So if you have data with discover_outputs (which I would understand) or also if you have a collection with discover_outputs? I will always have the later case.
... but I have to admit that I have a few cases where I abuses data+discover to set the format, but its always just a single data set .. so in this case the single data set is of use :) Nice
preprocessing += "${ ' && '.join([ \"ln -s '%s' '"+actual_parameter+"/%s.%s'\" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), _.ext) for _ in $" + actual_parameter + " if _ ]) } && \n"
looks like perl in terms of readability .. lol
Lets assume I have a select parameter with multiple="true"
. For a test can I somehow express a value that contains a comma?
value="Option A,Option B"
Can one have something like
<param>
<value="Option,A"/>
<value="Option,B"/>
</param>
yep:
<inputs>
<param name="sel" type="select" multiple="true" label="sel">
<option value="o 1"></option>
<option value="o 2"></option>
<option value="o,1"></option>
<option value="o,2"></option>
</param>
</inputs>
<outputs>
<data format="txt" name="sample"/>
</outputs>
<tests>
<test>
<param name="sel" value="o 1,o 2"/>
<data format="txt" name="sample"/>
</test>
<test>
<param name="sel" value="'o,1','o,2'"/>
<data format="txt" name="sample"/>
</test>
</tests>
gives:
RunToolException: Error creating a job for these tool inputs - parameter 'sel': an invalid option (u"'o") was selected (valid options: o,1,o,2,o 1,o 2)
I guess implementing something that allows something like
<test>
<param name="sel" >
<value>o,1</value>
<value>o,2</value>
</param>
<data format="txt" name="sample"/>
</test>
within galaxyproject/galaxy#9079 might be an option.
An alternative might be a sanitizer+mapping and to use the mapped value in the test, right?
no longer considers a zero-length file to be a valid SAM file
,