--- a/mashmap.xml	Fri Feb 23 09:13:49 2024 +0000
+++ b/mashmap.xml	Fri Feb 23 09:30:54 2024 +0000
@@ -1,6 +1,6 @@
 <tool name="mashmap" id="mashmap" version="3.1.3" profile="22.05">
   <!--Source in git at: https://github.com/fubar2/galaxy_tf_overlay-->
-  <!--Created by toolfactory@galaxy.org at 23/02/2024 20:10:51 using the Galaxy Tool Factory.-->
+  <!--Created by toolfactory@galaxy.org at 23/02/2024 20:28:46 using the Galaxy Tool Factory.-->
   <description>Fast local alignment boundaries</description>
   <requirements>
     <requirement version="3.1.3" type="package">mashmap</requirement>
@@ -8,13 +8,10 @@
   <version_command><![CDATA[echo "3.1.3"]]></version_command>
   <command><![CDATA[bash '$runme']]></command>
   <configfiles>
-    <configfile name="runme"><![CDATA[mashmap --pi '$perc_identity' -s '$seqLength' -f '$filtermode' \
+    <configfile name="runme"><![CDATA[mashmap --pi '$perc_identity' -s '$seqLength' -f '$filtermode' $dense \
 #if int($sketchSize) > 0:
 -J '$sketchSize' \
 #end if
-#if '$dense' == 'set':
---dense \
-#end if
 #if len($reflist) == 1:
  -r $reflist -q '$query' 
 #else
@@ -35,9 +32,9 @@
     <param name="perc_identity" type="float" value="85.0" label="Identity threshold" help="By default, it is set to 85, implying mappings with 85 or more identity should be reported. For example, it can be set to 80to account for more noisy long-read datasets or 95 for mapping human genome assembly to human reference."/>
     <param name="seqLength" type="integer" value="5000" label="Minimum segment length" help="Default is 5,000 bp. Sequences below this length are ignored. Mashmap provides guarantees on reporting local alignments of length twice this value."/>
     <param name="sketchSize" type="integer" value="0" label="Sketch size - leave 0 for automatic setting based" help="This parameter sets the seed density of the winnowing scheme, gauranteeing that the minhash will be calculated from a sample of sketchSize k-mers for each segment. It is set automatically based on --pi but can be manually set as well."/>
-    <param name="dense" type="select" label="Dense sketching" help="This flag will increase the seed density substantially, resulting in a density of roughly 0.02 * (1 + (1 - pi) / .05) where pi is the perc_identity threshold. This leads to longer runtimes and higher RAM usage, but significantly more accurate estimates of ANI." display="radio">
-      <option value="notset">Do not set this flag</option>
-      <option value="set">Set this flag</option>
+    <param name="dense" type="select" label="Dense sketching" help="This flag will increase the seed density substantially, resulting in a density of roughly 0.02 * (1 + (1 - pi) / .05) where pi is the perc_identity threshold. This leads to longer runtimes and higher RAM usage, but significantly more accurate estimates of ANI.">
+      <option value="">No dense sketching</option>
+      <option value="--dense">Dense sketching</option>
     </param>
     <param name="filtermode" type="select" label="Filter mode" help="Mashmap implements a plane-sweep based algorithm to perform the alignment filtering. Similar to delta-filter in nucmer, different filtering options are provided that are suitable for long read or assembly mapping. Option -f map is suitable for reporting the best mappings for long reads, whereas -f one-to-one is suitable for reporting orthologous mappings among all computed assembly to genome mappings.">
       <option value="map">map - best mapping for long reads</option>
@@ -56,7 +53,7 @@
       <param name="perc_identity" value="85.0"/>
       <param name="seqLength" value="5000"/>
       <param name="sketchSize" value="0"/>
-      <param name="dense" value="notset"/>
+      <param name="dense" value=""/>
       <param name="filtermode" value="map"/>
     </test>
   </tests>