Mercurial > repos > iuc > data_manager_groot_database_downloader
changeset 1:0c255951902a draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_groot_database_downloader commit 15ce75a21f8a3b314b0a8a420fc5b4fffe846171
| author | iuc |
|---|---|
| date | Mon, 18 Nov 2024 15:09:58 +0000 |
| parents | 641ac96ab63a |
| children | |
| files | data_manager/data_manager_groot_database_downloader.xml data_manager_conf.xml test-data/groot_database.loc |
| diffstat | 3 files changed, 8 insertions(+), 7 deletions(-) [+] |
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--- a/data_manager/data_manager_groot_database_downloader.xml Thu Oct 17 14:20:17 2024 +0000 +++ b/data_manager/data_manager_groot_database_downloader.xml Mon Nov 18 15:09:58 2024 +0000 @@ -2,7 +2,7 @@ <description> Download pre-clustered ARG database that are ready to be indexed</description> <macros> <token name="@TOOL_VERSION@">1.1.2</token> - <token name="@VERSION_SUFFIX@">0</token> + <token name="@VERSION_SUFFIX@">1</token> <token name="@PROFILE@">22.05</token> </macros> <requirements> @@ -12,7 +12,9 @@ </requirements> <command><![CDATA[ if [ -f '/usr/local/ssl/cacert.pem' ] ; then export SSL_CERT_FILE='/usr/local/ssl/cacert.pem' ; fi && + mkdir -p '$out_file.extra_files_path' && groot get -d '$database' --identity '$identity' && + mv ${database}.${identity} '$out_file.extra_files_path' && cp '$dmjson' '$out_file' ]]></command> <configfiles> @@ -24,7 +26,7 @@ { "value": "$database.$identity-@TOOL_VERSION@-#echo date.today().strftime('%d%m%Y')#", "name": "$database ($identity percent identity)", - "path": "/$database.$identity", + "path": "$database.$identity", "version": "@TOOL_VERSION@" } ] @@ -57,7 +59,7 @@ <has_text text='"version": "1.1.2"'/> <has_text_matching expression='"value": "arg-annot.90-1.1.2-[0-9]{8}"'/> <has_text text='"name": "arg-annot (90 percent identity)"'/> - <has_text text='"path": "/arg-annot.90"'/> + <has_text text='"path": "arg-annot.90"'/> </assert_contents> </output> </test>
--- a/data_manager_conf.xml Thu Oct 17 14:20:17 2024 +0000 +++ b/data_manager_conf.xml Mon Nov 18 15:09:58 2024 +0000 @@ -8,9 +8,9 @@ <column name="path" output_ref="out_file"> <move type="directory"> <source>${path}</source> - <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">groot_database/data/${value}</target> + <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">groot_database/${path}</target> </move> - <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/groot_database/data/${value}</value_translation> + <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/groot_database/${path}</value_translation> <value_translation type="function">abspath</value_translation> </column> <column name="version"/> <!-- columns that are going to be specified by the Data Manager Tool -->
--- a/test-data/groot_database.loc Thu Oct 17 14:20:17 2024 +0000 +++ b/test-data/groot_database.loc Mon Nov 18 15:09:58 2024 +0000 @@ -1,2 +1,1 @@ -arg-annot.90-16102024 arg-annot (90 percent identity) /tmp/tmpjmmj2x3o/galaxy-dev/tool-data/groot_database/data/arg-annot.90-16102024 1.1.2 -arg-annot.90-1.1.2-16102024 arg-annot (90 percent identity) /tmp/tmpqdkgcsoq/galaxy-dev/tool-data/groot_database/data/arg-annot.90-1.1.2-16102024 1.1.2 +arg-annot.90-1.1.2-18112024 arg-annot (90 percent identity) /tmp/tmprimr087u/galaxy-dev/tool-data/groot_database/arg-annot.90 1.1.2