# HG changeset patch
# User iuc
# Date 1721149516 0
# Node ID 91c1e57d5c7ff9fd2c2397069ec646a7f3717955
# Parent  3eac729e66c9f56694a2b806f55a0b727b8e3445
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit bfc4ff4956b94885638ae07a2560bac5f84fcca8

diff -r 3eac729e66c9 -r 91c1e57d5c7f bcftools_gtcheck.xml
--- a/bcftools_gtcheck.xml	Thu Jan 12 15:36:04 2023 +0000
+++ b/bcftools_gtcheck.xml	Tue Jul 16 17:05:16 2024 +0000
@@ -23,7 +23,7 @@
     bcftools index $genotypes_vcf &&
   #elif $section.genotypes.is_of_type('bcf')
     #set $genotypes_vcf = 'genotypes.bcf'
-    ln -s '$ection.genotypes' $genotypes_vcf &&
+    ln -s '$section.genotypes' $genotypes_vcf &&
     #if $section.genotypes.metadata.bcf_index:
       ln -s $section.genotypes.metadata.bcf_index ${genotypes_vcf}.csi &&
     #else
diff -r 3eac729e66c9 -r 91c1e57d5c7f macros.xml
--- a/macros.xml	Thu Jan 12 15:36:04 2023 +0000
+++ b/macros.xml	Tue Jul 16 17:05:16 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: