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update kmc.xml test section #139

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Oct 1, 2024
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update kmc.xml test section #139

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52 changes: 34 additions & 18 deletions tools/kmc/kmc.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -152,42 +152,52 @@
</section>
</inputs>
<outputs>
<data format="json" name="statistic" label="${tool.name} on ${on_string}">
<data name="statistic" format="json" label="${tool.name} on ${on_string}">
<filter>params['j']</filter>
</data>
<collection name="kmc_db" type="list" label="${tool.name} on ${on_string}: kmc db">
<discover_datasets pattern="(?P&lt;designation&gt;.+)" directory="output" format="binary" />
</collection>
</outputs>
<tests>
<test expect_num_outputs="2">
<!-- #1 test individual fasta file -->
<param name="individual_file" value="test.fasta.gz" ftype="fasta.gz"/>
<param name="k" value="27" />
<param name="ci" value="2" />
<param name="cs" value="255" />
<output_collection name="kmc_db" type="list">
<element name="kmer_27.kmc_pre" file="kmer_27.kmc_pre" ftype="binary" />
<element name="kmer_27.kmc_suf" file="kmer_27.kmc_suf" ftype="binary" />
</output_collection>
<output name="statistic" ftype="json">
<assert_contents>
<has_text text="1st_stage"/>
<has_text text="2nd_stage"/>
<has_text text="Stats"/>
</assert_contents>
</output>
</test>
<!-- output file is too large for testing; comment out to test on local machine with update_test_data option -->
<!-- <test expect_num_outputs="2"> -->
<!-- #1 test individual fastq with common parameters -->
<!-- #2 test individual fastq file -->
<!-- <param name="individual_file" value="filtered_1.fastq" ftype="fastq"/>
<param name="k" value="25" />
<param name="m" value="12" />
<param name="p" value="9" />
<param name="ci" value="2" />
<param name="cs" value="255" />
<output_collection name="kmc_db" type="list">
<element name="kmer_25.kmc_pre" file="kmer_25.kmc_pre" ftype="binary" />
<element name="kmer_25.kmc_suf" file="kmer_25.kmc_suf" ftype="binary" />
</output_collection>
<output name="statistic" file="statistic_25.json" ftype="json"/>
<output name="statistic" ftype="json">
<assert_contents>
<has_text text="1st_stage"/>
<has_text text="2nd_stage"/>
<has_text text="Stats"/>
</assert_contents>
</output>
</test> -->
<test expect_num_outputs="2">
<!-- #2 test individual fasta with common parameters -->
<param name="individual_file" value="test.fasta.gz" ftype="fasta.gz"/>
<param name="k" value="27" />
<param name="m" value="24" />
<param name="ci" value="2" />
<param name="cs" value="255" />
<output_collection name="kmc_db" type="list">
<element name="kmer_27.kmc_suf" file="kmer_27.kmc_suf" ftype="binary" />
<element name="kmer_27.kmc_pre" file="kmer_27.kmc_pre" ftype="binary" />
</output_collection>
<output name="statistic" file="statistic_27.json" ftype="json"/>
</test>
<!-- output file is too large for testing; comment out to test on local machine -->
<!-- <test expect_num_outputs="2"> -->
<!-- #3 test collection fastq with common parameters -->
Expand All @@ -209,7 +219,13 @@
<element name="kmer_29.kmc_suf" file="kmer_29.kmc_suf" ftype="binary" />
<element name="kmer_29.kmc_pre" file="kmer_29.kmc_pre" ftype="binary" />
</output_collection>
<output name="statistic" file="statistic_collection.json" ftype="json"/>
<output name="statistic" ftype="json">
<assert_contents>
<has_text text="1st_stage"/>
<has_text text="2nd_stage"/>
<has_text text="Stats"/>
</assert_contents>
</output>
</test>
-->
</tests>
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