Mercurial > repos > iuc > data_manager_build_coreprofiler
changeset 5:2870b4cdab18 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_coreprofiler commit db118f0726bf8a7d5e2c548c3e7470870accae16
| author | iuc |
|---|---|
| date | Thu, 05 Feb 2026 08:34:41 +0000 |
| parents | a1e8960e1629 |
| children | f9a82acae09e |
| files | data_manager/data_manager_build_coreprofiler_download.xml |
| diffstat | 1 files changed, 9 insertions(+), 9 deletions(-) [+] |
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--- a/data_manager/data_manager_build_coreprofiler_download.xml Thu Jan 08 10:29:36 2026 +0000 +++ b/data_manager/data_manager_build_coreprofiler_download.xml Thu Feb 05 08:34:41 2026 +0000 @@ -2,7 +2,7 @@ <description></description> <macros> <token name="@TOOL_VERSION@">2.0.0</token> - <token name="@VERSION_SUFFIX@">2</token> + <token name="@VERSION_SUFFIX@">3</token> <token name="@PROFILE@">22.05</token> <xml name="version_command"> <version_command><![CDATA[$ coreprofiler --version]]></version_command> @@ -47,11 +47,11 @@ 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" && + source "\$PUBMLST_COREPROFILER_SECRETS_PATH" && #elif $scheme_db == "bigsdb" - source "$BIGSDB_COREPROFILER_SECRETS_PATH" && + 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 + 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 @@ -71,10 +71,10 @@ #end if ## #if $db_version == "token" - -k "$COREPROFILER_CONSUMER_TOKEN" - -ks "$COREPROFILER_CONSUMER_SECRET" - -a "$COREPROFILER_ACCESS_TOKEN" - -as "$COREPROFILER_ACCESS_SECRET" + -k "\$COREPROFILER_CONSUMER_TOKEN" + -ks "\$COREPROFILER_CONSUMER_SECRET" + -a "\$COREPROFILER_ACCESS_TOKEN" + -as "\$COREPROFILER_ACCESS_SECRET" #end if && coreprofiler db makeblastdb @@ -458,4 +458,4 @@ <citations> <citation type="doi">10.3390/microorganisms10020292</citation> </citations> -</tool> \ No newline at end of file +</tool>