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Allow nest param in the dynamic_tool rule -> argument #3657

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merged 4 commits into from Apr 6, 2017

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@lecorguille
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commented Feb 23, 2017

I'm testing the dynamic tool with rule based on argument.
I failed to manage to use inputs.input and inputs|input

So, this is an awkwardness PR to allow param which are nest within <conditional>
For example:

<conditional name="inputs">
            <param name="input" type="select" label="Choose your inputs method" >
                <option value="zip_file" selected="true">Zip file from your history containing your chromatograms</option>
                <option value="single_file">mzXML file from your history</option>
            </param>
            <when value="zip_file">
                <param name="zip_file" type="data" format="no_unzip.zip,zip" label="Zip file" />
            </when>
            <when value="single_file">
                <param name="single_file" type="data" format="mzxml,netcdf" label="Single file" />
            </when>
</conditional>

My tool_destinations.yml

mytool:
    rules:
      - rule_type: arguments
        nice_value: 0
        arguments:
          "inputs|input": single
        destination: thread1-men_free10
    default_destination: thread4-men_free10

I sure that you already have method to browse the option dictionary.

@jmchilton

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commented Feb 23, 2017

I'd prefer a syntax like

arguments:
  inputs:
    input: single

Is that possible or reasonable?

xref #2579 - ping @ericenns

@galaxybot galaxybot added the triage label Feb 23, 2017

@galaxybot galaxybot added this to the 17.05 milestone Feb 23, 2017

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commented Feb 23, 2017

@jmchilton Sure, I can try/propose something around this syntax tomorrow.

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commented Feb 23, 2017

@lecorguille Great! Thanks a bunch.

@lecorguille

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commented Feb 28, 2017

@jmchilton What do think about this proposition?

@@ -121,7 +121,9 @@
# destination: fail
# fail_message: Don't do that
# arguments:
# careful: true
# my_section:

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bgruening Feb 28, 2017

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@lecorguille can you add a slightly more complex example, or more real world like?

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@lecorguille

lecorguille Mar 22, 2017

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For the real world example, I'm not really inspired and a bit lazy :P
To complexify, I can add a second statement?

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commented Mar 22, 2017

I just saw this PR now, this looks good to me. Thanks for the contribution.

@jmchilton jmchilton merged commit af37dd5 into galaxyproject:dev Apr 6, 2017

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commented Apr 6, 2017

Nice! Thanks @lecorguille!

@lecorguille lecorguille deleted the lecorguille:dynamic_tool_nest_param branch Apr 6, 2017

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