Translation of the Galaxy tool bcftools_reheader fails with error
RuntimeError: could not find wrapper for bcftools_reheader:b7be725976b6
It appears that this is caused by the tool id containing a macro which requires parsing. The bcftoolsreheader id attribute is `id="bcftools@EXECUTABLE@"`
The get_xml_id function in janis_core/ingestion/galaxy/utils/galaxy.py is not general enough to handle galaxy tools with macros in the id xml attribute. This leads to the get_xml_by_id function to incorrectly return None because the queryid does not match the "bcftools@EXECUTABLE@" string.
Translation of the Galaxy tool bcftools_reheader fails with error
RuntimeError: could not find wrapper for bcftools_reheader:b7be725976b6
It appears that this is caused by the tool id containing a macro which requires parsing. The bcftoolsreheader id attribute is `id="bcftools@EXECUTABLE@"`
The
get_xml_id
function in janis_core/ingestion/galaxy/utils/galaxy.py is not general enough to handle galaxy tools with macros in the id xml attribute. This leads to theget_xml_by_id
function to incorrectly return None because the queryid does not match the "bcftools@EXECUTABLE@" string.This can be reproduced with