# HG changeset patch
# User iuc
# Date 1721149203 0
# Node ID d58d2e8c7a57b59e8a5219827e63c966b33b735f
# Parent  cacc9970727a33b877f7e93ffe90daef958455f1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit bfc4ff4956b94885638ae07a2560bac5f84fcca8

diff -r cacc9970727a -r d58d2e8c7a57 bcftools_convert_from_vcf.xml
--- a/bcftools_convert_from_vcf.xml	Thu Jan 12 15:40:23 2023 +0000
+++ b/bcftools_convert_from_vcf.xml	Tue Jul 16 17:00:03 2024 +0000
@@ -145,7 +145,7 @@
         <data name="output_samples" format="tabular" label="${input_file.name.rsplit('.',1)[0]}.samples"/>
     </outputs>
     <tests>
-        <test>
+        <test expect_num_outputs="2">
             <param name="input_file" ftype="vcf" value="convert.vcf" />
             <param name="convert_to"  value="gen_sample" />
             <output name="output_gen">
@@ -159,7 +159,7 @@
                 </assert_contents>
             </output>
         </test>
-        <test>
+        <test expect_num_outputs="2">
             <param name="input_file" ftype="vcf" value="convert.vcf" />
             <param name="convert_to"  value="gen_sample" />
             <param name="tag"  value="GP" />
@@ -170,7 +170,7 @@
                 </assert_contents>
             </output>
         </test>
-        <test>
+        <test expect_num_outputs="2">
             <param name="input_file" ftype="vcf" value="check.vcf" />
             <param name="convert_to"  value="gen_sample" />
             <param name="tag"  value="GT" />
@@ -182,7 +182,7 @@
                 </assert_contents>
             </output>
         </test>
-        <test>
+        <test expect_num_outputs="2">
             <param name="input_file" ftype="vcf" value="convert.vcf" />
             <param name="convert_to"  value="hap_sample" />
             <output name="output_hap">
@@ -191,7 +191,7 @@
                 </assert_contents>
             </output>
         </test>
-        <test>
+        <test expect_num_outputs="3">
             <param name="input_file" ftype="vcf" value="convert.vcf" />
             <param name="convert_to"  value="hap_legend_sample" />
             <output name="output_hap">
@@ -212,7 +212,7 @@
             </output>
         </test>
         <!-- Test keep-duplicates option -->
-        <test>
+        <test expect_num_outputs="3">
             <param name="input_file" ftype="vcf" value="convert.vcf" />
             <param name="convert_to"  value="hap_legend_sample" />
             <param name="keep_duplicates" value="true"/>
@@ -237,7 +237,7 @@
             </assert_command>
         </test>
         <!-- Test region overlap -->
-        <test>
+        <test expect_num_outputs="2">
             <param name="input_file" ftype="vcf" value="convert.vcf" />
             <param name="convert_to"  value="gen_sample" />
             <section name="sec_restrict">
diff -r cacc9970727a -r d58d2e8c7a57 macros.xml
--- a/macros.xml	Thu Jan 12 15:40:23 2023 +0000
+++ b/macros.xml	Tue Jul 16 17:00:03 2024 +0000
@@ -174,7 +174,7 @@
   </token>
 
   <xml name="macro_AF_file">
-    <param name="AF_file" argument="--AF-file" type="data" format="tabular" optional="true" label="Allele frequencies file" help="Tab-delimited file containing the columns CHR,POS,REF,ALT,AF" />
+    <param argument="--AF-file" type="data" format="tabular" optional="true" label="Allele frequencies file" help="Tab-delimited file containing the columns CHR,POS,REF,ALT,AF" />
   </xml>
   <!-- This may need to bgzip and tabix the file -->
   <token name="@PREPARE_AF_FILE@">
@@ -191,7 +191,7 @@
   </token>
 
   <xml name="macro_estimate_AF">
-      <param name="estimate_AF" argument="--estimate-AF" type="data" format="data" optional="true" label="Estimate allele frequency" help="Calculate AC,AN counts on the fly, using either all samples (&quot;-&quot;) or samples listed in &lt;file&gt;" />
+      <param argument="--estimate-AF" type="data" format="data" optional="true" label="Estimate allele frequency" help="Calculate AC,AN counts on the fly, using either all samples (&quot;-&quot;) or samples listed in &lt;file&gt;" />
   </xml>
   <token name="@ESTIMATE_AF@">
 #if 'estimate_AF' in $section and $section.estimate_AF: