Locations of indexes in the BWA mapper format -->
<table name="bwa_indexes" comment_char="#">
<columns>value, dbkey, name, path</columns>
<file path="tool-data/bwa_index.loc" />
</table>
<!-- Locations of indexes in the Bowtie mapper format -->
<table name="bowtie_indexes" comment_char="#">
<columns>value, dbkey, name, path</columns>
<file path="tool-data/bowtie_indices.loc" />
</table>
<!-- Locations of indexes in the Bowtie2 mapper format -->
<table name="bowtie2_indexes" comment_char="#">
<columns>value, dbkey, name, path</columns>
<file path="tool-data/bowtie2_indices.loc" />
</table>
<!-- Locations of indexes in the Bowtie mapper format for TopHat to use -->
<table name="tophat_indexes" comment_char="#">
<columns>value, dbkey, name, path</columns>
<file path="tool-data/bowtie_indices.loc" />
</table>
<!-- Locations of indexes in the Bowtie2 mapper format for TopHat2 to use -->
<table name="tophat2_indexes" comment_char="#">
<columns>value, dbkey, name, path</columns>
<file path="tool-data/bowtie2_indices.loc" />
</table>
<!-- Location of SAMTools indexes and other files -->
<table name="sam_fa_indexes" comment_char="#">
<columns>index, value, path</columns>
<file path="tool-data/sam_fa_indices.loc" />
</table>
<!-- Location of Picard dict file and other files -->
<table name="picard_indexes" comment_char="#">
<columns>value, dbkey, name, path</columns>
<file path="tool-data/picard_index.loc" />
</table>
<!-- Location of Picard dict files valid for GATK -->
<table name="gatk_picard_indexes" comment_char="#">
<columns>value, dbkey, name, path</columns>
<file path="tool-data/gatk_sorted_picard_index.loc" />
</table>
<!-- Alignment and sequence data -->
<table name="alignseq">
<!-- XXX This has two different types of columns -->
<columns>index, dbkey, value</columns>
<file path="tool-data/alignseq.loc" />
</table>
<!-- UCSC twoBit indexed files -->
<table name="twobit">
<columns>dbkey, value</columns>
<file path="tool-data/twobit.loc" />
</table>
<!-- liftOver files -->
<table name="lift_over">
<columns>dbkey1, dbkey2, value</columns>
<file path="tool-data/liftOver.loc" />
</table>
<!-- Location of Mosaik files -->
<table name="mosaik_indexes" comment_char="#">
<columns>value, dbkey, name, path</columns>
<file path="tool-data/mosaik_index.loc" />
</table>
<!-- Novoalign indexes, not part of default Galaxy configurations -->
<table name="novoalign_indexes" comment_char="#">
<columns>value, dbkey, name, path</columns>
<file path="tool-data/novoalign_indices.loc" />
</table>
</tables>
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