Mercurial > repos > rhpvorderman > data_manager_select_index_by_path
changeset 38:bfc8a44fce75 draft
planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit daef12f8aec8822a48689b303cd216ef774f1110
| author | rhpvorderman |
|---|---|
| date | Wed, 25 Jul 2018 09:49:40 -0400 |
| parents | b40737d19954 |
| children | ad5d85570342 |
| files | data_manager/data_manager_select_index_by_path.xml data_manager/indexes.yml tool-data/centrifuge_indices.loc.sample tool-data/kraken_databases.loc.sample tool_data_table_conf.xml.sample |
| diffstat | 4 files changed, 40 insertions(+), 1 deletions(-) [+] |
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--- a/data_manager/data_manager_select_index_by_path.xml Mon Jul 16 10:42:19 2018 -0400 +++ b/data_manager/data_manager_select_index_by_path.xml Wed Jul 25 09:49:40 2018 -0400 @@ -7,7 +7,7 @@ </requirements> <description>Link to indexes on the filesystem that have already been built</description> <command detect_errors="exit_code"><![CDATA[ - python $__tool_directory__/path_name_value_key_manager.py + python3 $__tool_directory__/path_name_value_key_manager.py --value "${value}" --dbkey "${dbkey}" --name "${name}" @@ -39,6 +39,8 @@ <option value='picard_indexes'>picard_indexes</option> <option value='tophat2_indexes'>tophat2_indexes</option> <option value="rnastar_index2">rnastar_index2</option> + <option value="kraken_databases">kraken_database</option> + <option value="centrifuge_indices">centrifuge_indices</option> </param> <when value="rnastar_index2"> <param name="with_gtf" type="select" value="" label="Index with embedded gtf?">
--- a/data_manager/indexes.yml Mon Jul 16 10:42:19 2018 -0400 +++ b/data_manager/indexes.yml Wed Jul 25 09:49:40 2018 -0400 @@ -117,3 +117,15 @@ name: tophat2 index extensions: - .bt2 + +centrifuge_indices: + name: Centrifuge index + folder: [] + prefix: false + +kraken_databases: + name: Kraken database + folder: + - database.idx + - database.kdb + prefix: false \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/centrifuge_indices.loc.sample Wed Jul 25 09:49:40 2018 -0400 @@ -0,0 +1,17 @@ +# centrifuge_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 GOTTCHA. +# 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 three text columns seperated by TABS. +# +# <unique_id> <display_name> <file_base_path> +# +#bacteria_v20150825 Bacteria /depot/data2/galaxy/gottcha/GOTTCHA_BACTERIA_c4937_k24_u30_xHUMAN3x.species +#viruses_v20150825 Viruses /depot/data2/galaxy/gottcha/GOTTCHA_VIRUSES_c5900_k24_u30_xHUMAN3x.species +test test foo/bar/baz
--- a/tool_data_table_conf.xml.sample Mon Jul 16 10:42:19 2018 -0400 +++ b/tool_data_table_conf.xml.sample Wed Jul 25 09:49:40 2018 -0400 @@ -52,4 +52,12 @@ <columns>value, dbkey, name, path</columns> <file path="tool-data/tophat2_indices.loc" /> </table> + <table name="kraken_databases" comment_char="#"> + <columns>value, name, path</columns> + <file path="tool-data/kraken_databases.loc" /> + </table> + <table name="centrifuge_indices" comment_char="#"> + <columns>value, name, path</columns> + <file path="tool-data/centrifuge_indices.loc" /> + </table> </tables>