changeset 7:cb854f5d6a4b draft

planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a
author yhoogstrate
date Tue, 04 Aug 2015 08:57:24 -0400
parents 592cbca2c530
children 9750f8c1d3cb
files liftOver.loc.sample tool-data/all_fasta.loc.sample tool-data/liftOver.loc.sample
diffstat 3 files changed, 45 insertions(+), 27 deletions(-) [+]
line wrap: on
line diff
--- a/liftOver.loc.sample	Tue Aug 04 08:56:12 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,27 +0,0 @@
-#This is a sample file distributed with Galaxy that is used by the
-#liftOver tools.  The liftOver.loc file has this format (white space 
-#characters are TAB characters):
-#
-#<FromSpecies>	<ToSpecies>	<PathToChainFile>
-#
-#So, for example, if you had the chain file to convert from anoCar1 to galGal3
-#located at /depot/data2/galaxy/anoCar1/liftOver/anoCar1ToGalGal3.over.chain, 
-#then the liftOver.loc entry would look like this:
-#
-#anoCar1	galGal3		/depot/data2/galaxy/anoCar1/liftOver/anoCar1ToGalGal3.over.chain
-#
-#and your /depot/data2/galaxy/anoCar1/liftOver directory would 
-#contain all of your "chain" files (e.g.):
-#
-#-rw-rw-r-- 1 gua110 galaxy 24046079 2008-01-16 14:20 anoCar1ToGalGal3.over.chain
-#-rw-rw-r-- 1 gua110 galaxy 13216668 2008-01-16 14:20 anoCar1ToGasAcu1.over.chain
-#-rw-rw-r-- 1 gua110 galaxy 29597067 2008-01-16 14:20 anoCar1ToHg18.over.chain
-#...etc...
-#
-#Your liftOver.loc file should include an entry per line for each build you can
-#convert.  For example:
-#
-#anoCar1	galGal3	/depot/data2/galaxy/anoCar1/liftOver/anoCar1ToGalGal3.over.chain
-#anoCar1	gasAcu1	/depot/data2/galaxy/anoCar1/liftOver/anoCar1ToGasAcu1.over.chain
-#anoCar1	hg18	/depot/data2/galaxy/anoCar1/liftOver/anoCar1ToHg18.over.chain
-#...etc...
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/all_fasta.loc.sample	Tue Aug 04 08:57:24 2015 -0400
@@ -0,0 +1,18 @@
+#This file lists the locations and dbkeys of all the fasta files
+#under the "genome" directory (a directory that contains a directory
+#for each build). The script extract_fasta.py will generate the file
+#all_fasta.loc. This file has the format (white space characters are
+#TAB characters):
+#
+#<unique_build_id>	<dbkey>		<display_name>	<file_path>
+#
+#So, all_fasta.loc could look something like this:
+#
+#apiMel3	apiMel3	Honeybee (Apis mellifera): apiMel3		/path/to/genome/apiMel3/apiMel3.fa
+#hg19canon	hg19		Human (Homo sapiens): hg19 Canonical		/path/to/genome/hg19/hg19canon.fa
+#hg19full	hg19		Human (Homo sapiens): hg19 Full			/path/to/genome/hg19/hg19full.fa
+#
+#Your all_fasta.loc file should contain an entry for each individual
+#fasta file. So there will be multiple fasta files for each build,
+#such as with hg19 above.
+#
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/liftOver.loc.sample	Tue Aug 04 08:57:24 2015 -0400
@@ -0,0 +1,27 @@
+#This is a sample file distributed with Galaxy that is used by the
+#liftOver tools.  The liftOver.loc file has this format (white space 
+#characters are TAB characters):
+#
+#<FromSpecies>	<ToSpecies>	<PathToChainFile>
+#
+#So, for example, if you had the chain file to convert from anoCar1 to galGal3
+#located at /depot/data2/galaxy/anoCar1/liftOver/anoCar1ToGalGal3.over.chain, 
+#then the liftOver.loc entry would look like this:
+#
+#anoCar1	galGal3		/depot/data2/galaxy/anoCar1/liftOver/anoCar1ToGalGal3.over.chain
+#
+#and your /depot/data2/galaxy/anoCar1/liftOver directory would 
+#contain all of your "chain" files (e.g.):
+#
+#-rw-rw-r-- 1 gua110 galaxy 24046079 2008-01-16 14:20 anoCar1ToGalGal3.over.chain
+#-rw-rw-r-- 1 gua110 galaxy 13216668 2008-01-16 14:20 anoCar1ToGasAcu1.over.chain
+#-rw-rw-r-- 1 gua110 galaxy 29597067 2008-01-16 14:20 anoCar1ToHg18.over.chain
+#...etc...
+#
+#Your liftOver.loc file should include an entry per line for each build you can
+#convert.  For example:
+#
+#anoCar1	galGal3	/depot/data2/galaxy/anoCar1/liftOver/anoCar1ToGalGal3.over.chain
+#anoCar1	gasAcu1	/depot/data2/galaxy/anoCar1/liftOver/anoCar1ToGasAcu1.over.chain
+#anoCar1	hg18	/depot/data2/galaxy/anoCar1/liftOver/anoCar1ToHg18.over.chain
+#...etc...