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Tool test runs despite not giving input datasets to mandatory data parameter

Open bernt-matthias opened this issue 6 months ago • 1 comments

Describe the bug

The following test should fail in my opinion, since the dataset tab is not given.

<tool id="auto_fasta" name="auto_fasta" version="1.0" profile="23.1" license="MIT">
    <description></description>
    <command><![CDATA[
        echo success > '$out'
    ]]></command>
    <inputs>
        <param name="tab" type="data" format="tabular"/>
        <param name="fas" type="data" format="fasta"/>
    </inputs>
    <outputs>
        <data name="out" format="txt"/>
    </outputs>
    <tests>
        <test>
            <param name="fas" value="1.fasta"/>
            <output name="out">
                <assert_contents>
                    <has_line line="success"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
    ]]></help>
</tool>

Instead the tool test auto-converts the fasta to a tabular dataset and takes this.

Galaxy Version and/or server at which you observed the bug Galaxy Version: = 24.2

Browser and Operating System

planemo 0.75.29

To Reproduce

planemo test the above tool.

Expected behavior

The test should fail (as also indicated by the linter output)

Screenshots If applicable, add screenshots to help explain your problem.

bernt-matthias avatar May 17 '25 10:05 bernt-matthias

We should explore sending an explicit null here. This test would likely be invalid with a newer galaxy profile version.

mvdbeek avatar May 20 '25 14:05 mvdbeek