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    Marius
    @mvdbeek:matrix.org
    [m]
    If not we could kill it
    Jo-stfc
    @Jo-stfc
    Hi, I'm working with @elichad and have made a tool whose only output is a zip file. I was testing the output on file size, but the compression varies by more than 50% between my VM and the github testing. Any ideas on testing methods to be used in such cases? the file structure within the zip is deterministic
    Alex Ostrovsky
    @astrovsky01
    The compression varies that much on the same test files between the two?
    Jo-stfc
    @Jo-stfc
    yes
    Alex Ostrovsky
    @astrovsky01
    Can you check against the stdout/err?
    Jo-stfc
    @Jo-stfc
    checking against unzip output worked
    F. H.
    @heylf
    Sorry if I missed some information about this, but more and more user have some issues with RNA STAR. Jobs seem to stay in the queue for many days, whereas other are completed immediately. The error seems kinda arbitrary. See this post. https://help.galaxyproject.org/t/rna-star-will-not-load/6772
    Björn Grüning
    @bgruening
    @heylf is that ORG or EU?
    1 reply
    F. H.
    @heylf
    Seems a ORG problem so far.
    Jo-stfc
    @Jo-stfc
    is there any way to enable multiple select in conditionals? I found this issue galaxyproject/galaxy#7173 but the commit it links to doesnt seem to resolve the issue.
    Marius
    @mvdbeek:matrix.org
    [m]
    Can you elaborate what actions you would like to combine ?
    Jo-stfc
    @Jo-stfc
    i have a tool to generate a config file for 3 possible calculator types, and would like to enable selection of multiple calculator types to include their parameters as well in the output file, e.g. calculator A has params a,b; B has c,d so selecting AB would allow params a,b,c,d to be entered
    Alex Ostrovsky
    @astrovsky01:matrix.org
    [m]
    Could it have just been while Org was migrating/upgrading servers?
    Alex Ostrovsky
    @astrovsky01:matrix.org
    [m]
    @Jo-stfc: would a nested conditional work for what you need? And if the parameters are shared between, perhaps a macro?
    Jo-stfc
    @Jo-stfc
    macros would work, thanks
    Cristóbal Gallardo
    @gallardoalba:matrix.org
    [m]
    Hi, it seems that now is not possible to download the report from GitHub actions, is it intended?
    Björn Grüning
    @bgruening
    Not sure, probably a github UX issue.
    You can still find it here:
    grafik.png
    Cristóbal Gallardo
    @gallardoalba:matrix.org
    [m]
    Ok, thanks a lot!
    Jo-stfc
    @Jo-stfc
    is there a way to have inline html between parameters in tools? one of the parameters in a tool I'm developing needs a table format in its help text, but the help option only works inline
    3 replies
    Cristóbal Gallardo
    @gallardoalba:matrix.org
    [m]
    Anton Nekrutenko
    @nekruten:matrix.org
    [m]
    @jmchilton: @wm75 and myself we discussing various ways for creating tool categories and we came up with the following ideas:
    • by package (e.g., samtools from parsing <requirements> tag
    • by input datatype (from <input> tags)
    • by output datatype
    • by .eu URL-specific application type (e.g., RNA-seq)
    these can be generated automatically and then edited (e.g., parsing <requirements> tag may produce some interesting results that need to be manually edited)
    for input/output types we need to somehow bungle multiple versions of the same format (fastqsanger.gz, fastq, fastqsanger.bz2) into a single "type"
    bgruening
    @bgruening:matrix.org
    [m]

    fastqsanger.gz, fastq, fastqsanger.bz2

    you probably want to use Ontologies for that, EDAM annotations we have for some datatypes

    Anton Nekrutenko
    @nekruten:matrix.org
    [m]
    or galaxy classes?
    Anton Nekrutenko
    @nekruten:matrix.org
    [m]
    John Chilton: ☝️any thoughts?
    John Chilton
    @jmchilton:matrix.org
    [m]
    Is this for defining new categories or for defining new ways that users can filter the side panel?
    wm75 (Wolfgang Maier)
    @wm75:matrix.org
    [m]
    This is about additional Tool Panel views (in addition to the new EDAM Ontology ones).
    Anton Nekrutenko
    @nekruten:matrix.org
    [m]
    tool panel views
    John Chilton
    @jmchilton:matrix.org
    [m]
    I think that is reasonable but I also think I'd like to be able to apply like filtering to the list based on different contexts. Like if a tool specifies some EDAM tags - it would be nice to be able to click on the tag and filter the tool panel to just that tag. We could do the same with package requirements for instance. I think some of those lists are going to be quite large those.
    Anton Nekrutenko
    @nekruten:matrix.org
    [m]
    yes, the list based on requirements tag will be quite large, but that we can edit!
    Jo-stfc
    @Jo-stfc
    Hi, is there any way to apply scripts to tests? This would be to avoid the overhead of generating additional outputs just to be used in testing every time the tool is run
    Björn Grüning
    @bgruening
    @Jo-stfc can you explain this a little bit more?
    Jo-stfc
    @Jo-stfc
    one of the tools I made uses a software to generate some configurations of a molecule given an input and parameter file. The output of the tool is a folder containing all generated configurations. For testing, I want to validate one of the output configurations' files. Is it possible to have a validation script that will only run when testing, and not for production (when users are using the tool)?
    Björn Grüning
    @bgruening
    mh, you can add a hidden parameter (run_test) and set this one to true when you test
    then you can add a command in the end of your command section that does whatever you want iff run_test = true
    Jo-stfc
    @Jo-stfc
    that would help, thanks!
    Jo-stfc
    @Jo-stfc
    Hi, Im trying to run a test on a tool that I expect to fail, written as follows
    <test>
    <param name="folder" value="muonated-default-folder.zip" ftype='zip'/>
    <param name="castep_log" value="Si.castep" ftype="txt"/>
    <param name="charge_density" value="Sifail.den_fmt" ftype="txt"/>
    <assert_stderr>
    <has_text text="Error"/>
    </assert_stderr>
    </test>
    the test still fails saying job is in error state
    am I getting the syntax wrong?
    wm75 (Wolfgang Maier)
    @wm75:matrix.org
    [m]
    @Jo-stfc: you need to use expect_failure on the test itself (see here: https://docs.galaxyproject.org/en/latest/dev/schema.html#id91)
    In your example you're declaring that you're expecting certain stderr content, but that is not the same as the job ending in an error.
    Jo-stfc
    @Jo-stfc
    thanks!
    Björn Grüning
    @bgruening
    Anyone here, that can review and merge: galaxyproject/tools-iuc#4185