Mercurial > repos > iuc > data_manager_build_coreprofiler
changeset 6:f9a82acae09e draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_coreprofiler commit d4c7bfd623ecf2599435c71353052359a5ec63d2
| author | iuc |
|---|---|
| date | Fri, 06 Feb 2026 11:08:48 +0000 |
| parents | 2870b4cdab18 |
| children | |
| files | data_manager/data_manager_build_coreprofiler_download.xml |
| diffstat | 1 files changed, 18 insertions(+), 17 deletions(-) [+] |
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--- a/data_manager/data_manager_build_coreprofiler_download.xml Thu Feb 05 08:34:41 2026 +0000 +++ b/data_manager/data_manager_build_coreprofiler_download.xml Fri Feb 06 11:08:48 2026 +0000 @@ -2,7 +2,7 @@ <description></description> <macros> <token name="@TOOL_VERSION@">2.0.0</token> - <token name="@VERSION_SUFFIX@">3</token> + <token name="@VERSION_SUFFIX@">4</token> <token name="@PROFILE@">22.05</token> <xml name="version_command"> <version_command><![CDATA[$ coreprofiler --version]]></version_command> @@ -44,7 +44,7 @@ #end if mkdir -p '$out_file.extra_files_path' && -mkdir -p coreprofiler_${scheme_name}_${scheme_db}_${db_version}_${today}/scheme_$scheme_name/ && +mkdir -p 'coreprofiler_${scheme_name}_${scheme_db}_${db_version}_${today}/scheme_$scheme_name/' && #if $db_version == "token" #if $scheme_db == "pubmlst" source "\$PUBMLST_COREPROFILER_SECRETS_PATH" && @@ -52,21 +52,22 @@ source "\$BIGSDB_COREPROFILER_SECRETS_PATH" && #end if if [[ -z "\$COREPROFILER_CONSUMER_TOKEN" || -z "\$COREPROFILER_CONSUMER_SECRET" || -z "\$COREPROFILER_ACCESS_TOKEN" || -z "\$COREPROFILER_ACCESS_SECRET" ]]; then - echo "Error: Missing required bash variables for CoreProfiler authentication." >&2 - echo "Please set the following variables before running this tool:" >&2 - echo " COREPROFILER_CONSUMER_TOKEN" >&2 - echo " COREPROFILER_CONSUMER_SECRET" >&2 - echo " COREPROFILER_ACCESS_TOKEN" >&2 - echo " COREPROFILER_ACCESS_SECRET" >&2 - echo "Please refer to the data manager help section for more information on how to generate these tokens." >&2 - fi && + echo "Error: Missing required bash variables for CoreProfiler authentication." >&2 ; + echo "Please set the following variables before running this tool:" >&2 ; + echo " COREPROFILER_CONSUMER_TOKEN" >&2 ; + echo " COREPROFILER_CONSUMER_SECRET" >&2 ; + echo " COREPROFILER_ACCESS_TOKEN" >&2 ; + echo " COREPROFILER_ACCESS_SECRET" >&2 ; + echo "Please refer to the data manager help section for more information on how to generate these tokens." >&2 ; + exit 1; + fi ; #end if coreprofiler db download - -s $scheme_name - -o coreprofiler_${scheme_name}_${scheme_db}_${db_version}_${today}/scheme_$scheme_name + -s '$scheme_name' + -o 'coreprofiler_${scheme_name}_${scheme_db}_${db_version}_${today}/scheme_$scheme_name' ## Used only for test - #if str($hide_test) == 'true': + #if $hide_test -t #end if ## @@ -78,11 +79,11 @@ #end if && coreprofiler db makeblastdb - -s coreprofiler_${scheme_name}_${scheme_db}_${db_version}_${today}/scheme_$scheme_name - -n $scheme_name - -p coreprofiler_${scheme_name}_${scheme_db}_${db_version}_${today}/db_$scheme_name && + -s 'coreprofiler_${scheme_name}_${scheme_db}_${db_version}_${today}/scheme_$scheme_name' + -n '$scheme_name' + -p 'coreprofiler_${scheme_name}_${scheme_db}_${db_version}_${today}/db_$scheme_name' && -mv coreprofiler_${scheme_name}_${scheme_db}_${db_version}_${today} '$out_file.extra_files_path' && +mv 'coreprofiler_${scheme_name}_${scheme_db}_${db_version}_${today}' '$out_file.extra_files_path' && cp '$dmjson' '$out_file' ]]></command>