--- a/mashmap.xml	Sat Feb 24 06:58:16 2024 +0000
+++ b/mashmap.xml	Sat Feb 24 08:20:07 2024 +0000
@@ -1,6 +1,6 @@
 <tool name="mashmap" id="mashmap" version="1.19.2" profile="22.05">
   <!--Source in git at: https://github.com/fubar2/galaxy_tf_overlay-->
-  <!--Created by toolfactory@galaxy.org at 24/02/2024 15:58:22 using the Galaxy Tool Factory.-->
+  <!--Created by toolfactory@galaxy.org at 24/02/2024 19:18:09 using the Galaxy Tool Factory.-->
   <description>Fast local alignment boundaries</description>
   <requirements>
     <requirement version="3.1.3" type="package">mashmap</requirement>
@@ -9,7 +9,8 @@
   <version_command><![CDATA[echo "1.19.2"]]></version_command>
   <command><![CDATA[bash '$runme']]></command>
   <configfiles>
-    <configfile name="runme"><![CDATA[#if len($reflist) > 1:
+    <configfile name="runme"><![CDATA[ln -s '$query' 'query' &&
+#if len($reflist) > 1:
 #for i, mash in enumerate($reflist):
    #if i == 0:
        echo '$mash' > 'reflist' &&
@@ -18,15 +19,15 @@
    #end if
 #end for
 #end if
-samtools faidx '$query' &&
+samtools faidx 'query' &&
 mashmap --pi '$perc_identity' -s '$seqLength' -f '$filtermode' $dense \
 #if int($sketchSize) > 0:
 -J '$sketchSize' \
 #end if
 #if len($reflist) == 1:
- -r '$reflist' -q '$query' && 
+ -r '$reflist' -q 'query' && 
 #else
---rl 'reflist' -q '$query' && 
+--rl 'reflist' -q 'query' && 
 #end if
 cp 'mashmap.out'  '$mashout']]></configfile>
   </configfiles>