Created
October 15, 2024 09:34
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testing tool(s) for galaxy
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<?xml version="1.0"?> | |
<tool id="metadataFetch" name="Metadata" version="1.0" profile="16.04"> | |
<description></description> | |
<command detect_errors="aggressive"><![CDATA[ | |
echo "==tags==" >> $output; | |
#for tag in $input.tags: | |
echo "${tag.user_tname}" >> $output; | |
#end for | |
echo "==meta1==" >> $output; | |
echo "id: ${__app__.security.encode_id($input.id)}" >> $output; | |
echo "hid: ${input.hid}" >> $output; | |
echo "history_id: ${__app__.security.encode_id($input.history_id)}" >> $output; | |
echo "size = ${input.get_size(nice_size=True)}" >> $output; | |
echo "datatype.edam_format = ${input.datatype.edam_format}" >> $output; | |
echo "datatype.fileext = ${input.datatype.file_ext}" >> $output; | |
echo "==meta2==" >> $output; | |
#for (key, value) in $input.get_metadata().items(): | |
echo "${key} = ${value}" >> $output; | |
#end for | |
echo "==history==" >> $output; | |
echo "history.user = ${input.history.user.email}" >> $output; | |
echo "history.user_id = ${input.history.user_id}" >> $output; | |
echo "history.get_display_name = ${input.history.get_display_name()}" >> $output; | |
echo "==tool==" >> $output; | |
echo "tool_id = ${input.creating_job.tool_id}" >> $output; | |
echo "tool_version = ${input.creating_job.tool_version}" >> $output; | |
echo "job_runner_name = ${input.creating_job.job_runner_name}" >> $output; | |
echo "handler = ${input.creating_job.handler}" >> $output; | |
echo "==trans==" >> $output; | |
echo "Infra URL: ${__app__.config.galaxy_infrastructure_url}" | |
echo "==builtin==" >> $output; | |
echo "__tool_directory__ = ${__tool_directory__}" >> $output; | |
echo "__new_file_path__ = ${__new_file_path__}" >> $output; | |
echo "__tool_data_path__ = ${__tool_data_path__}" >> $output; | |
echo "__root_dir__ = ${__root_dir__}" >> $output; | |
echo "__datatypes_config__ = ${__datatypes_config__}" >> $output; | |
echo "__user_id__ = ${__user_id__}" >> $output; | |
echo "__user_email__ = ${__user_email__}" >> $output; | |
echo "__app__ = ${__app__}" >> $output; | |
]]></command> | |
<inputs> | |
<param label="Data" name="input" type="data" /> | |
</inputs> | |
<outputs> | |
<data format="txt" name="output"/> | |
</outputs> | |
<citations> | |
</citations> | |
<help>Dumps out all of the available metadata for inspection - hexylena</help> | |
</tool> |
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