# HG changeset patch
# User iuc
# Date 1721148707 0
# Node ID 5970245e85259fe21d9a82005a940bad11dc6144
# Parent  f86b9f21af7f770a19158ef3948222db934587d0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit bfc4ff4956b94885638ae07a2560bac5f84fcca8

diff -r f86b9f21af7f -r 5970245e8525 bcftools_consensus.xml
--- a/bcftools_consensus.xml	Thu Jan 12 15:18:50 2023 +0000
+++ b/bcftools_consensus.xml	Tue Jul 16 16:51:47 2024 +0000
@@ -139,7 +139,7 @@
         </data>
     </outputs>
     <tests>
-        <test>
+        <test expect_num_outputs="2">
             <expand macro="test_using_reference" ref="consensus.fa" />
             <param name="input_file" ftype="vcf" value="consensus.vcf" />
             <param name="mask" ftype="tabular" value="consensus.tab" />
@@ -155,7 +155,7 @@
                 </assert_contents>
             </output>
         </test>
-        <test>
+        <test expect_num_outputs="2">
             <expand macro="test_using_reference" select_from="cached" ref="consensus" />
             <param name="input_file" ftype="vcf" dbkey="?" value="consensus.vcf" />
             <param name="mask" ftype="tabular" value="consensus.tab" />
@@ -171,7 +171,7 @@
                 </assert_contents>
             </output>
         </test>
-        <test>
+        <test expect_num_outputs="1">
             <expand macro="test_using_reference" ref="consensus.fa" />
             <param name="input_file" ftype="vcf" value="consensus.vcf" />
             <param name="mask" ftype="tabular" value="consensus.tab" />
@@ -186,7 +186,7 @@
                 </assert_contents>
             </output>
         </test>
-        <test>
+        <test expect_num_outputs="1">
             <expand macro="test_using_reference" ref="consensus.fa" />
             <param name="input_file" ftype="vcf" value="consensus.vcf" />
             <section name="sec_restrict">
@@ -199,7 +199,7 @@
             </output>
         </test>
         <!--Test absent option-->
-        <test>
+        <test expect_num_outputs="1">
             <expand macro="test_using_reference" ref="consensus.fa" />
             <param name="input_file" ftype="vcf" value="consensus.vcf" />
             <section name="sec_restrict">
@@ -216,7 +216,7 @@
             </assert_command>
         </test>
         <!--Test mask options -->
-        <test>
+        <test expect_num_outputs="1">
             <expand macro="test_using_reference" ref="consensus.fa" />
             <param name="input_file" ftype="vcf" value="consensus.vcf" />
             <section name="sec_restrict">
diff -r f86b9f21af7f -r 5970245e8525 macros.xml
--- a/macros.xml	Thu Jan 12 15:18:50 2023 +0000
+++ b/macros.xml	Tue Jul 16 16:51:47 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: