Mercurial > repos > rhpvorderman > data_manager_select_index_by_path
changeset 3:afd01fcbea26 draft
planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 5db36ba46db15647fd3206c23114b7671e4b4f79
| author | rhpvorderman |
|---|---|
| date | Fri, 08 Sep 2017 08:57:33 -0400 |
| parents | 2898c6feeb9f |
| children | 7bdc452bec9b |
| files | data_manager/data_manager_select_index_by_path.xml data_manager_conf.xml tool-data/all_fasta.loc.sample tool-data/bowtie2_indices.loc.sample tool-data/bowtie_indices.loc.sample tool-data/bowtie_indices_color.loc.sample tool-data/bwa_mem_index.loc.sample tool-data/bwameth_indexes.loc.sample tool-data/fasta_indexes.loc.sample tool-data/gatk_sorted_picard_index.loc.sample tool-data/gemini_databases.loc.sample tool-data/gene_transfer.loc.sample tool-data/hisat2_indexes.loc.sample tool-data/kallisto_indexes.loc.sample tool-data/picard_index.loc.sample tool-data/tophat2_indices.loc.sample tool_data_table_conf.xml.sample |
| diffstat | 17 files changed, 416 insertions(+), 39 deletions(-) [+] |
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--- 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 @@ <option value='gene_transfer'>gene_transfer</option> <option value='hisat2_indexes'>hisat2_indexes</option> <option value='kallisto_indexes'>kallisto_indexes</option> - <option value='mosaik_indexes'>mosaik_indexes</option> - <option value='ngs_sim_fasta'>ngs_sim_fasta</option> <option value='picard_indexes'>picard_indexes</option> - <option value='srma_indexes'>srma_indexes</option> <option value='tophat2_indexes'>tophat2_indexes</option> </param> </inputs>
--- 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 @@ <column name="name" /> <column name="path" /> </output> -<!-- </data_table> <data_table name="bowtie2_indexes"> <output> @@ -98,22 +97,6 @@ <column name="path" /> </output> </data_table> - <data_table name="mosaik_indexes"> - <output> - <column name="value" /> - <column name="dbkey" /> - <column name="name" /> - <column name="path" /> - </output> - </data_table> - <data_table name="ngs_sim_fasta"> - <output> - <column name="value" /> - <column name="dbkey" /> - <column name="name" /> - <column name="path" /> - </output> - </data_table> <data_table name="picard_indexes"> <output> <column name="value" /> @@ -122,14 +105,6 @@ <column name="path" /> </output> </data_table> - <data_table name="srma_indexes"> - <output> - <column name="value" /> - <column name="dbkey" /> - <column name="name" /> - <column name="path" /> - </output> - </data_table> <data_table name="tophat2_indexes"> <output> <column name="value" /> @@ -138,7 +113,6 @@ <column name="path" /> </output> </data_table> ---> </data_manager> </data_managers>
--- 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): # #<unique_build_id> <dbkey> <display_name> <file_path> # @@ -14,4 +16,3 @@ #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/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. +# +# <unique_build_id> <dbkey> <display_name> <file_base_path> +# +# 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 +# +#
--- /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): +# +#<unique_build_id> <dbkey> <display_name> <file_base_path> +# +#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. +#
--- /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): +# +#<unique_build_id> <dbkey> <display_name> <file_base_path> +# +#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. +#
--- /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): +# +#<unique_build_id> <dbkey> <display_name> <file_path> +# +#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. +#
--- /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: +# +# <unique_build_id> <dbkey> <display_name> <genome_fasta_file_path> +# +# 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 +# +#
--- /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): +# +# <unique_build_id> <dbkey> <display_name> <file_base_path> +# +#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
--- /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): +# +#<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 +# +#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. +#
--- /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)
--- /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): +# +#<unique_build_id> <dbkey> <display_name> <file_path> +# +#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. +# +
--- /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. +# +# <unique_build_id> <dbkey> <display_name> <file_base_path> +# +# 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 +# +#
--- /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. +# +# <unique_build_id> <dbkey> <display_name> <file_base_path> +# +# 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 +# +#
--- /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): +# +#<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 +# +#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. +#
--- /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. +# +# <unique_build_id> <dbkey> <display_name> <file_base_path> +# +# 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 +# +#
--- 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 @@ <!-- 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> - <table name="all_fasta" comment_char="#"> + <table name="all_fasta" comment_char="#" allow_duplicate_entries="False"> <columns>value, dbkey, name, path</columns> <file path="tool-data/all_fasta.loc" /> </table> -<!-- - <table name="bowtie2_indexes" comment_char="#"> + <table name="bowtie2_indexes" comment_char="#" allow_duplicate_entries="False"> <columns>value, dbkey, name, path</columns> <file path="tool-data/bowtie2_indices.loc" /> </table> - <table name="bowtie_indexes" comment_char="#"> + <table name="bowtie_indexes" comment_char="#" allow_duplicate_entries="False"> <columns>value, dbkey, name, path</columns> <file path="tool-data/bowtie_indices.loc" /> </table> - <table name="bowtie_indexes_color" comment_char="#"> + <table name="bowtie_indexes_color" comment_char="#" allow_duplicate_entries="False"> <columns>value, dbkey, name, path</columns> <file path="tool-data/bowtie_indices_color.loc" /> </table> - <table name="bwa_mem_indexes" comment_char="#"> + <table name="bwa_mem_indexes" comment_char="#" allow_duplicate_entries="False"> <columns>value, dbkey, name, path</columns> <file path="tool-data/bwa_mem_index.loc" /> </table> ---> + <table name="bwameth_indexes" comment_char="#" allow_duplicate_entries="False"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/bwameth_indexes.loc" /> + </table> + <table name="fasta_indexes" comment_char="#" allow_duplicate_entries="False"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/fasta_indexes.loc" /> + </table> + <table name="gatk_picard_indexes" comment_char="#" allow_duplicate_entries="False"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/gatk_sorted_picard_index.loc" /> + </table> + <table name="gemini_databases" comment_char="#" allow_duplicate_entries="False"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/gemini_databases.loc" /> + </table> + <table name="gene_transfer" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/gene_transfer.loc" /> + </table> + <table name="hisat2_indexes" comment_char="#" allow_duplicate_entries="False"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/hisat2_indexes.loc" /> + </table> + <table name="kallisto_indexes" comment_char="#" allow_duplicate_entries="False"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/kallisto_indexes.loc" /> + </table> + <table name="picard_indexes" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/picard_index.loc" /> + </table> + <table name="tophat2_indexes" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/tophat2_indices.loc" /> + </table> </tables>