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Planemo lint unaware of assert_command #260

peterjc opened this Issue Jul 6, 2015 · 0 comments


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peterjc commented Jul 6, 2015

Planemo lint complained about this test:

    <param name="fastq_input1" value="bwa-mem-fastq1.fq" />
    <param name="ref_file" value="bwa-mem-mt-genome.fa" />
    <param name="set_algorithm_params" value="true" />
    <param name="k" value="20" />
        <has_text text="-k 20" />

taken from

$ planemo lint bwa-mem_v5.xml
Linting tool /Users/peterjc/repositories/planemo/docs/writing/bwa-mem_v5.xml
Applying linter top_level... CHECK
.. CHECK: Tool defines a version.
.. CHECK: Tool defines a name.
.. CHECK: Tool defines an id name.
Applying linter tests... WARNING
.. WARNING: No outputs or expectations defined for tests, this test is likely invalid.
.. CHECK: 2 test(s) found.
Applying linter output... CHECK
.. INFO: 1 outputs found.
Applying linter inputs... CHECK
.. INFO: Found 6 input parameters.
Applying linter help... CHECK
.. CHECK: Tool contains help section.
.. CHECK: Help contains valid reStructuredText.
Applying linter command... CHECK
.. INFO: Tool contains a command.
Applying linter citations... CHECK
.. CHECK: Found 1 likely valid citations.
Failed linting

Reported during the GCC2015 training day by @cganote

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