I was talking about the history
the history should be as simple as possible IMO
though heterogenous collections are a pain as well
as you would create there
hmm, not sure we have a great solution there
I guess discovering the output and sniffing could work ?
but if you know the formats it’s probably best to rename as the sniffers aren’t perfect
do you have the tool somewhere ?
In the end I just want to set the format of the output and I know that it is the same as the input, but there are multiple possible input formats.
I am still lost here. This should work fine with collection input if you set inherit_format. If you use multiple=“true” you need to create an arbitrary number of outputs using discover_datasets. This will be difficult to impossible to use in workflows
there’s no output to attach them to
there is a single, primary dataset, but I guess that won’t be of much/any use
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
Sounds better than looking at the line of code that might do the workaround:
preprocessing += "${ ' && '.join([ \"ln -s '%s' '"+actual_parameter+"/%s.%s'\" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), _.ext) for _ in $" + actual_parameter + " if _ ]) } && \n"
Lets assume I have a select parameter with multiple="true". For a test can I somehow express a value that contains a comma?
- for options without comma (e.g. "Option A" and "Option B") it would be
value="Option A,Option B" - but what if the option value contains a comma (e.g. "Option,A" and "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?
There’s a new samtools version out with lots of nice new things: https://github.com/samtools/samtools/releases/tag/1.10
Can write index files during sort, sam.gz seems recommended for huge contigs,
no longer considers a zero-length file to be a valid SAM file,
Making good progress:
list of failing test is at https://mvdbeek.github.io/iuc-tool-test-results/, as usual
we also have some regressions (this is testing against the current dev, which will probably become 20.01 pretty soon), so that’s good to see as well
