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As with all the Harvester command-line tools, you can provide all the arguments as parameters is a configuration file (X/-config). Here is a sample configuration for PubmedFetch.
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<?xml version="1.0" encoding="UTF-8"?>
<Task>
<Param name="email">sample.email@mydomain.tld</Param>
<Param name="termSearch">sample AND edu[ad]</Param>
<!-- these are set inside the example scripts, so are not needed
<Param name="output">config/recordhandlers/tfrh.xml</Param>
<Param name="outputOverride">fileDir=harvested-data/examples/pubmed</Param>
-->
<Param name="numRecords">ALL</Param>
<Param name="batchSize">1000</Param>
</Task>
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To execute the PubmedFetch tool from the commandline, there is a convenient environment config file that, when loaded in a bash shell, will allow you to execute PubmedFetch with a simple $PubmedFetch [args]. For information about that, see Environment Config File.
Or you can simply call (paths relative to base harvester folder):
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java -cp bin/harvester-<version>.jar:bin/dependency/* -Dprocess-task=PubmedFetch org.vivoweb.harvester.fetch.PubmedFetch
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