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Fix graphing of tool inputs

Alex Pearce requested to merge apearce-graph-flow-fixups into master

Graphing of tool inputs to algorithms was broken by !225 (merged) and this was causing the nightlies to fail. After fixing that I noticied some other funky features so fixed those to.

This is the current HLT2 reconstruction data flow after the changes:

HLT2 reconstruction data flow

Edited by Alex Pearce

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