MAGEtab export: skip protocols in protocols in the IDF that are not used in the SDRF

[agbeltran]

Reported by @sneumann in ISA-tools/ISAcreator#281

When exporting a transcription profiling assay from a multi-assay ISAtab file,
all protocols in i_Investigation are exported to idf.txt. This confuses ArrayExpress.
A solution could be to include all protocols in idf.txt which are referenced
from the sample and assay tables and hence in the sdrf.txt.
Otherwise, I will have to manually clean the ISAtab files before exporting
for the respective repositories. Yours, Steffen