# HG changeset patch
# User iuc
# Date 1721149478 0
# Node ID bf8325a07ce71ef525339c7ec4341db925b993a8
# Parent  a2f8dc22d7c0f4b1abbe4f41465192118e58187d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit bfc4ff4956b94885638ae07a2560bac5f84fcca8

diff -r a2f8dc22d7c0 -r bf8325a07ce7 bcftools_stats.xml
--- a/bcftools_stats.xml	Thu Jan 12 15:33:09 2023 +0000
+++ b/bcftools_stats.xml	Tue Jul 16 17:04:38 2024 +0000
@@ -157,13 +157,13 @@
         </param>
     </inputs>
     <outputs>
-        <data name="output_file" format="txt"/>
-        <data name="output_pdf" format="pdf" from_work_dir="plot_tmp/summary.pdf">
+        <data name="output_file" format="txt" label="${tool.name} on ${on_string}: txt" />
+        <data name="output_pdf" format="pdf" label="${tool.name} on ${on_string}: PDF" from_work_dir="plot_tmp/summary.pdf">
             <filter>plot_title</filter>
         </data>
     </outputs>
     <tests>
-        <test>
+        <test expect_num_outputs="1">
             <param name="input_file" ftype="vcf" value="stats.b.vcf" />
             <param name="inputB_file" ftype="vcf" value="stats.a.vcf" />
             <output name="output_file">
@@ -173,7 +173,7 @@
                 </assert_contents>
             </output>
         </test>
-        <test>
+        <test expect_num_outputs="1">
             <param name="input_file" ftype="vcf" value="mpileup.vcf" />
             <section name="sec_default">
                 <expand macro="test_using_reference" select_from="cached" ref="mpileup" />
@@ -186,7 +186,7 @@
                 </assert_contents>
             </output>
         </test>
-        <test>
+        <test expect_num_outputs="2">
             <param name="input_file" ftype="vcf" value="mpileup.vcf" />
             <param name="plot_title" value="Plot for mpileup.vcf" />
             <output name="output_file">
@@ -199,7 +199,7 @@
             <output name="output_pdf" file="summary.pdf" compare="sim_size" delta="25000" />
         </test>
         <!-- Test region overlap option-->
-        <test>
+        <test expect_num_outputs="1">
             <param name="input_file" ftype="vcf" value="stats.b.vcf" />
             <param name="inputB_file" ftype="vcf" value="stats.a.vcf" />
             <section name="sec_restrict">
@@ -216,7 +216,7 @@
             </assert_command>
         </test>
         <!-- Test VCF.gz input file -> REQUIRES https://github.com/galaxyproject/galaxy/pull/14605
-        <test>
+        <test expect_num_outputs="1">
             <param name="input_file"  value="mpileup.vcf.gz" />
             <output name="output_file">
                 <assert_contents>
@@ -228,7 +228,7 @@
         </test>
         -->
         <!-- Test modification in samples option -->
-        <test>
+        <test expect_num_outputs="1">
             <param name="input_file" ftype="vcf" value="mpileup.vcf" />
             <section name="sec_restrict">
                 <param name="samples" value="-" />
diff -r a2f8dc22d7c0 -r bf8325a07ce7 macros.xml
--- a/macros.xml	Thu Jan 12 15:33:09 2023 +0000
+++ b/macros.xml	Tue Jul 16 17:04:38 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: