A graph-based approach for designing extensible pipelines

BMC Bioinformatics

Table 1 Tool Registry example for format conversion pipelines

Input	Output	Tool	Language	Code	XI	XO	Performance
PolyPhred	PrettyBase	PolyPhred2PrettyBase.pl	perl	1	-	-	0.004
PrettyBase	SDAT	PrettyBase2SDAT.pl	perl	2	-	-	0.01
SDAT	StructureFormat	SDAT2Structure.pl	perl	5	-	mainparam,	0.15
						extraparam
SDAT	RHierfstat	SDAT2Rhierfstat.pl	perl	7	SDAT	-	0.02
PHASEOUT	Fasta	Phase2Fasta.pl	perl	9	Fragments,	-	0.02
					RefSeq

Columns Input and Output are file formats that are accepted and generated by a conversion tool; Tool and Language are the conversion tool’s name and its programming language; Code is the identifier of the tool; XI is the list of extra input files required for the tool’s execution; XO is the list of extra output files that is generated by the tool; and Performance is a measure related to the tool’s execution time. Other information not represented on this table can be found in the Additional file 1: Table S1.

ISSN: 1471-2105