tool_data_table_conf.xml

<!-- 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-->
<tables>
    <!-- Locations of all fasta files under genome directory -->
    <table name="all_fasta" comment_char="#" allow_duplicate_entries="False">
        <columns>value, dbkey, name, path</columns>
        <file path="tool-data/all_fasta.loc" />
    </table>
    <!-- Locations of indexes in the BFAST mapper format -->
    <table name="bfast_indexes" comment_char="#" allow_duplicate_entries="False">
        <columns>value, dbkey, formats, name, path</columns>
        <file path="tool-data/bfast_indexes.loc" />
    </table>
    <!-- Locations of nucleotide BLAST databases -->
    <table name="blastdb" comment_char="#" allow_duplicate_entries="False">
        <columns>value, name, path</columns>
        <file path="tool-data/blastdb.loc" />
    </table>
    <!-- Locations of protein BLAST databases -->
    <table name="blastdb_p" comment_char="#" allow_duplicate_entries="False">
        <columns>value, name, path</columns>
        <file path="tool-data/blastdb_p.loc" />
    </table>
    <!-- Locations of protein domain BLAST databases -->
    <table name="blastdb_d" comment_char="#" allow_duplicate_entries="False">
        <columns>value, name, path</columns>
        <file path="tool-data/blastdb_d.loc" />
    </table>
    <!-- Locations of indexes in the BWA mapper format -->
    <table name="bwa_indexes" comment_char="#" allow_duplicate_entries="False">
        <columns>value, dbkey, name, path</columns>
        <file path="tool-data/bwa_index.loc" />
    </table>
    <!-- Locations of indexes in the BWA color-space mapper format -->
    <table name="bwa_indexes_color" comment_char="#" allow_duplicate_entries="False">
        <columns>value, dbkey, name, path</columns>
        <file path="tool-data/bwa_index_color.loc" />
    </table>
    <!-- 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 fasta files appropriate for NGS simulation -->
    <table name="ngs_sim_fasta" comment_char="#" allow_duplicate_entries="False">
        <columns>value, dbkey, name, path</columns>
        <file path="tool-data/ngs_sim_fasta.loc" />
    </table>
    <!-- Locations of PerM base index files -->
    <table name="perm_base_indexes" comment_char="#" allow_duplicate_entries="False">
        <columns>value, name, path</columns>
        <file path="tool-data/perm_base_index.loc" />
    </table>
    <!-- Locations of PerM color-space index files -->
    <table name="perm_color_indexes" comment_char="#" allow_duplicate_entries="False">
        <columns>value, name, path</columns>
        <file path="tool-data/perm_color_index.loc" />
    </table>
    <!-- Location of Picard dict file and other files -->
    <table name="picard_indexes" comment_char="#" allow_duplicate_entries="False">
        <columns>value, dbkey, name, path</columns>
        <file path="tool-data/picard_index.loc" />
    </table>
    <!-- Location of SRMA dict file and other files -->
    <table name="srma_indexes" comment_char="#" allow_duplicate_entries="False">
        <columns>value, dbkey, name, path</columns>
        <file path="tool-data/picard_index.loc" />
    </table>
    <!-- Location of Mosaik files -->
    <table name="mosaik_indexes" comment_char="#" allow_duplicate_entries="False">
        <columns>value, dbkey, name, path</columns>
        <file path="tool-data/mosaik_index.loc" />
    </table>
    <!-- Locations of indexes in the 2bit format -->
    <table name="twobit" comment_char="#" allow_duplicate_entries="False">
        <columns>value, path</columns>
        <file path="tool-data/twobit.loc" />
    </table>
    <!-- Available IGV builds, loaded from URL -->
    <table name="igv_broad_genomes" comment_char="#" allow_duplicate_entries="False">
        <columns>name, url, value</columns>
        <file url="http://igv.broadinstitute.org/genomes/genomes.txt" />
    </table>
    <!-- Available liftOver chain file -->
    <table name="liftOver" comment_char="#" allow_duplicate_entries="False">
        <columns>dbkey, name, value</columns>
        <file path="tool-data/liftOver.loc" />
    </table>
    <!-- iobio bam servers -->
    <table name="bam_iobio" comment_char="#" allow_duplicate_entries="False">
        <columns>value, name, url</columns>
        <file path="tool-data/bam_iobio.loc" />
    </table>
    <!-- iobio vcf servers -->
    <table name="vcf_iobio" comment_char="#" allow_duplicate_entries="False">
        <columns>value, name, url</columns>
        <file path="tool-data/vcf_iobio.loc" />
    </table>
    <!-- simple biom servers -->
    <table name="biom_simple_display" comment_char="#" allow_duplicate_entries="False">
        <columns>value, name, url</columns>
        <file path="tool-data/biom_simple_display.loc" />
    </table>
    <!-- simple intermine servers -->
    <table name="intermine_simple_display" comment_char="#" allow_duplicate_entries="False">
        <columns>value, name, url</columns>
        <file path="tool-data/intermine_simple_display.loc" />
    </table>
    <table name="EnsemblPlants" comment_char="#" allow_duplicate_entries="False">
        <columns>name, value, url</columns>
        <file path="tools/1-PRE-ANALYSIS/Data_Preparation/species_EnsemblPlants.txt" />
    </table>
    <table name="EnsemblBacteria" comment_char="#" allow_duplicate_entries="False">
        <columns>name, value, url</columns>
        <file path="tools/1-PRE-ANALYSIS/Data_Preparation/species_EnsemblBacteria.txt" />
    </table>
    <table name="EnsemblFungi" comment_char="#" allow_duplicate_entries="False">
        <columns>name, value, url</columns>
        <file path="tools/1-PRE-ANALYSIS/Data_Preparation/species_EnsemblFungi.txt" />
    </table>
    <table name="EnsemblMetazoa" comment_char="#" allow_duplicate_entries="False">
        <columns>name, value, url</columns>
        <file path="tools/1-PRE-ANALYSIS/Data_Preparation/species_EnsemblMetazoa.txt" />
    </table>
    <table name="EnsemblProtists" comment_char="#" allow_duplicate_entries="False">
        <columns>name, value, url</columns>
        <file path="tools/1-PRE-ANALYSIS/Data_Preparation/species_EnsemblProtists.txt" />
    </table>
    <table name="EnsemblVertebrates" comment_char="#" allow_duplicate_entries="False">
        <columns>name, value, url</columns>
        <file path="tools/1-PRE-ANALYSIS/Data_Preparation/species_EnsemblVertebrates.txt" />
    </table>
    <table name="genome" comment_char="#" allow_duplicate_entries="False">
        <columns>name, value, url</columns>
        <file path="tools/1-PRE-ANALYSIS/Obtain_Genome_Sequences_Annotation/Genomes.txt"/>
    </table>
    <table name="gff" comment_char="#" allow_duplicate_entries="False">
        <columns>name, value, url</columns>
        <file path="tools/1-PRE-ANALYSIS/Obtain_Genome_Sequences_Annotation/GFF.txt"/>
</table>
    <table name="ensembl_plant_version" comment_char="#" allow_duplicate_entries="False">
        <columns>value, name</columns>
        <file path="tools/1-PRE-ANALYSIS/Data_Preparation/species_version.txt" />
    </table>
</tables>