# HG changeset patch
# User iuc
# Date 1721148740 0
# Node ID 9aa28226b77c9df0c7c697768c97e3fe31a7bce3
# Parent  07231f570130afe99c7ca010751a43347a88df66
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit bfc4ff4956b94885638ae07a2560bac5f84fcca8

diff -r 07231f570130 -r 9aa28226b77c bcftools_cnv.xml
--- a/bcftools_cnv.xml	Thu Jan 12 15:21:00 2023 +0000
+++ b/bcftools_cnv.xml	Tue Jul 16 16:52:20 2024 +0000
@@ -181,14 +181,14 @@
                     <param name="lrr_weight" type="hidden" value="0" />
                 </when>
             </conditional>
-            <param argument="--err-prob" name="err_prob" type="float" value="1e-4" label="Err Prob" help="Uniform error probability" />
-            <param argument="--same-prob" name="same_prob" type="float" value="0.5" min="0" max="1" label="Same Prob">
+            <param argument="--err-prob" type="float" value="1e-4" label="Err Prob" help="Uniform error probability" />
+            <param argument="--same-prob" type="float" value="0.5" min="0" max="1" label="Same Prob">
                 <help>
                     The prior probability of the query and the control sample being the same. 
                     Setting to 0 calls both independently, setting to 1 forces the same copy number state in both. (default: 0.5)
                 </help>
             </param>
-            <param argument="--xy-prob" name="xy_prob" type="float" min="0." max="1." label="Xy Prob" value="1e-9">
+            <param argument="--xy-prob" type="float" min="0." max="1." label="Xy Prob" value="1e-9">
                 <help>
                     The HMM probability of transition to another copy number state. 
                     Increasing this value leads to smaller and more frequent calls. 
diff -r 07231f570130 -r 9aa28226b77c macros.xml
--- a/macros.xml	Thu Jan 12 15:21:00 2023 +0000
+++ b/macros.xml	Tue Jul 16 16:52:20 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: