Merge pull request #6426 from bernt-matthias/lint-vcf2maf

vcf2maf: fix wrong test parameter
galaxyproject · Oct 5, 2024 · c36c44c · c36c44c
2 parents 9be97b7 + 652fbb9
commit c36c44c
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Showing 2 changed files with 4 additions and 5 deletions.
diff --git a/tools/vcf2maf/.lint_skip b/tools/vcf2maf/.lint_skip
diff --git a/tools/vcf2maf/vcf2maf.xml b/tools/vcf2maf/vcf2maf.xml
@@ -139,7 +139,7 @@
 			<param name="input1" dbkey="hg19" value="input_test1.vcf" ftype="vcf" />
 			<param name="ref_source" value="history" />
 			<param name="ref" dbkey="hg19" value="test1.fa" ftype="fasta" />
-			<param name="annotation_cache.source" value="no_vep" />
+			<param name="annotation_cache|source" value="no_vep" />
 			<assert_command>
 				<has_text text="--ncbi-build 'GRCh37'"/>
 			</assert_command>
@@ -149,7 +149,7 @@
 			<param name="input1" dbkey="hg19" value="input_test1.vcf" ftype="vcf" />
 			<param name="ref_source" value="cached" />
 			<param name="ref" value="hg19test" />
-			<param name="annotation_cache.source" value="no_vep" />
+			<param name="annotation_cache|source" value="no_vep" />
 			<assert_command>
 				<has_text text="--ncbi-build 'GRCh37'"/>
 			</assert_command>
@@ -159,7 +159,7 @@
 			<param name="input1" dbkey="hg19" value="input_test1.vcf" ftype="vcf" />
 			<param name="ref_source" value="cached" />
 			<param name="ref" value="hg19test" />
-			<param name="annotation_cache.source" value="no_vep" />
+			<param name="annotation_cache|source" value="no_vep" />
 			<param name="include_header" value="False" />
 			<output name="output1" ftype="tabular" >
 				<assert_contents>
@@ -172,7 +172,7 @@
 			<param name="input1" dbkey="dm6" value="input_test2.vcf" ftype="vcf" />
 			<param name="ref_source" value="history" />
 			<param name="ref" dbkey="dm6" value="test2.fa" ftype="fasta" />
-			<param name="source" value="restricted" />
+			<param name="annotation_cache|source" value="restricted" />
 			<param name="cache_file" value="drosophila_melanogaster_vep_106_BDGP6.32" />
 			<assert_command>
 				<has_text text="--ncbi-build 'BDGP6.32'"/>