Mercurial > repos > drosofff > sr_bowtier
changeset 2:32b97daad1f9 draft
Uploaded
author | drosofff |
---|---|
date | Mon, 12 May 2014 12:22:24 -0400 |
parents | 30f50368dd79 |
children | 752bd9400127 |
files | tool_data_table_conf.xml.sample |
diffstat | 1 files changed, 123 insertions(+), 0 deletions(-) [+] |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Mon May 12 12:22:24 2014 -0400 @@ -0,0 +1,123 @@ +<!-- 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 bowtie2 indexes --> + <table name="bowtie2_indexes" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/bowtie2_indices.loc" /> + </table> + <!-- Locations of bowtie2 indeces for tophat2 --> + <table name="tophat2_indexes" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/bowtie2_indices.loc" /> + </table> + <!-- Locations of GED indexes in the Bowtie GED wrappers format --> + <table name="ged_bowtie_indexes" comment_char="#"> + <columns>name, value</columns> + <file path="tool-data/bowtie_indices_ged.loc" /> + </table> + <!-- Locations of GED indexes in the Bowtie GED wrappers FOR single stranded RNAs --> + <table name="ged_bowtie_ssRNA_indexes" comment_char="#"> + <columns>name, value</columns> + <file path="tool-data/bowtie_ss_RNA_indices_ged.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 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, tools_valid_for</columns> + <file path="tool-data/picard_index.loc" /> + </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>