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Add test code for cancer.tab output file #6

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Add test code for cancer.tab output file #6

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3d0d25b
Add test code for cancer.tab output file
Oct 10, 2016
66b399b
More tests for non-empty files
Oct 12, 2016
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32 changes: 32 additions & 0 deletions mutation.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -66,6 +66,38 @@ rnaseq_mutation_pipeline.py
<!--<data format="json" name="m_i_json" label="JSON File" from_work_dir="mutation_inspector.json"/> -->
</outputs>
<tests>
<test>
<param name="left_input" value="FLI1.left.fq" />
<param name="right_input" value="FLI1.right.fq" />
<param name="index" value="hg19" />
<output name="cancertab">
<assert_contents>
<has_line line="CHROM&#009;POS&#009;REF&#009;ALT&#009;GENE&#009;DP&#009;QUAL&#009;MQ&#009;SAO&#009;NSF&#009;NSM&#009;NSN&#009;TUMOR&#009;TISSUE&#009;COSMIC_ID&#009;KGPROD&#009;RS&#009;PMC&#009;CRAVAT_PVALUE&#009;CRAVAT_FDR&#009;VEST_PVALUE&#009;VEST_FDR" />
<has_line_matching expression="^chr11.*" />
</assert_contents>
</output>
<output name="cancerVariants">
<assert_contents>
<has_line line="#CHROM&#009;POS&#009;ID&#009;REF&#009;ALT&#009;QUAL&#009;FILTER&#009;INFO&#009;FORMAT&#009;dataset_1" />
<has_line_matching expression=".+" />
</assert_contents>
</output>
<output name="cancerIndex">
<assert_contents>
<has_line_matching expression=".+" />
</assert_contents>
</output>
<output name="allVariants">
<assert_contents>
<has_line_matching expression=".+" />
</assert_contents>
</output>
<output name="bamFile">
<assert_contents>
<has_line_matching expression=".+" />
</assert_contents>
</output>
</test>
</tests>
<help>

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