add expect_num_outputs

galaxyproject · Sep 26, 2024 · 2ffe613 · 2ffe613
1 parent f328166
commit 2ffe613
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Showing 3 changed files with 8 additions and 10 deletions.
diff --git a/tools/gatk4/.lint_skip b/tools/gatk4/.lint_skip
@@ -1,2 +1 @@
-TestsExpectNumOutputs
 ToolVersionPEP404
diff --git a/tools/gatk4/gatk4_Mutect2.xml b/tools/gatk4/gatk4_Mutect2.xml
@@ -597,7 +597,7 @@
         </data>
     </outputs>
     <tests>
-        <test>
+        <test expect_num_outputs="1">
             <conditional name="mode">
                 <param name="mode_parameters" value="tumor_only"/>
                 <param name="tumor" ftype="bam" value="Mutect2-in1.bam" />
@@ -610,7 +610,7 @@
             <param name="output_parameters" value="no" />
             <output name="output_vcf" file="Mutect2-out1.vcf" lines_diff="2" />
         </test>
-        <test>
+        <test expect_num_outputs="1">
             <conditional name="mode">
                 <param name="mode_parameters" value="tumor_only"/>
                 <param name="tumor" ftype="bam" value="Mutect2-in2.bam" />
@@ -626,7 +626,7 @@
             <param name="output_parameters" value="no" />
             <output name="output_vcf" file="Mutect2-out2.vcf" lines_diff="2" />
         </test>
-        <test>
+        <test expect_num_outputs="1">
             <conditional name="mode">
                 <param name="mode_parameters" value="tumor_only"/>
                 <param name="tumor" ftype="bam" value="Mutect2-in3.bam" />
@@ -641,21 +641,21 @@
             <param name="output_parameters" value="no" />
             <output name="output_vcf" file="Mutect2-out3.vcf" lines_diff="2" />
         </test>
-        <test>
+        <test expect_num_outputs="1">
             <conditional name="mode">
                 <param name="mode_parameters" value="tumor_only"/>
                 <param name="tumor" ftype="bam" value="Mutect2-in4.bam" />
             </conditional>
             <param name="reference_sequence" value="hg38"/>
             <param name="gzipped_output" value="false" />
-	    <param name="reference_source_selector" value="cached" />
-	    <param name="reference_sequence" value="hg38"/>
+	        <param name="reference_source_selector" value="cached" />
+	        <param name="reference_sequence" value="hg38"/>
             <param name="optional_parameters" value="no" />
             <param name="advanced_parameters" value="no" />
             <param name="output_parameters" value="no" />
             <output name="output_vcf" file="Mutect2-out4.vcf" lines_diff="2" />
         </test>
-        <test>
+        <test expect_num_outputs="3">
             <conditional name="mode">
                 <param name="mode_parameters" value="tumor_only"/>
                 <param name="tumor" ftype="bam" value="Mutect2-in5.bam" />
@@ -672,7 +672,7 @@
             <output name="assembly_region_out" file="Mutect2-out5-1.tabular" />
             <output name="bam_output" file="Mutect2-out5.bam" />
         </test>
-        <test>
+        <test expect_num_outputs="1">
             <conditional name="mode">
                 <param name="mode_parameters" value="somatic"/>
                 <param name="tumor" ftype="bam" value="tumor.bam" />

diff --git a/tools/gatk4/macros.xml b/tools/gatk4/macros.xml
@@ -1,4 +1,3 @@
-<?xml version="1.0"?>
 <macros>
     <token name="@VERSION@">4.1.7.0</token>
     <token name="@WRAPPER_VERSION@">@VERSION@+galaxy1</token>