# HG changeset patch
# User iuc
# Date 1762713389 0
# Node ID 06c0a042a61d7c63e9c9a4735692eaa077b446cc
# Parent  fa43288f637cbb4d57fd8d2e492b9f870f12b926
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/meryl commit 6935ad9dddbbb913817552d682d0b2208481dc7f

diff -r fa43288f637c -r 06c0a042a61d filter-kmers.xml
--- a/filter-kmers.xml	Tue Oct 08 16:44:39 2024 +0000
+++ b/filter-kmers.xml	Sun Nov 09 18:36:29 2025 +0000
@@ -19,7 +19,7 @@
     #if $filter_type.type == 'times'
         $filter_type.N
     #elif $filter_type.type == 'frequency'
-        distinct=${operation_type.filter_type.distinct}
+        distinct=$filter_type.distinct
     #end if
     tmp.meryl
     output read-db.meryl &&
@@ -52,6 +52,7 @@
     <tests>
         <test expect_num_outputs="1">
             <conditional name="filter_type">
+                <param name="type" value="times"/>
                 <param name="N" value="100"/>
             </conditional>
             <param name="input_meryldb_02" value="read-db.meryldb" ftype="meryldb"/>
@@ -65,6 +66,7 @@
         </test>
         <test expect_num_outputs="1">
             <conditional name="filter_type">
+                <param name="type" value="times"/>
                 <param name="N" value="80"/>
             </conditional>
             <param name="input_meryldb_02" value="read-db.meryldb" ftype="meryldb"/>
@@ -78,6 +80,7 @@
         </test>
         <test expect_num_outputs="1">
             <conditional name="filter_type">
+                <param name="type" value="frequency"/>
                 <param name="distinct" value="0.9998"/>
             </conditional>
             <param name="input_meryldb_02" value="maternal.meryldb" ftype="meryldb"/>
@@ -91,6 +94,7 @@
         </test>
         <test expect_num_outputs="1">
             <conditional name="filter_type">
+                <param name="type" value="times"/>
                 <param name="N" value="100"/>
             </conditional>
             <param name="input_meryldb_02" value="read-db.meryldb" ftype="meryldb"/>
@@ -104,6 +108,7 @@
         </test>
         <test expect_num_outputs="1">
             <conditional name="filter_type">
+                <param name="type" value="times"/>
                 <param name="N" value="100"/>
             </conditional>
             <param name="input_meryldb_02" value="read-db.meryldb" ftype="meryldb"/>
diff -r fa43288f637c -r 06c0a042a61d macros.xml
--- a/macros.xml	Tue Oct 08 16:44:39 2024 +0000
+++ b/macros.xml	Sun Nov 09 18:36:29 2025 +0000
@@ -1,7 +1,7 @@
 <macros>
-    <token name="@TOOL_VERSION@">1.3</token>
+    <token name="@TOOL_VERSION@">1.4.1</token>
     <token name="@GALAXY_TOOL_VERSION@">galaxy</token>
-    <token name="@SUFFIX_VERSION@">7</token>
+    <token name="@SUFFIX_VERSION@">0</token>
     <token name="@PROFILE@">22.01</token>
     <xml name="edam_ontology">
         <edam_topics>                                                                                  
@@ -19,6 +19,21 @@
             <requirement type="package" version="2.8">pigz</requirement>
         </requirements>
     </xml>
+    <xml name="kmer_param">
+        <conditional name="options_kmer_size">
+            <param name="kmer_size" type="select" label="K-mer size selector">
+                <option value="provide">Set a k-mer size</option>
+                <option value="estimate">Estimate the best k-mer size</option>
+            </param>
+            <when value="provide">
+                <param name="input_kmer_size" type="integer" min="1" value="" label="K-mer size" help="For a human genome, the best k-mer size is k=21 for both haploid (3.1G) or diploid (6.2G).."/>
+            </when>
+            <when value="estimate">
+                <param name="genome_size" type="integer" min="1000" max="70000000000" value="1000" label="Genome size" help="Haploid genome size or diploid genome size, depending on what we evaluate. In bp. Only required if the k-mer size is not provided."/>
+                <param name="collision_rate" type="float" min="0.0001" max="0.01" value="0.001" label="Tolerable collision rate" help="Tolerable collision rate. By default is 0.001."/>
+            </when>
+        </conditional>
+    </xml>
     <xml name="meryldb_archive_assumptions">
         <has_archive_member path="^[^/]+.meryl$" n="1"/>  <!-- folder also counts -->
         <has_archive_member path="[^/]+.meryl/merylIndex" n="1" all="true">