# HG changeset patch
# User iuc
# Date 1728146447 0
# Node ID a175c35ccdce471af617423f01498b53c172010d
# Parent  ef842bb94d1fe3af058bbbdbca49d8c5e232f3ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hivclustering/ commit fb9914c1e5dc3555b3d57926259d76dd9a624039

diff -r ef842bb94d1f -r a175c35ccdce hivclustering.xml
--- a/hivclustering.xml	Thu Jun 14 07:04:38 2018 -0400
+++ b/hivclustering.xml	Sat Oct 05 16:40:47 2024 +0000
@@ -1,5 +1,4 @@
-<?xml version="1.0"?>
-<tool id="hivclustering" name="Make inferences" version="@VERSION@.0">
+<tool id="hivclustering" name="Make inferences" version="@TOOL_VERSION@.@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>on HIV-1 transmission networks using HIVClustering</description>
     <macros>
         <import>macros.xml</import>
@@ -47,14 +46,14 @@
             </param>
             <when value="ignore"/>
             <when value="report">
-                <param name="contaminant_file" argument="--contaminant-file" type="data" format="tabular" label="Input file with contaminant IDs"/>
+                <param argument="--contaminant-file" type="data" format="tabular" label="Input file with contaminant IDs"/>
             </when>
             <when value="remove">
-                <param name="contaminant_file" argument="--contaminant-file" type="data" format="tabular" label="Input file with contaminant IDs"/>
+                <param argument="--contaminant-file" type="data" format="tabular" label="Input file with contaminant IDs"/>
             </when>
         </conditional>
         <conditional name="edges">
-            <param name="edge_filtering" argument="--edge-filtering" type="select" label="Compute edge support and mark edges">
+            <param argument="--edge-filtering" type="select" label="Compute edge support and mark edges">
                 <option value="ignore" selected="True">Do not mark</option>
                 <option value="report">For display</option>
                 <option value="remove">For removal</option>
@@ -79,7 +78,7 @@
             <option value="plain">plain</option>
         </param>
         <param argument="--cluster" type="boolean" truevalue="--cluster hivcluster.csv" falsevalue="" label="Output a CSV file with cluster assignments for each sequence"/>
-        <param name="multiple_edges" argument="--multiple-edges" type="boolean" truevalue="--multiple-edges" falsevalue="" label="Permit multiple edges to link the same pair of nodes in the network"/>
+        <param argument="--multiple-edges" type="boolean" truevalue="--multiple-edges" falsevalue="" label="Permit multiple edges to link the same pair of nodes in the network"/>
         <param argument="--singletons" type="boolean" truevalue="--singletons" falsevalue="" label="Include singletons in output"/>
         <param argument="--centralities" type="boolean" truevalue="--centralities" falsevalue="" label="Output a CSV file with node centralities"/>
         <param argument="--threshold" type="float" value="0.015" label="Only count edges where the distance is less than this threshold"/>
@@ -94,7 +93,6 @@
             <param name="input" value="hivclustering-in1.csv" ftype="csv"/>
             <param name="format" value="plain"/>
             <param name="threshold" value="0.8"/>
-            <param name="json" value="True"/>
             <output name="graph" ftype="hivtrace">
                 <assert_contents>
                     <has_text text="Cluster sizes"/>
@@ -105,7 +103,6 @@
             <param name="input" value="hivclustering-in2.csv" ftype="csv"/>
             <param name="format" value="plain"/>
             <param name="threshold" value="0.8"/>
-            <param name="json" value="True"/>
             <output name="graph" ftype="hivtrace">
                 <assert_contents>
                     <has_text text="Cluster sizes"/>
diff -r ef842bb94d1f -r a175c35ccdce macros.xml
--- a/macros.xml	Thu Jun 14 07:04:38 2018 -0400
+++ b/macros.xml	Sat Oct 05 16:40:47 2024 +0000
@@ -2,10 +2,12 @@
 <macros>
   <xml name="requirements">
     <requirements>
-      <requirement type="package" version="@VERSION@">python-hivclustering</requirement>
+      <requirement type="package" version="@TOOL_VERSION@">python-hivclustering</requirement>
     </requirements>
   </xml>
-  <token name="@VERSION@">1.3.1</token>
+  <token name="@TOOL_VERSION@">1.3.1</token>
+  <token name="@VERSION_SUFFIX@">1</token>
+  <token name="@PROFILE@">23.1</token>
   <xml name="citations">
     <citations>
       <citation type="bibtex">