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 
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