# HG changeset patch
# User galaxyp
# Date 1765573860 0
# Node ID e967ba68bc427a97fbd887980d721c5acfb4a006
# Parent  e23eb82e7586cf6ca549662135b11db1c0528063
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pvactools commit 2727330d0394c8a1f178061abffe91fe621be7ee

diff -r e23eb82e7586 -r e967ba68bc42 pvacbind.xml
--- a/pvacbind.xml	Fri Dec 12 16:49:37 2025 +0000
+++ b/pvacbind.xml	Fri Dec 12 21:11:00 2025 +0000
@@ -34,9 +34,11 @@
         #if $binding_threshold
             --binding-threshold $binding_threshold
         #end if
-        #if $percentile_threshold_conditional.use_percentile_threshold == "true"
-            --percentile-threshold $percentile_threshold_conditional.percentile_threshold
-            --percentile-threshold-strategy $percentile_threshold_conditional.percentile_threshold_strategy
+        #if $percentile_threshold
+            --percentile-threshold $percentile_threshold
+        #end if
+        #if $percentile_threshold_strategy != 'default'
+            --percentile-threshold-strategy $percentile_threshold_strategy
         #end if
         #if $allele_specific_binding_thresholds
             --allele-specific-binding-thresholds
@@ -144,21 +146,12 @@
             <option value="30">30</option>
         </param>
         <param argument="--binding-threshold" type="integer" value="" optional="true" label="Binding Threshold"/>
-        <conditional name="percentile_threshold_conditional">
-            <param name="use_percentile_threshold" type="select" label="Use Percentile Threshold">
-                <option value="false" selected="true">No</option>
-                <option value="true">Yes</option>
-            </param>
-            <when value="true">
-                <param argument="--percentile-threshold" type="integer" optional="false" label="Percentile Threshold"/>
-                <param argument="--percentile-threshold-strategy" type="select" label="Percentile Threshold Strategy">
-                    <option value="conservative" selected="true">conservative</option>
-                    <option value="exploratory">exploratory</option>
-                </param>
-            </when>
-            <when value="false">
-            </when>
-        </conditional>
+        <param argument="--percentile-threshold" type="float" value="" optional="true" label="Percentile Threshold"/>
+        <param argument="--percentile-threshold-strategy" type="select" label="Percentile Threshold Strategy">
+            <option value="default" selected="true">Use default</option>
+            <option value="conservative">conservative</option>
+            <option value="exploratory">exploratory</option>
+        </param>
         <param argument="--allele-specific-binding-thresholds" type="boolean" checked="false" label="Use allele-specific binding thresholds"/>
         <param argument="--top-score-metric" type="select" label="Top Score Metric">
             <option value="default" selected="true">Use default</option>
@@ -191,7 +184,7 @@
         <param name="add_sample_name_reports_column" argument="--additional-report-columns" type="boolean" checked="false" label="Add sample name reports column"/>
         <param argument="--exclude-NAs" type="boolean" checked="false" label="Exclude NA values from the filtered output"/>
         <param argument="--aggregate-inclusion-binding-threshold" type="integer" value="" optional="true" label="Aggregate Inclusion Binding Threshold"/>
-        <param argument="--aggregate-inclusion-count-limit" type="integer" value="" optional="true" label="Aggregate Inclusion Binding Threshold"/>
+        <param argument="--aggregate-inclusion-count-limit" type="integer" value="" optional="true" label="Aggregate Inclusion Count Limit"/>
     </inputs>
 
     <outputs>
diff -r e23eb82e7586 -r e967ba68bc42 shared_macros.xml
--- a/shared_macros.xml	Fri Dec 12 16:49:37 2025 +0000
+++ b/shared_macros.xml	Fri Dec 12 21:11:00 2025 +0000
@@ -1,6 +1,6 @@
 <macros>
     <token name="@TOOL_VERSION@">6.0.2</token>
-    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@VERSION_SUFFIX@">1</token>
     <token name="@AA_RE@">[ACDEFGHIKLMNPQRSTVWY]</token>
     <token name="@PROBLEM_AA_RE@">(@AA_RE@+|@AA_RE@:-?\d+)</token>
     <token name="@PROBLEM_AA_ARG_RE@">@PROBLEM_AA_RE@(,@PROBLEM_AA_RE@)*</token>