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phac-nml / irida-wf-ga2xml

Create an IRIDA workflow from a Galaxy workflow file
Apache License 2.0
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The sequenceReadsPaired or sequenceReads is not filled out in <inputs> #13

Closed apetkau closed 4 years ago

apetkau commented 4 years ago

When exporting a workflow, there is an <inputs> section in the XML file:

  <inputs>
    <sequenceReadsPaired/>
    <requiresSingleSample>false</requiresSingleSample>
  </inputs>

Here, <sequenceReadsPaired> should correspond to the name given in the Galaxy workflow .ga file:

      "label" : "sequence_reads_paired",
      "id" : 0,
      "tool_state" : "{\"optional\": false, \"collection_type\": \"list:paired\"}",

That is, the XML file should contain <sequenceReadsPaired>sequence_reads_paired</sequenceReadsPaired> instead of being left empty.

apetkau commented 4 years ago

I cannot reproduce this issue. It seems to work properly for everything I've tried.