Mercurial > repos > bgruening > glimmer_hmm
changeset 2:2b0210a098ba draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm commit 2effed877a778e455c63a76e994a0f2bb8f4dba0
| author | rmarenco |
|---|---|
| date | Thu, 14 Jul 2016 15:15:24 -0400 |
| parents | 4da91bb244dc |
| children | 5e14355f802a |
| files | glimmerHMM/tool_data_table_conf.xml.sample tool_data_table_conf.xml.sample |
| diffstat | 2 files changed, 196 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/glimmerHMM/tool_data_table_conf.xml.sample Thu Jul 14 15:15:24 2016 -0400 @@ -0,0 +1,98 @@ +<!-- 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 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 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 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 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> + <!-- Location of Mosaik files --> + <table name="mosaik_indexes" comment_char="#"> + <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="#"> + <columns>value, path</columns> + <file path="tool-data/twobit.loc" /> + </table> + <!-- Available IGV builds, loaded from URL --> + <table name="igv_broad_genomes" comment_char="#"> + <columns>name, url, value</columns> + <file url="http://igv.broadinstitute.org/genomes/genomes.txt" /> + </table> + <!-- Available liftOver chain file --> + <table name="liftOver" comment_char="#"> + <columns>dbkey, name, value</columns> + <file path="tool-data/liftOver.loc" /> + </table> + <!-- iobio bam servers --> + <table name="bam_iobio" comment_char="#"> + <columns>value, name, url</columns> + <file path="tool-data/bam_iobio.loc" /> + </table> + <!-- iobio vcf servers --> + <table name="vcf_iobio" comment_char="#"> + <columns>value, name, url</columns> + <file path="tool-data/vcf_iobio.loc" /> + </table> + <!-- simple biom servers --> + <table name="biom_simple_display" comment_char="#"> + <columns>value, name, url</columns> + <file path="tool-data/biom_simple_display.loc" /> + </table> + <!-- glimmer_hmm trained_dir --> + <table name="glimmer_hmm_trained_dir" comment_char="#"> + <columns>value, name, path</columns> + <file path="tool-data/glimmer_hmm.loc" /> + </table> +</tables>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Thu Jul 14 15:15:24 2016 -0400 @@ -0,0 +1,98 @@ +<!-- 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 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 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 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 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> + <!-- Location of Mosaik files --> + <table name="mosaik_indexes" comment_char="#"> + <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="#"> + <columns>value, path</columns> + <file path="tool-data/twobit.loc" /> + </table> + <!-- Available IGV builds, loaded from URL --> + <table name="igv_broad_genomes" comment_char="#"> + <columns>name, url, value</columns> + <file url="http://igv.broadinstitute.org/genomes/genomes.txt" /> + </table> + <!-- Available liftOver chain file --> + <table name="liftOver" comment_char="#"> + <columns>dbkey, name, value</columns> + <file path="tool-data/liftOver.loc" /> + </table> + <!-- iobio bam servers --> + <table name="bam_iobio" comment_char="#"> + <columns>value, name, url</columns> + <file path="tool-data/bam_iobio.loc" /> + </table> + <!-- iobio vcf servers --> + <table name="vcf_iobio" comment_char="#"> + <columns>value, name, url</columns> + <file path="tool-data/vcf_iobio.loc" /> + </table> + <!-- simple biom servers --> + <table name="biom_simple_display" comment_char="#"> + <columns>value, name, url</columns> + <file path="tool-data/biom_simple_display.loc" /> + </table> + <!-- glimmer_hmm trained_dir --> + <table name="glimmer_hmm_trained_dir" comment_char="#"> + <columns>value, name, path</columns> + <file path="tool-data/glimmer_hmm.loc" /> + </table> +</tables>