# HG changeset patch
# User eugen
# Date 1344859932 14400
# Node ID d83e10016ed8ed515eacd0cb280e36ab780cac37
# Parent  a0d9b44f8db4dabb3d0df1a7cf110a52cd6a8ed4
Deleted selected files

diff -r a0d9b44f8db4 -r d83e10016ed8 tool_data_table_conf.xml
--- a/tool_data_table_conf.xml	Mon Aug 13 08:11:38 2012 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,123 +0,0 @@
-<!-- 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="#">
-        <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="#">
-        <columns>value, dbkey, formats, name, path</columns>
-        <file path="tool-data/bfast_indexes.loc" />
-    </table>
-    <!-- Locations of nucleotide (mega)blast databases -->
-    <table name="blastdb" comment_char="#">
-        <columns>value, name, path</columns>
-        <file path="tool-data/blastdb.loc" />
-    </table>
-    <!-- Locations of protein (mega)blast databases -->
-    <table name="blastdb_p" comment_char="#">
-        <columns>value, name, path</columns>
-        <file path="tool-data/blastdb_p.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 Bowtie color-space mapper format -->
-    <table name="bowtie_indexes_color" comment_char="#">
-        <columns>value, dbkey, name, path</columns>
-        <file path="tool-data/bowtie_indices_color.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 BWA Bisulfite mapper format -->
-    <table name="bismark_bs_indeces" comment_char="#">
-        <columns>value, dbkey, name, path</columns>
-        <file path="tool-data/bismark_bs_indeces.loc" />
-    </table>
-    <!-- Locations of FastA genomes for BSMAP -->
-     <table name="bsmap_fasta" comment_char="#">
-        <columns>value, dbkey, name, path</columns>
-        <file path="tool-data/bsmap_fasta.loc" />
-    </table>    
-    <!-- Locations of indexes in the BWA color-space mapper format -->
-    <table name="bwa_indexes_color" comment_char="#">
-        <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="#">
-        <columns>value, dbkey, name, path</columns>
-        <file path="tool-data/ngs_sim_fasta.loc" />
-    </table>
-    <!-- Locations of 2bit sequence files for use in Lastz -->
-    <table name="lastz_seqs" comment_char="#">
-        <columns>value, name, path</columns>
-        <file path="tool-data/lastz_seqs.loc" />
-    </table>
-    <!-- Locations of PerM base index files -->
-    <table name="perm_base_indexes" comment_char="#">
-        <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="#">
-        <columns>value, name, path</columns>
-        <file path="tool-data/perm_color_index.loc" />
-    </table>
-    <!-- Location of SAMTools indexes and other files -->
-    <table name="sam_fa_indexes" comment_char="#">
-        <columns>line_type, 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>
-    <!-- Available of GATK references -->
-    <table name="gatk_annotations" comment_char="#">
-        <columns>value, name, gatk_value, tools_valid_for</columns>
-        <file path="tool-data/gatk_annotations.txt" />
-    </table>
-    <!-- Location of SRMA dict file and other files -->
-    <table name="srma_indexes" comment_char="#">
-        <columns>value, dbkey, name, path</columns>
-        <file path="tool-data/picard_index.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 Bowtie color-space mapper format for TopHat to use -->
-    <table name="tophat_indexes_color" comment_char="#">
-        <columns>value, dbkey, name, path</columns>
-        <file path="tool-data/bowtie_indices_color.loc" />
-    </table>
-    <!-- Locations of configurations in the CCAT peak/region caller format -->
-    <table name="ccat_configurations" comment_char="#">
-        <columns>value, name, path</columns>
-        <file path="tool-data/ccat_configurations.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>
-</tables>
diff -r a0d9b44f8db4 -r d83e10016ed8 tool_data_table_conf.xml.sample
--- a/tool_data_table_conf.xml.sample	Mon Aug 13 08:11:38 2012 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,118 +0,0 @@
-<!-- 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 bismark converted bs-seq references -->
-    <table name="bismark_bs_indeces" comment_char="#">
-        <columns>value, dbkey, name, path</columns>
-        <file path="tool-data/bismark_bs_indeces.loc" />
-    </table>
-    <!-- Locations of all fasta files under genome directory -->
-    <table name="all_fasta" comment_char="#">
-        <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="#">
-        <columns>value, dbkey, formats, name, path</columns>
-        <file path="tool-data/bfast_indexes.loc" />
-    </table>
-    <!-- Locations of nucleotide (mega)blast databases -->
-    <table name="blastdb" comment_char="#">
-        <columns>value, name, path</columns>
-        <file path="tool-data/blastdb.loc" />
-    </table>
-    <!-- Locations of protein (mega)blast databases -->
-    <table name="blastdb_p" comment_char="#">
-        <columns>value, name, path</columns>
-        <file path="tool-data/blastdb_p.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 Bowtie color-space mapper format -->
-    <table name="bowtie_indexes_color" comment_char="#">
-        <columns>value, dbkey, name, path</columns>
-        <file path="tool-data/bowtie_indices_color.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 BWA color-space mapper format -->
-    <table name="bwa_indexes_color" comment_char="#">
-        <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="#">
-        <columns>value, dbkey, name, path</columns>
-        <file path="tool-data/ngs_sim_fasta.loc" />
-    </table>
-    <!-- Locations of 2bit sequence files for use in Lastz -->
-    <table name="lastz_seqs" comment_char="#">
-        <columns>value, name, path</columns>
-        <file path="tool-data/lastz_seqs.loc" />
-    </table>
-    <!-- Locations of PerM base index files -->
-    <table name="perm_base_indexes" comment_char="#">
-        <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="#">
-        <columns>value, name, path</columns>
-        <file path="tool-data/perm_color_index.loc" />
-    </table>
-    <!-- Location of SAMTools indexes and other files -->
-    <table name="sam_fa_indexes" comment_char="#">
-        <columns>line_type, 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>
-    <!-- Available of GATK references -->
-    <table name="gatk_annotations" comment_char="#">
-        <columns>value, name, gatk_value, tools_valid_for</columns>
-        <file path="tool-data/gatk_annotations.txt" />
-    </table>
-    <!-- Location of SRMA dict file and other files -->
-    <table name="srma_indexes" comment_char="#">
-        <columns>value, dbkey, name, path</columns>
-        <file path="tool-data/picard_index.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 Bowtie color-space mapper format for TopHat to use -->
-    <table name="tophat_indexes_color" comment_char="#">
-        <columns>value, dbkey, name, path</columns>
-        <file path="tool-data/bowtie_indices_color.loc" />
-    </table>
-    <!-- Locations of configurations in the CCAT peak/region caller format -->
-    <table name="ccat_configurations" comment_char="#">
-        <columns>value, name, path</columns>
-        <file path="tool-data/ccat_configurations.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>
-</tables>