Missing parameters in DEAnalysis.pm

There are several values in 5.2.DEAnalysis_Noiseq_miRNAs.ini that are not properly used, e.g. :

;Probability of differential expression to perform the DE analysis with Noiseq. qvalue=0.9 ;This value refers to filter processing in the reads (Should be "yes" or "no"). filter=yes ;Method that will be used to filter proccess with Noiseq software. filtermethod=1 ;Cutoff for the coefficient of variation per condition to be used in filter processing with method 1 in Noiseq analysis(in percentage cutoffvalue=80 ;Type of replicates to be used to perform the DE analysis with Noiseq. replicatevalue=biological ;Counts equal to 0 are replaced by k to perform the DE analysis with Noiseq kvalue=1 ;Length correction is done by dividing expression by length^lc to perform the DE analysis with Noiseq lcvalue=0.5

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