Hi list, I am currently writing a Galaxy wrapper (for SortMeRNA [1]) and I would have several questions. == Pre-processing an input == SortMeRNA filters rRNA reads against an indexed rRNA database. This database can either be one bundled together with SortMeRNA and defined in a relevant .loc file, or one from the history. Either way, it must have been processed beforehand with another binary (just like makeblastdb/blastp). I am not sure of the best design here. * Providing another wrapper for this other binary, with users explicitly using it beforehand in their workflow? *Assuming the databases have been processed outside of Galaxy beforehand ? (As the tool relies on the file name, this would work for databases in the .loc file but not ones from the history) *Providing an extra-smart wrapper which would check if the database has been indexed, and if not invisibly indexing before running SortMeRNA ? == Error handling == I have been trying to use <stdio><regex> to catch an error (the one defined in above section actually) and inform the user with a meaningful message. >From the console debug, it seems the error is correctly detected, since it displays the custom <regex description=""> : galaxy.jobs INFO 2013-01-22 19:02:04,198 Job 202: Fatal error: The database ${databases} has not been preprocessed using buildtrie before using SortMeRNA. But Galaxy only displays in the failed history a generic message « tool error An error occurred running this job: Unable to finish job » Am I missing something, or the <stdio><regex> is not meant to be used this way? == Using a previously set choice to set a default value later == Main option Alpha (a binary choice A/B) influence the default value of advanced option Beta (a float). Beta is buried into the "advanced options" section − I’d rather not have it just next to Alpha. Mirroring constructs seen in the <action>tag, I was hoping to do something like : <conditional name="Alpha"> <param name="Alpha_selector" type="select" format="text"> <option value="A">Option A</option> <option value="B">Option B</option> </param> </conditional> […] <conditional name="Alpha.Alpha_selector"> <when value="A"> <param name="Beta" type="float" value="0.15"/> </when> <when value="B"> <param name="Beta" type="float" value="0.25"/> </when> </conditional> But that does not seem to work. Am I missing something, or is it just not possible ? Alternatively, I looked into setting some hidden variable $default_value in the Alpha select, which would be used as <param name="Beta" value=$default_value/>, but that does not seem to work either Thanks for your help! [1] <http://bioinfo.lifl.fr/RNA/sortmerna/> -- Jean-Frédéric Bonsai Bioinformatics group