Mercurial > repos > jjohnson > ensembl_variant_report

changeset 1:a43d6ae3eb85 draft

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planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty
author jjohnson
date Fri, 06 Jan 2017 16:26:21 -0500
parents c3a9e63e8c51
children bf2687e2511e
files tool-data/twobit.loc.sample tool_data_table_conf.xml.sample
diffstat 2 files changed, 129 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/twobit.loc.sample	Fri Jan 06 16:26:21 2017 -0500
@@ -0,0 +1,26 @@
+#This is a sample file distributed with Galaxy that is used by some
+#tools.  The twobit.loc file has this format (white space characters 
+#are TAB characters):
+#
+#<Build>	<FullPathToFile>
+#
+#So, for example, if you had droPer1 twobit files stored in 
+#/depot/data2/galaxy/droPer1/, then the twobit.loc entry 
+#would look like this:
+#
+#droPer1	/depot/data2/galaxy/droPer1/droPer1.2bit
+#
+#and your /depot/data2/galaxy/droPer1/ directory would 
+#contain all of your twobit files (e.g.):
+#
+#-rw-rw-r--   1 nate   galaxy 48972650 2007-05-04 11:27 droPer1.2bit
+#...etc...
+#
+#Your twobit.loc file should include an entry per line for each twobit 
+#file you have stored.  For example:
+#
+#droPer1	/depot/data2/galaxy/droPer1/droPer1.2bit
+#apiMel2	/depot/data2/galaxy/apiMel2/apiMel2.2bit
+#droAna1	/depot/data2/galaxy/droAna1/droAna1.2bit
+#droAna2	/depot/data2/galaxy/droAna2/droAna2.2bit
+#...etc...
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample	Fri Jan 06 16:26:21 2017 -0500
@@ -0,0 +1,103 @@
+<!-- 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>
+</tables>