Sometimes tools generate multiple outputs and not all of them are of the same importance. For example a tool used for data visualisation might generate 2 outputs, the image (the visualisation of the data) and a config file (config file is useful only for reproducing that exact render). In this case we would not use the tool to generate only the config file, however, APE does not support such annotation. Ideally, we would like to be able to say that the image is a primary output and enforce (or set as preference) usage of that output before using the config file. This caused issues in proteomics domain, where some tools would output one of the inputs as a reference (it was a FASTA file), and the APE config was set to "use_all_generated_data": "one", which ment that using one output per tool was sufficient.
Sometimes tools generate multiple outputs and not all of them are of the same importance. For example a tool used for data visualisation might generate 2 outputs, the image (the visualisation of the data) and a config file (config file is useful only for reproducing that exact render). In this case we would not use the tool to generate only the config file, however, APE does not support such annotation. Ideally, we would like to be able to say that the image is a primary output and enforce (or set as preference) usage of that output before using the config file. This caused issues in proteomics domain, where some tools would output one of the inputs as a reference (it was a FASTA file), and the APE config was set to
"use_all_generated_data": "one",which ment that using one output per tool was sufficient.