diff mashmap.xml @ 5:10e4181a6443 draft

planemo upload

--- a/mashmap.xml	Fri Feb 23 09:30:54 2024 +0000
+++ b/mashmap.xml	Fri Feb 23 09:59:25 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 [e-mail] at 23/02/2024 20:28:46 using the Galaxy Tool Factory.-->
+  <!--Created by [e-mail] at 23/02/2024 20:50:55 using the Galaxy Tool Factory.-->
   <description>Fast local alignment boundaries</description>
   <requirements>
     <requirement version="3.1.3" type="package">mashmap</requirement>
@@ -8,21 +8,23 @@
   <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' $dense \
+    <configfile name="runme"><![CDATA[#if len($reflist) > 1:
+#for i, mash in enumerate($reflist):
+   #if i == 0:
+       echo $mash > 'reflist' &&
+   #else:
+       echo $mash >> 'reflist' &&
+   #end if
+#end for
+#end if
+mashmap --pi '$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
-#for i, mash in enumerate($reflist):
-   #if i == 0:
-       echo $mash > 'reflist'
-   #else:
-       echo $mash >> 'reflist'
-   #end if
-#end for
---rl  'reflist' -q '$query' 
+--rl 'reflist' -q '$query' && 
 #end if
 cp 'mashmap.out'  $mashout]]></configfile>
   </configfiles>