# HG changeset patch
# User rhpvorderman
# Date 1504875453 14400
# Node ID afd01fcbea26cc45cb9b3b00a986cdfc184ef315
# Parent 2898c6feeb9f66d38aee7f652ef10194a1946b18
planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 5db36ba46db15647fd3206c23114b7671e4b4f79
diff -r 2898c6feeb9f -r afd01fcbea26 data_manager/data_manager_select_index_by_path.xml
--- a/data_manager/data_manager_select_index_by_path.xml Fri Sep 08 08:12:20 2017 -0400
+++ b/data_manager/data_manager_select_index_by_path.xml Fri Sep 08 08:57:33 2017 -0400
@@ -27,10 +27,7 @@
-
-
-
diff -r 2898c6feeb9f -r afd01fcbea26 data_manager_conf.xml
--- a/data_manager_conf.xml Fri Sep 08 08:12:20 2017 -0400
+++ b/data_manager_conf.xml Fri Sep 08 08:57:33 2017 -0400
@@ -8,7 +8,6 @@
-
diff -r 2898c6feeb9f -r afd01fcbea26 tool-data/all_fasta.loc.sample
--- a/tool-data/all_fasta.loc.sample Fri Sep 08 08:12:20 2017 -0400
+++ b/tool-data/all_fasta.loc.sample Fri Sep 08 08:57:33 2017 -0400
@@ -1,6 +1,8 @@
#This file lists the locations and dbkeys of all the fasta files
-
-#This file has the format (white space characters are TAB characters):
+#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):
#
#
#
@@ -14,4 +16,3 @@
#fasta file. So there will be multiple fasta files for each build,
#such as with hg19 above.
#
-
diff -r 2898c6feeb9f -r afd01fcbea26 tool-data/bowtie2_indices.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/bowtie2_indices.loc.sample Fri Sep 08 08:57:33 2017 -0400
@@ -0,0 +1,37 @@
+# bowtie2_indices.loc.sample
+# This is a *.loc.sample file distributed with Galaxy that enables tools
+# to use a directory of indexed data files. This one is for Bowtie2 and Tophat2.
+# See the wiki: http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup
+# First create these data files and save them in your own data directory structure.
+# Then, create a bowtie_indices.loc file to use those indexes with tools.
+# Copy this file, save it with the same name (minus the .sample),
+# follow the format examples, and store the result in this directory.
+# The file should include an one line entry for each index set.
+# The path points to the "basename" for the set, not a specific file.
+# It has four text columns seperated by TABS.
+#
+#
+#
+# So, for example, if you had hg18 indexes stored in:
+#
+# /depot/data2/galaxy/hg19/bowtie2/
+#
+# containing hg19 genome and hg19.*.bt2 files, such as:
+# -rw-rw-r-- 1 james james 914M Feb 10 18:56 hg19canon.fa
+# -rw-rw-r-- 1 james james 914M Feb 10 18:56 hg19canon.1.bt2
+# -rw-rw-r-- 1 james james 683M Feb 10 18:56 hg19canon.2.bt2
+# -rw-rw-r-- 1 james james 3.3K Feb 10 16:54 hg19canon.3.bt2
+# -rw-rw-r-- 1 james james 683M Feb 10 16:54 hg19canon.4.bt2
+# -rw-rw-r-- 1 james james 914M Feb 10 20:45 hg19canon.rev.1.bt2
+# -rw-rw-r-- 1 james james 683M Feb 10 20:45 hg19canon.rev.2.bt2
+#
+# then the bowtie2_indices.loc entry could look like this:
+#
+#hg19 hg19 Human (hg19) /depot/data2/galaxy/hg19/bowtie2/hg19canon
+#
+#More examples:
+#
+#mm10 mm10 Mouse (mm10) /depot/data2/galaxy/mm10/bowtie2/mm10
+#dm3 dm3 D. melanogaster (dm3) /depot/data2/galaxy/mm10/bowtie2/dm3
+#
+#
diff -r 2898c6feeb9f -r afd01fcbea26 tool-data/bowtie_indices.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/bowtie_indices.loc.sample Fri Sep 08 08:57:33 2017 -0400
@@ -0,0 +1,37 @@
+#This is a sample file distributed with Galaxy that enables tools
+#to use a directory of Bowtie indexed sequences data files. You will
+#need to create these data files and then create a bowtie_indices.loc
+#file similar to this one (store it in this directory) that points to
+#the directories in which those files are stored. The bowtie_indices.loc
+#file has this format (longer white space characters are TAB characters):
+#
+#
+#
+#So, for example, if you had hg18 indexed stored in
+#/depot/data2/galaxy/bowtie/hg18/,
+#then the bowtie_indices.loc entry would look like this:
+#
+#hg18 hg18 hg18 /depot/data2/galaxy/bowtie/hg18/hg18
+#
+#and your /depot/data2/galaxy/bowtie/hg18/ directory
+#would contain hg18.*.ebwt files:
+#
+#-rw-r--r-- 1 james universe 830134 2005-09-13 10:12 hg18.1.ebwt
+#-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 hg18.2.ebwt
+#-rw-r--r-- 1 james universe 269808 2005-09-13 10:12 hg18.3.ebwt
+#...etc...
+#
+#Your bowtie_indices.loc file should include an entry per line for each
+#index set you have stored. The "file" in the path does not actually
+#exist, but it is the prefix for the actual index files. For example:
+#
+#hg18canon hg18 hg18 Canonical /depot/data2/galaxy/bowtie/hg18/hg18canon
+#hg18full hg18 hg18 Full /depot/data2/galaxy/bowtie/hg18/hg18full
+#/orig/path/hg19 hg19 hg19 /depot/data2/galaxy/bowtie/hg19/hg19
+#...etc...
+#
+#Note that for backwards compatibility with workflows, the unique ID of
+#an entry must be the path that was in the original loc file, because that
+#is the value stored in the workflow for that parameter. That is why the
+#hg19 entry above looks odd. New genomes can be better-looking.
+#
diff -r 2898c6feeb9f -r afd01fcbea26 tool-data/bowtie_indices_color.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/bowtie_indices_color.loc.sample Fri Sep 08 08:57:33 2017 -0400
@@ -0,0 +1,37 @@
+#This is a sample file distributed with Galaxy that enables tools
+#to use a directory of Bowtie indexed sequences data files. You will
+#need to create these data files and then create a bowtie_indices.loc
+#file similar to this one (store it in this directory) that points to
+#the directories in which those files are stored. The bowtie_indices.loc
+#file has this format (longer white space characters are TAB characters):
+#
+#
+#
+#So, for example, if you had hg18 indexed stored in
+#/depot/data2/galaxy/bowtie/hg18/,
+#then the bowtie_indices.loc entry would look like this:
+#
+#hg18 hg18 hg18 /depot/data2/galaxy/bowtie/hg18/hg18
+#
+#and your /depot/data2/galaxy/bowtie/hg18/ directory
+#would contain hg18.*.ebwt files:
+#
+#-rw-r--r-- 1 james universe 830134 2005-09-13 10:12 hg18.1.ebwt
+#-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 hg18.2.ebwt
+#-rw-r--r-- 1 james universe 269808 2005-09-13 10:12 hg18.3.ebwt
+#...etc...
+#
+#Your bowtie_indices.loc file should include an entry per line for each
+#index set you have stored. The "file" in the path does not actually
+#exist, but it is the prefix for the actual index files. For example:
+#
+#hg18canon hg18 hg18 Canonical /depot/data2/galaxy/bowtie/hg18/hg18canon
+#hg18full hg18 hg18 Full /depot/data2/galaxy/bowtie/hg18/hg18full
+#/orig/path/hg19 hg19 hg19 /depot/data2/galaxy/bowtie/hg19/hg19
+#...etc...
+#
+#Note that for backwards compatibility with workflows, the unique ID of
+#an entry must be the path that was in the original loc file, because that
+#is the value stored in the workflow for that parameter. That is why the
+#hg19 entry above looks odd. New genomes can be better-looking.
+#
diff -r 2898c6feeb9f -r afd01fcbea26 tool-data/bwa_mem_index.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/bwa_mem_index.loc.sample Fri Sep 08 08:57:33 2017 -0400
@@ -0,0 +1,38 @@
+#This is a sample file distributed with Galaxy that enables tools
+#to use a directory of BWA indexed sequences data files. You will need
+#to create these data files and then create a bwa_index.loc file
+#similar to this one (store it in this directory) that points to
+#the directories in which those files are stored. The bwa_index.loc
+#file has this format (longer white space characters are TAB characters):
+#
+#
+#
+#So, for example, if you had phiX indexed stored in
+#/depot/data2/galaxy/phiX/base/,
+#then the bwa_index.loc entry would look like this:
+#
+#phiX174 phiX phiX Pretty /depot/data2/galaxy/phiX/base/phiX.fa
+#
+#and your /depot/data2/galaxy/phiX/base/ directory
+#would contain phiX.fa.* files:
+#
+#-rw-r--r-- 1 james universe 830134 2005-09-13 10:12 phiX.fa.amb
+#-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 phiX.fa.ann
+#-rw-r--r-- 1 james universe 269808 2005-09-13 10:12 phiX.fa.bwt
+#...etc...
+#
+#Your bwa_index.loc file should include an entry per line for each
+#index set you have stored. The "file" in the path does not actually
+#exist, but it is the prefix for the actual index files. For example:
+#
+#phiX174 phiX phiX174 /depot/data2/galaxy/phiX/base/phiX.fa
+#hg18canon hg18 hg18 Canonical /depot/data2/galaxy/hg18/base/hg18canon.fa
+#hg18full hg18 hg18 Full /depot/data2/galaxy/hg18/base/hg18full.fa
+#/orig/path/hg19.fa hg19 hg19 /depot/data2/galaxy/hg19/base/hg19.fa
+#...etc...
+#
+#Note that for backwards compatibility with workflows, the unique ID of
+#an entry must be the path that was in the original loc file, because that
+#is the value stored in the workflow for that parameter. That is why the
+#hg19 entry above looks odd. New genomes can be better-looking.
+#
diff -r 2898c6feeb9f -r afd01fcbea26 tool-data/bwameth_indexes.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/bwameth_indexes.loc.sample Fri Sep 08 08:57:33 2017 -0400
@@ -0,0 +1,15 @@
+# This is a sample file distributed with Galaxy that is used to define a
+# list of bwa-meth indices, using three columns tab separated:
+#
+#
+#
+# An index can be created with the following command:
+#
+# bwameth.py index /some/path/genome.fa
+#
+# "/some/path/genome.fa" would then be the last column in the line
+# If this were for the mm10 mouse genome, the resulting entry would look like:
+#
+#mm9 mm9 Mouse (mm9) /some/path/genome.fa
+#
+#
diff -r 2898c6feeb9f -r afd01fcbea26 tool-data/fasta_indexes.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/fasta_indexes.loc.sample Fri Sep 08 08:57:33 2017 -0400
@@ -0,0 +1,29 @@
+#This is a sample file distributed with Galaxy that enables tools
+#to use a directory of Samtools indexed sequences data files. You will need
+#to create these data files and then create a fasta_indexes.loc file
+#similar to this one (store it in this directory) that points to
+#the directories in which those files are stored. The fasta_indexes.loc
+#file has this format (white space characters are TAB characters):
+#
+#
+#
+#So, for example, if you had hg19 Canonical indexed stored in
+#
+# /depot/data2/galaxy/hg19/sam/,
+#
+#then the fasta_indexes.loc entry would look like this:
+#
+#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa
+#
+#and your /depot/data2/galaxy/hg19/sam/ directory
+#would contain hg19canon.fa and hg19canon.fa.fai files.
+#
+#Your fasta_indexes.loc file should include an entry per line for
+#each index set you have stored. The file in the path does actually
+#exist, but it should never be directly used. Instead, the name serves
+#as a prefix for the index file. For example:
+#
+#hg18canon hg18 Human (Homo sapiens): hg18 Canonical /depot/data2/galaxy/hg18/sam/hg18canon.fa
+#hg18full hg18 Human (Homo sapiens): hg18 Full /depot/data2/galaxy/hg18/sam/hg18full.fa
+#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa
+#hg19full hg19 Human (Homo sapiens): hg19 Full /depot/data2/galaxy/hg19/sam/hg19full.fa
diff -r 2898c6feeb9f -r afd01fcbea26 tool-data/gatk_sorted_picard_index.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/gatk_sorted_picard_index.loc.sample Fri Sep 08 08:57:33 2017 -0400
@@ -0,0 +1,26 @@
+#This is a sample file distributed with Galaxy that enables tools
+#to use a directory of Picard dict and associated files. You will need
+#to create these data files and then create a picard_index.loc file
+#similar to this one (store it in this directory) that points to
+#the directories in which those files are stored. The picard_index.loc
+#file has this format (longer white space is the TAB character):
+#
+#
+#
+#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
+#
+#and your /depot/data2/galaxy/srma/hg18/ directory
+#would contain the following three files:
+#hg18.fa
+#hg18.dict
+#hg18.fa.fai
+#
+#The dictionary file for each reference (ex. hg18.dict) must be
+#created via Picard (http://picard.sourceforge.net). Note that
+#the dict file does not have the .fa extension although the
+#path list in the loc file does include it.
+#
diff -r 2898c6feeb9f -r afd01fcbea26 tool-data/gemini_databases.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/gemini_databases.loc.sample Fri Sep 08 08:57:33 2017 -0400
@@ -0,0 +1,3 @@
+## GEMINI databases
+#Version dbkey Description
+#08_08_2014 hg19 Database (08-08-2014)
diff -r 2898c6feeb9f -r afd01fcbea26 tool-data/gene_transfer.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/gene_transfer.loc.sample Fri Sep 08 08:57:33 2017 -0400
@@ -0,0 +1,14 @@
+#This file lists the locations and dbkeys of all the gene transfer files
+
+#This file has the format (white space characters are TAB characters):
+#
+#
+#
+#So, gene_transfer.loc could look something like this:
+#
+#vm5 vm5 vM5 annotation /path/to/vM5.annotation.gtf
+#
+#Your gene_transfer.loc file should contain an entry for each individual
+#gtf file.
+#
+
diff -r 2898c6feeb9f -r afd01fcbea26 tool-data/hisat2_indexes.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/hisat2_indexes.loc.sample Fri Sep 08 08:57:33 2017 -0400
@@ -0,0 +1,39 @@
+# hisat2_indexes.loc.sample
+# This is a *.loc.sample file distributed with Galaxy that enables tools
+# to use a directory of indexed data files. This one is for HISAT2.
+# See the wiki: http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup
+# First create these data files and save them in your own data directory structure.
+# Then, create a hisat2_indexes.loc file to use those indexes with tools.
+# Copy this file, save it with the same name (minus the .sample),
+# follow the format examples, and store the result in this directory.
+# The file should include an one line entry for each index set.
+# The path points to the "basename" for the set, not a specific file.
+# It has four text columns seperated by TABS.
+#
+#
+#
+# So, for example, if you had sacCer3 indexes stored in:
+#
+# /depot/data2/galaxy/sacCer3/hisat2_indexes/
+#
+# containing sacCer3 genome and sacCer3.*.ht2 files, such as:
+#
+# -rw-rw-r-- 1 dave dave 12M Sep 23 13:57 sacCer3.1.ht2
+# -rw-rw-r-- 1 dave dave 2.9M Sep 23 13:57 sacCer3.2.ht2
+# -rw-rw-r-- 1 dave dave 161 Sep 23 13:57 sacCer3.3.ht2
+# -rw-rw-r-- 1 dave dave 2.9M Sep 23 13:57 sacCer3.4.ht2
+# -rw-rw-r-- 1 dave dave 7.3M Sep 23 13:57 sacCer3.5.ht2
+# -rw-rw-r-- 1 dave dave 3.0M Sep 23 13:57 sacCer3.6.ht2
+# -rw-rw-r-- 1 dave dave 128K Sep 23 13:57 sacCer3.7.ht2
+# -rw-rw-r-- 1 dave dave 32K Sep 23 13:57 sacCer3.8.ht2
+#
+# then the hisat2_indexes.loc entry could look like this:
+#
+#sacCer3 sacCer3 S. cerevisiae Apr. 2011 (SacCer_Apr2011/sacCer3) (sacCer3) /depot/data2/galaxy/hisat2_indexes/sacCer3
+#
+#More examples:
+#
+#mm10 mm10 Mouse (mm10) /depot/data2/galaxy/hisat2_indexes/mm10
+#dm3 dm3 D. melanogaster (dm3) /depot/data2/galaxy/hisat2_indexes/dm3
+#
+#
diff -r 2898c6feeb9f -r afd01fcbea26 tool-data/kallisto_indexes.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/kallisto_indexes.loc.sample Fri Sep 08 08:57:33 2017 -0400
@@ -0,0 +1,33 @@
+# kallisto_indexes.loc.sample
+# This is a *.loc.sample file distributed with Galaxy that enables tools
+# to use a directory of indexed data files. This one is for kallisto.
+# See the wiki: http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup
+# First create these data files and save them in your own data directory structure.
+# Then, create a kallisto_indexes.loc file to use those indexes with tools.
+# Copy this file, save it with the same name (minus the .sample),
+# follow the format examples, and store the result in this directory.
+# The file should include an one line entry for each index set.
+# The path points to the "basename" for the set, not a specific file.
+# It has four text columns seperated by TABS.
+#
+#
+#
+# So, for example, if you had sacCer3 indexes stored in:
+#
+# /depot/data2/galaxy/sacCer3/kallisto_indexes/
+#
+# containing sacCer3 genome and sacCer3.*.ht2 files, such as:
+#
+# -rw-rw-r-- 1 dave dave 12M Sep 23 13:57 sacCer3.fa
+# -rw-rw-r-- 1 dave dave 2.9M Sep 23 13:57 sacCer3.kallisto
+#
+# then the kallisto_indexes.loc entry could look like this:
+#
+#sacCer3 sacCer3 S. cerevisiae Apr. 2011 (SacCer_Apr2011/sacCer3) (sacCer3) /depot/data2/galaxy/sacCer3/kallisto_indexes/sacCer3.kallisto
+#
+#More examples:
+#
+#mm10 mm10 Mouse (mm10) /depot/data2/galaxy/kallisto_indexes/mm10
+#dm3 dm3 D. melanogaster (dm3) /depot/data2/galaxy/kallisto_indexes/dm3
+#
+#
diff -r 2898c6feeb9f -r afd01fcbea26 tool-data/picard_index.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/picard_index.loc.sample Fri Sep 08 08:57:33 2017 -0400
@@ -0,0 +1,26 @@
+#This is a sample file distributed with Galaxy that enables tools
+#to use a directory of Picard dict and associated files. You will need
+#to create these data files and then create a picard_index.loc file
+#similar to this one (store it in this directory) that points to
+#the directories in which those files are stored. The picard_index.loc
+#file has this format (longer white space is the TAB character):
+#
+#
+#
+#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
+#
+#and your /depot/data2/galaxy/srma/hg18/ directory
+#would contain the following three files:
+#hg18.fa
+#hg18.dict
+#hg18.fa.fai
+#
+#The dictionary file for each reference (ex. hg18.dict) must be
+#created via Picard (http://picard.sourceforge.net). Note that
+#the dict file does not have the .fa extension although the
+#path list in the loc file does include it.
+#
diff -r 2898c6feeb9f -r afd01fcbea26 tool-data/tophat2_indices.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/tophat2_indices.loc.sample Fri Sep 08 08:57:33 2017 -0400
@@ -0,0 +1,37 @@
+# tophat2_indices.loc.sample
+# This is a *.loc.sample file distributed with Galaxy that enables tools
+# to use a directory of indexed data files. This one is for Bowtie2 and Tophat2.
+# See the wiki: http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup
+# First create these data files and save them in your own data directory structure.
+# Then, create a bowtie_indices.loc file to use those indexes with tools.
+# Copy this file, save it with the same name (minus the .sample),
+# follow the format examples, and store the result in this directory.
+# The file should include an one line entry for each index set.
+# The path points to the "basename" for the set, not a specific file.
+# It has four text columns seperated by TABS.
+#
+#
+#
+# So, for example, if you had hg18 indexes stored in:
+#
+# /depot/data2/galaxy/hg19/bowtie2/
+#
+# containing hg19 genome and hg19.*.bt2 files, such as:
+# -rw-rw-r-- 1 james james 914M Feb 10 18:56 hg19canon.fa
+# -rw-rw-r-- 1 james james 914M Feb 10 18:56 hg19canon.1.bt2
+# -rw-rw-r-- 1 james james 683M Feb 10 18:56 hg19canon.2.bt2
+# -rw-rw-r-- 1 james james 3.3K Feb 10 16:54 hg19canon.3.bt2
+# -rw-rw-r-- 1 james james 683M Feb 10 16:54 hg19canon.4.bt2
+# -rw-rw-r-- 1 james james 914M Feb 10 20:45 hg19canon.rev.1.bt2
+# -rw-rw-r-- 1 james james 683M Feb 10 20:45 hg19canon.rev.2.bt2
+#
+# then the bowtie2_indices.loc entry could look like this:
+#
+#hg19 hg19 Human (hg19) /depot/data2/galaxy/hg19/bowtie2/hg19canon
+#
+#More examples:
+#
+#mm10 mm10 Mouse (mm10) /depot/data2/galaxy/mm10/bowtie2/mm10
+#dm3 dm3 D. melanogaster (dm3) /depot/data2/galaxy/mm10/bowtie2/dm3
+#
+#
diff -r 2898c6feeb9f -r afd01fcbea26 tool_data_table_conf.xml.sample
--- a/tool_data_table_conf.xml.sample Fri Sep 08 08:12:20 2017 -0400
+++ b/tool_data_table_conf.xml.sample Fri Sep 08 08:57:33 2017 -0400
@@ -1,25 +1,59 @@
-