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"
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?
no longer considers a zero-length file to be a valid SAM file,
tetyper tool to allow users to load variant profiles from tool data tables? galaxyproject/tools-iuc#2772
Is there a galaxy datatype that would be close to bedpe: https://bedtools.readthedocs.io/en/latest/content/general-usage.html#bedpe-format
tetyper for loading variant profiles from tool data tables? Thanks! galaxyproject/tools-iuc#2772
I'm working with a lab doing research with bacterial genomes and I'm working on introducing their pipeline into Galaxy. In many cases the bacterial data consists of a combination of species, so mapping to a specific genome is tricky.
Mapping bacterial data to a referencce genome has 3 options:
the genome is known, so is selected from local cache as is often done in Galaxy
a custom reference is selected - these custom references are a composition of files, and I'm not aware if/how this is currently handled in Galaxy. For example, for the custom reference for Brucella_abortus1 consists of the following 7 files:
- Bab1_define_filter.xlsx
- Bab1_remove_from_analysis.xlsx
- NC_006932-NC_006933.fasta
- NC_006932-NC_006933.gbk
- NC_006932-NC_006933.genome
- NC_006932-NC_006933.gff
The input data is inspected to determine the optimal genome to be mapped.
Does anyone know if this is currently being done in Galaxy? I've done some searching and only found this so far https://help.galaxyproject.org/t/mapping-rna-seq-data-to-a-composite-build-of-bacterial-genomes/1443.
I can wrap the tool for Galaxy that the lab is using, but I want to make sure I'm not re-inventing the wheel.
select tsv data sets(s)