Hi Galaxy team,
I am using the TargetFinder tool for plant small RNA target prediction
(Galaxy tool version: 1.7.0+galaxy1).
I may have found a possible issue with the Prediction score cutoff value parameter.
In the tool form I set the cutoff to 5. I also previously tried 5.0, but to avoid any decimal-format issue I repeated the run with the integer value 5. However, the output still appears to contain only predictions consistent with the default cutoff 4. In other words, changing the cutoff value does not seem to change the result, and the tool behaves as if the default threshold is always used.
My settings were approximately:
Galaxy instance: usegalaxy.eu
Tool: TargetFinder
Tool version: 1.7.0+galaxy1
Input small RNA sequences: mature Arabidopsis miRNAs
Target sequence database: Araport11 cDNA FASTA
Prediction score cutoff value: 5
Search reverse strand: false
Output format: tab-delimited
Expected behavior:
Predicted targets with TargetFinder scores up to and including 5 should be reported.
Observed behavior:
The output seems to be restricted to predictions with scores up to 4, as if the cutoff parameter was not passed to the underlying command or was overwritten by the default value.
Could someone please check whether the score cutoff parameter is being correctly passed by the Galaxy wrapper? Has anyone else observed similar behavior with this TargetFinder wrapper?
Many thanks!
Martin
