Syntax of configuration

Column 1         - tool name
Column 2         - input parameter name
Column 3 or more - substitution rules in the format of match, match=, or match=replacement

Example

tophat2 input1
cufflinks input .accepted_hits.bam tabular=txt
cuffquant samples.sample accepted_hits.bam.out_file=quan
cuffnorm PREFIX=cuffnorm tabular=txt
cuffdiff

• 'input1', 'input', and 'samples.sample' are used to rename output files of 'tophat2', 'cufflinks', and 'cuffquant', respectively.
• 'PREFIX' for cuffnorm generates the original output files with a specified prefix.
• For cuffdff, the original file names are used.
• From the output file names of cufflinks '.accepted_hits.bam' is removed and 'tabular' is replaced by 'txt'.
• From the output file names of cuffquant 'accepted_hits.bam.out_file' is replaced by 'quan'.

Output