Merge pull request #587 from dannon/retab_loc_samples

Retab .loc.samples
galaxyproject · Aug 11, 2015 · a04147d · a04147d
2 parents 7baab04 + ee4f077
commit a04147d
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diff --git a/tool-data/all_fasta.loc.sample b/tool-data/all_fasta.loc.sample
@@ -4,13 +4,13 @@
 #all_fasta.loc. This file has the format (white space characters are
 #TAB characters):
 #
-#<unique_build_id>	<dbkey>		<display_name>	<file_path>
+#<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
+#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,

diff --git a/tool-data/faseq.loc.sample b/tool-data/faseq.loc.sample
@@ -20,7 +20,7 @@
 #Your faseq.loc file should include an entry per line for each set of fasta 
 #sequence files you have stored.  For example:
 #
-#hg18			/depot/data2/galaxy/faseq/hg18
-#mm9			/depot/data2/galaxy/faseq/mm9
+#hg18	/depot/data2/galaxy/faseq/hg18
+#mm9	/depot/data2/galaxy/faseq/mm9
 #Arabidopsis	/depot/data2/galaxy/faseq/Arabidopsis
 #...etc...
diff --git a/tool-data/liftOver.loc.sample b/tool-data/liftOver.loc.sample
@@ -8,7 +8,7 @@
 #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
+#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.):

diff --git a/tool-data/mosaik_index.loc.sample b/tool-data/mosaik_index.loc.sample
@@ -5,13 +5,13 @@
 #the directories in which those files are stored. The mosaik_index.loc 
 #file has this format (longer white space is the TAB character):
 #
-#<unique_build_id>		<dbkey>		<display_name>		<fasta_file_path>
+#<unique_build_id>	<dbkey>	<display_name>	<fasta_file_path>
 #
 #So, for example, if you had hg18 indexed and stored in 
 #/depot/data2/galaxy/mosaik/hg18/
 #then the mosaik_index.loc entry would look like this:
 #
-#hg18	hg18	hg18 Pretty		/depot/data2/galaxy/mosaik/hg18/hg18.fa
+#hg18	hg18	hg18 Pretty	/depot/data2/galaxy/mosaik/hg18/hg18.fa
 #
 #and your /depot/data2/galaxy/mosaik/hg18/ directory
 #would contain the following files:

diff --git a/tool-data/ngs_sim_fasta.loc.sample b/tool-data/ngs_sim_fasta.loc.sample
@@ -4,7 +4,7 @@
 #in this directory) that points to the locations of those files. The ngs_sim.loc
 #file has this format (white space characters are TAB characters):
 #
-#<unique_build_id>		<dbkey>		<display_name>		<file_base_path>
+#<unique_build_id>	<dbkey>	<display_name>	<file_base_path>
 #
 #So, for example, if you had hg18chrM.fa in 
 #/data/path/hg18/seq/, 
@@ -16,5 +16,5 @@
 #have stored.
 #
 #hg18chrM	hg18	hg18chrM	/data/path/hg18/seq/hg18chrM.fa
-#phiX174	phiX	phiX174		/data/path/genome/phiX/seq/phiX.fa
-#pUC18		pUC18	pUC18		/data/path/genome/pUC18/seq/pUC18.fa
+#phiX174	phiX	phiX174	/data/path/genome/phiX/seq/phiX.fa
+#pUC18	pUC18	pUC18	/data/path/genome/pUC18/seq/pUC18.fa
diff --git a/tool-data/perm_base_index.loc.sample b/tool-data/perm_base_index.loc.sample
@@ -5,23 +5,23 @@
 #the directories in which those files are stored. The perm_base_index.loc 
 #file has this format (longer white space characters are TAB characters):
 #
-#<build_seed_readlength>	<display_name>		<file_base>
+#<build_seed_readlength>	<display_name>	<file_base>
 #
 #Because each PerM index is built with a specific seed and a specific read
 #length, this needs to be specified so the user can choose the appropriate
 #one. So, for example, if you had phiX indexed with seed F3 and read length 
 #50, and stored in /depot/data/galaxy/phiX/perm_index/,
 #then the perm_base_index.loc entry would look something like this:
 #
-#phiX_F3_50		phiX: seed=F3, read length=50		/depot/data/galaxy/phiX/perm_index/phiX_base_F3_50.index
+#phiX_F3_50	phiX: seed=F3, read length=50	/depot/data/galaxy/phiX/perm_index/phiX_base_F3_50.index
 #
 #and your /depot/data/galaxy/phiX/perm_index/ directory
 #would contain the file phiX_base_F3_50.index:
 #
 #Your perm_base_index.loc file should include an entry per line for each
 #index set you have stored. For example:
 #
-#phiX_F3_50		phiX: seed=F3, read length=50	/data/galaxy/phiX/perm_index/phiX_base_F3_50.index
-#phiX_F4_50		phiX: seed=F4, read length=50	/data/galaxy/phiX/perm_index/phiX_base_F3_50.index
-#hg19_F3_50		hg19: seed=F3, read length=50	/data/galaxy/hg19/perm_index/hg19_base_F3_50.index
-#hg19_F4_50		hg19: seed=F4, read length=50	/data/galaxy/hg19/perm_index/hg19_base_F3_50.index
+#phiX_F3_50	phiX: seed=F3, read length=50	/data/galaxy/phiX/perm_index/phiX_base_F3_50.index
+#phiX_F4_50	phiX: seed=F4, read length=50	/data/galaxy/phiX/perm_index/phiX_base_F3_50.index
+#hg19_F3_50	hg19: seed=F3, read length=50	/data/galaxy/hg19/perm_index/hg19_base_F3_50.index
+#hg19_F4_50	hg19: seed=F4, read length=50	/data/galaxy/hg19/perm_index/hg19_base_F3_50.index
diff --git a/tool-data/perm_color_index.loc.sample b/tool-data/perm_color_index.loc.sample
@@ -5,24 +5,24 @@
 #the directories in which those files are stored. The perm_color_index.loc 
 #file has this format (white space characters are TAB characters):
 #
-#<build_seed_readlength>	<display_name>		<file_base>
+#<build_seed_readlength>	<display_name>	<file_base>
 #
 #Because each PerM index is built with a specific seed and a specific read
 #length, this needs to be specified so the user can choose the appropriate
 #one. So, for example, if you had phiX indexed with seed F3 and read length 
 #50, and stored in /depot/data/galaxy/phiX/perm_index/,
 #then the perm_color_index.loc entry would look something like this:
 #
-#phiX_F3_50		phiX: seed=F3, read length=50		/data/galaxy/phiX/perm_index/phiX_color_F3_50.index
+#phiX_F3_50	phiX: seed=F3, read length=50	/data/galaxy/phiX/perm_index/phiX_color_F3_50.index
 #
 #and your /depot/data/galaxy/phiX/perm_index/ directory
 #would contain the file phiX_color_F3_50.index:
 #
 #Your perm_color_index.loc file should include an entry per line for each
 #index set you have stored. For example:
 #
-#phiX_F3_50		phiX: seed=F3, read length=50		/data/galaxy/phiX/perm_index/phiX_color_F3_50.index
-#phiX_F4_50		phiX: seed=F4, read length=50		/data/galaxy/phiX/perm_index/phiX_color_F3_50.index
-#hg19_F3_50		hg19: seed=F3, read length=50		/data/galaxy/hg19/perm_index/hg19_color_F3_50.index
-#hg19_F4_50		hg19: seed=F4, read length=50		/data/galaxy/hg19/perm_index/hg19_color_F3_50.index
+#phiX_F3_50	phiX: seed=F3, read length=50	/data/galaxy/phiX/perm_index/phiX_color_F3_50.index
+#phiX_F4_50	phiX: seed=F4, read length=50	/data/galaxy/phiX/perm_index/phiX_color_F3_50.index
+#hg19_F3_50	hg19: seed=F3, read length=50	/data/galaxy/hg19/perm_index/hg19_color_F3_50.index
+#hg19_F4_50	hg19: seed=F4, read length=50	/data/galaxy/hg19/perm_index/hg19_color_F3_50.index
 #
diff --git a/tool-data/picard_index.loc.sample b/tool-data/picard_index.loc.sample
@@ -5,13 +5,13 @@
 #the directories in which those files are stored. The picard_index.loc 
 #file has this format (longer white space is the TAB character):
 #
-#<unique_build_id>		<dbkey>		<display_name>		<fasta_file_path>
+#<unique_build_id>	<dbkey>	<display_name>	<fasta_file_path>
 #
 #So, for example, if you had hg18 indexed and stored in 
 #/depot/data2/galaxy/srma/hg18/, 
 #then the srma_index.loc entry would look like this:
 #
-#hg18	hg18	hg18 Pretty		/depot/data2/galaxy/picard/hg18/hg18.fa
+#hg18	hg18	hg18 Pretty	/depot/data2/galaxy/picard/hg18/hg18.fa
 #
 #and your /depot/data2/galaxy/srma/hg18/ directory
 #would contain the following three files:

diff --git a/tool-data/regions.loc.sample b/tool-data/regions.loc.sample
@@ -8,7 +8,7 @@
 #/depot/data2/galaxy/regions/encode_regions_coords_hg16.bed, then the
 #regions.loc entry would look like this:
 #
-#hg16	encode_hg16		ENCODE Regions	/depot/data2/galaxy/regions/encode_regions_coords_hg16.bed
+#hg16	encode_hg16	ENCODE Regions	/depot/data2/galaxy/regions/encode_regions_coords_hg16.bed
 #
 #and your /depot/data2/galaxy/regions/ directory would 
 #contain all of your regions files (e.g.):

diff --git a/tool-data/srma_index.loc.sample b/tool-data/srma_index.loc.sample
@@ -8,7 +8,7 @@
 #the directories in which those files are stored. The srma_index.loc 
 #file has this format (longer white space is the TAB character):
 #
-#<unique_build_id>	<dbkey>		<display_name>	<fasta_file_path>
+#<unique_build_id>	<dbkey>	<display_name>	<fasta_file_path>
 #
 #So, for example, if you had hg18 indexed and stored in 
 #/depot/data2/galaxy/srma/hg18/,